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PMx User Manual v1.0

1. Primary Input File O ghi EXCHANGE CSY BL PMxCENS C5 My Recent Documents My Computer File name EXCHANGE CSV My Network Files of type SPARKS CSV File csv 4 No Demography Input File needs to be specified because SPARKS 1 6 places into the Primary Input File exchange csv the demographic information that is required by PMx However additional records of moves of individuals into or out of the population can optionally be specified either as CSV files or as Moves files see Appendix D for details on the format of these additional demography files If additional demographic data are provided in files other than the Primary Input File then these data can be applied only to demographic analyses or can be used also to define which individuals were in or out of the population throughout the Genetic History see Genetic Overview and Graphs tabs in Section 4 of the manual 5 Under Additional Optional Input Files add the pmxcens csv file found in the studbook folder to the Census You may also add any of the fed files usually found in the SPARKS folder but possibly in the studbook folder to Associations and or rgn files to Regions 6 No additional files are needed for UDFs as they are already included in the SPARKS 1 6 export although new UDFs that were not in the studbook can be added as an optional UDF udf file 7 Click on Create
2. A Contribution of the IUCN SSC Conservation Breeding Specialist Group e About this Manual This PMx User Manual was developed in concert with the programmers of the PMx software program for intensive population management and with contributions by zoo population management advisors from around the globe This version 1 0 is written to reflect the options and functionality of PMx version 1 0 20120115 The IUCN SSC Conservation Breeding Specialist Group will oversee periodic revisions to the user manual as PMx continues to be expanded and updated This manual is distributed free of charge with the PMx software and is available on the PMx and CBSG websites Please send any suggestions additions or corrections to Kathy Traylor Holzer IUCN SSC Conservation Breeding Specialist Group CBSG email kathy cbsg org This manual is currently being translated into Chinese Mandarin Japanese and Spanish Please contact CBSG or the programmers if you are interested in providing translation for other languages for either the PMx software program and or the user manual Many thanks to the following manual contributors Kathy Traylor Holzer IUCN SSC Conservation Breeding Specialist Group Robert Lacy Chicago Zoological Society Jonathan Ballou Smithsonian Conservation Biology Institute Laurie Bingaman Lackey International Species Information System Cara Groome Population Management Center Lincoln Park Zoo Katelyn Marti Population Man
3. PMx User Manual version 1 0 Page 108 Delta GD Rank GD Rank Diff Rank F MSI Ext MSI 0 00005 0 00635 0 00010 0 00062 0 00011 0 00237 0 00001 0 01212 0 00001 0 01474 0 00009 0 00019 0 00008 0 00194 0 00001 0 01350 0 00004 0 00876 0 00003 0 00966 0 00001 0 01560 0 00005 0 00751 0 00006 0 00516 0 00013 0 00512 0 00007 0 00364 0 00008 0 00211 0 00006 0 00501 N hb N NN e NW BWW Wn bBwWe ND ANU DW ETH PO kKY KY HOON amp A Anm PNY PNY NNN NSN Ww ANUA DB DRATAAN NN NNN F Defining Bins The default definitions for the Bins Break Points and No Way points are as follows Delta GD The break point is 0 change in GD Default values are set so that categories 1 3 each contain 33 of the range above the break point and categories 4 6 each contain 33 of the range below the break point There is no No Way category GV Diff The upper limit top of Bin 1 is set at the best possible i e smallest MK Diff from a pairing The lower limit bottom of Bin 6 is set by the worst possible MK Diff from a pairing The break point is the average MK Diff of all rated pairings As above default values are set so that categories 1 3 each contain 33 of the range above the break point and categories 4 6 each contain 33 of the range below the break point There is no No Way category Only the pairs with inbreeding coefficients less than the No Way point set for F are included here F The upper limit is set at 0
4. PMx User Manual version 1 0 Page 148 Sample file blank AMUR SIBERIAN TIGER PANTHERA TIGRIS ALTAICA Year Tot_sex Male Female Unk_sex Tot_born Wildborn Capt Unk_born Captures_M Captures_F Captures_U Births_M Births_F Births_U Stillb_M Stillb_F Stillb U Releases_M Releases_F Releases_U Deaths_M Deaths_F Deaths_U LTFS_M LTFS_F LTFS_U lmports_M Ilmports_F lmports_U Exports_M Exports_F Exports_U 1934 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1935 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1936 3 1 2 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 1937 3 1 2 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1938 6 2 4 0 6 3 3 0 0 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1939 6 2 4 0 6 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1940 9 3 6 0 9 3 6 0 0 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1941 10 3 7 0 10 2 8 0 0 0 0 1 2 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1942 5 1 4 0 5 1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 2 3 0 0 0 0 0 0 0 0 0 0 Etc Other Optional Input Files UDFs Input File UDFs can be provided within a separate file rather than or in addition to being included within the primary input file First line must be UDF labels UDFs UDFilabel UDF2Ilabel but there does not have to be a label for every UDF and there can be extra labels for UDFs never entered for any animals Any label of STUD_ID will be skipped which allows t
5. SIRE sire1lD prob1 SIRE sire2ID prob2 with the sire Ds being the possible sires and prob being the probability or proportional contribution for a possible sire Or equivalently SIRES sire1ID sire2ID SIREPROBS prob2 prob2 Note the difference between SIRE one sire per line with its probability and SIRES multiple sires with probabilities on another line starting with SIREPROBS If probabilities are not specified in either style above they are assumed to be equal across all possible sires Optional lines for specifying multiple possible dams follow the same formats with DAM rather than SIRE Multiple possible parents of unknown sex can be entered similarly with UNK UNKS and UNKPROBS in which case they will be assigned as both possible sires and possible dams with probabilities in each case set to the total probability that the animal was a parent of one kind or the other For Individuals parentage probabilities are rescaled to add to 1 0 if sum gt 1 If sum lt 1 then the missing part is assigned to an UNK parent For Groups if sum gt 1 probabilities are assumed to be number of diploid genomes contributed by each sire or dam and sum of Probs becomes the Group size If sum lt 1 then the missing part is assigned to an UNK parent and Group size is set to 1 Special codes for SirelD and DamID WILD animal is wild caught can also be WLDx with x being a number UNK animal oth
6. A variety of optional further data on an individual can be provided following an individual s record with lines starting with as follows Records of moves of an individual into and out of the population can optionally be inserted immediately after a record with the format MOVE Dateln InEst Intype DateOut OutEst OutType Location Notes The date fields coded as specified above Est estimate fields are coded as Exact a blank or None is also treated as exact U for an unknown date Y or Year known only to year M or Month known only to month or D or Day with each of Y M and D optionally followed by an integer to indicate the number of years months or days to which a date is known Currently accepted Typeln values are birth capture found import leftentry entry Currently accepted TypeOut values are death release lost export alive Location and Notes are optional and can be any text string rightexit exit Optional UDF records can be inserted after an individual with format UDF UDF1value UDF2value Note that UDFs can instead be provided as extra variables appended to the line of primary data for each individual PMx User Manual version 1 0 Page 139 Optional specification of multiple or uncertain sires the line after an individual record Note that there are several currently acceptable formats
7. Graf Birth Flow is Pulse Continous Age Classes are 1 years mi Report results using time unit as For early mortality use 30 days Project for 20 time steps Distribute Unassigned Mx In prop to known Exdude Number of Iterations for simulations 500 Select Confidence Interval Add 2 age dasses to life tables 95 90 75 D 68 Assign sex to births in Life Table Use actual sex Stochastic Projections 0 50 Treat each birth as male Maximum Females bred per Male 1 Ratio of Male Female Mx 1 05 When calculating Life Table Unknown sex are 0 50 male For projections births are treated as 0 50 male Multiple Parents Most Likely X Defaults OK Assumptions Overall Statistics Stochastic Runs Age Classes are years Birth Flow Continuous CI 95 Iterations 500 Projections 20 time Growth in terms of years r 0 013 lambda 0 987 Ro 0 907 T steps 7 9 N20 102 Up to date The Settings tab in Demography allows the user to e Change the number of iterations default 500 maximum 1000 e Change the time interval for reporting results default years to days weeks months or decades This changes only how population growth ambda r are reported the rates are relative to the interval chosen here e Change the number of time intervals to project into the future default 20 maximum 100 e Change the birth sex ratio for projections default 0 50 male e Change the conf
8. Kleiman K V Thompson and C K Baer eds Chicago IL University of Chicago Press Faust L J Y M Bergstrom S D Thompson and L Bier 2009 PopLink ver 2 1 Chicago IL Lincoln Park Zoo ISIS 2011 SPARKS Single Population Analysis and Records Keeping System ver 1 6 Eagan MN International Species Information System Ivy J A and R C Lacy A comparison of strategies for selecting breeding pairs to maximize genetic diversity retention in managed populations Journal of Heredity in press Lacy R C Extending pedigree analysis for uncertain parentage and diverse breeding systems Journal of Heredity in press Lacy R C J D Ballou and J P Pollak PMx Software package for demographic and genetic analysis and management of pedigreed populations Methods in Ecology and Evolution in press Pollak J P R C Lacy and J D Ballou 2000 Population Management 2000 Brookfield IL Chicago Zoological Society PMx User Manual version 1 0 Page 24 SECTION 2 SELECTION SCREEN Purpose The Selection screen allows the user to fully define which individuals are included in the demographic and genetic population analyses The individuals selected are used for both historical analyses as well as analysis of the current living population and therefore generally should include both living and dead individuals Usually the selected individuals comprise the population that is being managed demographically Individuals may
9. PMx User Manual version 1 0 Page 82 Empirical kinship data can be weighted differently from the data calculated from the pedigree Click the Change button in the Assumptions section at the bottom of the screen to open the Genetic Assumptions box and change Weight to assign to empirical kinships the value must be between 0 and 1 This box will only be accessible if empirical data has been imported Weights can also be changed on the Genetics Settings Tab Clicking the Clear Empirical Kinships button will reset the matrix to the original data calculated from the pedigree file To export the kinship matrix click the Write Kinships button on the lower left hand corner of the screen A box will appear that allows the user to specify which individuals to include the managed individuals only i e the selected population for genetic analysis chosen on the Selection screen the living individuals only and or the entire half matrix The kinship matrix can also be saved as a txt csv or xls file by clicking the Export button at the bottom of the screen Write Kinship to File Kinship Matrix File Managed Only Living Only Half Matrix Terms and Concepts Kinship value KV The weighted mean kinship of an individual with the weights being the reproductive values of each of the kin The mean kinship value of a population predicts the loss of gene diversity expected in the subsequent generation if all animals were to mate ra
10. years Males Females Others Age Class Actual Stable Actual Stable Actual 24 22 20 18 1 Select Locations MANHATTAN MILWAUKEE MINNESOTA NY BRONX OMAHA PHILADELP PITTSBURG M F Non breeding Age M F Breeding Age Fiter Non breeding Age Sex Breeding Age Sex D a a o Animate Reset aa Display Export Count Summary IDs Assumptions Overall Statistics Stochastic Runs Age Classes are years Birth Flow Continuous CI 95 Iterations 500 Projections 20 time Growth in terms of years r 0 011 lambda 1 011 Ro 1 088 T teps 7 4 N20 159 Up to date A title can be added above the age pyramid using the Add title button The table on the left side of the screen provides the data from which the age distribution graph is created This table can be displayed by Counts default Summary and IDs the display can be changed underneath the table Counts Displays the actual numbers Actual and the numbers expected for a stable age distribution Stable for males females and other sex types A stable age distribution is the number of animals that would be expected in each age and sex class if the life table rates had been constant over time indicated by the red lines on the graph Summary Displays the total N for males females and unknowns as well as a breakdown of these totals to known and unknown age animals PMx User Manual
11. After each pair is selected the measures of genetic value of the remaining animals and the Dynamic Population Variables will be updated PMx does this by adding the number of offspring indicated to the population and recalculating all genetic variables The section below the Selected Pairs table will display a cumulative total of the Pairs recommended Offspring Attempted and Offspring Expected based on the indicated Success Setting the Success variable to 0 is equivalent to the Pair Only option in PM2000 and is the same as the Static MK method that is available in the Auto Pair tool see below With that setting no offspring are expected and the genetic calculations for the population will not be updated The UniquelD of individuals that have been added to the Selected Pairs will be highlighted blue on the Males and Females tables for easy identification of individuals that have already been selected for breeding Check the Do not show Paired box in the upper right corner to remove these individuals from the tables Checking this box does not affect the genetic calculations it only visually removes them from the displayed table so that the list of remaining unpaired individuals is more clearly visible and shorter Checking and unchecking this box will toggle these individuals in and out of the display but does not affect the genetic calculations Overview Individuals Kinship Matrix i Pairing Culling Managem
12. Assumes that each individual will produce a number of future offspring equal to its reproductive value Vx Modeling Terms Confidence interval Cl This defines the range of values upper and lower limits that the pararmeter in this case mean population size will take in relation to a specific level of likelihood For example a 95 Cl means that 95 of the simulations result in values between the lower and upper limits Deterministic Deterministic means predictable with no variation or determined In deterministic calculation exact values are applied to formulas that define relationships e g first year mortality will always be 24 Since there is no variation in input values the result will always be the same Iteration A single stochastic simulation of the population over the specified time period Because events in a stochastic simulation are based on probabilities the outcome of each iteration will be different therefore many iterations should be run to accurate estimate results P Extinction Probability that the population will go to zero measured as the proportion of stochastic simulations in which the population goes to 0 Stochastic Stochastic means variable due to chance or based on probabilities In stochastic calculations input values are based on probabilities e g every individual has a 24 chance of not surviving its first year Actual values used in the calculations will vary with each application and
13. Cumulative Frequency Interval 0 20 Another Variable Founder Certainty v Filter Individuals Sort on v Filtered showing 47 Sort Founders on v Assumptions Dynamic Population Variables Do Not Include Founders Unknown Weight 0 00 GD 0 9526 GV 0 9485 MK 0 0474 Known 96 N 47 0 Terms and Concepts See Appendix B Glossary for definitions of genetic terms used on this tab Helpful Hints e If the labels on the graph axes are bunched together double clicking on the graph and dragging the corner of the graph to increase its size will spread out the labels e Export the historical genetic Population graphs before excluding post reproductive sterilized or other permanent non breeders from the genetic analysis on the Selection screen in order to include them in the genetic calculations Cautions While it is possible to create a large number of different graphs with Custom graphs be aware that many of these would be relatively meaningless or very had to interpret Pay attention to the graph settings in order to create a useful graph PMx User Manual version 1 0 Page 104 SETTINGS TAB Genetics Purpose The Settings tab in the Genetics module allows the user to customize settings for genetic assumptions and analyses specifically it provides the ability to modify the way in which multiple and unknown parents are treated in the pedigree analysis how founders are treated and how MSI values
14. False 6 La 72 HOUSTON Urka Female False 15 5 LEIPZIG Amur Male False 10 127 SIOUX FAL 0050 Katrina Female False 18 57 MAGDEBURG Kerula Female False 16 129 SAN FRAN 16212 Nicholas Male False 18 15 ROTTERDAM Baboeska Female False 15 167 PITTSBURG 29 Igor Male False 15 14 ROTTERDAM Nicolajev Male False 15 168 PITTSBURG 30 Sasha Female False 19 121 LEIPZIG Chingan Male False 18 177 SANDIEGOZ 169049 Seja Female False 16 58 MAGDEBURG Altai Female False 19 183 PITTSBURG 219 Kumarsk Male False 16 13 PRAHA Tapka Female False 15 187 FERNDALE Alexis Ti Male False 13 11 PRAHA Amur Male False 11 188 FERNDALE Tasha Female False 13 Fa 107 ROTTERDAM Ghabarowsk Female False 20 a QC piama Ts ze oxy p yy Pm m 9 r Apply changes in Selection to Genetics Assumptions Dynamic Population Variables Do Not Tndude Founders Uningan Weight 0 00 GD 0 9645 GV 0 9600 MK 0 0359 Known 100 N 143 0 eS Helpful Hints Cautions See Section 2 Selection screen for helpful hints and cautions PMx User Manual version 1 0 Page 115 SECTION 5 GOALS SCREEN Purpose The Goals Section of PMx provides deterministic projections for the retention of genetic diversity in the population over time given a particular set of biological and management conditions Various options can be explored to assess how they perform in terms of meeting long term genetic program goals How to Use This Section The first step is to spec
15. GDt GDt GDw GDt with each GD calculated as 1 MK for its parallel MK and with the means across subpopulations weighted by the number of kinships that are included in each calculation Thus the Fst for the overall set of subpopulations will be more heavily influenced by the divergence among the larger subpopulations and is not simply the average of all pairwise Fst values Note that there are other formulations of Fst that do weight each subpopulation equally regardless of its size PMx User Manual version 1 0 Page 100 New Features This feature is comparable to the META MK software previously available from Jonathan Ballou 2006 Helpful Hints e The Filter button can be used to refine the view of the Full Population or other subpopulation selected as the Current Set However this does not alter the contents of the Current Set Metrics are not recalculated based on filter settings and still reflect the pre filtered population The filter simply creates smaller views of the population For example it can be useful to limit the Current Set view to show only those individuals that meet certain criteria for transfer e g females over 3 years of age e It can be useful to add a column to the Current Set table to indicate the management set s to which each individual belongs This can be done by right clicking on the column header and adding the Management Sets column This individual variable can also be added to other PMx ta
16. Kinship Matrix Tab ccccccssssccccccecsssesseaecesecscecseeaaecececsceeseaeaeseeecuseeeeaeaecesecesecseeaeaeeeeeesssesesaeaeeeseesseeegs 81 Pai WISCsI ALO Ma air E T RT OTOOTO E EOE O OAO TOOTA OA TRO A 84 Pairings Tabien noer a e E EEEE E RE E E E EERE 87 C lling Ta Disses netan eae e e a e E T ea eea EAE REE E 93 Management Sets TabDicsitaroatainiaerno mirige eaa eae eiee Ra a eE eE aeS EREEREER 95 Genetics Graphs TaD ostira a a Ee E a Ae E Sa 101 G netics Settings Taisson sine ee a eae eea eea e aa eae Re E r aE EE E ea Eaa 104 Genetics Selection Tab iiirecasticceccecevecaeeGeseecedetentecdieccce EARE RAE EARE AEA E AEA EARI ESTARES 114 PMx User Manual version 1 0 Section 5 Goals Screen Using the Goal Screen irinari ii rna EEA A tees eee ansehen EAA AES 115 Section 6 Recommendations Screen Using the Recommendations Screen ccseeccccesseneececseeeeceeceeeececeeeeececceeaeceeeeeeeceseeeaecseeueaeeeeseeeeseeeaeess 118 Appendices Appendix A Description of Individual Variables ccsscccssssececsesnececeeseeecseseeeceeueeeceeseeeeseneeeesees 122 Appendix B GlOSSARY eair cee tes Ghee ened A TEOT ANA OE ATO O AOO 128 Appendix C Frequently Asked Questions ecccececeesnececeenneeeeeeaeeececaaeeececsaeeececaueeeeeesueeeeseqaeeeeeeiaeeeeseas 132 Appendix D Input File Formats ccccccccsssceeessnececeesneeececceeecseaeeeeeeaeeeceeaeeeseeaeeesseaeeeseeqeeeeseieeeseeed 136 Appendix E PMX Output Files as
17. Seasonality Projections Reproductive Planning Add Remove Availablity Graphs Settings years Males Females Others Age Class Actual Stable Actual Stable Actual aL 0 0 0 0 0 0 0 0 0 0 1 23 0 0 0 0 0 0 0 0 0 0 2 L N 51 2 0 0 0 0 0 0 0 0 0 0 B 2 oo oo oo o 0 9 2 L 20 oo oi oo 02 0 0 19 0 0 03 0 0 0 5 0 0 18 i 18 10 os o 10 0 0 7 10 os o 15 0 9 16 16 20 13 40 18 0 0 15 4 0 17 4 0 2 2 0 0 44 14 1000 210405 0 0 1 oo 23 40 30 0 0 peel 12 4 0 24 2 0 4 0 0 4 11 4 0 2 6 3 0 37 0 0 10 10 60 27 40040 0 0 9 oo 29 oo 42 0 9 Peo 5 0 3 0 8 0 44 0 0 a 7 10 340704 0 0 ga 6 30 3248 0 0 5 oo 33 o0 49 oo kak 4 3 0 3 4 7 0 5 0 0 0 a 3 30 35 50 5i 0 0 ao i 2 so 35 30 52 0 0 1 7 0 37 5 0 52 0 0 0 0 3 0 48 3 0 67 0 0 T T 10 5 0 5 10 Years Males El m F Non breeding Age E m F Breeding Age Fiter SIDI dne i 3 E Non breeding Age Sex q Export ome Summary IDs Breeding Age Sex 77 eerondes es LeO Unproven Breeders i Assumptions Overall Statistics erie k Age Classes are years Birth Flow Continuous CI 95 Iterations 500 Projections 20 time Growth in terms of years r 0 011 lambda 1 01 Sterle ws PD cee Regions The default view for the age pyramid is the living population indicated as All Living in the drop down menu beneath the figure These are all individuals in the selected population that were living as of the Analysis Date according to their age on that date Other views subsets
18. Selection Summary Founders Individuals Kinship Matrix pairwise Info Pairing Culling Management Sets Graphs Settings UniquelD 29 38 48 49 54 55 61 65 68 Location DUKEPRIM DUKEPRIM DUKEPRIM DUKEPRIM DUKEPRIM CHEHAW CINCINNAT CINCINNAT DUKEPRIM CHEF Enter the IDs of two animals in the DUKE PRIM 0 6719 0 4453 0 4453 0 2227 0 3359 0 2109 0 2109 0 3359 0 3359 0 22 axes below to views thet insti 38 DUKEPRIM 0 4453 0 6719 0 4453 0 3359 0 2227 0 2109 0 2109 0 2227 0 2227 0 33 48 DUKEPRIM 0 4453 0 4453 0 6719 0 2227 0 2227 0 2109 0 2109 0 2227 0 2227 0 22 i 49 DUKEPRIM 0 2227 0 3359 0 2227 0 5000 0 1113 0 1055 0 1055 0 1113 0 1113 0 29 J 54 DUKEPRIM 0 3359 0 2227 0 2227 0 1113 0 5000 0 1680 0 1680 0 2930 0 2930 0 11 55 CHEHAW 0 2109 0 2109 0 2109 0 1055 0 1680 0 5000 0 2500 0 1680 0 1680 0 108 Kinship Matrix 61 CINCINNAT 0 2109 0 2109 0 2109 0 1055 0 1680 0 2500 0 5000 0 1680 0 1680 0 10 65 CINCINNAT 0 3359 0 2227 0 2227 0 1113 0 2930 0 1680 0 1680 0 5000 0 2930 0 11 n 68 DUKE PRIM 0 3359 0 2227 0 2227 0 1113 0 2930 0 1680 0 1680 0 2930 0 5000 0 11 Read in Empirical Kinships 69 CHEHAW 0 2227 0 3359 0 2227 0 2930 0 1113 0 1055 0 1055 0 1113 0 1113 0 501 70 DUKE PRIM 0 2109 0 2109 0 2109 0 1055 0 1680 0 2500 0 2500 0 1680 0 1680 0 10 74 CHEHAW 0 3359 0 2227 0 2227 0 1113 0 2930 0 1680 0 1680 0 2930 0 2930 0 11 76 WAHPETON 0 2734 0 2168 0 2168 0 1084 0 2305 0 2090 0 3340 0 3340 0 2305
19. conjunction with other adjustments to the Population Variables and Founder Related Variables r Pfr PMx Sumatran Tiger GSMP 28Jul11 lola Fie Language Help Project Notes selection I Demography Genetics Goals Recommendations Goal 90 0 Gene Diversity at the END of X 100 ran Population Variables Founder Related Variables Generation Length years f New Fndrs per Addition Event Maximum Potential Lambda 1 Year to Start Adding Fndrs Current N Years between events o io Aysuaaig aua5 Current Effective Size g Year to Stop Ne N FGE per founder Current Gene Diversity Maximum Allowable N Solve For Send to Project Notes Managed N 289 Pedigree Known 100 0 Current Gene Diversity 0 948 Potential Gene Diversity 0 985 Lambda 1 044 The Send to Project Notes button will export the currently displayed management goal and strategy to the Project Notes screen Terms and Concepts See Demography Section 3 and Glossary Appendix B for explanations of the Population Variables New Features The ability to set a minimum genetic goal to be maintained During a time period is now functional this feature was disabled in PM2000 Helpful Hints e When using the Solve For feature be sure to Reset the values before solving for a different variable e Although the retention of 90 gene diversity for 100 years is a standard goal for most managed populations in some case
20. entry or exit dates are not to be included Line 1 Header Studbook ID Sex Birth Type Birth Date Birth Date Est Entry Date Entry Date Est Entry Age In Days Entry Method Exit Date Exit Date Est Exit Age In Days Exit Method Censored Complete Lines 2 to n data with the following format fields separated by Studbook ID Up to 6 characters long Sex Male Female Unknown Birth Type Wild Born Captive Born Unknown Birth Date MM DD YYYY Birth Date Est None Month Year x Years Entry Date MM DD YYYY Entry Date Est None Month Year x Years Entry Age XXX Entry Method alive at start of window born into window imported into window Exit Date MM DD YYYY Exit Date Est None Month Year x Years Exit Age XXX Exit Method died LTF alive at end of window exported out of window Censored Complete Complete if animal died or alive Censored if animal exported or LTF Sample format Studbook ID Sex Birth Type Birth Date Birth Date Est Entry Date Entry Date Est Entry Age In Days Entry Method Exit Date Exit Date Est Exit Age In Days Exit Method Censored Complete 1 Male Captive Born 9 19 1974 None 1 1 1990 None 5583 alive at start of window 5 22 1993 None 6820 died complete 2 Male Captive Born 1
21. from a PMx Export as exchange csv from SPARKS 1 6 from the ped file created by PM2000 from a ped file exported by PopLink or from a csv file that could be created from an Excel data set or with a text editor The required format for each of these files is described below Note that the fields for pedigree records can be ordered differently than specified below as long as a header line identifies the sequence used 1 Exchange dbf produced by Genetics Export from SPARKS 1 5 PMx will accept and translate the exchange dbf file that is currently produced by SPARKS 1 5 This is perhaps not the preferred method because PMx relies on an old MS DOS program to do the translation from exchange dbf to a ped file see format below PMx User Manual version 1 0 Page 137 Fields in the exchange dbf are as follows SPARKS labels some of these fields differently but either the SPARKS labels or the field names below are acceptable Those fields in brackets are ignored by PMx and can be omitted ID DamID SirelD BirthDate BirthDateEst Sex ID DID SID Dateln InEst DateOut OutEst 6 ignored fields DeathDate Location Local ID InstCode SocialGroup Selected T F Dead T F 14 ignored fields OtherID Sex is coded as 0 7 with the following meanings 0 fertile female 1 fertile male 2 sterile male 3 sterile female 4 sterile unknown or abnormal 5 fertile unknown 6 contracepted male
22. required Values are separated by tab space or A value of 1 is a code for a missing value in which case PMx will assign the kinship calculated from the pedigree for that pair 12 25 31 522 0 50 0 10 0 50 0 00 0 10 0 55 0 25 0 00 0 25 0 45 The file can instead provide the coefficients of relatedness in which case it would normally have the extension re but can have any extension If PMx is told that the file contains relatedness values then each value will be divided by two to obtain the kinship PMx User Manual version 1 0 Page 150 Pairing File A set of pairs can be specified within a file for later reading into PMx The first line is a header that will be skipped If the header contains F as its third specified variable then the reading of the data lines will assume that the inbreeding of the pairing in included Otherwise it is assumed that F is not included in each row of the file The subsequent lines list one per line the pairings with variables separated by or tab The field delimiter cannot be a comma because that would cause misreading of numeric data in many regional data formats The Sire D and DamID must be listed as the first two variables F if included in the header is given next followed by the probability of success the number of offspring to be produced the location of the pairing and any notes However any line can be truncated at any vari
23. set the target size at the current size and lambda will change to 1 0 The number of births needed will be only that number needed to replace expected deaths If the goal is to decrease the population size Births Needed may show negative numbers This reflects the number of individuals that must be removed from the population to cause the population to decline to the target size The Reset button will restore the default values which provide births and pairs needed in the next year in the current population to achieve the historic lambda shown in the Overall Statistics in the footer of the screen The graph on the right side of the tab displays the projected growth and stabilization of the population based upon the exact achievement of this growth rate and target population size x PMx Demography Overview Male Life Table Female Life Table Age Distribution Census Projections Reproductive Planning Add Remove Avaiabiity Graphs Settings Births needed to increase the population from 55 Projected N toanewsizeof 70 0 witha growth ratec 1 0494 Births Needed a over the next 5 _ time interval 1 year years Births Pairs Assume birth sex ratio Reset a s2 70 s ne Ss i cs 4 6 A 3 j Maes IESS Females 2 75 5 0 ms a 7 2 48 x Reproductive Needs per Time Interval 1 year 4 84 5 6 int P 50 Births Needed 2 4 lt gt 5 2 lt gt 8 0 j 4 7 3 1 15 Average Litter Size 2 5 6 38 40 7 5 8 3 9
24. txt extension Genetics institution information will be exported to location tt Click on the Select Filters buttons to set your demographic and genetic views for export The filters displayed in the boxes are defaults Demographics Genetics Select Filters Select Filters The following are default fiters a The following are default fiters Locations N AMERICA AND During Locations N AMERICA AND As of 1 1 1900 2 11 2011 AND Status 2 11 2011 AND Status Living Living Ok The file names in the top three boxes are chosen based on the database name these can be changed if desired but do not change the extensions prn for demography files ped for genetics files The Demography filters chosen will limit the studbook database to a specific population that will be used to calculate life table parameters Mx Qx Lx etc The chosen filters will be displayed in the filter box change the default filters to the desired demographic window which is generally the period of modern management for the species Filters in addition to date and geographic windows can also be set The Genetic filters are used to create the list of individuals that will be considered living individuals in the current population PopLink exports this list of specimens and their pedigree information to PMx If desired change the default filters using the Select Filters button After the desired filters have been set click OK to create
25. 0 108 78 WAHPETON 0 2734 0 2168 0 2168 0 1084 0 2305 0 2090 0 3340 0 3340 0 2305 0 108 Write Kinships 80 INDIANAPL 0 2734 0 2168 0 2168 0 1084 0 2305 0 2090 0 3340 0 3340 0 2305 0 108 81 HATTIESBG 0 2734 0 2168 0 2168 0 1084 0 2305 0 2090 0 3340 0 3340 0 2305 0 1084 gt s Addl Data Location Sort on UniqueID Filtered showing 21 Assumptions Dynamic Population Yariables Bo Nou Ix Ride OUD des GD 0 7582 GV 0 7122 FGE 2 07 Known 100 N 21 0 Clear Empirical Kinships A window will open that provides the option to attach a kinship matrix text file that contains either kinship coefficients between any two individuals or coefficients of relatedness Kinships are symmetrical by definition but the imported file of empirical kinships only needs to contain the diagonal values and the below diagonal values Values can be included that are nonsensical from a genetics standpoint for example true kinships must range from 0 to 1 but PMx will accept any numerical values that are provided Read in Empirical Kinships Kinship Matrix File The file contains Kinship Coefficients Coefficients of Relatedness Example of a Kinship Matrix File text in bold NOT entered 123 124 201 202 300 0 50 056 0 57 0 87 0 50 0 56 050 066 0 50 0 45 0 57 0 66 0 53 0 38 10 55 0 87 0 50 0 38 0 50 0 90 0 50 0 45 0 55 0 90 0 60 List of individuals with kinships to be specified Kinship f matrix
26. 1 0 Page 97 Click the Plot button above the Management Sets table to produce a plot indicating the effect change in gene diversity of moving any single individual from one subpopulation to another The impact on the source population is given on the horizontal x axis while the impact on the destination population is given on the vertical y axis The subpopulations and direction of the transfer can be selected at the bottom of the window click the Plot button to redraw the plot for the new subpopulations The sample plot below shows that transfer of the majority of individuals if moved from the EAST subpopulation to the WEST subpopulation would reduce GD in the EAST subpopulation while increasing GD in the WEST subpopulation The preferred genetic situation would be to transfer individuals whose transfer would result in an increase in GD for both the source and destination subpopulations These are the individuals located in the upper right corner of the plot Transfer of individuals in the lower left corner of the plot should be avoided as this causes a decrease in gene diversity in both populations 0 002 0 001 GD in DESTINATION WEST m 2 Change in GD in SOURCE EAS O Select Populations to Plot From EAST aj To WEST PMx provides two methods for exploring the genetic impact of moving specific individuals between subpopulations and for making these transfers within the program in order to evaluate the cumul
27. AgeYears are given for each individual as with other tables in PMx other columns can be added or deleted by right clicking on the column header to customize the table PMx provides the following additional columns to specify the recommendation for each individual Disposition Indicates the recommended action regarding the physical placement of the individual Default setting is Hold remain at current location alternate choices on the pull down menu are Send To Export Receive From Import From Available Other Unknown New Location Indicates the recommended destination of the individual if it is recommended to be moved e g Send To Export Default setting is blank The pull down menu provides a list of ISIS mnemonics included in the data files used to create the PMx project other location names can be manually typed into the cell which is set to fill in from the list Breeding Indicates the recommended action regarding the breeding or placement of an individual in a social group Default setting is Do Not Breed alternate choices on the pull down menu are Breed Surplus i e not needed in the managed population Social i e to be kept with other animals for social reasons but not for breeding Other Unknown With Indicates the Unique ID of the recommended mate of the individual if recommended to breed can take on alternate meanings e g Group X if Breeding Social Default setting is blank offspring Indicates th
28. Documents PopLink 2 1 PopLink Databases CHIMPANZEE mCHIMPA aaan REPLACE primary demographic data with these data ADD to primary demographic data with these data Additional Optional Input Files SPARKS Census 1 C Users faust Documents PopLink 2 1 PopLink Databases CHIMPANZEE Exchcens csv SPARKS Census 2 UDFs Associations Regions PMx User Manual version 1 0 Page 12 Advanced Export from PopLink Follow the directions above under Basic Export from PopLink to create the Genetic export and Census export files To create the advanced Demographic export 1 2 Run the Survival Tool Reports gt Survival Tool selecting the Analytical Survival Statistics option Set the appropriate filters for the export aj i Survival Tool Selection lec me Select the types of survival analyses to conduct below 3 Select your window for survival analyses below p Descriptive Survival Statistics for Fe Start Date 2 11 00 x communication purposes e MM DD YYYY v Analytical Survival Statistics for population f i End Date 2 11 2011 X management a MM DD YYYY Expert Survival Statistics Customize my Institution erre F analyses by using _ as the starting age in days where Lx 1 r Generate a Comparative Advanced Results a Additional No Fitters Applied table for the analyses selected above Filters N Ok Cancel 5 Ok Cancel 4 A pop up box may appear indicating that the oldest indivi
29. MGHLT_I prn FGHLT_I prn If you are using DEMOG and e your data Run the Genes or Demog program accept the default names lt gt Run the program immediately lt gt Do not run the program now Names should not include any Program command DEMOG4 2 spaces or amp characters PMx User Manual version 1 0 Page 8 Census export 1 From the Reports menu select Analysis gt Census gt Census Report Run the report to the screen 2 Use the ESCape key to close the report There is no need to adjust the View Criteria for this report Various reports will be created and stored in the studbook folder Import into PMx 1 Open PMx Pick New Project and enter a project name Including the species name and a date can be helpful as projects accumulate over time 2 The Project File to Create name will automatically update to reflect this project name 3 Either manually type in the Primary Input File information or click on the eS button at the end of this field and browse to the appropriate SPARKS studbook folder Change the file type to display dbf files Choose exchange dbf and click on Next PMx Create a new project Project Name GHLT Intl data pm2000 export files Project Description Example for using pm2000 style Files For import Project File to Create GHLT Intl data pm2000 export Files pmxproj Primary Input File C SparksDYglt_i EXCHANGE DBF 4 Add the required prn files for females and ma
30. Once PMx opens to the opening Project Notes screen select File gt Save Project PMx User Manual version 1 0 Page 5 a PMx Create a new proj Demography Input File Optional PRN Female Male csv Moves Apply moves to both Demographic and Genetic views Apply moves to Demographic view only Additional Optional Input Files Census UDFs Associations mas Regions r _ qom N lt oo aan a a JQ OS C ISISdosbox SPARKS gt NA Mal v Search NA_Mal p J la Organize 7 New folder v ie Favorites Name Date Type af 1 LI EE Desktop 3 25 2011 9 04 PM Microsoft Off J Downloads a EXCHANGE CSV 3 25 2011 9 04 PM Microsoft Off lt gt Recent Places Sa PMXCENS3 CSV 3 13 2011 3 04 PM Microsoft Off PMx User Manual version 1 0 Page 6 Creating a Project from SPARKS 1 5x Export from SPARKS Data are exported in three parts from SPARKS 1 54 or 1 56 similar to how exports are done for PM2000 Genetic export 1 Fromthe SPARKS main menu select Reports 2 Use the Left arrow key m to open the View Criteria as needed Set the Date Span for the export from yesterday s date to today s date During the date span Also set Living Dead LTF to Lived during date span Geographic or Association views may be used as well as User Defined Fields The ESCape key will return you to the Reports menu ct SPARKS15 E
31. Other Unknown ReproStatus Current reproductive status of the individual Options are Fertile Contracepted Sterile PostReproductive Other Unknown based upon the status designated in the exported data default Fertile BirthType Birth origin of the individual Wild Born Captive Born Other or Unknown Associations Lists the current zoo association s for this individual based on the last location of the individual and the zoo associations for which this institution is a member The appropriate association fed file s must be specified either during data import or on the Genetics Settings tab Country Lists the country of the last location for this individual provided with SPARKS 1 6 exports Region Lists the geographic region based on the last location of the individual SPARKS 1 6 exports will provide this information automatically using the following regions Europe Africa North America PMx User Manual version 1 0 Page 126 Latin America Middle East South Asia Southeast Asia East Asia and Australasia Regions can also be specified using rgn file s ManagementSets Lists the Management set s in which the individual is included Imported from the Management Sets tab by use of the Update Table button SocialGroup Social groupings as assigned at the Location from SPARKS UDF1 UDF7 User Defined Fields displayed using the actual UDF name_udf Up to seven will be individually available UDFs All U
32. Page 41 Cautions Model data currently are not saved with a PMx project rather Model Data default back to Actual Data when a saved project is reopened This will affect projections reproductive planning and other similar demographic calculations Be sure to export and save Model Data files so that these values can be recreated Future versions of PMx may provide the ability to import model data files Individuals with unknown birth date estimates are not used in any life table calculations as the individual s age cannot be calculated If possible make sure all individuals in the population have birth date estimates prior to exporting to PMx in order to ensure these individuals are included in the life tables Individuals with birth date age estimates will have their entered birth date used in calculations i e the estimation range is ignored and the entered date is used Individuals of unknown sex are distributed as 0 5 male and 0 5 female throughout the life table calculations The default when adding births into the life tables is to treat each birth as 50 male and 50 female If the population has a sex bias the user may want to consider using the Use Actual Sex option on the Settings tab Caution should be used with the Smooth tool as too much alteration of data may misrepresent or alter trends within the life tables Reproduction in the first age class typically will be overestimated since PMx uses the N at the midpoint of th
33. Probability of reproductive success for each pair Success expected default 1 0000 e Maximum allowable level of inbreeding F upper limit default 0 20 e Auto Pair Scheme for creating pairs either Static MK Dynamic MK or Ranked Mk Automatic Selection of it TS a Offspring will be automatically added to your population based on the criteria be low when you dick Accept Pairs desired 10 Offspring per pair 4 Auto Pair Scheme Static MK Dynamic MK Max Pairs for Male 1 Max Pairs for Females 1 Ranked MK Success expecte 1 0000 F upper limit 0 20 Accept Cancel PMx User Manual version 1 0 Page 89 Static MK This breeding scheme creates pairs by attempting to pair the next available male with the lowest MK value with the next available female with the lowest MK value within the limits set by maximum allowable F and maximum of mates This process is repeated until the desired number of pairs has been reached The MK of all individuals and the genetic calculations remain static no hypothetical offspring are created This option may be considered for populations with a low breeding success rate Dynamic MK This breeding scheme is similar to Static MK with one exception after each pair is selected the genetic calculations are updated to reflect the expected number of offspring from that pair meaning that the MK of an individual is dynamic and increases as its relatives reproduce successfully
34. Settings F break point UseAverageF Genetic Value Type Mean_Kinship GV Diff Method ExcludeUnknowns MSI Method Tulsa For Unknown Sexes ExcludeUnknowns Advanced settings PMx User Manual version 1 0 Page 107 Click on Advanced settings The default view is to display Bin data which shows how each variable is defined across the rankings of 1 to 6 referred to as Bins Each variable has a value that sets the Break Point between Beneficial and Detrimental pairings with respect to that variable The variables Inbreeding Coefficient and Unknown Pedigree also define values as No Way points individuals are too related and or too much of the pedigree is unknown to make a meaningful assessment The Bins for each variable Delta Gene Diversity Difference in GV Inbreeding Coefficient and Unknown Pedigree are defined in terms of e Percentiles Percent of the range of values that fall into that bin e g 33 indicates that the bin contains pairs with values in the first third of the range e Value Value that defines the lower limit starting point of that bin e Number of total pairings that fall into that bin e Percent of total pairings that fall linto that bin IMn Advanced Seti Detrimental Break Point 4 Percentiles 0 33 0 67 1 00 0 33 0 67 1 00 Value 0 00013 0 00006 0 00000 0 00000 0 00005 0 00009 0 00014 1 00000 430 3241 7657 6923 2329 199 0 02 0 16 0 37 0 33 0 11 0 01 Differen
35. System Requirements PMx version 1 0 is written in the C programming language developed with Microsoft Visual Studio 2010 for the Microsoft NET Framework version 4 running on Windows operating systems It has been tested on Windows XP and Windows 7 but it is likely that it will work also on older versions of Windows It can probably be run on Apple Mac OS running Windows emulators but no versions have been compiled specifically for Mac Unix Linux or other operating systems PMx can run on 32 bit or 64 bit processors Users should have the latest service packs for their OS and must also have installed the Microsoft NET Framework version 4 The web installer for the NET is available at the Microsoft download center www microsoft com downloads The memory requirements of PMx depend on the size of the studbook being analyzed The minimum RAM increases proportional to the square of the population size and the required RAM can be quite large A population with 1000 animals selected for analysis usually the living animals will typically require about 10 MB of RAM to hold the calculations a population of 10 000 will require about 1 GB of available RAM Moreover if the population is large more than about 1000 the program can be very slow and require large graphics memory to hold the extensive tables of data that are available for viewing in PMx Some of the tables that require the most memory can be optionally disabled in PMx and the default
36. The amount of unknown ancestry in the male and female Incomplete pedigree information means that the genetic value and relatedness of a pair cannot be accurately calculated These variables are combined using a default set of definitions that can be modified on the genetic Settings tab to assign a MSI score of 1 to 6 for each pair which can be thought of as follows 1 very beneficial genetically to the population 2 moderately beneficial 3 slightly beneficial 4 slightly detrimental 5 detrimental should only be used if demographically necessary 6 very detrimental should be considered only if demographic considerations override preservation of genetic diversity very highly detrimental should not be paired due to high level of kinship of pair The View MateRx settings button and the demographic Settings tab give more detailed information regarding how the MSI values are calculated and also allow these settings to be modified also see the MateRx documentation Ballou et al 1999 for more information on MateRx and these calculations Using Pairwise Info The default table of MSI values for pairs can be used to quickly assess the relative genetic value of a pair subset of pairs potential mates for one individual and many other valuable data when making breeding recommendations This can be especially helpful to quickly explore options for pairing individuals at one facility that houses numerous individuals of ea
37. The sum of allelic retentions of the individual founders i e the product of the mean allelic retention and the number of founders The average of the inbreeding coefficients among the living individuals weighted by the known for each individual The mean inbreeding coefficient of a population will be the proportional decrease in observed heterozygosity relative to the expected heterozygosity of the founder population When the Genetics Screen is first opened the right side will display options to change the Genetic Assumptions and Other Settings related to the genetic analysis These options are also available on the Genetics Settings tab under Genetic Details but are duplicated on this screen for convenience see the manual section on Genetic Settings for detailed explanations of these options e Parentage Assumptions Default is Probabilistic parents applicable to datasets with MULT parents Value proportion WILD to assign to Unknown parents Default is zero applicable to datasets with UNKnown parents Include Founders Checkbox to include founders rather than just the captive born population into the genetic calculations Weight Groups Applicable to datasets with groups Weight to assign to empirical Kinships Default is 1 00 applicable to datasets with imported empirical kinships Analysis Date End date of the analysis Default is the end of the export filter window and typically is the date of export unless other
38. YULEE 9300 Ingasu I Female 9 True False ANTWERP Congo I 437 OMAHA 1159 Kengo Ili Male True False ANTWERP Tele o ifrenae 8 te Tee wie 447 9910 Jamal l Male 7 True False ANTWERP Kadanga 452 10M1 Nanoki 0c Male 7 LONDON RP Congo Ii 453 COLUMBUS 2000 El Jewar 0t Male 7 True False ANTWERP Nn 7 6 True False 457 YULEE 9500 Siri 0C Female ANTWERP Roubi 463 NYBRONX 9604 Hiari 0C Male True False LONDON RP Buta e2 ae CE todmale 6 Tue True i NYBRONX 371618 Congo ee ZOORASIA a ee a PARIS ZOO Nn 478 DISNEYAK 0002 Zenzelle 0C Female True False KISAN OKA Epulu anr NV RDANY O71N Kwali MI Female 5 True Eales lt HE Export import Export Revert to originally imported data Update Selection V Apply changes in Selection to Genetics V Apply changes in Selection to Demography True False won nnpwn m o u o m D Managed N 45 Pedigree Known 100 0 Current Gene Diversity 0 931 Potential Gene Diversity 0 953 Lambda 1 051 Additional changes to the Selected Population can be made on this screen First decide if the new Selected Population will apply to the demographic analyses and or to the genetic analyses Specify which analyses should use the new Selected Population by checking one or both of the boxes Apply changes in Selection to Genetics and Apply changes in Selection to Demography at the bottom right of the screen Different selections can be applied in a series f
39. a txt file as well as a csv file of the recommendations table with individuals as lines rows similar to the format in PMx This file can be opened in Word Excel or other programs and used to generate reports regarding individual recommendations The Export Insitutional Recs button will create a txt file of the recommendations grouped by institution for each institution that currently has or is recommended to receive an individual recommendations are first listed for Animals currently at the institution if any and then recommendations are listed for Animals planned to be moved to this institution if any as seen in the example below This file can also be opened in various programs to create a master plan report Animals currently at the institution 4562 MINNESO T 10470 Male Hold DoNotBreed 4930 MINNESO T 13238 Female Hold Breed 4984 MINNESO T 12317 Female Hold DoNotBreed 5200 MINNESO T 13204 Female Hold DoNotBreed TA TA TA TA Animals planned to be moved to this institution 4825 RACINE Male 8 SendTo MINNESOTA The exported text file for individual recommendations or any similarly formatted text file can be imported into PMx to modify the recommendations table There are two options mport Recs will import the individual recommendations in the text file replacing any existing recommendations in the table The Import List button will import the individuals in the text file but will not overwrite the existing re
40. a minimum estimate Rearing Rearing situation of the individual recorded in the studbook options are Parent Hand Foster Peer Supplemental Unknown None Colony Group ReproGoals A projection of the total desired number of future progeny for each individual given the current genetic and demographic structure of the population and taking into account optimal matings and optimal removals of over represented animals Exact achievement of all reproductive goals and optimal removals would maximize gene diversity in the next generation Offspring UniquelDs of the individual s offspring PriorMates UniquelDs of the known mates involved in producing individual s offspring ReproYears Years in which the individual produced offspring LastReproDate Date of last known reproduction date of birth of last offspring MyFounders UniquelDs of founders that are genetically represented in the individual MyFounderContribs Proportion of each founder represented in the individual in same order as MyFounders MyDescendants UniquelDs of the individual s descendants up to the first 25 Entity Whether this animal represents an individual or a group Count Number of individuals represented by this entity count 1 for an individual count group size for a group MatingType Indicates the process by which the entity was created Options are Sexual Clonal Selfing Merge for groups Split for groups Haploid
41. actual historical managed population over time For example if current living post reproductive individuals are removed from the genetic analysis these individuals will not be included in the historical genetic analyses even during their early and reproductive years see Section 2 Selection screen for more discussion on this topic EE PMx tapir_UNK Genetics Selection Summary Founders Individuals Kinship Matrix Pairwise Info Pairing Culling Management Sets Graphs Settings Population Founder Individual Custom Gene Diversity Founders 1 30 25 50 8 25 pf 2 20 6 215 c B ai 9 C 5 J85 1 199C 1 Founder Genome Equivalents Mean Inbreeding w T f 5 1 199C 19 Ji 1 Assumptions Dynamic Population Variables uona eae a SOME GD 0 9526 GV 0 9485 MK 0 0474 Known 96 N 47 0 PMx User Manual version 1 0 Page 102 Founder Graphs This screen shows histogram plots displayed one of four measures for each founder e Representation number of copies of each founder s genes present in the living descendant population e Descendants number of living descendants e Contribution proportion of the genes in the living descendant population that are derived from each founder e Retention probability that each founder s alleles are still present in at least one living descendant pir_UNK Genetics Selection Summary Founders Individuals Kinship Matrix Pairwise Info Pai
42. as an Administrator Short cuts to PMx should also specify that the program should run in Administrator mode On some Windows systems the hassle of needing additional rights to run the program can be avoided by installing the program within folders for user documents rather than within Program Files but on other systems programs are required to be placed within Program Files If you have trouble getting PMx to install and run try installing it in a different folder We know of no reason why PMx could not be installed on and run from a server but such configurations have not been tested and no support can be provided to troubleshoot site specific installation problems If you wish to reinstall PMx you may be required to first uninstall the prior version If you wish to keep a backup of prior versions save the installation package files rather than having multiple versions of PMx installed simultaneously Uninstalling PMx will not remove any project files that you created PMx User Manual version 1 0 Page 3 Creating a New Project To create a new PMx project open PMx and click New Project Specify a Project Name and Project Description to identify the project and the name of the PMx project file default name is the project name with the extension pmxproj Type in or browse using the button and choose the primary input file which will differ depending upon the program and version that was used to create the export files s
43. because neither this individual nor any of its relatives pass on the allele to an offspring Assumes that each individual will produce a number of future offspring equal to its reproductive value AgeDays Age of individual in days based on the Analysis Date on the Settings tab for living individuals or age at death for dead individuals AgeDays for individuals lost to follow up is designated by AgeYears Age of individual truncated to years based on the analysis date on the Settings tab for living individuals or age at death for dead individuals AgeYears for individuals lost to follow up is designated by AgeClass Age class of the individual based on the age class length designated on the Demography Settings tab AgeClass is the same as AgeYears for living individuals if age class length one year AgeClass for dead individuals is designated by Vx The expected number of offspring produced this year and in each future year by this individual based on its age and sex NOffspring The number of offspring already produced by this individual all offspring recorded in the studbook not affected by date span of the project NLivingOffspring The number of offspring already produced that are currently living PMx User Manual version 1 0 Page 125 NBroods The number of litters broods clutches produced by this individual based on birth dates only without regard to identity of mate and therefore
44. can be completely identified Certain exact identity of both parents is known and traceable back to known founders Individuals that are 100 Certain do not have any MULTs or UNKs in their pedigree Certainty represents a higher degree of knowledge than Known and therefore is always less than or equal to Known PMx User Manual version 1 0 Page 70 Gene Diversity Proportional gene diversity as a proportion of the source population is the probability Gene Value Founder Genome Equivalents Founder Genomes Surviving Mean Inbreeding that two alleles from the same locus sampled at random from the population are not identical by descent from a common ancestor Gene diversity is the heterozygosity of founder alleles 1 inbreeding expected in progeny produced by random mating Gene value is the gene diversity of the living individuals weighted for the reproductive value of individuals Gene value is the heterozygosity of founder alleles expected in progeny produced by random mating and if each individual were to produce the number of offspring expected from its age based reproductive value The number of unrelated individuals founders that would represent the same amount of gene diversity as does the population of currently living individuals A population s FGE becomes smaller than the actual number of population founders over time as founder representations vary and gene diversity is lost from the population
45. creating a project none of these formats currently generates ped files with the MOVE information PMx User Manual version 1 0 Page 144 The formats of these file types follow 1 prn Formats PopLink and SPARKS both can export a life table for import to PMx These are not the preferred import files for demography as they do not let the user define their own age classes There needs to be one PRN file for the males and another for the females These files can be produced as txt files manually if life table information is available from another source Format of file is as follows Line 1 Header Studbook Data for Not used for any purpose Line 2 Common name Line 3 Latin name Line 4 Sex Line 5 Data exported on mm dd yyyy Line 6 Data compiled by name Line 7 Contact info address Line 8 Data current thru mm dd yyyy Line 9 Scope of data international regional etc Line 10 Header Line 11 blank Line 12 beginning of data in following format Space number alive space Qx space Mx space Age class format x x 1 space sample size for Qx space sample size for Mx Line 12 n repeat data for each age class until no more animals at risk Data are followed by a blank line Next line Filter conditions in effect All following lines are optional Any additional lines will be interpreted as additional filter information For ex
46. is opened again e By selecting Save PMx settings in the File menu the current table configuration can be saved so that it will be the default lay out when new projects are created e Data within a table can be copied to the Windows clipboard for pasting into other programs using the standard highlighting Ctrl C copy and Ctrl V paste Windows commands e Clicking on an Export button will open a dialog box for saving the table as a tab delimited text txt file a comma delimited csv file or as an Excel x s file e Clicking on a Filter button will open a form for specifying the criteria on which the rows of the table can be filtered to a subset see below Filtering a Table View Rows on many tables can be filtered so that only a subset of individuals is displayed Note however that filtering only subsets the individuals that are viewed and does not affect the calculations It can be helpful to use a filter to create a subset of individuals that is then selected for another reason e g to create a Management Set in such cases calculations will be based on those individuals that were selected Some tables are filtered by default but these filters can be changed For example Males on the Pairing tab will initially be filtered to living males but unknown sex can be added if desired To filter the rows of a table click on Filter In the following window Filter Display for Table select one of the three buttons either 1 to disp
47. is that PMx will not display the largest tables e g the kinship matrix for large studbooks Installation The PMx installation package can be downloaded from www vortex9 org PMx PMx html This installation package should be saved to the local computer and then run It is likely that Administrator rights will be required to install PMx and during installation it may be necessary to authorize the installation program to make changes to the computer PMx is believed to be free of any malicious code and we do not collect any information about you or your system during the download installation or use of program However we can make no warranty that the copy of PMx you download and install is valid and cannot change your system in unwanted ways Always protect yourself through the use of anti virus software PMx can be installed in the default location usually C Program Files PMx or in any location on your hard disk Depending on the version of Windows under which it is installed and the system settings on your computer it may be beneficial or even required to install it in a specific location to which you have installation rights Also depending on the security settings on the computer it may be necessary to run it under Administration rights or to specify when PMx is opened that the program is authorized to make changes to files and folders If the program does not run when you try to start it right click on the program file and run it
48. number of births needed into an estimation of the number of litters and breeding pairs As a general rule boxes with white colored background may be changed by the user Note that the default values are not population specific e g default litter size equals 1 for all populations Boxes with shaded background show resulting calculated values Calculated values are all given as a range mean 95 Confidence Interval Enter the average litter clutch size for this population often reported in the studbook software this will allow PMx to estimate how many litters need to be produced next year to meet the goal This often is not the same however as the number of breeding pairs that are needed Two additional factors affect the number of pairs needed the probability that a recommended pair breeds i e produces a litter and the number of litters produced during the year by each pair The Reproductive Planning tab only allows for a single average probability of breeding to be entered to represent the success rate of all pairs however different probabilities of breeding can be attributed to specific pairs on the Pairing tab in the Genetics section Use your experience and knowledge of the biology husbandry and behavior as well as knowledge of the individuals in the population to estimate the overall probability that each pair will breed Probabilities lt 1 will result in the need for more recommended breeding pairs Another factor that a
49. other regional settings with automatic adjustment to reading and displaying data in the local format e g 1 00 in USA being the same as 1 00 in Germany and in both cases meaning the number one However some data management programs that are used to prepare pedigree data for input into PMx may use region specific data formats causing problems in the transfer of data into PMx In addition differences in regional data formats may cause problems for transferring PMx projects to other computers that have regional settings different from the computer on which the PMx project was created PMx has a Language option on the main menu tool bar that can translate the text on the screens into languages other than English At this time translations into Japanese Chinese Mandarin and Spanish are provided but these are still being completed and tested Other language translations will be included as options in the Language menu as volunteers provide the translated texts contact PMx vortex9 org if you want to offer to provide a translation When the language is changed not all labels within PMx screens will necessarily be translated immediately e g some labels already set on the tabs may not be updated but the text will appear in the last selected language when PMx is closed and then re opened If a translation is incomplete text for which we do not yet have the translations will appear on the screens in English Updates to PMx will include
50. population size Non Breeding Populations No Births option PMx provides the option to easily project population size given no reproduction This is useful for estimating population size and decline for populations being phased out and managed to extinction through attrition i e no reproduction normal survival How to Use This Tab The table on the left provides the numerical projections for each interval over time these projections are depicted on the graph on the right Default projection settings are for 20 years using one year intervals The number of time intervals projected can be changed on the demographic Settings tab a PMx NA MAL 25Mar Demography Overview Male Life Table Female Life Table Age Distribution Census Projections Reproductive Planning Add Remove Avaiabity Graphs Settings Display projections for Total years Intervals 1 year Agedass 0 1 2 3 4 5 6 7 8 9 10 1 Stochastic Projections Total 55 00 57 33 59 26 58 03 59 96 60 22 62 06 63 13 64 15 63 31 66 46 68 1 Births 442 566 336 522 459 652 440 664 5 90 806 66 o 3 00 4 22 540 321 498 438 621 420 634 563 769 63 100 284 4 01 513 3 05 473 416 591 399 603 535 73 140 2 10 00 1 00 281 398 5 09 303 4 70 413 587 396 598 53 3 200 979 0 99 275 3 90 499 296 460 4 05 575 388 58l 420 4 0 00 197 961 097 2 70 383 490 291 452 398 564 38 5 200 0 00 193 949 096 266 378 483 287 44
51. population size to census size of living captive born individuals PMx User Manual version 1 0 Page 75 Genetic Footer The footer across the bottom of the Genetic Overview tab contains reminders of the Assumptions with respect to the genetic analysis these assumptions can be changed on the genetics Settings tab Also displayed are a few genetic Dynamic Population Variables GD GV population MK Known N which are updated as Selected Pairs and Selected Culls are added to or removed from the analysis This footer is displayed at the bottom of all Genetic section tabs Cautions e Individuals that are toggled out of the selected population on the Selection tab for genetic analysis will not be included in either the current or historical genetic calculations e Since historical genetic values are based on the individuals in the current selected population for the genetic analysis they may not accurately reflect the actual genetic status of the population at those points in the past For example individuals that were excluded from the genetic analysis because they are currently sterilized or post reproductive permanent non breeders will not be tallied in the historical genetic values even if they were part of the managed population in the past e The Current Ne and therefore Ne N may be underestimated if living individuals such as permanent non breeders are removed from the genetic analysis on the Selection tab if these individuals
52. project If a saved PMx project is reopened the Actual Data values will be used for the Model Data Smoothing and or other desired changes to the Model Data will need to be re entered PMx User Manual version 1 0 Page 63 GRAPHS TAB Demography Purpose The demographic Graphs tab provides the user with graphical representation of basic Model Data life table values Standard as well as options to graph all life table and census table values Custom How to Use This Tab Standard Graphs Data for the four Standard graphs Mx Vx Qx Lx are taken from the Model Data life table on the Life Table tabs Any alteration or smoothing of data in the Model Data life tables will automatically be updated in the relevant graphs Peaks and dips in the graphs may be removed or smoothed by altering life table data see Life Table tab for more information Double clicking on a graph allows the user to print the graph export the graph to a png file or send the graph to the report Graphs sent to the report can be found on the Project Notes tab Overview Male Life Table Female Life Table Age Distribution Census Projections Reproductive Planning Add Remove Availability Graphs j Settings Standard Custom Mx Vx Males x E Males Females Females Model Qx Model Lx Males 5 0 5 Males Females Females 4 Ag Assumptions Overall Statistics Stochastic Runs Age Cl
53. provides an estimation of future population size total N males females given the model life table demographic rates applied to the actual current age and sex distribution Both deterministic and stochastic projections are provided as well as a deterministic projection based ona starting stable age distribution Projections can also be generated for non breeding populations Actual vs Stable The difference between the actual and stable projections demonstrates the impact of the current age structure For example if there are relatively few individuals of breeding age as compared to a stable age distribution growth will be lower and the population might even decrease in size The impact of non stable age distribution modulates and lessens over time as the age structure approaches a stable distribution Deterministic vs Stochastic Life table rates represent average rates over a period of time and across individuals In reality reproduction and survival varies for each individual these chance stochastic variations tend to even out in large populations but can have an impact on small populations These impacts accumulate over time producing more variation more uncertainty in projected N over time The mean stochastic projection provides a more realistic projection by incorporating these effects variation around this mean is provided as confidence intervals Cls which can be helpful in conveying the range of projected future
54. r Instantaneous rate of change of the population averaged for males and females If r gt 0 the population is increasing if r lt 0 it is decreasing Ro Net reproductive rate which is the rate of change per generation average number of offspring that an individual will produce in its lifetime averaged for males and females Ro gt 1 for increasing populations and Ro lt 1 for declining populations T Mean generation time averaged for males and females which is the average age of reproduction production of offspring It is also the average time from reproduction in one generation to reproduction in the next generation T is not the age of first reproduction Once stochastic projections are run the averages and bracketed Confidence Intervals are shown Default setting for the confidence intervals is 95 CI may be changed on the demographic Settings tab Click on Send to Project Notes to copy the table data to the Project Notes tab Double click on the graph for options to print the graph export it to a file or send it to the Project Notes tab Click on the Demographic Details tab to open the full Demography section of PMx an expansive demography module that includes tabs for more complex demography overview information male and female life tables age distribution and census graphs population projections reproductive planning supplementation and removal harvesting schemes and pre set and user defined demographic graph
55. recommended for the most reproduction over their lifetime and conversely which individuals are unlikely to ever receive a breeding recommendation The algorithm first uses dynamic MK pairing to produce enough offspring from the genetically top ranked males and females to increase the population to the user entered Limit Then the algorithm uses Auto Cull to remove the least valuable animals from the current generation until the population returns to the Target N again The algorithm goes back and forth between the dynamic MK pairing and Auto Cull until the entire next generation is created and the entire current generation has been culled see Appendix F for more information To calculate Life Time Reproductive Goals specify Target N The target population size in the next generation default current population size Limit The maximum population size allowed default value current population size 20 PMx User Manual version 1 0 Page 90 Max Pairs If Vx Multiplier box is not checked Enter the maximum number of times that each Male Female male female is allowed to reproduce i e the number of offspring each individual is allowed to produce as PMx assumes that each reproductive event produces only one offspring If Vx Multiplier box is checked PMx uses the numbers entered for Max Pairs as multipliers of the Vx demographic reproductive value based on the individual s sex and age to determine the maximum number of times
56. reproduced in the past A more accurate calculation for Current Ne and Ne N can be obtained by noting these values before removing any living individuals for the genetic analysis PMx User Manual version 1 0 Page 76 FOUNDERS TAB Purpose The Founders tab shows a list of all founders and several statistics about their genetic contributions to the living captive born population based on the selected population How to Use This Tab When opening this tab the default sorting of founders is by Unique ID As in most other tables in PMx the table can be sorted by any of the headings by clicking on the column heading and the individuals listed in the table can be filtered by clicking on the Fi ter button in the lower right hand corner Age Alive Representation Contribution Allele Retention Potential Retention Descendants 0 0105 0 0105 0 0118 0 0203 0 0075 0 0075 0 0085 0 0085 0 0228 0 0134 0 0134 0 0455 0 0475 0 0475 0 0205 0 0320 0 0320 0 0300 Anson Filtered showing 57 iter Dynamic Population Variables Do Not Indude Founders Unknown Weight 0 00 GD 0 9645 GV 0 9600 MK 0 0359 Known 100 N 143 0 The genetic contribution of each founder is described using the following five variables Representation Contribution Allele Retention Potential Retention Descendants Proportion of the genes in the descendant population that de
57. s lifetime PMx User Manual version 1 0 Page 73 GENETICS OVERVIEW TAB Purpose The Genetics Overview tab provides more detailed genetic information for the current and historical population as defined on the Selection tab when the box Apply Updated Selection to Genetics is checked This includes the number of living animals living descendants founders potential founders percent ancestry known and certain gene diversity and gene value population mean kinship founder genome equivalents founder genomes surviving mean inbreeding current and historical mean Ne and Ne N Projected values of select variables are also given based on management recommendations hypothetical offspring from recommended breeding pairs and the impact of recommended culls How to Use This Tab This tab is accessed from the Genetics Details button on the Genetics Summary Statistics screen The table on the left side of the screen provides a number of genetic statistics pertaining to the Current population Values in the Dynamic column incorporate the effect of hypothetical offspring produced by recommended breeding pairs as well as the removal of individuals recommended to be culled The remaining columns provide annual genetic values for the historical population during the selected filter window for analysis If individuals are added to or removed from the Selected Population on the Selection tab and the box Apply Updated Selection to Genetics is checked thes
58. so the result will be variable PMx User Manual version 1 0 Page 132 APPENDIX C FREQUENTLY ASKED QUESTIONS Questions occasionally come up about PMx during masterplanning or training courses Here are some frequently asked questions FAQs regarding the use of PMx We hope to continue to expand this section If you have suggestions for additional FAQs please send them to Kathy Traylor Holzer kathy cbsg org and include the answer if you know it General How can add additional input files after have already created the project Some files can be added after a project has been created the association files e g fed region files e g rgn moves files e g mov and UDF files e g udf can be added on the Genetics Settings tab Other files e g census files can only be added when creating a project When opening my PMx export files in Excel the numbers are converted to text How can I convert them back to numbers Text and comma delimited files can be imported into Excel Numbers exported to an Excel file will be converted as text a small green triangle may appear in the upper left of the cell To convert to numbers format in Excel 2007 select a range of cells and use the Number Format option to change the format of the cells to Number In Excel 2003 use the following For one cell Select the cell click the button that appears and click Convert to Number For a range of cells e Inan empty cell
59. the PopLink Database Folder Creates a male and female annual age class life table Age class lengths cannot be modified as the export consists of an already calculated life table not raw data Exchange csv SPARKS 1 6 Under Analysis Export to PMx for a given Provides the raw data for PMx to calculate filter condition male and female life tables Since the raw data are included users can modify the File will be in the SPARKS studbook folder age class width to different time lengths ANALYTICAL PopLink 1 Under Reports Menu select Survival Provides the raw data for PMx to calculate SURVIVAL Tool Check Analytical Survival male and female life tables Since the raw STATISTICS Statistics for Population data are included users can modify the INCLUDED Management age class width to different time lengths INDIVIDUALS 2 Set desired filter TABLE csv 3 With Analytical Survival Statistics Report click on the Included Individuals Table 4 Select Export 5 File will be in the PopLink Database Folder mov No software Manually Provides information on every move into currently and out of the population by any produces this individual Provides the raw data to file calculate male and female life tables ped None Manually For a ped file to be used it must contain MOVE information as specified above While a ped file is created by PM2000 PopLink and PMx but only after successfully
60. the desired association file Geographic Area Assocaton PMx User Manual version 1 0 Page 14 Go to the UDF tab in the main window Select one of the cells right click and select Export to Excel This will create a file called gc_UDF csv in the studbook folder the file will automatically open in Excel simply close the file and it will be saved in the appropriate format When creating the PMx project choose the UDF file on the second Create a New Project screen under Additional Optional Input Files and select the gc_UDF csv file from the studbook folder To specify an association select a fed file under Additional Optional Input Files In PopLink 2 1 these FED files are stored in C Users UserName Documents PopLink 2 1 Federation Files In PopLink 1 3 they are stored in C Program Files PopLink1 3 Federation Files Creating a Project from other Data Sources Although it is much easier to prepare the data files for use in PMx from the studbook programs SPARKS or PopLink it is possible to create the required Primary Input File and optional other data files from databases maintained in other programs or for example from data in an Excel spreadsheet The various formats of data files that can be read by PMx are provided in Appendix D Using Associations in PMx Associations are used to represent national or regional zoo associations such as EAZA JAZA AZA ALPZA etc SPARKS and PopLink provide fed files for
61. the file if started with The data record for each individual must begin with ID Special coding of Sire and Dam can be used to specify mating types other than sexual reproduction of a single diploid male with a single diploid female and optional lines can be inserted after a record to further specify multiple possible sires or dams move records or UDFs The formats for these special codes can be the same as specified above for the ped file but additional formats are also accepted as follows Multiple possible sires can be entered on lines following the animal as described above in the ped format These possible parent data can be entered on lines starting with SIRE SIRES and PMx User Manual version 1 0 Page 142 SIREPROBS rather than SIRE SIRES and SIREPROBS but when the asterisk is omitted then the probabilities are taken to be percents 0 to 100 rather than proportions 0 to 1 ISIRE ID sire1ID prob1 ISIRE ID sire2ID prob2 with the sirelDs being the possible sires and prob being the probability or proportional contribution for a possible sire and the ID being the offspring for whom that possible sire is being assigned Or equivalently ISIRES ID sire1ID sire2ID ISIREPROBS ID prob2 prob2 The ISIRE lines can be preceded with as in ISIRE And similarly for DAMS If possible sires or dams for an animal are listed several times in a
62. the population PMx will automatically only use individuals living in the population at the end of the analysis date span analyzed to calculate the genetic and demographic characteristic of the current population If different selections have been made for demographic and genetic analyses either selection can be viewed by checking the appropriate Apply changes box Checking the Apply to Demography box only will display the demographic Selected Population on the left checking the Apply to Genetics box whether or not the Apply to Demography box is checked will display the genetic Selected Population on the left Each table Selected Population or Not Selected may be exported at any time using the relevant Export button underneath the table and saved as a txt csv or xls file PMx User Manual version 1 0 Page 27 To return to the originally imported selection click on the Revert to originally imported data button and then on Update Selection button The original data selection will be applied to the demographic and or genetic analyses depending on which box es Apply changes box es are checked NOTE Reverting to the original data will reset modifications made in the project for example all Management Sets will be deleted Use this button with caution For SPARKS 1 5 and PopLink basic demographic exports If the studbook data export filters are set for a living today setting rather than a historical genetic filter as recom
63. this pair The default threshold is F 0 125 but will be set higher for populations in which the average F gt 0 125 The threshold set automatically by PMx for a particular dataset is given to the left of the table as No Way for F 0 125 Click on View MaterRx settings for more information or to modify MSI definition settings Modifying the MateRx settings will cause PMx to recalculate the Pairwise Info table and may reset the Filter Sort on variables and Addl Data variable to the default settings Dead individuals currently cannot be added to the Pairwise Info table Cautions MSI scores may not be suitable to use for managing every captive population Be cautious when using this feature for managing populations with unusual histories or structures few founders very small N large amount of unknown pedigree high levels of inbreeding PMx User Manual version 1 0 Page 86 PAIRING TAB Purpose The Pairing tab provides detailed information on the impact of breeding specific pairs on the genetic status of the population Recommended breeding pairs can be documented and their cumulative impact given a certain probability of success incorporated dynamically into PMx genetic calculations How to Use This Tab The default setting is for all males to be displayed in the left table and all females in the right table with unsexed individuals omitted from both tables These settings can be changed using the Filter button although th
64. to any individuals in the derived population except for its own descendants Founders are often wild caught but for some regional populations animals imported from another unrelated captive population might be considered founders as well If an unrelated living animal has no descendants that animal is considered to be a potential founder until it contributes progeny to the captive population then it becomes a true founder Living Animals The number of living animals in the currently selected population Living The number of living animals descended from founders This may be a fractional Descendants number because PMx normally excludes all animals with unknown parents from genetic analyses and includes only those parts of individuals that can be traced back to known founders For example an animal with a known dam but an unknown sire will be tallied as half an animal in genetic analyses unless otherwise specified under the Settings tab Ancestry The percentage of the living individuals pedigree that can be traced back to known Known founders either through positive identification of all ancestors or all possible ancestors Thus 100 Known individuals can have completely identified ancestors or can have MULTs multiple possible parents in their pedigree provided that the identity of all possible parents is specified in the Sire and or Dam fields in the database Ancestry The percentage of the living individuals pedigree that
65. version 1 0 Page 44 IDs Displays a variation of the age distribution figure indicating each animal by their UniquelD Clicking on one of these IDs in the table will provide a button that will open a window with summary information on this specimen The Animate button uses the demographic assumptions and overall statistics outlined in the footer at the bottom of the page and as seen in the other PMx demography tabs to animate the projected changes in the age distribution over time default projection 20 years The Animate feature works only when viewing the graph of the total living animals filter Alive The Reset button will reset the graph back to the original age distribution for the selected population Both the data table and the age distribution graph can be exported by clicking on the Export buttons Terms and Concepts Age distribution A two way classification showing the numbers or percentages of individuals in various age and sex classes Founder An individual obtained from a source population often the wild that has no known relationship to any individuals in the derived population except for its own descendants New Features e Animate button Animates the projected changes under assumed and current statistics outlined in footer of page in the age distribution of the total living population over time e Ability to view the age distribution of selected subsets of the population e g proven breeders by location
66. will be assigned 4 consecutive MKRanks but the 4th assigned is equivalent to the 1st assigned FOKE First Order Kin Equivalents The number of first order kin siblings or offspring that would contain the same number of copies of an individual s alleles identical by descent as are present in the entire captive born population Thus an offspring or sibling contributes 1 to FOKE each grand offspring contributes 0 5 to FOKE each cousin contributes 0 25 to FOKE FOKE 4 N MIK in which N is the number of living animals in the captive population KV Kinship Value The weighted mean kinship of an individual with the weights being the reproductive values Vx of each of the kin The mean KV of a population predicts the loss of gene diversity expected in the subsequent generation if all individuals were to mate randomly and all were to produce the numbers of offspring expected for individuals of their age GUAII Genome Uniqueness All The probability that a random allele from the individual is not present in any other living individual in the population founders included i e same allele descended from a common ancestor GUDescend Genome Uniqueness Descendants The probability that a random allele from the individual is not present in any other living non founder individual in the population descendants ProbLoss Probability that a random allele from the individual will be lost from the population in the next generation
67. 0 19 1980 None 1 1 1990 None 3361 alive at start of window 4 22 1996 None 5664 died complete 4 Male Captive Born 11 8 1981 None 1 1 1990 None 2976 alive at start of window 1 2 2001 Year 6995 died complete 15 Male Captive Born 10 18 1983 None 1 1 1990 None 2267 alive at start of window 12 3 2003 None 7351 died complete 23 Male Captive Born 10 11 1984 None 1 1 1990 None 1908 alive at start of window 3 28 1990 None 1994 died complete PMx User Manual version 1 0 Page 146 4 MOVE file Formats There should be a record for every instance an individual entered the filter window PMx will normally expect such files to have extension mov but they can be any text file Skips comment lines starting with Record format ID Dateln InEst InType DateOut OutEst OutType Location Notes Formats for the dates move types and date estimates are the same as specified above for the MOVE records that can be inserted into a ped file Location and Notes are optional ped Formats To be used for demography the ped file must contain MOVE information See above for format of the ped file with MOVE information Census File Formats The table below shows the types of input files that can be optionally imported to generate Census content in PMx the software that creates them how they are created and their content File Type Created Using Created by Contents Uses exchcens txt SPARKS 1 56 In SPARKS Under Analysis run a Yea
68. 00 The lower limit is set at 0 1249 or a user defined level The break point is the average F of all possible pairs Bin 1 is limited to F 0 00 Bins 2 and 3 are each 50 of the range between 0 00 and the break point Bins 4 6 are each 33 of the range between the break point and 0 1249 or upper limit The default No Way point is 0 125 however this point is modified for inbred populations in which the average F is greater than 0 125 as follows If average F gt 0 5 No Way 1 0 If average F gt 0 25 No Way 0 5 If average F gt 0 125 No Way 0 25 Otherwise No Way 0 125 PMx User Manual version 1 0 Page 109 It is possible to edit the bin definitions On the genetics Settings tab use the pull down menu for Edit Bin to select the variable to edit and click the Go button This will open a window that allows the bin definitions to be modified either by specifying Values default or Percentiles The Break Point and No Way point can also be modified The right side of the window provides a summary of the number of pairs that fall into each Bin based on the variable being edited left column and based on the composite MSI values using the definitions in this window The box in the lower right corner gives the Minimum Mean and Maximum values for the variable being edited for those pairs evaluated here those above the No Way point for F and for all possible pairs Global Editing Delta_GD Select wh
69. 2 Ebola 10 4 m 4 m pE Export import _ Export Revert to originally imported data Update Selection 7 Apply changes in Selection to Genetics V Apply changes in Selection to Demography n Managed N 170 Pedigree Known 100 0 Current Gene Diversity 0 953 Potential Gene Diversity 0 977 Lambda 1 030 Exactly which individuals are included in the Managed N when the PMx project is first created can be checked by sorting the Selected Population table by the column Alive and checking which individuals have Alive True and Gone False The Gone column checks which individuals have left the population before the end of the date span analyzed through Death Lost To Follow up Release or Export individuals that left the population are marked as Gone True while those that are still in the population at the end of the date span are marked as Gone False For example an individual that was exported from the population e g went to another zoo region but is not dead would be marked as Alive True and Gone True and would not be included in the Managed N PMx User Manual version 1 0 Page 26 Project Notes Selection Demography Genetics Goals Recommendations Selected Population Number Induded 137 Number Not Induded 576 UniqueID Location Loca HouseName Otl Sex AgeYears Alivee Gone Location LocalID HouseName OtherID a 423 OKLAHOMA 7295 Malaika Ill Female g True False ANTWERP O jeta 432
70. 2M1490 CHIKO UN Male 1 0000 1 0000 2008 10 14 Exact True DeathDateEst LANGKEA __ CHKI UNJ Female 1 0000 1 0000 2008 10 14 Exact True DeathCode MELAKA e E Male 1 0000 1 0000 2008 10 14 Exact False Dam MELAKA a Cl Unknow 1 0000 1 0000 2008 10 14 Exact False Sire MELAKA NICOLE UNJ Female 1 0000 1 0000 2008 02 07 Exact False R s l SireProb Update Table Unfiltered showing 277 Gen F Assumptions Dynamic Population Variables MK Do Not Include Founders Unknown Weight 0 00 GD 0 9125 GV 0 9164 MK 0 0875 MKRank FOKE Kv PMx User Manual version 1 0 Page 79 Some columns include multiple pieces of information Clicking on one of the individual data cells in the column will display a button Click on this button to open a box that displays each piece of data This applies to Other ID Sire Dam SireProb DamProb Offspring PriorMates ReproYears MyFounders MyFounderContribs UDFs DemMoves and GenMoves It is possible to edit some of the data directly in this table rather than having to import a new dataset For example the Sex or House Name of an individual can be changed in this table Other data fields such as the mean kinship value of an individual cannot be edited Clicking on one of these cells will display the message This variable cannot be edited Once changes have been made clicking on another tab will bring up two messages Would you like to update Genetics to include your data changes and Wou
71. 35 Litters year 2 35 8 6 5 43 30 Prop Pair Breeds 0 3 9 5 1 34 i T Litters Needed 1 0 lt gt 2 1 lt gt 3 2 10 5 1 3 4 0 Pairs Needed 1 6 lt gt 3 5 lt gt 5 3 j Export 5 0 Includes infant mortality Mean 95 CI 5 0 0 10 1 1 years Assumptions Overall Statistics Stochastic Runs Age Classes are years Birth Flow Continuous CI 95 Iterations 500 Growth in terms of years r 0 065 lambda 1 067 Projections 20 time steps Ro 1 946 T 8 6 N20 87 Up to date The Births Needed table in the center of the tab show how many births are needed in the next year and each subsequent year to grow or reduce and maintain the population at the target size The demographic rates from the Model Data life tables are applied to the age and sex distribution of the PMx User Manual version 1 0 Page 55 current population to make these calculations These calculations take into consideration the neonatal mortality rates so the number of Births Needed represents the actual projected number of births needed as opposed to the number of surviving births The Pairs column in the table displays the estimated number of pairs needed each year this calculation takes into consideration the probability that a pair will breed and number of litters produced per year see further discussion below The Reproductive Needs per Time Interval section on the lower left side of the screen can be used to translate the
72. 56 0 56 0 00 4 0 1 50 0 00 0 02 18 100 050 0 00 40 056 0 56 000 4 0 1 50 0 00 0 02 19 0 00 0 00 1 00 0 0 056 0 28 0 00 0 0 1 00 0 00 0 01 19 0 00 0 00 1 00 0 0 0 56 0 28 0 00 0 0 1 00 0 00 0 01 20 0 00 0 00 1 00 0 0 0 00 0 00 0 00 0 0 0 00 0 00 0 00 20 000 0 00 1 00 0 0 0 00 0 00 0 00 0 0 0 00 0 00 0 00 21 0 00 0 00 1 00 0 0 0 00 0 00 0 00 0 0 0 00 0 00 0 00 0 00 0 00 1 00 0 0 0 00 0 00 0 00 0 0 0 00 0 00 0 00 Growth in terms of years r 0 060 lambda 1 062 Ro 1 447 T 6 1 N20 60 Export Growth in terms of years r 0 060 lambda 1 062 Ro 1 447 T 6 1 N20 60 Export Reset Smooth Table has been smoothed 0 times Settinas Overall Statistics Stochastic Runs Age Classes are years Birth Flow Continuous CI is95 Iterations 500 Growth in terms of years r 0 078 lambda 1 081 Projections 20 time steps Ro 2 089 T 8 3 N20 114 Outdated On the left side of the screen is the Actual Data life table which represents the true demographic rates imported into PMx and cannot be modified On the right side of the screen is the Model Data life table Initially both life tables display the same data however the Model Data life table can be manually altered or smoothed Editable values in the Model Data life table are highlighted in gray and bolded Px Qx and Mx Once any of these values is altered PMx will automatically update the other values affected by the change both in the Model Data table and a
73. 6 392 55 6 7 8 3 00 1 88 0 00 1 82 9 21 0 96 2 56 3 67 4 70 2 79 4 33 38 3 00 2 82 175 0 00 1 69 8 71 0 92 2 40 3 47 4 44 2 64 4 1 3 00 2 90 2 73 1 70 0 00 1 65 8 40 0 88 2 33 3 35 4 28 2 54 kd 4 00 2 95 2 88 2 70 1 70 0 00 1 65 8 28 0 86 2 30 3 30 4 2 10 5 00 3 89 2 84 2 82 2 65 1 70 0 00 1 65 8 03 0 81 2 26 3 21 11 11 00 4 86 3 75 2 71 2 76 2 59 1 70 0 00 1 65 7 75 0 75 2 2 40 12 0 00 10 84 4 79 3 68 2 64 2 73 2 56 1 70 0 00 1 65 7 60 0 7 13 1 00 0 00 10 00 4 43 3 44 2 52 2 50 2 35 1 50 0 00 1 45 7 1 14 2 00 0 86 0 00 8 80 3 90 3 05 2 26 2 19 2 06 1 29 0 00 1 24 1 00 1 82 0 85 0 00 8 45 3 74 2 90 1 00 1 00 1 82 0 72 0 00 7 62 3 38 3 00 0 70 1 00 1 82 0 50 0 00 6 30 0 00 3 00 0 59 1 00 1 82 0 43 0 00 m lt Export E Project with no births Deterministic Settinas Overall Statistics Stochastic Runs Age Casses are years Birth Flow Continuous CI is95 Iterations 500 Growth in terms of years r 0 078 lambda 1 081 Projections 20 time steps Ro 2 089 T 8 3 N20 114 Up to date PMx User Manual version 1 0 Page 50 The initial projection displayed is deterministic for the total population and possibly also stochastic depending upon version of PMx used Projections can be viewed for males and females separately using the pull down menu above the table Projections can be toggled between reproducing and non reproducing populations using the check box below the table The table
74. 7 contracepted female any other code will be interpreted as unknown sex with unknown fertility 2 exchange csv created by translation of exchange dbf The exchange dbf file created by SPARKS can be transformed into a csv or txt text file for example through importing and then saving the data using Excel An advantage to taking this extra step is that the text file can be easily edited to insert additional data fields that are not included in the exchange dbf file created by SPARKS Although Excel commonly creates a csv comma separated values file as one possible text format PMx actually requires that the delimiter between fields NOT be a comma so it may be necessary to use a text editor to replace all comma delimiters The fields can be separated by a colon semi colon or tab Commas as field delimiters are not permitted by PMx because they cause confusion when used with regional data formats in which the comma is the decimal delimiter The first line of the file is a header listing the exchange fields It must be there The second line is an optional header that contains optional UDF labels with the format UDFS UDFiLabel UDF2Label Any number of comment lines can be inserted in the file if the comment lines are started with The list of fields for each individual is the same as for the exchange dbf above except that each line can be extended with any number of UDFs Special coding of
75. 7122 FGE 2 07 Known 100 N 21 0 Kinship Matrix Clear Empirical Kinships On each axis in the main kinship matrix one additional column of data can be displayed following the Unique ID The default variable displayed is Location Use the Addl Data pull down menu at the bottom of the screen to choose a different variable to be displayed Unique ID is the default order of individuals The Sort on pull down menu at the bottom of the screen can be used to choose a different variable for sorting individuals As in the other Genetic tabs the individuals displayed in the kinship matrix can be filtered to display a particular subset of individuals by clicking on Filter in the lower right hand corner of the screen To include kinship coefficient data that were calculated from a data source different from the pedigree analysis e g molecular data from microsatellite analyses click the Read in Empirical Kinships button This option allows the user to specify a matrix of relatedness or kinship s among pairs of individuals For example this method can be used to define kinships among founders rather than using the default assumption that founders are not related Founder kinships may be available because of known familial relationships such as a clutch or littermates or from molecular genetic evidence that indicates close kinship among some founders PMx User Manual version 1 0 Page 81 EE PMx Crowned lemur Genetics
76. 91 0 90 0 36 25 2 12 30 1 26 0 07 5 1 00 1 00 0 00 25 0 0 89 0 89 0 15 25 0 11 40 0 97 0 07 5 1 00 1 00 0 00 25 0 0 89 0 89 O45 25 0 11 40 0 97 0 07 6 1 00 0 96 0 00 24 3 0 89 0 89 0 29 243 10 40 0 87 0 07 6 1 00 0 96 0 00 24 3 0 89 0 89 0 29 243 10 40 0 87 0 07 7 0 92 0 96 0 08 218 0 89 085 0 14 21 8 9 81 0 65 0 06 7 0 92 0 96 0 08 218 0 89 085 O44 218 9 81 0 65 0 06 8 1 00 0 97 0 00 20 7 0 82 0 82 0 29 207 9 21 0 57 0 05 8 1 00 0 97 0 00 20 7 0 82 0 82 0 29 207 9 21 0 57 0 05 9 0 95 0 94 0 05 18 8 0 82 0 79 0 00 18 8 8 43 0 30 0 05 9 0 95 0 94 0 05 188 0 82 0 79 0 00 18 8 8 43 0 30 0 05 10 0 94 0 93 0 06 143 0 77 0 75 0 18 14 3 7 89 0 34 0 04 10 0 94 0 93 0 06 14 3 0 77 0 75 O48 14 3 7 89 0 34 0 04 11 0 92 096 0 08 96 0 73 0 70 0 00 96 7 40 0 18 0 04 11 0 92 0 96 0 08 96 0 73 0 70 0 00 96 7 40 0 18 0 04 12 100 1 00 0 00 8 0 0 67 0 67 0 20 80 6 67 0 20 0 03 12 100 1 00 0 00 80 0 67 067 0 20 80 6 67 0 20 0 03 13 100 092 0 00 80 067 067 0 00 80 5 67 0 00 0 03 13 100 0 92 0 00 80 0 67 067 0 00 80 5 67 0 00 0 03 140 83 091 017 68 067 061 0 00 68 5 09 0 00 0 03 14 0 83 0 91 017 68 0 67 061 0 00 68 5 09 0 00 0 03 15 100 1 00 0 00 44 056 0 56 0 00 4 4 4 50 0 00 0 02 15 1 00 1 00 0 00 44 0 56 056 0 00 44 450 0 00 0 02 16 1 00 1 00 0 00 40 056 056 0 00 4 0 3 50 0 00 0 02 16 100 1 00 0 00 4 0 0 56 0 56 0 00 4 0 3 50 0 00 0 02 17 100 1 00 0 00 4 0 0 56 0 56 0 00 4 0 2 50 0 00 0 02 17 100 100 0 00 40 0 56 0 56 000 4 0 2 50 0 00 0 02 18 100 050 0 00 4 0 0
77. DFs including the first seven are combined into this column with UDFs separated by DemMoves Displays the conditions for how the individual entered and left the project window This will match GenMoves unless a separate Moves file is imported Options for entering the project are Capture Birth LeftEntry Unknown Options for leaving the project are AliveOut Lost Release Death GenMoves Displays the conditions for how the individual entered and left the project window Options for entering the project are Capture Birth LeftEntry Unknown Options for leaving the project are AliveOut Lost Release Death Gone True if the individual is not in the population at the end of the date span defined by the project The individual may have left the project through death or transfer or be Lost to Follow up Itf Inverse of the variable Alive GoneDate Date on which the individual left the population if it left by some means other than death such as by transfer export or lost to follow up This is the true exit date and is not restricted to the date span defined by the project Individuals that are either alive at the end of the project or have died have a GoneDate of Flag Click the button to set a color flag for one or more individuals Multiple sequential individuals can be flagged using the Shift key Once flagged individuals can be sorted or filtered by color similar to a UDF Notes Notes of any kind may be typ
78. Ex cannot be calculated or plotted Why is the Census tab blank What does the message that the census is not available mean You must attach the correct census file in the second screen when creating a project For SPARKS 1 5x or PopLink this is the exchcens txt file if you exported from SPARKS 1 6 then the census input file is pmxcens csv You must run the Census Report in SPARKS 1 5x or PopLink to create the necessary exchcens txt file SPARKS 1 6x creates the pmxcens csv file automatically during the PMx export Why does the stochastic projection for my population show a decline while the deterministic projection shows positive population growth Stochastic projections incorporate additional factors not considered by deterministic projections Skewed sex ratio in particular has no effect on deterministic projections but can have a significant impact on stochastic projections Monogamous species with skewed adult sex ratios will suffer from a limitation of mates leaving unpaired unbred adults of the more common sex For polygynous species e g many herd species too few females lead to a similar problem however fewer males is typically not a problem and in fact may be an intentional management strategy For such species it is important that the maximum number of females bred per male is set correctly on the Demographic Settings tab so that female biased populations are modeled correctly Other factors such as very small popu
79. ID she will be treated as an UNK founder unless an animal with that ID is actually in the studbook 4 Exchange csv created by a PMx export from SPARKS 1 6 SPARKS 1 6 exports the pedigree to PMx as a semi colon delimited text file that contains more information than the data exported by SPARKS 1 5 or by PopLink Although semi colon delimiters are used to avoid confusion with numeric formats the file must have a csv extension so that PMx can recognize it as a SPARKS 1 6 export The first few lines of the file are headers each beginning with These header lines are ignored by PMx Another header line provides the date window used in the export with the following format Dates 01 01 1970 lt 28 02 2011 A mandatory header line lists the exchange fields with format ID ID Sire Dam Sex Selected BirthType ReproStatus Living DOB DOBest DOD DODest DeathCodes Location LocallD Social Program Country HouseName Transpond TagBand Tattoo ColorPhase Litt erSize No_Litters Litter_List UDFs Note that this line specifies the sequence of data fields in all individual records so it is critical that it be included and correct The next line is an optional list of UDF labels UDFs UDF1label UDF2label Several further header lines describe the format of lines that specify multiple possible parents and move records These lines begin with and are ignored by PMx Any number of comment lines can be inserted later in
80. Male Female Unk_sex Tot_born Wildborn Capt Unk 1962 Tairas E PAES UE Tesvesstea 1a R Banua 0 R ke SE Tairnissia Lorssa D savdeee l R y En 7a secens Sieve 0 1964 Toisia 1 EE PANE A iiesia batt A OE Ce S ERNE 0 n LIG Bisso O aiite Divvecsees Baaai N o O Oorarrgei Jori 0 1966 S T Dires Boccdintay 7 AAE o TEE Oori e O 0 1967 E SE T esite A E Dakaesaes 163 svete Be asias e Ni 0 1968 L Linviceres De cents SAE Ibiri a be Peery Betis 0 Etc 2 PMxCensus csv format This should be a semi colon separated file Line 1 is blank Line 2 followed by species name This line is not used for anything Line 3 followed by variable names not used for anything but data are expected to be in this order for each record Variables need to be in this order separated by names of variables are irrelevant Order Content Order Content Order Content 1 Year 11 Females captured 21 Sex released 2 Total alive 12 Sex captured 22 Males died 3 Male alive 13 Male born 23 Females died 4 Female alive 14 Females born 24 Sex died 5 Sex alive 15 Sex born 25 Males imported 6 Total alive 16 Males stillborn 26 Females imported 7 Wildborn alive 17 Females stillborn 27 Sex reported 8 Captive born alive 18 Sex stillborn 28 Males exported 9 Origin alive 19 Males released 29 Females exported 10 Males captured 20 Females released 30 Sex exported
81. NE 5456 5200 0 0274 0 3500 25 0 0321 0 0363 COLUMBUS 0 0276 0 0203 SAN FRAN 5341 4970 0 0000 0 6000 2 5 0 0341 0 0381 CALGARY 0 0276 0 0203 STPAUL 5464 4969 0 0625 0 4000 25 0 0341 0 0359 CHICAGOBR 0 0285 0 0251 DES MOINE 5286 5287 0 0000 0 2500 25 0 0341 0 0277 NY BRONX 0 0287 0 0223 CHICAGOBR o 0 0347 0 0356 RACINE 0 0300 0 0265 MADISON Pairs 18 Offspring attempted 45 0 0356 0 0359 CLEVELAND 8 Woss e m a Offspring expected 19 13 Export Filtered showing 43 Filtered showing 74 Assumptions Dynamic Population Variables Do Not Indude Founders Unknown Weight 0 00 GD 0 9645 GV 0 9601 MK 0 0359 Known 100 N 144 1 Success 0 4 Selected Pairs PMx User Manual version 1 0 Page 87 Once a pair has been highlighted for breeding enter the estimated probability of success for that pair range is 0 to 1 in the Success field Enter the Offspring attempted for this breeding e g mean litter size x number of litters The default for both variables is 1 i e 100 chance of producing 1 offspring These variables can be different for each pair allowing for different expected breeding success rates for different pairs e g due to health age needed transfers etc Click on the Accept button to accept a highlighted pair This will add the pair to the Selected Pairs table on the right Breeding Location and other Notes about the recommendation can be entered into this table
82. SI is a composite score that integrates four l ene er peren genetic components Delta GD MKDiff Inbreeding and Unknown into a single index These variables _ Edit how unknown pedigree affects MSI are combined using specific definitions that can be Edit Weights ae Sells modified to assign a MSI score of 1 to 6 for each pair with MSI of 1 3 being genetically beneficial and 4 6 being genetically detrimental to the population and indicating No Way pairs that aioe dema should not be bred due to high kinship level of pair Viewing MSI Information Click on Details at the bottom center of this screen or View MateRx settings on the Pairwise Info tab to open a new window that give the Minimum Mean and Maximum values for Delta GD GV Diff MK Diff Inbreeding Coefficient and Mean Kinship for all pairs in the population Also given are the current settings for several factors related to the calculation of MSI many of which can be changed on the Settings tab Displayed on the right is a histogram of the MSI scores for all pairs in the population see the Pairwise Info tab for further explanation of MS and other variables Click the Export button to save the table as a txt file Click the Edit button to return to the Settings tab Minimum Mean Maximum 0 0001 0 0000 0 0002 Distribution of MSI values 0 0000 0 0116 0 0482 Inbr Coeff 0 0000 0 0217 0 5000 Mean Kinship 0 0000 0 0251 0 0482 Parameters
83. Sire and Dam can be used to specify mating types other than sexual reproduction of a single diploid male with a single diploid female and optional lines can be inserted after a record to further specify multiple possible sires or dams move records or UDFs The formats for these special codes are the same as specified below for the ped file PMx User Manual version 1 0 Page 138 3 ped file created by either PM2000 or PopLink The ped file is a simple text file that is produced automatically when a PM2000 project is created or can be exported from PopLink Like the exchange csv file above it has the advantage that optional additional data can be inserted that are not automatically included in the exports from PM2000 or PopLink Comment lines starting with will be skipped except for special types of lines as described below First line specifies the analysis date as Analysis date 20091231 Next line is a header starting with Number of animals and it will be skipped UDF labels can be optionally specified in a header line as UDFs UDF1Label UDF2Label Primary data record format must be all on one line with fields in the following order ID SirelD DamID Sex Selected T F Dead T F Birth Date blank if unknown Death Date blank if not dead or not known Location Local ID Other ID Any number of UDF fields can be appended to each data line Sex is coded as 0 7 interpreted as in SPARKS see above
84. Subpopulations can also be created by manually selecting individuals To do this use the Ctrl and or Shift keys to right click and highlight all of the individuals that are to be grouped as a subpopulation With these individuals highlighted click the button and select Create a subpopulation from selected individuals Name the subpopulation and click OK Empty subpopulations can also be created e g wild habitat into which captive individuals will be reintroduced PMx User Manual version 1 0 Page 96 Create a sub population from the Full Population Create a sub population from each Location Create a sub population from each Assodation Create a sub population from each Region Create a sub population from each Country Create a sub population from each Socal Group Subpopulations can also be removed Highlight the subpopulation on the list of Management Sets and click the button to remove the selected subpopulation Clicking the Reset button will remove all of the subpopulations Once created individual subpopulations can be selected and viewed by using the drop down list for Current Set Clicking on a Management Set in the table on the left will also open that subpopulation as the Current Set on the right Like most tables in PMx the Management Sets and Current Set tables can be saved as txt csv or x s files using the Export button sat PMx Samp ect Feader s
85. This option is a good scheme for populations with a good probability of success for pairs Ranked MK This breeding scheme goes through the entire list of possible breeding pairs uses iterative culling to remove the worst options based on Mk from the list and then recommends that the last remaining male and female as a pair repeating this process until the desired number of pairs are selected This option is a good scheme for populations that get one opportunity for breeding and then die i e use for discreet generations reintroductions or at least have relatively little overlap of generations Repro Goals This button at the top of the screen estimates the lifetime reproductive goals for the currently living individuals in the population This is a new tool that has not yet been extensively tested Only use if you are familiar with the underlying algorithms in this tool This tool projects the number of offspring that each currently living individual is expected to be recommended to produce over its lifetime if everything were to happen perfectly as planned e g survival and reproduction is predictable and realized according to the life table data in order to replace the entire living population with the entire next generation WARNING this tool indicates the number of offspring to produce over an individual s lifespan not just in the next year This should be considered as an approximate benchmark to identify which individuals may be
86. Type Plot Variable s For Line Graph Plot from year Earliest 1934 7 Total E Males Bar Graph 1990 E Females E Sex Assumptions Overall Statistics Stochastic Runs Age Classes are years Birth Flow Continuous CI 95 Iterations 500 Projections 20 time Growth in terms of years r 0 013 lambda 0 987 Ro 0 907 T steps 7 9 N20 197 Up to date Ex Life expectancy or the average number of additional years an individual in age class x can expect to live Vx Reproductive value or the expected number of offspring produced this year and in future years by an animal of age x Cx Proportion of population expected for this age and sex class under a stable age distribution Risk Qx Number of individuals at risk of dying during that age class sample size for Qx Risk Mx Number of individuals at risk of reproducing during that age class sample size for Mx Lambda Proportional change in population size from one year to the next Lambda N is based on observed changes in population size due to all causes Lambda Repro is based on population changes due to births and deaths only New Features PMx greatly increases the variables that can be plotted over time Notable new variables include Institutions Sex Ratio Lambda N and Lambda Repro under Custom Census graphs Helpful Hints e Ifthe model data have not been altered the Model line s will overwrite the Actual data line s making it appear as if t
87. XE Geographic rea During Date Span Dates During 25 Feb 2611 gt 26 Feb 2611 Age Unknown ge Sex Event Type Coop Mgmt Plan Birth Origin Founder Mult Breeder Rearing Association VLiving Dead LIF Necropsy info Inbreeding Parent Inbreeding Permanent Temp cimen report and other reports User Defined Flds her key returns to previous menu User Selected Flag tt Change Bi lt Select p en Othe StudBook Report uestionnaire nalysis sort elationships order asterplan Social Groups abe ls Cards Sa OA ONL 3 From the Reports menu select Analysis gt Export Data Use the Down arrow key i i move to Genetic and then use the Space bar on the keyboard to choose Genetic Use the Down arrow key to move to the next field The default name for the export will be EXCHANGE dbf you may change this Select Do not run the program now Use the Down arrow key to move through the rest of the screen To run Genes or Demog consult the SPARKS manual 4 You will be asked if you wish to include animals released to the wild in the calculations It would be unusual to answer yes 5 The export will be created and stored in the studbook folder 6 Close SPARKS or reset the View Criteria for a demographic import see below PMx User Manual version 1 0 Page 7 cx SPARKS15 EXE Export Data Analysis File Report End Date Data File Names Export type lt gt Demographic fccept the default export fi
88. a GD GV Diff and F is referred to as the Tulsa method based on a set of rules by the MateRx software design team and other members of the AZA Small Population Management Advisory Group SPMAG First each pair is assigned a rank of 1 to 6 for each of the factors Delta GD GV Diff and F Their rank is 1 if the value for that pair falls in the first bin 2 if the value falls in the second bin etc Thus each pair will have three ranks e g 1 2 1 These three ranks are then evaluated to derive a final MSI as follows If all ranks lt 4 e If ranks are 111 then MSI 1 MSI 2 for ranks of 222 MSI 3 for ranks of 333 e If sum of ranks lt 5 then MSI 1 i e 112 121 211 otherwise e If sum of ranks lt 6 or GD 1 then MSI 2 i e 113 131 311 122 123 132 133 e All others are MSI 3 i e 223 232 233 322 323 332 For ranks with at least one 4 e If F 6or GV Diff 5 or 6 then MSI 6 otherwise e If GD 1 2 3 or 4 then MS 4 e 6 If GD 6 then MS 5 e IfGD 5andF 5 then MS 5 e IfGD SandF lt 5 then MS 4 These three genetic components are based on pedigree data If there is an unknown parentage in the pedigree of an individual PMx cannot calculate these measures accurately Individuals with partially unknown pedigree will have these variables calculated using the known portion of the pedigree The more uncertainty there is about the pedigree the less valuable these estimates become The general management st
89. abels until then Demography setting Genetics setting Use Probabilities Probabilistic Parents Most Likely Most Likely Parents Treat Mult as Unknown Omit Uncertain Parents Note that the default setting for Demography is different than the default setting for Genetics PMx User Manual version 1 0 Page 68 Time unit for results default years Change the time interval for reporting results default years to days weeks months or decades This changes only how population growth lambda r is reported the rates are relative to the interval chosen here This setting does not change the age class length Length of projections default 20 time steps Change the number of time intervals to project into the future maximum 100 This applies to deterministic projections stochastic projections age distribution projections reproductive planning add remove plans and availability projections Number of iterations default 500 Change the number of iterations maximum 1000 Confidence interval default 95 Change the confidence interval for stochastic projections options are 95 90 75 and 68 Maximum females bred per male default determined by relative values of average reproduction of males and females Change the average number of females that breed with each breeding male PMx uses this number in stochastic projections to account for limited availability of breeding males in female biased popul
90. able after the Sire D and DamID in which case the missing values will be assigned as probability 1 0 offspring 1 location and notes both blank The inbreeding coefficient is ignored as PMx will calculate the inbreeding for the pair For example Sire Dam F Success Offspring Location Notes 391 390 0 0000 0 8000 4 CHICAGOBR High priority 412 417 0 1016 1 0000 1 LONDONRP Nice animals 437 425 0 1016 0 2500 1 ST LOUIS Mean Culling File A set of animals to be culled from the population can be specified within a file for later reading into PMx The first line can be an optional header with UniquelD Location or anything that starts with UniquelD and it will be skipped The subsequent lines list one per line the IDs to be culled These can be optionally followed by Location or any other information separated from the ID by v or tab For example UniquelD Location 317 DALLAS 338 SAN ANTON 377 COLO SPRG PMx User Manual version 1 0 Page 151 APPENDIX E PMX OUTPUT FILES Most of the work with PMx is interactive assessing population status via analyses shown on screens and working through demographic and genetic decisions to obtain population management goals Tables graphs and final recommendations can be exported in various formats to facilitate the documentation and dissemination of management plans However hidden within the pmxproj file that is created when PMx saves a proje
91. about 20 zoo associations which are text files that list the ISIS mnemonic for each institution that is a current member of that association as of the date that the fed file was created These fed files are updated approximately annually and are available from ISIS If an association fed file is attached in PMx then this association will be listed in the Association column on the Individual tab for all individuals whose last Location was a member of that association Although only one fed file can be attached during the creation of a project additional multiple fed files can be added on the Settings tab in the Genetics section Individuals can belong to more than one association because institutions themselves can be members of more than one zoo association Management sets can also be created automatically based on Association Caution Note that Association is accurate at the point in time that the fed file was created since institutions move in and out of zoo association membership over time the Association member list may not be accurate for historical or future data Using Regions in PMx Regions are used in PMx to represent the geographic region in which the individual physically lives based on its last Location This means that an individual cannot be in more than one region at a particular point in time SPARKS 1 6 exports data to PMx that include the Country and Region for each individual based on last Location when the individual exit
92. ade it in the analyses should always be documented otherwise it is almost certain that you will later forget what you did in your analyses Project notes can be copied and pasted into Word documents or other editors When analyzing a pedigreed population and planning population management within PMx the most logical sequence in which to work is to follow the order of the tabs After creating the project first examine the Project Notes to confirm that the imported data were what was intended Then add to those Project Notes any additional documentation for the project Next the Selection section can be used to refine which individuals from the studbook are in or not in the analyzed and managed population The Demography section would normally be visited next to determine the demographic trends and prospects for the population The Genetics section is then used to determine both the genetic health of the population and which pairings will be best to maintain that health The Goals section can then be used to integrate demographic and genetic analyses to decide what long term population goals can be achieved Finally the Recommendations section provides a table for documenting the decisions made about each individual In actual use of PMx the user will probably move back and forth between these sections for example to revisit demographic planning after the goals are refined but it will often be useful to work initially through the sections in or
93. agement Center Lincoln Park Zoo Kristin Leus European Association of Zoos and Aquaria CBSG Europe Caroline Lees CBSG Australasia Kristine Schad Population Management Center Lincoln Park Zoo Gina Ferrie Disney s Animal Kingdom Jamie Ivy San Diego Zoo Global Colleen Lynch Lincoln Park Zoo Karin Schwartz Lisa Faust Lincoln Park Zoo Manual citation Traylor Holzer K ed 2011 PMx Users Manual Version 1 0 IUCN SSC Conservation Breeding Specialist Group Apple Valley MN USA PMx software citation Ballou J D R C Lacy and J P Pollak 2011 PMx software for demographic and genetic analysis and management of pedigreed populations version 1 0 Chicago Zoological Society Brookfield IL USA PMx User Manual version 1 0 Table of Contents Section 1 Using PMx Introduction to PMx overview history new features ccccesccesssscssseecssecesseceesseeseeeecseeeesseessseeesenees 1 Getting Started installation creating PMX Projects cccccsssccesssssececsssseeesesseecessssseeessssseeeeseseeesesssaeees 3 Using PMx program COMPONENES ccccsscccsessececeessececeeseeeceeseeeeceesaseecsesseeecsesseeeesesaeeeceesaeeeceeteeeeeees 19 Section 2 Selection Screen Using the Selection Screen sce sece c zescascasareds cageedaianseecaadegesaseceadecss cagendaecabeceacedavsascoatecdscegsestbecsbecedeeyssadbecee 25 How to Create Seletin siderinte icpn coa aeaa an a iea aeaaea aG Eei stent 28 Sect
94. al Captive populations Individuals also do not need to be in any of the created management sets PMx User Manual version 1 0 Page 136 APPENDIX D INPUT FILE FORMATS General Issues Every individual in the pedigree entered into PMx must have a unique identifier This Unique D can be the studbook number in a SPARKS or PopLink database or the GAN Global Accession Number of ZIMS or any other identifier that is uniquely assigned to each individual The only other data fields that are mandatory for every individual are Dam Sire is optional because an asexual species might have no sires Selected a flag to indicate if an individual is to be included in the analysis and Alive a flag to indicate if an individual is alive Constraints on data fields For data fields that are string variables such as the Unique D OtherlDs Location and UDFs user defined fields PMx places no limitations on the string length The only characters that cannot be used within string variables are colon semi colon and tab Date fields in text files must be formatted as yyyymmdd e g 20110315 yyyy mm dd or mm dd yyyy e g 3 15 2011 The first format is preferred as it is less likely to cause confusion in regions with different data formats Data fields that are true false Boolean variables can be entered as any of True T 1 Y or Yes all case insensitive with all other values being interpreted as False Extra spaces arou
95. all recommendations to the default settings Hold Do Not Breed The Reset from Pairs and Culls button will reset all recommendations to only those from the Selected Pairs and Selected Culls on the Pairing and Culling tabs all other individuals will reset to the default settings The default set of individuals that are displayed in the recommendations table are usually the living individuals in the last Selection more specifically those for which Gone false and Selected true This may or may not be the exact list of individuals desired As with other tables in PMx the Filter button can be used to modify the list of individuals included on the recommendations table either by setting different filters or highlighting and Adding or Removing specific individuals The Reset to default filter button will return the filter to the initial settings Fiter Dipl or Tane S Do not filter the display of animals in this table Only show animals where Only show animals where ar gt of the following are true Column Name Op Value Gone false Selected true Highlight animals to add to the table Highlight animals to remove from the table a a Reset to default filter PMx User Manual version 1 0 Page 120 Exporting and Importing Files The buttons at the bottom of the screen can be used to export and import data for the recommenda tions table The Export button will create
96. ample Next line optional During mm dd yyyy mm dd yyyy Next line optional Status status Sample file Studbook Data for Check after data for filter conditions CALIFORNIA CONDOR GYMNOGYPS CALIFORNIANUS female Data exported on 20 Apr 2010 Data compiled by Michael Mace Contact info Data current thru 18 Dec 2008 Scope of data International North America HOST Zoological Society of San Diego Number Alive Qx Mx Age Class Sample Size Qx Sample Size Mx 10 000 0 150 0 000 0 1 268 6 218 4 8 000 0 060 0 000 1 2 164 7 151 1 8 000 0 130 0 000 2 3 120 1 109 1 etc etc etc 0 000 0 000 0 000 44 45 0 0 0 0 0 000 0 000 0 000 45 46 0 0 0 0 Filter conditions in effect During 1 1 1990 3 23 2010 End of sample file Note Data are fixed format space delimited PMx User Manual version 1 0 Page 145 2 Exchange csv Formats This is the same format as specified above Exchange csv created by a PMx export from SPARKS 1 6 3 Analytical Survival Statistics Included Individuals Table csv Formats For every animal that has been in the population under conditions that match the set filter e g alive between 1 1 1990 and 1 1 2011 in North America needs to have a record for every time it entered the filter Each record needs to have the entry information date type age and then the exit information associated with that entry still alive died exported Animals with unknown birth
97. an rate of inbreeding as that observed in the population or b result in the same rate of random change in gene frequencies genetic drift as observed in the population These two definitions are identical only if the population is demographically stable because the rate of inbreeding depends on the distribution of alleles in the parental generation whereas the rate of gene frequency drift is measured in the current generation First Order Kin Equivalents FOKE The number of first order kin siblings or offspring that would contain the number of copies of an individuals alleles identical by descent as are present in the living captive born population Thus an offspring or sib contributes 1 to FOKE each grand offspring contributes 1 2 to FOKE each cousin contributes 1 4 to FOKE FOKE 4 N MK in which N is the number of living individuals in the captive population Founder An individual obtained from a source population often the wild that has no known relationship to any individuals in the derived population except for its own descendants Founder Contribution Number of copies of a founder s genome that are present in the living descendants Each offspring contributes 0 5 each grand offspring contributes 0 25 etc PMx User Manual version 1 0 Page 130 Founder Genome Equivalents FGE The number of wild caught individuals founders that would produce the same amount of gene diversity as is present in the living descendant
98. are calculated This tab also provides options to change the analysis date window start and end dates and allows the user to attach optional additional files after the project has been created How to Use This Tab This tab is divided into three sections The left column provides options for modifying the Genetic Assumptions in the data analysis and for setting the Analysis Date The center column provides options to modify the MateRx Settings that contain the definitions and rules used in calculating MSI for the Pairwise Info tab The right column can be used to attach and read in Additional Data Files after the project has been created After changing any options click Implement changes to apply these changes i PMx Amur Tiger Test Pop Genetics x Overview Founders Individuals Kinship Matrix Pairwise Info Pairing Culing Management Sets Graphs Settings Selection Genetic Assumptions MateRx Settings Additional Data Files Parentage Assumptions F Break Point UseAverageF v Associations s Probabilistic parent v mm Genetic Value Type Mean Kinship X ces ae a Value proportion WILD to assign to Unknown parents Optional specification of moves in and out of Genetic 0 00 if ca MK Diff Method AbsoluteDiffs b Moves fle E Include Founders Weight Groups For Unknown Sexes ExdudeUnknowns v i CSV file ey Weight to assign to empirical Kinships MSI Method Tu
99. arison of strategies for selecting breeding pairs to maximize genetic diversity retention in managed populations Journal of Heredity in press Keyfitz N 1968 Introduction to the Mathematics of Populations Addison Wesley Reading Mass Lacy R C 1987 Loss of genetic diversity from managed populations Interacting effects of drift mutation immigration selection and population subdivision Conservation Biology 1 143 158 Lacy R C 1993 Impacts of inbreeding in natural and captive populations of vertebrates Implications for conservation Perspectives in Biology and Medicine 36 480 496 PMx User Manual version 1 0 Page 154 Lacy R C A M Petric and M Warneke 1993 Inbreeding and outbreeding depression in captive populations of wild species Pages 352 374 in The Natural History of Inbreeding and Outbreeding N W Thornhill ed University of Chicago Press Chicago IL Lacy R C 1994 Managing genetic diversity in captive populations of animals Pages 63 89 in Restoration and Recovery of Endangered Plants and Animals M L Bowles and C J Whelan eds Cambridge University Press Cambridge UK Lacy R C 1995 Clarification of genetic terms and their use in the management of captive populations Zoo Biology 14 565 577 Lacy R C 1997 Importance of genetic variation to the viability of mammalian populations Journal of Mammalogy 78 320 335 Lacy R C 2000 Should we select genetic alleles in our conservation bre
100. ase Because these results are stochastic the values will vary if the stochastic projection is re run although these differences should be slight if a large number of iterations are run a Stochastic Projections P Extinction p 00 Overall Stochastic Lambda 0 987 1 024 1 055 Stochastic lambda next 1 year 0 964 1 027 1 127 Probability that the Population will DECLINE next 1 year INCREASE next 1 year be the SAME SIZE next 1 year Export Graph Rerun Sim Close Time step PMx User Manual version 1 0 Page 51 Because stochastic projections incorporate the effects of skewed sex ratio it is important to set the correct ratio of female mates to males in the Settings tab The default setting is based on the relative average reproductive rates of males and females In species in which a single male can breed with multiple females during the same breeding season year such as herd species this number will be greater than 1 0 It is important to set this parameter to the appropriate value otherwise the stochastic projections may be erroneously pessimistic for a female biased population as PMx will leave some females unbred due to the apparent shortage of male mates x PMx Amur Tiger SSP 24Jul11 Demography eE Overview Male Life Table Female Life Table Age Distribution Census Seasonality Projections Reproductive Planning Add Remove Availability
101. asses are years Birth Flow Continuous CI 95 Iterations 500 Projections 20 time Growth in terms of years r 0 071 lambda 1 073 Ro 1 695 T steps 7 3 N20 112 Up to date Custom Graphs Life Table This screen allows the user to create custom graphs from life table data e Select Life table in the upper left box e Next select one of the 10 variables under Variable to Plot in the center left box one box must be checked e Select whether to plot Actual and or Model life table data at least one of these boxes must be checked in the lower left box e Select whether to plot data for Males and or Females at least one of these boxes must be checked in the lower left box e Select whether to plot as a Line or Bar graph under the graph e The resulting graph will be displayed on the right Double clicking on the graph will provide options to print export or send the graph to the report PMx User Manual version 1 0 Page 64 Overview Male Life Table Female Life Table Age Distribution Census Projections Reproductive Planning Add Remove Availability l Graphs Settings Standard Custom Select Graph Type Life table Census Life Table Graphs oe Variable to Plot Lx Mid Mx Px Mid Qx m E Male Actual Ex Vx on Female Actual Cx LxMx 12 4 Risk Qx Risk Mx ee Graph Type Plot Variable For Line Graph V Actual Data Model Data ia Bar Graph 7 Males As
102. at to edit Percentiles D Values Break Point No Way Percentiles Values Frequency BIN From To Delta GD MSI E 0 00 lt x lt 050 0 000081 108 51 Bl 050 lt x lt 075 0 000040 252 82 3 075 lt x lt 100 0 000000 Break Point 685 84 4 0 00 lt x lt 933 0 0 000040 937 1913 Bl 033 lt x lt 067 0 000082 1043 357 E 0s7 lt x lt 10 0 000122 Max NoWay mn 270 740 m 1 000000 0 331 Validate Restore Finished Statistics Used in MateRx Global Changes Defaults Close m 0 000122 0 000123 Mean 0 000021 0 000023 Max 0 000161 0 000161 Values OK To edit a bin choose Percentiles Values or Break Point No Way in the Select what to edit box at the top of the window The editable values will be highlighted and others grayed out Make the desirable revisions and then click the Validate Changes button PMx will check the values for validity and will return the message Values OK in the lower left if they are accepted otherwise PMx will return an error message such as MateRx Values Out of Sequence Try Again or Cancel The frequencies in the columns on the right will be updated if new definitions are accepted Click the Restore Defaults button to reset to the default definitions for this variable and click Validate Changes again Click the Finished Close button to exit this window PMx User Manual version 1 0 Page 110 Calculating MSI Tulsa method The default method for combining the various bin rankings for Delt
103. ata on the second section underneath The right side of the screen displays a histogram of number of events births or deaths per month a table giving these frequencies are displayed to the left of each histogram These tables can be exported as txt csv or x s files using the Export button below them similarly the graphs can be exported as png files The left section of the tab specifies the data used for these analyses The total default sample size is given for birth and deaths and then is divided into the number of events used in the tables and graphs Usable dates the number of events omitted from the analyses due to date span estimates to the year or greater Date estimates too wide and the number of events with Unknown dates also removed from the analyses PMx conducts a Chi square statistical test on each distribution to determine the probability that the observed data would occur by chance Generally if the P Uniform Distribution lt 0 05 this indicates a non random pattern of event distribution across months If the distribution shows a strong peak and the analysis is statistically significant i e P Uniform Distribution lt 0 05 the user might consider choosing a Pulse birth flow on the demographic Settings tab Overview Male Life Table Female Life Table Age Distribution Census Seasonality Projections Reproductive Planning Add Remove Availabilty Graphs Settings _ Events Shown Birt
104. ations Birth ratio for projections default 0 50 male Birth ratio used for all projections Terms and Concepts Mx fecundity Average number of offspring born to individuals in that age class Iteration A single stochastic simulation of the population over the specified time period Because events in a stochastic simulation are based on probabilities the outcome of each iteration will be different therefore many iterations should be run to accurate estimate results Confidence interval Cl This defines the range of values upper and lower limits that the parameter in this case mean population size will take in relation to a specific level of likelihood For example a 95 Cl means that 95 of the simulations result in values between the lower and upper limits New Features Many of the setting options on this tab were not available in PM2000 The ability to change age class length and other life table settings allow for greater flexibility in modeling different life histories The ability to run stochastic population projections provides more realistic estimates of future population trends The addition of these options will improve demographic planning for managed populations Helpful Hints e Be sure to adjust the maximum number of females per breeding male as appropriate otherwise stochastic projections will be misleading especially for polygynous species e Consider shortening age classes for short lived species e g sma
105. ative impacts of multiple moves Individual Mgt Set the Current Set to the desired source population Click the Individual Mgt button above the Current Set table to open a table containing all of the individuals in the Current Set source population Unlike most PMx tables the column variables cannot be modified but are set to UniquelD Sex Age Location and sub Population Also displayed is the change in GD or MK if selected in lower left corner to the source in brackets and destination without brackets subpopulations if that individual alone were to be moved to that subpopulation Click on the column header to sort by any column e g change in GD in the source population Use the pull down menu in the Action column for a specific individual to simulate the transfer of the individual to another subpopulation Multiple transfers can be designated to multiple subpopulations from this source subpopulation Clicking on the Accept Actions button will transfer these individuals to the designated destination subpopulations and recalculate all of the individual and population statistics The new N and GD of each subpopulation will be displayed in the upper left corner of this window Selecting Copy to instead of Move to will place the individual in both subpopulations copying it to the destination subpopulation while leaving it in the source population e g transfer of gametes PMx User Manual version 1 0 Page 98 Location j j EastAs
106. be excluded from demographic and or genetic management because they are in other regions or are held by private individuals or institutions that will not be participating in the cooperative breeding program or due to behavioral physiological or husbandry reasons Sometimes a different set of individuals either a larger set or a subset are believed to be a better representation of the demographic or genetic characteristics of the managed population There are two selection screens in PMx the primary Selection screen on the main PMx window and another on the Selection tab in the Genetics module The two screens operate in a similar manner with some minor differences see the Genetics Selection Tab section of the manual for more information The Selection tab is provided under Genetics for convenience so that the user can quickly modify the population for genetic analysis within the Genetics module A good understanding of the Selection screen is crucial for successful and correct use of PMx It is recommended to read the manual section for this screen completely before proceeding with analysis How to Use This Tab In many cases the user will have already used geographic association date span and or other filters in the studbook database software SPARKS PopLink etc when creating the export files for PMx in order to define which individuals should be included in the population analyses If required the Selection screen in PMx can be used
107. be the same Stochastic Stochastic means variable due to chance or based on probabilities In stochastic calculations input values are based on probabilities e g every individual has a 24 chance of not surviving its first year Actual values used in the calculations will vary with each application and so the result will be variable Iteration A single stochastic simulation of the population over the specified time period Because events in a stochastic simulation are based on probabilities the outcome of each iteration will be different therefore many iterations should be run to accurate estimate results Confidence interval CI This defines the range of values upper and lower limits that the parameter in this case mean population size will take in relation to a specific level of likelihood For example a 95 Cl means that 95 of the simulations result in values between the lower and upper limits P Extinction Probability that the population will go to zero measured as the proportion of stochastic simulations in which the population goes to 0 New Features Stochastic projections While PM2000 provides deterministic population projections PMx provides both deterministic and stochastic projections Deterministic projections are derived from applying Px and Mx values to the total N of individuals in each age sex class For stochastic projections each individual has a probability of surviving each age class based on Px Mx is appli
108. ble parents from which the split was made CLONE Entity is a Clone of the Dam and of the same EntityType as the Dam If Dam D is MULT or GROUP then there were multiple possible parents from which the clone was made SELF Entity is an Individual formed by selfing the Dam If Dam D is MULT or GROUP then there were multiple possible parents from which the selfing occurred EXTRACT Entity is an Individual formed by extracting an individual from the Dam presumed normally to be a group entity If DamID is MULT or GROUP then there were multiple possible parents from which the extract occurred If Dam is an Individual then extract is the same as a clone Genetically Clone Split and Extract all have the same consequences for kinships PMx User Manual version 1 0 Page 141 HAPLOID Entity is an Individual formed from a haploid gamete possibly then duplicated to make a completely homozygous diploid individual from the Dam If DamID is MULT or GROUP then there were multiple possible parents from which the gamete came Of the above special codes for MatingTypes the only one that can be applied also to the Dam is GROUP The other codes in place of the Sire D all imply that the set of possible parents will be specified in the Dam If Dam D and SirelD are both GROUP or MULT then the reproduction was a sexual merge see description above under SirelD GROUP If any of MERGE SPLIT CLONE SELF EXTRACT or HAPLOID are listed for the Dam
109. ble for births as well in a future version of PMx There is also an option to Use Only Exact Dates omitting estimated dates from the analysis A title can be provided for each graph r Select Items Events Deaths X Sex Male X Title Births Filter On None a Associations E Use Only Ex Regions Countries Locations Filters can be used to specify and compare two distributions for example the seasonality of births for males vs female births can be compared by selecting Births for both distributions and filtering each by a different sex The Compare Seasonality check box in the lower left will perform a Chi square statistical test to compare whether or not these two distributions are significantly different from each other Terms and Concepts Chi square A statistical test that compares a distribution of observed frequency data to that expected based on a particular hypothesis e g that there is no pattern in frequency or that two distributions are the same and estimates the statistical probability based on sample size see a statistical reference or text for more detailed and precise information New Features This is a new feature seasonality data and analyses are not provided in PM2000 Helpful Hints e Remember to change the Title of the histogram when you change the Events Sex and or Filter PMx User Manual version 1 0 Page 49 PROJECTIONS TAB Purpose The Projections tab
110. bles e If the Selected Population is reset by clicking the Revert to originally imported data button on the main Selection screen all Management Sets will be deleted e Individual MK values reported in Management Set tab are the MK value calculated with respect to the Full Population not for the subpopulation defined by the Management Set Cautions Fst and MKb are contextual metrics in this application the values sometimes reflect the pairwise relationship between two subpopulations and sometimes represent a mean level of relationship or conversely divergence among the set of subpopulations being considered In the Comparisons button these values are reported between pairs of subpopulations In the Management Sets tab the values reported refer to relationships between the Management Set subpopulation in the list on the left of the screen and the Current Set selected on the right side of the screen Selecting a different Current Set will cause values on the left side of the screen to be repopulated reflecting the relationship to the new Current Set Note that when the Current Set is selected on the right of the screen is Full Population the values for Fst and MKb to each subpopulation on the left of the screen are not populated To generate a true Fst subpopulation to total population and populate these fields a subpopulation called Total Population should be created This subpopulation should contain the same animals as in the Full Popu
111. book software Faust et a 2009 as well as Laurie Bingaman Lackey of ISIS who provides support and ongoing improvements to SPARKS have worked closely with the developers of PMx to ensure that data can smoothly move to PMx PMx can also accept data maintained in other studbook database systems and specifications for PMx input files are provided in Appendix D New Features From PM2000 to PMx PMx includes all of the data analyses available in PM2000 as well as many additional features The major new options in PMx include e Ability to set age class length to intervals other than one year shorter or longer e Stochastic population projections e Projections for non reproducing populations e Projections based on scheduled supplementations and or removals e Ability to project availability of individuals for reintroduction over time e Ability to handle breeding systems other than bi sexual reproduction e g cloning selfing e Inclusion of probabilities for multiple possible parents e Ability to assign probability of success to recommended breeding pairs e Mate Suitability Index matrices previously available in MateRx e Ability to assess genetic impact of transfers between management groups e Increased ability to incorporate group management strategies e Increased ability to import data from a variety of datasets Additional new features will be added over time in subsequent versions PMx User Manual version 1 0 Page 2 GETTING STARTED
112. calculations will take to display The user can reduce the calculation time by turning off some of the more time intensive calculations using these check boxes at the bottom of the screen e Include Genetic History Turns historical genetic calculations on and off e Include MateRx Turns the pairwise display calculations on and off see Pairwise Info Tab section e Show Kinship Matrix Turns the kinship matrix display calculations on and off see Kinship Matrix Tab section The default setting is for these calculations to be activated for smaller datasets studbooks with fewer than N 1000 individuals in the selected population When datasets become large these settings will turn off automatically as a default setting These calculations require pairwise calculations which can become a very large number of calculations as the number of individuals in the dataset increases The default settings can be changed by checking or unchecking any of the boxes as desirable An additional check box Allow Pairing Dead is provided to allow the pairing of dead individuals This is useful for example when assisted reproduction with cryopreserved gametes may be used in some of the pairing recommendations The default setting is for this option to be turned off to speed up PMx processing Checking this box will allow dead individuals to be added to the Pairing and Management Set Tabs if the filter is modified to include them Dead individuals will not be include
113. ce in GV Percentiles 0 33 0 67 1 00 0 33 0 67 1 00 Value 0 00398 0 00796 0 01193 0 01193 0 02402 0 03610 0 04818 1 00000 4708 4171 3438 5849 2231 382 0 23 0 20 0 17 0 28 0 11 0 02 Inbr Coefficient Percentiles 0 00 0 50 1 00 0 33 0 67 1 00 Value 0 00000 0 00632 0 01264 0 01264 0 04989 0 08713 0 12438 0 12500 13383 607 715 3873 1793 408 0 60 0 03 0 03 0 17 0 08 0 02 Unknown Pedigree 5 Individual data At the bottom of the table not visible in the above screenshot is the total number of pairings that receive an MSI equal to ratings indicated by the name of the Bin i e 1 6 and No Way These MSI values are calculated from the four individual variable rankings using one of two methods The default method is known as the Tulsa method and is based on a set of logic rules An alternative is to use a Weighted method in which weights can be assigned to the first three variables to determine the final MSI see below Click the Individual data button at the bottom of the screen to view detailed information for each male female pair This table contains one row for each pair the values for each of the four variables Delta GD GV Diff F and Known the bin rating for dGD GVDiff and F and the composite final MSI score as well as the extended MSI This table can be sorted by clicking on the heading of any column Both the Individual data table and Bin data table can be saved as an txt file by clicking the Export button
114. center table on the Add Remove tab displays the total number of males and females added or removed each year time interval in the future with all age classes grouped for each sex Additions and removals in the same year are combined to display the net change in N If insufficient individuals are available in the specified age and sex class to meet the removal plan then removals will be incomplete for that time interval e g if the plan calls to remove 4 six year old males and only 3 males are projected to be in that age class in that time interval then 3 will be removed and no additional males will be taken from other age classes or from other time intervals The Export button can be used to export this table The Projections graph at the top right corner of the tab displays the projected population size over time The Numbers Removed or Added graph in the lower right displays the projected additions above the zero baseline and removals below the baseline over time these are a visual representation of the numbers in the center table New Features The Add Remove tab is a new feature and was not available in PM2000 It incorporates aspects of the Supplementation and Harvest features available in the Vortex population simulation program Helpful Hints e Be sure to enter NEGATIVE numbers for removing individuals e Use the Availability tab instead to assess the ability of the population to provide individuals available for removal while ma
115. ch sex or to quickly identify an alternative suitable mate if a recommended breeding fails PMx User Manual version 1 0 Page 84 Other variables besides MSI can be displayed in the table by using the pull down menu for Data to display to the left of the table additional variables are eMSI DeltaGD MKDiff F Known and Ranks the individual rankings for dGD MKDiff and F in that order used to calculate the MSI The value for any of these variables for a particular male female pair can be quickly viewed by entering the UniquelD for each of the two individuals in the boxes on the left and clicking the Calculate button The table lists the UniquelD of each male rows and female columns followed by an additional row or column The default for this additional variable is Location however other variables such as House Name or Age can be selected by using the pull down menu for Addl Data at the bottom of the screen Individuals are sorted by UniquelD as a default setting this can be changed for rows and or columns using the pull down menus for Sort Rows on and Sort Cols on at the bottom of the screen Use the Filter to subset the data for example to view only reproductive age individuals or individuals at only one Location or small number of Locations Data in the table can be updated Dynamic based on Selected Pairs and Selected Culls by clicking the Update Table with Pairs and Culls button on the left The displayed table can be
116. cking the Accept button will cause the individual s to be moved or copied Clicking Cancel will cause the individual s to remain in the source subpopulation PMx testmeta Genetics 12 62 i 1 0000 ADVENTURE 79 0 9679 0 0000 1 0000 ADVENTURE 41 0 9525 0 0054 0 0093 a 1 0000 AUDUBON 1 0000 AUDUBON n 1 0000 AUDUBON scendants 0000 1 0000 BIRMINGHM 1 0000 BIRMINGHM 1 0000 BIRMINGHM 1 0000 BIRMINGHM Delete button The Delete button in the upper right corner of the main window can be used to delete the highlighted individual s from the Current Set PMx User Manual version 1 0 Page 99 Terms and Concepts Subpopulation Any group of individuals selected from the Full Population or from another subpopulation Subpopulations do not have to be mutually exclusive or exhaustive pairwise MKb Mean kinship between a pair of subpopulations the mean of all pairwise kinships for all combinations of an individual from subpopulation 1 with an individual from subpopulation 2 See cautions below pairwise Fst A measure of the genetic divergence between two subpopulations Technically defined as the proportion of the genetic variance of the combined pair of subpopulations that is due to the genetic differences between the subpopulations Equivalently the extra genetic variance contained in the combined pair of subpopulations over the mean genetic variance within each subpopulation expressed as a propor
117. commendations New individuals that are added to the table via an imported file will have Not Selected added in the RecNotes field A common practice for some managers is to conduct the demographic analysis for a population and then to exclude some individuals e g sterile or post reproductive individuals from the genetic analysis through selection applied only to genetics see Selection screen This process will result in only those individuals used in the genetic analysis being included in the recommendations table as the default filter is Selected true based on the last selection In this case excluded individuals can be added to the table using filtering options An alternate and often easier method is to follow this process 1 While using the Selection for demography entire managed living population go to the Recommendations screen and Export the table that includes all individuals in the management program 2 Goto the Selection screen make the new selection that is applied to genetics only excluding permanent non breeders and or other individuals from the genetic analysis 3 Make Pairs and Culls as appropriate 4 Goto the Recommendations screen and choose mport List Import the exported text file from the full demographic selection population 5 The result should be that the recommended pairs and culls should remain unaffected but that the excluded individuals are added to the Recommendations table These indiv
118. commended to remove living individuals that can never breed or will never be bred again e g post reproductive sterilized poor health hybrid from the genetic mean kinship calculations as these individuals can no longer pass on their genetic material to the next generation and their inclusion influences the mean kinship values of other individuals in the population However these non reproductive individuals may occupy cage space and need to be managed in other ways In addition their demographic information is valuable Managers therefore often chose to include these individuals in the demographic analysis but to exclude them from genetic analysis There are two options for removing these individuals from the analysis and each method has its own set of consequences Different people generally prefer PMx User Manual version 1 0 Page 29 different methods and one is not more correct than the other as long as the user is aware of how to interpret the results Option 1 Remove permanent non breeders in the Selection screen either on the main Selection screen or on the Selection tab within the Genetics module Uncheck the box Apply changes in Selection to Demography and make sure that the box Apply changes in Selection to Genetics is checked so that the selection will only be applied to the genetic calculations Deselect the non reproductive individuals by moving them to the table on the right and click the Update Selection button These in
119. ct are a number of files that contain output that sometimes will be useful The pmxproj file is actually a compressed zipped file that uses the standard file compression format Therefore access to the contents of the file requires only the following few steps e Make a copy of the file so that the PMx project itself is not damaged e Rename the copy changing the extension to zip e g ions pmxproj becomes lions zip e Extract any files of interest from the zip file using any of the standard programs e g PKZip or Windows 7 Explorer Pmxproj File Contents The pmxproj file contains e Copies of all input files that were used to create the PMx project e g the ped or csv primary input file orn or csv or txt files with demographic and census input and additional files such as fed and rgn files e Various csv files that contain tables of demographic results such as the life tables and population projections e Six files with the calculated kinship matrices for each possible combination of genetic assumptions These files are stored in binary bin format and will be readable only via programs able to read this format i e the files will not be readable in a text editor For studbooks that have no unknown or uncertain parents several or all of these kinship files will be exact copies because the genetic assumptions will have no effect on the kinship calculations e A pmi file that contains the full list of the indi
120. ctive population size Ne and Ne N will be misleading as it will not include these individuals Living individuals that bred in the past but are now sterilized or post reproductive will not contribute to the tally of breeders in the current population on which the calculation of Ne is based Option 2 Remove permanent non breeders in the Culling tab in the Genetics module of PMx Rather than deselecting non reproductive individuals on one of the Selection screens it is possible to exclude them from genetic analyses by culling them on the Culling tab in the Genetics module Consequences e The Managed N and genetic information in the PMx main footer will display the information for the total living population being managed including the individuals that can never breed again However within the detailed Genetic module the Dynamic Population Variables will display the information for the population with culled animals removed and with any chosen pairings having bred PMx User Manual version 1 0 Page 30 e When making pairings under the Pairing tab the displayed change in GD resulting from the pairings is the change relative to the Dynamic value which includes the effects of any culls and pairs already executed for the entire living population being managed e The Recommendations table will include rows for all individuals in the management program including the non reproductive ones e The unselected individuals excluded f
121. d by typing in the first year to plot and clicking Update Chart but PMx will not accept a date earlier than the exported data Click on the lt lt button to reset date to earliest date The graph can be exported by double clicking on the graph and selecting either Export to File or Send to Report Graphs of additional census data information are available under Custom gt Census graphs on the Graphs tab in the Demography section r z PMx Demography ll E zsm Overview Male Life Table Female Life Table Age Distribution Census Projections Reproductive Planning Add Remove Avaiabiity Graphs Settings Year Institutions Lambda from Census Lambda from Reproduction Total N Male Female Sex 1990 0 000 1 000 a 1 2 o By Sex 1991 1 1 000 3 1 2 o 1992 2 1 333 0 667 4 1 3 o Z 1993 2 2 500 10 4 6 o 1994 2 1 000 10 4 6 o 1995 4 1 000 10 4 6 o 1996 4 0 900 0 900 9 4 5 o E Males 1997 4 1 222 11 4 7 0 Z o Females 1998 4 0 909 0 909 10 3 7 o a 1999 6 2 200 22 11 11 o 2000 10 1 500 1 500 33 16 17 o 2001 14 1 121 1 121 37 18 19 0 1990 1995 2000 2005 2002 16 1 081 40 19 21 o di 2003 17 1 175 1 050 47 Z 4 B o 2004 20 0 936 0 936 4 2 22 o Standard Graphs Graph Type 2005 20 1 091 1 091 48 26 22 ok Td Line Graph Plot from year Fariest 1990 o o o o 1990 Update Chart 4 m gt By Sex Bar Graph ee n Export By Origi
122. d in the genetic status calculations on the living population e g GD MKs of living individuals This option will require a historical genetic export Click on Send to Project Notes to copy the table data to the Project Notes tab Double click on the graph for options to print the graph export it to a file or send it to the Project Notes tab New Features Several of the genetic statistics are new in PMx such as Percent Ancestry Certain as well as some of the settings and assumptions such as the ability to use multiple parent data Helpful Hints e If data in some of the tabs are not available e g kinship matrix check to see if the check boxes on this screen defaulted to Off due to the size of the dataset e An Appendix detailing how to use PMx genetic tools for genome resource banking including identification of individuals to bank given certain GRB goals and strategies for using these samples by pairing dead individuals is being developed for inclusion in a future edition of this manual Cautions e If the Analysis Date is set to some date other than the date on which the studbook data were exported the Location for each individual will not change to match the new Analysis Date but will reflect the Location of the individual at the end of the export filter window This is because SPARKS and PopLink currently only export the last Location in the filter window to PMx PMx does not have the ability to track moves over an individual
123. d then will not be calculated e Use ReproGoals to help estimate how close intensive management might allow the population to approach the Potential GD e A powerful addition to this tab is the ability to add variables to the tables that are especially relevant to the species or population For some populations these might include Rearing type Prior Mates past ReproYears etc Since space is limited in these tables to display multiple columns less useful columns can be removed or if they are fixed can be hidden by pulling the right edge of the column to the left to reduce its width e To view dead individuals on the Pairing tables make sure that the Allow Pairing Dead check box is checked on the main Genetics Summary Statistics screen and change the table filters to include dead individuals e AutoPair and ReproGoals create pairs from only the individuals on the displayed filter view Cautions Only use Repro Goals if you are very familiar with the underlying algorithms This is a new tool that has not yet been extensively tested for its best uses in population management PMx User Manual version 1 0 Page 92 CULLING TAB Purpose The Culling tab allows the identification of those individuals that are genetically overrepresented in the population and provides the ability to assess the effect of removing individuals on the genetic status of the population Individuals may be removed culled to promote genetic management surplu
124. data can be exported to txt x s or csv files using the Export button below the table Double clicking on the graph provides options for exporting the graph as a png file or sending it to the report Depending upon the version of PMx that you are using the stochastic projections may have been run automatically or may need to be run before the results can be viewed The word Outdated will appear in the lower right either if stochastic projections have not been run or if relevant data have been changed in PMx that could affect these projections and indicating that the stochastic projection should be run again This will change to Up to date once stochastic projections have been run Use the Stochastic button below the graph to run stochastic simulations of future population trends This will open a new window that displays a line for each simulation of the population over time The default settings run 500 iterations Use the Export button to export the graph the Rerun Sim button to run a new set of iterations and the Close button to close this window Numerical results provided in this window include e Probability of population extinction P Extinction over the projected time period e Mean stochastic lambda over the projected time period and Cls e Mean stochastic lambda for the next year and Cls e Probability that the population will Decline Increase or be the Same Size in the next year as defined by the proportion of simulations for each c
125. ded reproduction in the selected population Latest Age of latest recorded reproduction in the selected population Average Mx Average overall reproductive rate Mx for age classes in which Mx gt 0 births to unknown age parents Given in relation to all births Projections time step Results of the stochastic projections once they have been run Prob Extinction Probability that the population will go to zero measured as the proportion of stochastic simulations in which the population goes to 0 Size next 1 time step Projected size of the population based on stochastic projections after 1 time step mean Cls Life table Lambda Growth rate based on the deterministic life table calculations Long Term Stoch Lambda Growth rate based on the stochastic projection calculations including Cls Lambda next 1 time step Growth rate in the next time step based on stochastic projections Prob Increase next 1 time step Probability that the population will increase in the next time step based on the stochastic projections Prob Decrease next 1 time step Probability that the population will decrease in the next time step based on the stochastic projections Age Structure Impact Life table lambda is based on the exact demographic values in the male and female life tables and do not take the actual population age and sex structure into consideration However deviations of the age and sex structure from a stable a
126. defines the end of the analysis window This is the ending date for the genetic historical calculations This date also defines the current population the genetic status of the living population is calculated with respect to this date Default date is the end of the date window for the exported data Checking the Apply date also to Demographic Age Structure box will apply the new date to all historical and current demographic calculations default setting Start Date Date that defines the beginning of the analysis window for historical genetic analyses default is the start of the date window for the exported data Gene drop Iterations Number of iterations for gene drop simulations default 1000 More iterations will provide more precise results but usually 1000 is sufficient for most purposes PMx User Manual version 1 0 Page 106 MateRx Settings These settings apply to how MSI scores and ranks are calculated for pairwise comparisons and are MateRx Settings accessible from both the genetic Settings tab and F Break Point UseAverageF the Pairwise Info tab These subscreens provide information on the characteristics of the population Genetic Value Type Mean Kinship with respect to pairwise comparisons and also aes TRANE MK Diff Method AbsoluteDiffs provide the ability to modify the definitions weights and calculation method for computing MSI For Unknown Sexes ExcludeUnknowns values MSI Method Tulsa M
127. der Even within the Demography and Genetics sections the tabs are arranged in the order that most people will want to explore the data PMx User Manual version 1 0 Page 19 Working with Tables Most of the features of tables within PMx are consistent from table to table Although some features are disabled or not applicable to some tables the primary features of working with tables in PMx are e Vertical and horizontal scroll bars will appear if they are needed for viewing parts of the table that do not fit in the window Windows can be resized by clicking and dragging their edges e Column widths can be changed by clicking and dragging the dividing lines between columns e The rows can be sorted based on the data in any column by clicking on the column header Clicking on the same header again will reverse the order of the sorting e Except for key initial columns often Unique D that are frozen indicated by light shading the order of columns can be changed by clicking and dragging e Right clicking on the table will open a list of variables that can be displayed Clicking to check a variable name will cause that variable to be added to the table Unchecking a variable will remove it from the table Most tables have some key variables that are always displayed whether or not the variable is checked in the list e Changes to variables and column order will be saved with a project so that tables will appear the same when the project
128. dividuals now are not counted in the genetic calculations but do appear in the age pyramid population projections and other demographic analysis NOTE Only remove individuals that can definitely never breed again do not remove contracepted or pre reproductive individuals those with temporary health problems or other individuals that still hold the potential to breed later Consequences e The Managed N and genetic information in the PMx main footer will display the information for the subset of the population used for genetic analyses not for the total living managed population e When making pairings under the Pairing tab the displayed change in GD resulting from the pairings is the change compared to the GD in the subset of the current population used for genetic analysis rather than the GD of the entire living population being managed e The Recommendations table will only include rows for the genetically managed individuals and those individuals excluded from the genetic analysis may need to be manually added to the table if recommendations are to be included for these individuals e The unselected individuals excluded from genetic analyses in this way are also removed from the historical genetic analyses for their entire lifetime even if earlier in their lifetime they were capable of reproducing and should legitimately contribute to the genetic statistics of the population at that time e The calculation of current effe
129. dual in the demographic window is still alive and will provide information on this individual Specify an age greater than the age of the oldest living individual to use as the maximum longevity and the end of the PMx life table for this sex You may enter the age of this individual rounded up to the next highest integer age Alternately if credible information is available that the species and sex can live to an older age an older maximum longevity can be entered For example this might be appropriate if the population has not been maintained very long in captivity has not had enough old individuals to represent the entire lifespan of the species or if there are credible data from a field study or alternate captive population either the same species or a related species that can be used to make an estimate Note the maximum longevity can also be changed by adding age classes to the PMx lifetable through changing the Demography Settings in PMx Your oldest female in the window is still alive ID cll et ly birth puede Hog type What age gt 23 1184 yrs Cancel Leet would you like to use for your maximum longevity the max age to which an individual of this species and sex can live _e Kr v S When the Analytical Survival Statistics Report pops up click the Export button in the upper right hand corner This will create a file called ANALYTICALSURVIVAL STATISTICS INCLUDING INDIVIDUALS TABLE CSV that will b
130. duals to be culled and click OK The Cull File can be created in two different ways It is created if the Selected Culls box is exported and later if necessary these individuals may be added or removed manually from the list Alternatively a cull file can be created manually as a text file listing the individuals to be culled with one individual UniquelD per line New Features The ability to automatically generate a list of optimal individuals to cull Auto cull is new to PMx Cautions PMx User Manual version 1 0 Page 94 The default column widths may hide some details particularly in the dGD column Unless the column is stretched wider it may not initially display the minus signs for the negative values PMx User Manual version 1 0 Page 95 MANAGEMENT SETS TAB Purpose The Management Sets tab is used to divide a studbook population into subpopulations or Management Sets and to examine the genetic divergence and similarities between subpopulations as well as to test the genetic effects of the movement of individuals among these subpopulations These subpopulations could represent population subsets such as e large herds or flocks within a managed population e operational distinctions such as education specimens vs breeding specimens within a population e separately managed regions within a global population e animals managed within a zoo association vs outside of a zoo association or e captive and wild population
131. e EWN oue PRm 0 6719 0 4453 0 4453 0 2227 0 3359 0 2109 0 2109 0 3359 0 3359 0 22 boxes beige towiew iher kinship DUKE PRIM 0 4453 0 6719 0 4453 0 3359 0 2227 0 2109 0 2109 0 2227 0 2227 0 33 23 in e t DUKE PRIM 0 4453 0 4453 0 6719 0 2227 0 2227 0 2109 0 2109 0 2227 0 2227 0 22 i ee DUKE PRIM 0 2227 0 3359 0 2227 0 5000 0 1113 0 1055 0 1055 0 1113 0 1113 0 2 7 DUKE PRIM 0 3359 0 2227 0 2227 0 1113 0 5000 0 1680 0 1680 0 2930 0 2930 0 11 CHEHAW 0 2109 0 2109 0 2109 0 1055 0 1680 0 5000 0 2500 0 1680 0 1680 0 108 Kinship 0 3359 CINCINNAT 0 2109 0 2109 0 2109 0 1055 0 1680 0 2500 0 5000 0 1680 0 1680 0 108 CINCINNAT 0 3359 0 2227 0 2227 0 1113 0 2930 0 1680 0 1680 0 5000 0 2930 O 11 a DUKE PRIM 0 3359 0 2227 0 2227 0 1113 0 2930 0 1680 0 1680 0 2930 0 5000 oar CHEHAW 0 2227 0 3359 0 2227 0 2930 0 1113 0 1055 0 1055 0 1113 0 1113 0 50 DUKE PRIM 0 2109 0 2109 0 2109 0 1055 0 1680 0 2500 0 2500 0 1680 0 1680 0 105 CHEHAW 0 3359 0 2227 0 2227 0 1113 0 2930 0 1680 0 1680 0 2930 0 2930 0 11 WAHPETON 0 2734 0 2168 0 2168 0 1084 0 2305 0 2090 0 3340 0 3340 0 2305 0 108 WAHPETON 0 2734 0 2168 0 2168 0 1084 0 2305 0 2090 0 3340 0 3340 0 2305 0 108 INDIANAPL 0 2734 0 2168 0 2168 0 1084 0 2305 0 2090 0 3340 0 3340 0 2305 0 108 HATTIESBG 0 2734 0 2168 0 2168 0 1084 0 2305 0 2090 0 3340 0 3340 0 2305 0 108 lt gt Addl Data Location Sort on UniqueID i Filtered showing 21 Assumptions Dynamic Population Variables ee GD 0 7582 GV 0
132. e PMx will indicate both how long the genetic goal can be maintained and also the projected genetic diversity at the end of the projected time period Pi Vr PMx Sumatran Tiger GSMP 28Jul11 a Fie Language Help Project Notes I Selection Demography Genetics Goals Recommendations Gene Diversity at the END of X Population Variables Founder Related Variables Generation Length years New Fndrs per Addition Event Maximum Potential Lambda Year to Start Adding Fndrs Current N Years between events S io Current Effective Size g Year to Stop Ne N I FGE per founder Q D 5 a e d a lt Current Gene Diversity Maximum Allowable N Solve For Nothing Use values X Reset You can exceed goals and maintain 90 5 You can maintain over 90 0 for up to 112 years Send to Project Notes Managed N 289 Pedigree Known 100 0 Current Gene Diversity 0 948 Potential Gene Diversity 0 985 Lambda 1 044 PMx User Manual version 1 0 Page 116 The graph on the right hand side of the page illustrates the modeled scenario specifically the population size projection and the gene diversity retained over the specified time period specified in the Goal Double clicking on the graph will open it in a new window that allows the graph to be exported to file sent to Project Notes or printed If the goal cannot be met then the Population Variables may be changed to assess their effect
133. e Tabular data can be viewed as Counts Summary or IDs only Counts were provided in PM2000 Helpful Hints Take a look at the age distribution e Are there any impossibly old animals if so check your studbook data as these may be errors e Does the age structure show a baby boom or is it top or bottom heavy e Are there enough animals in breeding age classes to provide the desired amount of reproduction e Are unproven breeders aging indicating a possible loss of breeding potential e How does the actual age distribution compare to the stable age distribution If they are quite different then population growth may behave quite differently in the future than it has in the past Cautions The various age structure filters views will only be as good as the studbook data e Example 1 A population that has a large portion of its pedigree recorded as unknown in the studbook may show very few proven breeders e Example 2 If contracepted animals are not recorded in the studbook they will not be displayed on the graph e Example 3 If there are few reproductive data available because the population has not been in zoos for very long or parentage is not always recorded the Post Reproductive view or the non reproductive animals indicated in a light blue on the graph may not be correct PMx User Manual version 1 0 Page 45 CENSUS TAB Purpose The Census tab provides both numerical and graphical information on population size over time i
134. e based on bisexual reproduction and some of the terminology and data presentation in PMx implies such a breeding system However algorithms have been added to PMx that allow comparable calculations to be conducted on species with other breeding systems such as cloning hermaphroditic selfing and haplodiploidy In addition PMx provides some methods for estimating genetic parameters when pedigree data are partly missing when there are multiple possible parents or when the entities being managed are groups of organisms rather than diploid individuals derived from mixing and or sampling of ancestral groups or individuals With these new extensions of pedigree analysis methods PMx may be useful for management of some plant fungus or prokaryote populations although no attempt has been made to facilitate analyses of non animal populations PMx contains sections modules for Demography Genetics determining Goals for population management and recording Recommendations The Demography section provides life table projections of population growth and associated parameters from observed birth and death rates the ability to model the effects of changes in rates tools for exploring the impacts of different management strategies e g harvest or supplementation and means to determine the numbers of births or deaths needed to achieve demographic goals The Genetics section provides analysis of the genetic diversity retained over generations kinsh
135. e can be exported to txt csv and Xls formats by clicking on the Export button In the example shown below the population has been set to increase from 55 to 80 individuals Removals are set to consist only of males and are to be split equally across the 1 2 3 and 4 year old age classes i e 25 from each class The results indicate that no animals are available for harvest until year 16 when the population has reached its target of 80 individuals Beyond that the population is able to provide 1 3 males per year across all age classes z stprojections Demography E WE O a Llak a PMx NA MAL test projections Demography n A Overview Male Life Table Female Life Table Age Distribution Census Projections Reproductive Planning Add Remove Availability Graphs Settings How Many Animals Can Be Removed Numbers and ages of animals that could be removed Time Intervals 1 year Enter what proportion of years Interval 16 oe Interval 17 Interval 18 Interval 19 a that can be removed while Gare rlia 3 from each age sex dass Age Males Females Males Females Males Females Males Females Keeping Pop at size 80 44 36 Each sex should am to L0 Total ese ae 5 Maintaining Lambda at 1 081 Le Reset Export m Total Projections ie m r Assumptions Overall Statistics Stochastic Runs Age Unit years Birth Flow Continuous CI is95 Iterations 500 Pro
136. e end of the row using the Delete button Multiple plans can be added and applied separately or in combination Buttons are provided to Enable All Plans Disable All Plans or Delete All Plans Overview Male Life Table Female Life Table Age Distribution Census Projections I Reproductive Planning Add Remove Availability Graphs Settings Add and or Remove Individuals Total Removed Added each year Projections Define Supplementation or Removal Plans that each specify the number of animals of SSS Foma rR different sex and age classes to add or remove Each plan can have a different time k x H schedule 0 0 0 ag 1 00 0 0 Zg Currently Defined Plans 2 1 0 1 0 Name Start Stop Interval Affect RP Enable Edit 3 0 0 0 0 Periodic Supplementation 2 10 2 Edit 4 10 10 2 A 8 i 1 2 Exports 5 20 5 W Edit pam 20 23 6 1 0 1 0 7 0 0 0 0 8 1 0 1 0 Numbers Removed or Added ae a Mm r m 0 0 0 0 Add Plan 10 1 0 1 0 11 0 0 0 0 Enable Al Pions 12 0 0 0 0 Disable All Plans 13 00 0 0 14 0 0 0 0 Delete All Plans 15 20 2 0 16 0 0 0 0 4 17 0 0 0 0 a 4 11 3 J Export Assumptions Overall Statistics Stochastic Runs Age Classes are years Birth Flow Continuous CI 95 Iterations 500 Projections 20 time Growth in terms of years r 0 071 lambda 1 073 Ro 1 695 T steps 7 3 N20 112 Up to date PMx User Manual version 1 0 Page 59 The
137. e in a particular geographic region SPARKS 1 6 will automatically export Region for each individual as well as Country for other data exports or to customize the definitions of regions it is necessary to create an rgn file similar to a fed file and attach it here See Section 1 of the manual for more information on Regions Optional specification of moves in and out of Genetic view provide more flexibility in determining when individuals move in and out of the selection for genetic analysis in order to more accurately assess historical genetic status of a population Files can be imported that Replace or Add Moves to the existing imported data This is an advanced option still under testing more information on this feature will be available in a later version of this manual UDFs are udf files that are User Defined Fields that can be custom created to provide information on individuals specific to the needs of the data analysis or population planning e g taxonomic information UDFs can be read in during studbook exports e g SPARKS 1 6 when the PMx project is created or at a later point using the Settings tab PMx gives the option to specify if the data in these files should be added to or should replace UDF data already imported for the individuals Adding data will create new UDF fields while keeping any existing UDF data intact Replacing UDF data will cause all existing UDF fields to be deleted and the new data inserted Read Emp
138. e interval while reproduction likely occurs near the end when few individuals are alive To avoid this bias PMx will automatically convert the age class length to a shorter time interval e g month instead of year when reproduction occurs in the first age class Age class length can be changed on the Settings tab PMx User Manual version 1 0 Page 42 AGE DISTRIBUTION TAB Purpose This tab provides the user with the population s age structure data and graph and also allows the user to project and visualize changes in the age distribution into the future How to Use This Tab To the right of the screen the Age Distribution graph shows the number males on left and females on right in different age classes Y axis Each horizontal bar represents one age class default age class one year The total number N of males and females is given on the figure at the top left and right corners respectively The light blue color indicates those individuals that are out of the range of Mx gt 0 and thus considered to be non reproductive immatures at the bottom of the distribution post reproductive individuals at the top Unknown sex animals of breeding age are indicated in green unknown sex animals of non breeding appear in yellow Unknown aged animals are not shown PM Amur Tiger SSP 24Jul11 Demography eo Overview Male Life Table Female Life Table Age Distribution Census
139. e number of animals at risk Risk Qx The number of animals that are alive during an age class This is the sample size from which Qx is calculated Risk Qx values are used to calculate mortality Qx by dividing the number of deaths that occurred during an age class by the total number of animals at risk of dying during that age class Survivorship Lx The probability that a new individual e g age 0 will be alive at age x Survivorship is a cumulative measure that represents the proportion of individuals that survive from birth to the beginning of a specific age class i e the survivorship of age class 5 is influenced by all of the survival rates in the age classes from birth until age class 5 Mid Lx The proportion of individuals surviving to the mid point of age class x Fecundity Mx The average number of same sex young born to individuals in that age class For each offspring each parent gets 0 5 of the birth attributed to him her Risk Mx The number of animals that are alive during an age class This is the sample size from which Mx is calculated Risk Mx values are used to calculate fecundity Mx by dividing the number of births that occurred during an age class by the total number of animals at risk of reproducing during that age class Life Expectancy Ex The average number of additional years an individual in age class x can expect to live Reproductive Value Vx The expected number of offspring produced in this year and i
140. e of SirelD or DamID UNK WILD or MULT including MLTx However for other matings types non sexual reproduction or various forms of group formation the SirelD data field can be used to enter a special code to describe the mating type If Sire D is GROUP Entity is assumed to be a Group formed by a sexual merge in which sum of contributions from sire side are scaled to equal sum of contributions from dam side Sires contributing to this Group should be specified on subsequent lines of SIRE and or SIRES The contributions of these sires to the Group if unequal should be specified on SIRE and or SIREPROB lines Group size is the sum of the contributions unless specified otherwise with GROUPXx as the SirelD in which case x gives the total size of the new group and contributions of parents are re scaled to sum to x MERGE Entity is assumed to be a Group formed by a merge Dam would normally be listed as GROUP or MULT and the parents contributing to this merge should be specified on subsequent lines of DAM and or DAMS The contributions to the Merge if unequal should be specified on DAM and or DAMPROB lines A single Dam D other than GROUP or MULT could be listed in which case the merge would be the same as a clone of that dam SPLIT Entity is assumed to be a Group formed by a split DamID can be a single entity e g the group from which a split was made or can be GROUP or MULT if there are multiple possi
141. e recommended number of offspring from the individual with respect to the breeding recommendation Default setting is blank Fills automatically from Pairing tab RecNotes Provides a field for the user to add miscellaneous notes about the individual and or detailed recommendations for that individual Default setting is blank Examples of entries include Excluded from genetic analysis Breed via Al Has contraceptive implant Priority breeder Include in research study etc If pairs have been selected on the Pairing tab these recommendations will be automatically transferred to the recommendations table for both the male and female If an ISIS mnemonic is typed into the Location column in the Selected Pairs table on the Pairing tab then the Disposition of any individual in that pair that is not at that location will be changed to Send To and the New Location will be filled in on the recommendations table Recommended culling of individuals are also transferred to the recom mendations table The Disposition of any individuals that were selected to be culled on the Culling tab will be changed to Available All of these entries can be manually altered PMx User Manual version 1 0 Page 119 PMx Amur Ti File Language Help Project Notes Selection Demography Genetics Goals Recommendations UniqueID Location is LocalID Sex AgeYears Disposition New Locati
142. e statistics will be updated to reflect the new selection Click the Export button to export the data as a txt csv or xls file Overview Individuals Kinship Matrix Pairwise Info Management Sets Graphs Settings Selection Current Dynamic 1994 1995 1996 1997 1998 2006 2007 2008 57 42 45 45 47 49 58 58 58 Potential additional 0 Living Animals N Individuals 174 168 166 161 155 151 149 144 142 132 140 132 134 129 129 Living Descendants 174 00 168 00 166 00 161 00 155 00 151 00 144 00 142 00 141 00 132 00 140 00 132 00 134 00 129 00 Ancestry Known 100 100 100 100 100 100 100 100 100 100 100 100 100 100 Ancestry Certain 100 100 100 100 100 100 100 100 100 100 100 100 100 100 Gene Diversity Based on Kinship Matrix 0 9525 0 9636 0 9681 Based on Gene Drop Potential Gene Value 0 9419 0 9360 0 9578 0 9585 0 9588 Population Mean Kinship 0 0475 0 0364 0 0319 0 0321 0 0322 Founder Genome Equivalents Based on Kinship Matrix Based on Gene Drop Potential Founder Genomes Surviving Mean Inbreeding 0 0457 0 0299 0 0156 0 0158 0 0144 Mean Ne Over Generations Current Ne Based on Breeding Males and Breeding Females Ne N 4 Assumptions Dynamic Population Variables Do Not Indude Founders Unknown Weight 0 00 GD 0 9645 GV 0 9600 MK 0 0359 Known 100 N 143 0 PMx User Manual version 1 0 Page 74 The following information is p
143. e steps if current trends continue Default time step is one year but this can be changed in the Settings tab Mortality Mortality proportion of individuals that died during an age class is given with sample size provided in parentheses 30 Day Proportion of individuals that die within 30 days of birth or hatch The length of time defined as early mortality may be changed on the demographic Settings tab 0 Age Class Proportion of individuals that die during the first age class Avg Pre Repro Average of mortalities for all Pre Reproductive age classes where Mx 0 Avg Repro Average of mortalities for all reproductive Breeding Age age classes where Mx gt 0 Avg Post Repro Average of mortalities for all Post Reproductive age classes where Mx returns to 0 PMx User Manual version 1 0 Page 36 Survival time step Survival Lx of the selected population during the exported date window and other filters Lx 0 50 0 25 etc The age to which various proportions of the population survive from 50 to 1 Life Expectancy Average life expectancy at birth Will display if the oldest animal s ever existing is still living Oldest Living Oldest living individual will display UniquelD if only a single individual or n if more than one individual Reproduction time step Reproductive summary of the selected population during the exported date window and other filters Earliest Age of earliest recor
144. e table labels Wales Females will not change The default columns for each table are UniquelD MKdynamic Rank KVdynamic Known AgeYears Location ReproStatus F Result and MSI As with most tables in PMx the variables displayed can be customized by right clicking on the header and adding and or removing variables Note that the variables UniquelD MKdynamic KVdynamic Rank and F Result are required and cannot be deleted Data can be sorted by clicking on the column header The Results table in the upper right corner displays information regarding the pair of individuals highlighted blue rows in the two tables The top right gives information about the pair inbreeding coefficient F of the offspring and the MSI score for the pair The rest of the table gives the new values and net change for Gene Diversity Gene Value Founder Genome Equivalents FGE and Percent of pedigree Known if that pair produces surviving offspring Offspring produced by a pair can be changed from the default value of one in the field below the table The blue columns in the Males and Females tables give the F of resulting offspring and MSI score for all possible mates of the individual highlighted in blue in the other table The MSI column can be changed to display other variables eMSI DeltaGD MKDiff or Ranks instead of MSI using the Pairwise data to display button at the top of the screen In this example male 4193 and female 4074 are highlighted blue
145. e that can be traced back to known founders Balanced Ranks Difference between the MK or KV ranking within sex for the male and for the female eMSI Extended MS For each factor Delta GD GV Diff and F a percentile is calculated as the percentile of the range that the factor s value falls within the bin For example if the F value for a pair falls 2 3 of the way between the lower value of that bin and the upper value of that bin then its percentile is 67 The percentiles are then averaged or weighted averaged across the three factors and this average is then appended to the MSI value in decimal format See the Pairwise Info tab for other MateRx related definitions New Features Most of the setting options on this tab were not available in PM2000 including more flexibility in dealing with multiple MULT and unknown UNK parents specifying the zoo association or geographic region of an individual revising individuals moves in and out of the genetic window and all settings for MateRx type analysis Helpful Hints e Check that your association fed files are current before using them for inter regional analysis e Use Associations to create your own management sub groups of institutions e Be sure to click on Read Files after specifying additional data files otherwise the new data will not be read into PMx PMx User Manual version 1 0 Page 114 SELECTION TAB Genetics Purpose The Selection tab in the Genetics sectio
146. e used in the demographic import into PMx PMx User Manual version 1 0 Page 13 Advanced Import into PMx Follow the same process described for the Basic Import except for the Demography Input File select the Analytical Survival Statistics Included Individuals Table csv file from the studbook folder Female Male C Users LFaust LPZ_DOMAIN Documents PopLink 2 1 PopLink Databases Sav Tam09 ANALYTIC REPLACE primary demographic data with these data ADD to primary demographic data with these data Additional Optional Input Files Census C Users LFaust LPZ_DOMAIN Documents PopLink 2 1 PopLink Databases SavTam09 Exchcenst 2 Exporting Additional Files from PopLink UDFs Associations Regions PMx can also display additional information about individuals Files for User Defined Fields UDFs Associations and Regions can be specified in the second Create a New Project screen in PMx under Additional Optional Input Files UDF studbook data can be exported from PopLink 2 1 Click on the Select Filters button at the top left main window and click on the Clear All Filters button on the bottom left of the resulting pop up window Reproductive Event 1D Status Date Parent Age Institution Specimen Notes Birth Type UDF Sex Use this filter to limit your data geographically OR using a FED file For geographic filtering type in the SPARKS mnemonics e g N AMERICA For FED file filtering select
147. each male female will be allowed to reproduce in the calculations of the lifetime reproductive goals e g PMx assumes post reproductive individuals can no longer reproduce and young animals will have the highest reproduction Caution Be sure to check Vx values in the life tables found in Demography section before using this tool If Vx values are considered unreliable as indicators of future reproductive success consider not checking the Vx Multiplier box otherwise the results from this tool may be inaccurate for this population In addition be aware that it might be normal for the maximum reproduction that can be obtained from an individual to be several fold to many fold greater than the Vx estimated from the life table based on past management conditions Once these variables have been specified click the Calculate button to calculate the Reproductive Goals for each individual and the Resulting GD for the population in the next generation if all reproductive goals are perfected reached i e if everything happens as ideally as possible This value of GD could be used in goal setting because it calculates a more realistic upper limit of gene diversity given the currently living animals in the population i e indicates what is biologically possible than GD calculated from Potential Founder Genome Equivalents that is given on the Genetic Overview tab However this may still be an unrealistically high projection for the population GD dependi
148. ecking the Apply culls to demography box before individuals are culled The Current Population table and list of Selected Culls can be exported using the Export buttons under each respective section If the Selected Culls box is exported a Cull File will be created see below As with most PMx tables the list of individuals displayed in the Current Population table can be filtered using the Filter button Auto button This feature can be used to identify the best x number of individuals for culling so that the overall population gene diversity is optimized Clicking the Auto button will open the Auto Cull window Enter the number of individuals to be culled default value is 10 Click Accept The optimal x individuals to be culled will now appear in the Selected Culls box and all genetic calculations will be updated Entering 0 for the Culls will cause PMx to cull until GD is maximized Check the Restrict culls to filtered list box to limit Autocull to only those individuals displayed e g one sex older individuals Animals will be automatically culled from the population optimizing gene diversity Culls Restrict culls to filtered list Enter 0 culls to optimize Gene Diversity cone Read Cull File button This feature will read in a previously created list of individuals to be culled Clicking on the Read Cull File button will open the Read in Cull List window Navigate to and select the file containing the lists of indivi
149. ed into the field Recommendation Information The following fields display information entered into the Recommendations tab Click on the Update Table button on this tab to update these fields Recommendations should be edited on the Recommendations tab and not on the Individual tab RecDisposition Recommendation for the possible transfer of an individual Options are Hold SendTo Export ReceiveFrom ImportFrom Available Other Unknown RecDestination Location at which the individual is recommended to live in the future either remain at the current location or be transferred to a different location PMx User Manual version 1 0 Page 127 RecBreed Recommendation for this individual with respecdt to breeding Standard options are DoNotBreed Breed Surplus Social Other Unknown Npairs Number of pairings assigned to this individual in the breeding recommendations count of entries in With field on the Recommendations tab RecMates List of the Unique lDs of mates assigned to this individual in the breeding recommendations list of entries in With field on the Recommendations tab RecNotes Notes about the breeding and transfer recommendations RecNotes field on the Recommendations tab DemSelected True if the individual is in the Selected Population for demographic analysis PMx User Manual version 1 0 Page 128 APPENDIX B GLOSSARY OF TERMS Demographic Terms Age Distribution A two way classif
150. ed only to females and takes into account the availability of breeding males Stochastic projections are more realistic as the impact of small population size skewed sex ratio and other chance events are incorporated and provides a range of probable outcomes rather than a fixed number Projections with no reproduction PMx provides the option to easily project the impact of halting reproduction in a population useful in projecting decline in populations being managed to extinction Age structure status ratings Once stochastic projections are run PMx compares the stochastic growth rate lambda for the next year to the deterministic growth rate life table lambda and provides a warning if either 1 the actual stochastic growth rate deviates substantially from the predicted deterministic growth rate e g the population will grow much more slowly or 2 there is a moderate or significant chance that the direction of actual growth increase vs decrease will be different than the direction predicted e g the population will decline instead of increase This information can be found at the bottom of the table on the Overview tab in Demography once stochastic projections have been run See Demography Overview in this manual for more information PMx User Manual version 1 0 Page 53 Helpful Hints e Donot interrupt stochastic simulations but allow PMx to compete simulation runs before proceeding with other computer functions e D
151. ed the filter window The Regions used in this export are designated by country as follows e North America Canada Greenland US Bermuda e Latin America from Mexico south through the Caribbean Islands Central America and South America e Europe including Russia Armenia Azerbaijan Belarus Estonia Georgia Kazakhstan Kyrgyzstan Latvia Lithuania Moldova Tajikistan Turkmenistan Ukraine Uzbekistan e Africa all of Africa PMx User Manual version 1 0 Page 15 e Middle East Bahrain Iran Iraq Israel Jordan Kuwait Lebanon Oman Qatar Saudi Syria UAE Yemen e South Asia Afghanistan Bangladesh Bhutan BIOT India Maldives Nepal Pakistan Sri Lanka e South East Asia Myanmar Laos Vietnam Cambodia Thailand Malaysia Singapore Indonesia Philippines e East Asia China Hong Kong Macao Taiwan Japan North Korea South Korea Mongolia e Australasia Australia New Zealand Papua New Guinea Fiji New Caledonia plus nearby island groups Designations for Asia and Middle East approximately follow the UN designations for these regions as depicted here East Asia r i For projects created from SPARKS 1 6 exports the Country and Region will appear on the Individual tab even if no rgn file is attached Management sets can be created automatically based on either Country or Region If a different custom Region is desired than those outlined above a custom Region file s can be created and attac
152. eding programs Zoo Biology 19 279 282 Lacy R C 2009 Stopping evolution Genetic management of captive populations Pages 58 81 in Conservation Genetics in the Age of Geonomics G Amato R SeSalle O A Ryder and H C Rosenbaum eds Columbia University Press New York Lacy R C Extending pedigree analysis for uncertain parentage and diverse breeding systems Journal of Heredity in press Lacy R C and J D Ballou 2002 Population Management 2000 User s Manual Chicago Zoological Society Brookfield IL Lacy R C J D Ballou and J P Pollak 2011 PMx software package for demographic and genetic analysis and management of pedigreed populations Methods in Ecology and Evolution in press Lacy R C J D Ballou and J P Pollak PMx Software package for demographic and genetic analysis and management of pedigreed populations Methods in Ecology and Evolution in press Lacy R C J D Ballou F Princ e A Starfield and E Thompson 1995 Pedigree analysis Pages 57 75 in Population Management for Survival amp Recovery Analytical Methods and Strategies in Small Population Conservation J D Ballou M Gilpin and T J Foose eds Columbia University Press New York Lande R and G F Barrowclough 1987 Effective population size genetic variation and their use in population management Pages 87 123 in Viable Populations for Conservation M E Soul ed Cambridge University Press Cambridge UK Lee
153. ee below Click Next On the following screen you have the ability to include optional data input files Click Create and PMx will create your project and open the main PMx window at the Project Notes screen The name of the project will appear in the top window bar Note The PMx window may disappear temporarily while the project is being created this can take several seconds for large studbooks please wait for the PMx window to reappear Below is asummary table of those files needed to create a PMx project from various versions of the SPARKS and PopLink database programs see the detailed instructions on how to create these data exports from each program SPARKS 1 6x SPARKS 1 5x PopLink 2 1 PopLink 1 3 Primary Input File exchange csv exchange dbf ped ped Demography Input Not needed included prn files prn files basic File s in exchange csv Analytical Survival Statistics Included Individuals Table csv advanced Census File pmxcens csv exchcens txt Exchcens txt Exchcens txt UDFs File Not needed included gc_UDF csv Not possible in exchange csv Creating a Project from SPARKS 1 6x Export from SPARKS 1 From the SPARKS main menu select Reports 2 Use the Left arrow key to open the View Criteria as needed The Date Span for the export will default to 1 Jan 1800 today s date otherwise set a date span sufficient to include sensible demographic data associated with m
154. emale Life Table Age Distribution Census Projections Reproductive Planning Add Remove Availability Graphs Settings Total Males Females Survival years Census Lx 0 50 6 2 4 2 8 1 Lx 0 25 17 0 16 7 17 3 Lx 0 10 23 8 24 2 23 3 Lx 0 05 29 1 30 5 27 7 Lx 0 01 32 2 33 5 30 9 Life Expectancy o 11 2 C3 Oldest Age 28 6 ID 358 28 6 ID 358 28 6 ID 317 Reproduction years Earliest 3 Latest 28 Females Others Average Mx 0 1 150 births to unknown age par 11 out of 486 Stochastic Projections Mx Projections years Prob Extinction 0 00 500 Size next 1 year 154 lt gt 164 lt gt 175 Life table Lambda 1 002 Long Term Stoch Lambda 0 974 lt gt 0 992 lt gt 1 008 Lambda next 1 year 0 963 lt gt 1 027 lt gt 1 094 ProblIncrease next 1 year 0 77 Prob Decrease next 1 year 0 17 lt L95 Det Males Females Assumptions Overall Statistics Stochastic Runs Age Classes are years Birth Flow Continuous CI 95 Iterations 500 Projections 20 time Growth in terms of years r 0 002 lambda 1 002 Ro 1 015 T steps 11 2 N20 166 Up to date Totals This section gives the number of living individuals in the current selected population i e living as of the Analysis Date Total counts as well as counts broken down by sex are listed for the following categories Pre Reproductive Number of living individuals not yet of breeding age defined by those i
155. empt to check for updates when opened if the computer is connected to the internet Within the Help menu there is also an option to check the PMx website manually and download any upgrades more recent than the version running on your system Attempts will be made to make all upgrades backward compatible to accept PMx project files created with prior versions but no guarantee can be provided Cautions PMx is distributed free of charge It is provided without any promise of support The primary developers of PMx and a large number of collaborating colleagues have attempted to provide the best most current methods and tools to assist with the management of pedigreed populations PMx is distributed with no guarantee that the methods perform as intended or described that the computer code is without bugs that could influence results or that the program is suitable for any particular purpose PMx User Manual version 1 0 Page 23 Acknowledgements PMx was designed and written by Jonathan Ballou Smithsonian Conservation Biology Institute Robert Lacy Chicago Zoological Society and JP Pollak Cornell University with considerable and essential input and testing by a large number of colleagues including Rajan Amin Zoological Society of London Laurie Bingaman Lackey International Species Information System ISIS Lisa Faust Lincoln Park Zoo Jamie Ivy Zoological Society of San Diego Kristin Leus CBSG Europe EAZA Sarah Long AZA Popula
156. en by a relevant variable such as Age ReproStatus Known Location or appropriate UDF can be useful to quickly identify living individuals to exclude from the genetically managed population e If changes are made to the Selected Population it is recommended to document these changes in the Project Notes otherwise it is easy to forget why some individuals were included and others excluded Cautions e A good understanding of the Selection option is crucial for successful and correct use of PMx It is recommended to read the manual section for this tab completely before proceeding with analysis e Some results may be misleading depending upon how and where filters and selections are applied to the population data e The membership of regional zoo Associations is dynamic and changes over time PMx does not have access to this information and therefore treats the Association list as static and equal to the list of institutions in the imported fed file for that Association For example if an institution was a past member of an Association but recently left the Association individuals at this institution in the past when it was part of the Association will not be included in the historical analyses PMx User Manual version 1 0 Page 31 e The current version of PMx will save the separate selections for demography and genetics but only if the correct boxes Apply changes to are checked unchecked before highlighting individuals and moving
157. ent Sets Graphs Settings Selection Males SpecifyPairs Read Pair Fie Females Pairwise data to display MST UniquelD MKdys Rank KVdynd Location AgeY F Result MSI a UniqueID MKdys Rank KVdynai Location AgeYe F Result MSI Offspring F and Pair MSI 0 0718 P 4203 0 0240 1 0 0283 OMAHA 1s al 4407 0 0215 1 0 0277 PITTSBURG 3 ODay New Value Change 0 0264 2 0 033 TANAPL 4074 0 0244 2 0 0191 MANHATTAN 17 Gene Diversity 0 9646 0 0001 4 4 7 0 01 NHATTAN 4983 0 0247 0 0247 COLUMBUS Gene Value 0 9605 0 0003 0 0233 COLUMBIA 4984 0 0247 0 0247 MINNESOTA 14 1414 0 0438 0 0223 NY BRONX 4073 0 0259 0 0215 COLO SPRG n 0 0000 0 0270 0 0272 0 0276 0 0276 4541 0 0283 0 0280 LOUISVILL 4916 0 0270 0 0260 BRIDGEPRT Sire Dam F Success Offspring Location Notes 0 0292 10 0 0370 COLO SPRG 4194 0 0270 0 0198 RACINE 5456 5200 0 0274 0 3500 25 4755 0 0321 11 0 0363 COLUMBUS 4500 0 0276 0 0203 SAN FRAN 5341 4970 0 0000 0 6000 25 4586 0 0341 13 0 0381 CALGARY 4501 0 0276 0 0203 STPAUL 5464 4969 0 0625 0 4000 25 4168 0 0341 12 0 0359 CHICAGOBR 4413 0 0285 0 0251 DES MOINE 5286 5287 0 0000 0 2500 25 4304 0 0341 14 0 0277 NY BRONX 4195 0 0287 0 0223 CHICAGOBR E S aaa a aag 4825 0 0347 15 0 0356 RACINE 0 0300 0 0265 MADISON Pairs 18 Offspring attempted 45 4748 0 0356 16 0 0359 CLEVELAND 8 0 0134 6 m Offspring expected 19 13 Expo
158. enter the number 1 e Select the cell containing 1 and on the Edit menu click Copy e Select the range of numbers stored as text that you want to convert e Onthe Edit menu click Paste Special then under Operation click Multiply e Click OK e Delete the content of the cell entered in the first step An alternative method which will convert all non integers to numbers is Open the Excel worksheet Hit Ctrl F to open the Find and Replace dialogue window Click on the Replace tab Inthe Find what box type a period if using American style numbers or a comma if using European style numbers Type the same character period or comma into the Replace with box Click on Replace All PMx User Manual version 1 0 Page 133 Demography Why are there so many age classes on the age pyramid And why so many points on the life table graphs Check the age class length to see if it is shorter than you expect or intend A shorter age class means more age classes in the life tables more points on the graphs and more bars on the age pyramid If your data included reproduction in the first age class PMx may have automatically shortened age class length to avoid this problematic situation Why does PMx give me a message that Ex is not available for the life table In some studbook datasets life expectancy Ex cannot be defined because the Lx value does not go to zero i e the life table is infinite In this case
159. eory and practice International Zoo Yearbook 27 26 41 Foose T J R Lande N R Flesness G Rabb amp B Read 1986 Propagation plans Zoo Biology 5 139 146 Frankham R amp D A Loebel 1992 Modeling problems in conservation genetics using captive Drosophila populations Rapid genetic adaptation to captivity Zoo Biology 11 333 342 Frankham R J D Ballou and D A Briscoe 2010 Introduction to Conservation Genetics Cambridge University Press Cambridge UK 2 edition Frankham R J D Ballou M D B Eldridge R C Lacy K Ralls M R Dudash and C B Fenster 2011 Predicting the risk of outbreeding depression Conservation Biology in press Hedrick P W and P Miller 1992 Conservation genetics theory and management of captive populations Pages 70 87 in Conservation of Biodiversity for Sustainable Development O T Sandlund K Hindar and A H D Brown eds Oxford University Press Oxford ISIS 2011 SPARKS Single Population Analysis and Records Keeping System ver 1 6 Eagan MN International Species Information System Ivy J A and R C Lacy 2010 Using molecular methods to improve the genetic management of captive breeding programs for threatened species Pages 267 295 in Molecular Approaches in Natural Resource Conservation and Management J A DeWoody J W Bickham C H Michler K N Nicols O E Rhodes and K E Woeste eds Cambridge University Press Cambridge Ivy J A and R C Lacy A comp
160. er as under Dam Gen Generation in captivity Founding wild caught individuals are considered to be generation 0 Offspring from two founding individuals are generation 1 and so on Parents of an individual are often not of the same generation in which case the average generation value for that individual will be the average of the values of each of its parents plus one F inbreeding coefficient The probability that the two alleles at a genetic locus are identical by descent from an ancestor common to both parents The mean inbreeding coefficient of a population will be the proportional decrease in observed heterozygosity relative to the expected heterozygosity of the founder population MK mean kinship Coefficient between an individual and all individuals including itself in the living captive born population The mean kinship of a population is equal to the proportional loss of gene diversity of the descendant captive born population relative to the founders and is also the mean inbreeding coefficient of progeny produced by random mating Mean kinship is also the reciprocal of two times the founder genome equivalents MK 1 2 FGE MK 1 GD PMx User Manual version 1 0 Page 124 MKRank Ordered rank by mean kinship within sex 1M the top male lowest MK value 1F top female in the list In the case of ties in MK individuals are assigned MKRanks in random order i e if there are 4 individuals with MK 0 1597 they
161. ersed i e British rgn attached first and then Europe rgn individuals in the British Isles will be listed as Europe under Region PMx User Manual version 1 0 Page 16 Differences in Feature Availability SPARKS and PopLink Exports Most analyses and features of PMx are available using data exports from all versions of SPARKS and PopLink however there are some new features that are only available when using particular studbook keeping programs and versions for export The additional features listed in the table below are not available using SPARKS 1 5x or PopLink 1 3 but are available with data exports from SPARKS 1 6x and in some cases with PopLink 2 1 using the Advanced option for demographic exports Feature PopLink 2 1 SPARKS 1 6x using Advanced export Ability to change age class length X X Ability to redefine early mortality X X Ability to model continuous vs seasonal X X pulse reproduction Detailed census data i e captures X releases imports exports stillbirths LTFs x lt Provides past litters broods per individual gt x lt Ability to designate potential multiple parent IDs and probabilities Calculation of both Known and Certain Historical genetic analyses Ability to import social groups gt lt gt X lt gt X lt gt X lt Country and geographic Region for individuals provided in Primary Input File Opening an Existing Pro
162. erwise has unknown parent can also be coded as NONE or just left blank Note if an animal is wild caught both parents should be listed as WILD unless it is one of the forms of asexual or non sexual reproduction see below SPLIT CLONE SELF HAPLOID EXTRACT MERGE If only one parent is WILD and similarly with UNK then that wild parent will be replaced by a pseudo founder an animal that is inserted into the pedigree and is itself a founder The pseudo founder is given the ID of MateOf ID of the known parent An animal should not be given parents WILD x UNK because PMx won t know if it is WILD or UNK PMx User Manual version 1 0 Page 140 MULT or MULTx or MLTx with x being a number listed as a parent can be followed by lines specifying who are the possible sires or dams with probabilities using the format described above for SIRES SIRE DAMS DAM etc If not followed by specification of the possible parents MULT will be treated the same as UNK If a single sire and dam are listed in the Individual record and SIRE or DAM lines are also provided PMx will ignore the SIRE and DAM lines Any unrecognized SirelD or Dam D will be treated as a founder animal inserted into the pedigree with UNK x UNK parents Acceptable specifications of various Mating Types The mating type that created an offspring is assumed to be Sexual diploid individual if parents are each given as on
163. es are calculated All of these options can also be found in the Genetics Settings tab so changing them in one location will also change them in the other see Genetics Settings tab section for more information Terms and Concepts See the Genetics Summary Statistics screen Genetic Overview tab and Pairwise Info tab sections and the Appendix B Glossary for definitions of the variables on this tab New Features e New ways to incorporate multiple potential parents into the genetic analysis e New ways to deal with animals with unknown parentage e User can add or remove more variables from the male and female tables and customize them for the needs of a particular managed population e The relative suitability of many potential mates can be seen simultaneously on the tables e Paired individuals can be visibly removed from the tables to see who is left to pair e User can incorporate likelihood of reproductive success for each recommended breeding pair e User can indicate the number of offspring recommended for each breeding pair e PMx calculates the cumulative expected number of offspring e Lifetime reproductive goals can be estimated e Optimal breeding pairs can be automatically calculated Helpful Hints e PMx automatically uses a dynamic MK list i e genetic calculations are revised after each pair is selected For pairing using a static MK list enter 0 for Success for each pair note that the Offspring expecte
164. esired and click Update e The resulting graph will be displayed on the right Double clicking on the graph will provide options to print export or send the graph to the report Click Clear to uncheck all boxes and clear the Custom graph Terms and Concepts Mid Lx mid Survivorship or the proportion of individuals surviving from birth to the mid point of age class x Px mid Survival or the proportion of individuals which survive from the beginning of age class x to the mid point of age class x 1 Mx Fecundity or the average number of offspring born to individuals in that age class Qx Mortality or the probability that an individual of age x dies during age class x PMx User Manual version 1 0 Page 65 PMc Amur Tiger SSP 24Jul11 D cy I Overview il Male Life Table Female Life Table Age Distribution I Census I Seasonality Projections Reproductive Planning Add Remove Availabilty Graphs Settings Standard Custom Select Graph Type Ufe table Census Census Graphs Sex Ratio Males Variable s to Plot EN E Institutions V Sex Ratio E Birth Sex Ratio 0 6 E Births E Deaths E Lambda N E Lambda Repro 2 0 5 2 Sex Ratio Captures E Releases Wild Born E Captive Born ie Sex Ratio 0 5 Bos E Imports E Exports E Origin 22 0 3 1960 1965 1970 1975 1980 1985 1990 1995 2000 2005 2010 Stillbirths E Lost Year Graph
165. exported using the Export button and saved as a txt csv or xls file Pairwise Info Matrix UniqueID Females gt 4407 5050 4074 4073 4984 4983 4828 4542 4194 4916 4195 Males V Location PITTSBURG COLUMBUS MANHATTAN COLO SPRG MINNESOTA COLUMBUS INDIANAPL SYRACUSE RACINE BRIDGEPRT CHICAGOBR GLE 4203 OMAHA 1 4 4 4 4 4 4 5049 INDIANAPL Enter the IDs of two animals in the 5286 COLO SPRG boxes below to view pairwise info 3640 NY BRONX Data to display 7 7 4 4193 MANHATTAN 4 COLUMBIA 4 COLUMBUS 4 LOUISVILL 6 DES MOINE 6 CHICAGOLP 6 DETROIT 6 7 6 6 6 6 6 6 6 6 Update Table with Pairs and F maias Culls CALGARY SEDGWICK CHICAGOBR TORONTO View MateRx settings NY BRONX NoWay for F 0 12 RACINE LANSING Anh bhR hh RWWWHWNNY ENE N hha Reh RWYHYWYWNNN ENN A A Php he PRWNNNNWNH EEN D hhh RAR RWNNNNWN PEN DD PND DHHMHVNVN SE HHH RHE ENN NY pepe eHW HON NN ENN DEEN SA heheh RR WUYUYNNNNN ENN w A hep D hp he Y HW Pe EeN EN PEW hhh ehh RWW Hehehe HN EN Nw A Sortronson sotcosc SS Assumptions Dynamic Population Variables Do Not Indude Founders Unknown Weight 0 00 Terms and Concepts MSI Mate Suitability Index MSI is a numerical genetic assessment of a male female pair that incorporates several variables into one ranking MSI range is 1 to 7 with 1 being the most genetically beneficial eMSI MSI score that includes the exten
166. f individuals which survive from the beginning of one age class to the next Mid Px The probability that an individual survives to the mid point of age class x Survivorship Age Specific Lx The probability that a new individual e g age 0 is alive at the beginning of age x Alternatively the proportion of individuals which survive from birth to the beginning of a specific age class Mid Lx The proportion of individuals surviving to the mid point of age class x Genetic Terms Allele Retention The probability that a gene contributed by a founder individual exists in at least one individual in the living descendant population Coefficient of Relatedness r The probability that at a given locus an allele sampled from one individual is identical by descent to at least one of the alleles at that locus in a second individual In a population with no inbreeding r is two times the kinship value Coefficient of Kinship Kinship Coefficient or Coefficient of Consanguinity often symbolized f or k The probability that at a given locus an allele sampled from one individual is identical by descent to an allele sampled at random from that locus in a second individual Cull Remove an individual from the managed population used for genetic analysis Effective Population Size Ne The size of a randomly mating population of constant size with equal sex ratio and a Poisson distribution of family sizes that would a result in the same me
167. ffects the number of pairs needed is the number of litters produced per year per pair Many species produced only one litter per year for species that can produce more than one litter per year entering a number gt 1 for Litters year will cause PMx to calculate the minimum number of pairs needed This assumes that each pair will be recommended to produce this number of litters in many cases there may be genetic or other reasons why managers may decide not to produce multiple litters from the same pair within one year but distribute the same number of litters among a large number of pairs The reproductive plan can be saved to a file using the Export button The graph also can be exported sent to the Project Notes or printed by double clicking on the graph Terms and Concepts Population Growth Rate or Lambda A The proportional change in population size from one year to the next A lambda of 1 11 means a 11 per year increase lambda of 0 97 means a 3 decline in size per year New Features e Ability to specify multiple litters per year e Provides the number of litters needed in the next year e Provides the confidence interval ranges for number of births litters and pairs needed for the next year PMx User Manual version 1 0 Page 56 Helpful Hints Remember that the results of each reproductive plan are only calculated after clicking on another field In many cases in population planning using this screen for determinin
168. file then those sets of possible parents are collectively considered to be the possible parents of the animal An advantage of this format in which the ID of the offspring is listed is that the lines with these parentage data do not have to follow immediately after the offspring in the pedigree file but can instead be inserted anywhere within the file For example the records listing the possible parents can all be inserted at the bottom of the pedigree file If a parent of an animal is listed as MULT1 MULT2 or GROUP1 GROUP2 then another alternative to listing the possible parents on the subsequent data line is to give later in the file the animals that comprise that MULT or GROUP with data lines in the following format ID MULT1 SIRE 123 0 50 SIRE 124 0 50 Or equivalently ID MULT1 SIRES 123 124 SIREPROBS 0 50 0 50 And similarly with Dam instead of Sire for multiple possible dams and the Sire and Dam labels can be preceded or not by an The initial ID tag can be any of ID INDIVIDUAL MULT or GROUP or any of these preceded by an ox The advantage of using this format to specify which animals are included in a MULTx parent with x being a number is that a number of animals with the same set of possible parents can be assigned MULTx as the parent and then only once in the file do the parents in that MULTx set need to be identified The exchange csv file can also contain move reco
169. g the box e Columns may be moved from one position to another by clicking on the header for a particular column and dragging it to the desired position e The overall data may be sorted by clicking on any header As all of the information is treated as text information will be ordered by characters then numbers then letters Data may be sorted in ascending or descending order by clicking repeatedly on the header e Individuals can be marked using different colors in the Flags column which can then be used for sorting a EE PMx test Genetics UniqueID Location LocalID HouseName OtherID Sex Known Certainty BirthDate BirthDateEst Alive LocallD DORTMUND US2544 KARA m Female 0 937 5 0 93 75 2006 10 06 Exact True HouseName TAIPING 270238 DURGA Cl Female 1 0000 10 Exact True OtherID TAIPING ZT0178 DINA UNJ Male 0 9375 0 9375 2000 09 27 Exact True on TAIPING ZT0278 GAYA 00 01BC 86B8 Female 0 9375 0 9375 2000 09 27 Exact True Per TAIPING ZT0277 YANI 00 01E7 23BE Female 0 9375 0 9375 2000 09 27 Exact True HALLE 207305 SIRIUS 968000004754586 Male 0 9375 0 9375 2007 10 02 Exact True E P BERLIN TP TAREK 968000004262588 Male 0 9375 0 9375 2007 10 02 Exact True ee HALLE 207307 JOHANN 968000004765399 Male 0 9375 0 9375 2007 10 02 Exact True BirthDateEst SEDGWICK 12427 MALIK UI Male 1 0000 1 0000 2007 07 30 Exact True Alive SEDGWICK 12428 HAKIM EJ Male 1 0000 1 0000 2007 07 30 Exact True DeathDate MELAKA
170. g the number of pairs needed may not be a useful or accurate tool For most populations it is necessary to assess the probability of each pair breeding on a case by case basis and a general value for probability of breeding cannot be determined for the population For example an older pair who has been together for some time but has had no breeding success will have a lower probability of breeding than a proven breeding pair currently at peak reproductive age For this reason Births Needed may be the most useful calculation This can be compared to Offspring Expected on the Pairing tab as a series of breeding pairs are created with different estimated probabilities of success Always keep in mind what is realistic for the population when reproductive planning Are there enough animals in breeding age classes to provide the desired amount of reproduction Is there enough space available to hold that many offspring in a year s time Approximately how many offspring has this population produced annually historically On how basis was the target population size chosen Cautions As noted above the calculations take neonatal mortality rates into consideration so the results indicate the number of births needed as opposed to the number of surviving births The default current population size may change before and after genetic analyses are conducted Example if animals are unselected for the genetic analyses the default value for t
171. ge distribution SAD will cause the short term population growth rate to vary from the deterministic life table lambda PMx compares the average stochastic lambda for the next two time intervals S to the life table lambda L and reports on the Status of the potential impact of this deviation from SAD One of five Status messages is displayed PMx User Manual version 1 0 Page 37 Okay Life table and stochastic lambdas are in the same direction both positive or both negative the two lambdas differ by less than 2 and there is less than 10 chance that the stochastic lambda S will be in a different direction than the life table lambda Actual growth rate deviates moderately from predicted growth rate Growth is in the same direction but stochastic lambda deviates from life table lambda by 2 5 Actual growth rate deviates significantly from predicted growth rate Growth is in the same direction but stochastic lambda deviates from life table lambda gt 5 Moderate chance that the population will increase decrease instead of decrease increase as predicted There is a 10 20 change that stochastic lambda is in a different direction than life table lambda Significant chance that the population will increase decrease instead of decrease increase as predicted There is a gt 20 change that stochastic lambda is in a different direction than life table lambda Demographic Footer The footer across the bottom of the Demo
172. ger mean kinships e Add the column MyDescendants to display a list of the first 25 descendants of each founder which can be useful to identify descendants of underrepresented founders or those of lineages of particular interest PMx User Manual version 1 0 Page 78 INDIVIDUALS TAB Purpose The Individuals tab is used to display all of the specific information that is either imported for an individual or group or accrues as various analyses are run Subsets of this information are utilized on many other screens but by default all possible information is displayed here More details on Groups will be added as they are developed How to Use This Tab Upon opening the tab all of the information currently available for each individual or entity i e group in the selected population will be displayed i e data are unfiltered A short description of most variables can be viewed by placing the cursor on either the header label or on a cell in that column for one of the individuals More detailed descriptions of each variable can be found in Appendix A This table can be modified as follows e Right click on the header line and a menu of all variables will appear By default all are checked Unchecking any variable will remove that column from the display This does not remove the data from the project just from the current table view Any variable can be added back to the table at any time by right clicking on the header and checkin
173. graphy Overview tab contains reminders of many of the variables that affect the demography Assumptions many of these assumptions can be changed on the demographic Settings tab Also displayed are a few demographic Overall Statistics r lambda Ro T projected N as well as the status of the Stochastic Runs Outdated or Up to date This footer is displayed at the bottom of all Demography section tabs Cautions e The age classes to be considered as Pre Reproductive Breeding Age and Post Reproductive are based upon past reproduction as indicated in the calculate Mx values for each sex in the life tables It is possible that the population may simple not have bred at those ages yet this is especially true if the overall population is relatively young or has not been in captivity long Revision of the Mode Data to Mx gt 0 in early or late age classes may be needed to more appropriately defined the biological reproductive lifespan for the species e The reproductive status of individuals Fertile Contracepted Sterilized is based on the designation of these individuals in the exported studbook database If individuals are not listed as Contracepted or Sterilized in the studbook they will appear as Fertile in PMx by default which may or may not be accurate e Be sure to rerun the Stochastic Projections after making any changes in the Model Data or demographic Settings PMx User Manual version 1 0 Page 38 LIFE TABLES TABS Purpose T
174. he actual data are not being plotted e Ex life expectancy cannot be calculated if the life table is infinite i e Lx does not go to zero e Plotting both Lambda N and Lambda Repro on the same graph can illustrate the impact of managerial captures imports releases exports vs biological births and deaths events on population size and trends e lf both the N and Institutions boxes are checked you will be given the option of using a combined line for N and bar for Institutions graph PMx User Manual version 1 0 Page 66 SETTINGS TAB Demography Purpose The Settings tab allows the user to customize settings for demographic planning specifically it provides the ability to modify the way in which some life table calculations are made to change the length of the time interval used for calculations to something different than one year and to set factors related to population projections Information about these options can also be found on the Life Tables tab and Projections tab How to Use This Tab In general options in the left column relate primarily to life table settings Settings for projections can be found in the right column After changing any of the values click OK to apply these changes The tab label will display to indicate that changes from the default values have been made and the Stochastic Runs box in the lower right corner will change to Outdated indicating the need to rerun the
175. he current population size on the Reproductive Planning tab will reflect the new smaller size Remember that changes to Model Data are not saved with a project If a saved PMx project is reopened the Actual Data values will be used for the Model Data and therefore for projections of needed births to achieve a particular growth rate Smoothing and or other desired changes to the Model Data will need to be re entered PMx User Manual version 1 0 Page 57 ADD REMOVE TAB Purpose The Add Remove tab allows the user to define population management plans that include the addition of new individuals to the population and or the removal of individuals from the population over a projected future time period and to assess the demographic impacts of these plans on population size How to Use This Tab This tab is divided into three sections Left section provides the ability to create enable disable or delete one or multiple supplementation or removal plans Center table displays the tabular results number of individuals added and or removed of the enabled plans over the projected time period and Right section displays the projected population size top and the projected number of individuals added or removed bottom under the enabled plans over the projected time period To create a new plan click on Add Plan to open the Define a Supplementation or Removal Plan window 1 9 The table on the left shows the current number of individ
176. hed The format is similar to a fed file it is a text file containing a list of ISIS mnemonics in that geographic region and is designated as a rgn file Imports from SPARKS 1 5x or PopLink do not contain Country or Region information and so these columns will appear blank in PMx unless a rgn file is attached Like a custom fed file a rgn file can be created fairly easily by editing and renaming an existing fed file in a text editor SPARKS offers an option under the Association filter to Create a comprehensive custom fed file that includes all Locations in the studbook which can then be renamed saved and edited into a custom fed or rgn file Caution It is possible to attach multiple rgn files to a PMx project one at creation and or multiple files on the Settings tab in the Genetics section However since an individual can only physically be in one region at a time if multiple region files are attached that are not mutually exclusive then the last rgn file attached will take precedence i e overwrite previous regional designations for an individual For example if a complete Europe region file is attached first and then a British Isles region file containing a subset of European mnemonics specific to the British Isles is subsequently attached individuals at mainland European institutions will be listed as Europe under Region while those in the British Isles will be listed as British under Region If the order of attachment were rev
177. hese two tabs Male Life Table and Female Life Table provide the user with separate male and female life tables that provide the average survival and reproductive rates for the time period view for the data imported into PMx The life tables allow for visualization of the demographic history of the chosen population How to Use This Tab Life tables are created for males and females using life history data from all individuals in the selected time frame when data are exported from PopLink or SPARKS a PMx NA MAL 25Mar Demography a Overview Male Life Table Female Life Table age Distribution Census Projections Reproductive Planning Add Remove Avaiiabiity Graphs Settings Females Actual Data Females Model Data Age years Px Mid Px Qx RiskQx Lx Mid Lx Mx RiskMx Ex VK amp Age years Px MidPx Qx RiskQx Lx MidLx Mx RiskMx Ex Vx amp E o o 0 07 324 100 0 96 0 00 324 15 35 1 04 0 10 o 9 os 0 07 324 1 00 096 0 00 32 4 15 35 1 04 0 10 1 1 00 1 00 0 00 31 0 0 93 0 93 0 00 31 0 14 92 1 15 0 09 1 1 00 1 00 0 00 31 0 0 93 0 93 0 00 31 0 14 92 1 15 0 09 2 1 00 0 99 0 00 30 8 0 93 0 93 0 00 30 8 13 92 1 22 0 09 2 1 00 0 99 0 00 308 0 93 0 93 0 00 308 13 92 1 22 0 09 3 0 98 0 98 0 02 264 0 93 0 92 0 14 26 4 13 06 1 31 0 08 3 0 98 0 98 0 02 264 0 93 092 014 264 13 06 1 31 0 08 4 0 98 0 99 0 02 25 2 0 91 0 90 0 36 25 2 12 30 1 26 0 07 4 0 98 0 99 0 02 25 2 0
178. his file to be created by converting the SPARKS udf dbf file into a csv file Comment lines starting with will be ignored Record format ID UDFivalue UDF2value Note that UDFs are stored as strings even if they have a numerical format Association Input File This can be a text file with any name although PMx will specifically look for files with extension fed The file should be just a list of MNEMONICs one per line of all Locations that are to be considered part of that association The Association s for each animal will be listed in PMx as a label that is the filename minus the fed extension Multiple fed files can be read and an animal can be listed as being within more than one Association e g fed files might be used to read AZA CAZA WAZA and even FRIENDSOFJON Region Input File This can be any text file although PMx will specifically look for files with extension rgn The file should be just a list of MNEMONICs one per line of all Locations that are part of that region The Region for each individual will be listed in PMx as the filename minus the rgn extension Multiple rgn files can be read but each individual will be listed as within only the last of the regions in which it was a member PMx User Manual version 1 0 Page 149 Locations File When SPARKS or PopLink creates an export for PM2000 or PMx it also creates a Location txt file that lists contact informat
179. hs Month Filtered On None Title Births ay Total Births 1462 Merch Usable dates 1404 April Date estimates too wide 45 Unknown dates 13 may P Uniform Distribution lt 0 05 Chi square 535 18 df 11 June January ES el ay nen gt August September October November December Month a Events Shown Deaths Deaths Fitered On None Sen Title Deaths Prusy Total Deaths 1798 r Usable dates 1404 April Date estimates too wide 11 Unknown dates 383 ny Uniform Distribution lt 0 05 Chi square 40 75 df 11 Jna Edt Gear uly August September October November December W Compare Seasonality The two distributions are statistically significantly different from each other at ithe 0 05 level Chi Square 153 18 df 11 Assumptions Overall Statistics Stochastic Runs Age Classes are years Birth Flow Continuous CI 95 Iterations 500 Projections 20 time Growth in terms of years r 0 013 lambda 0 987 Ro 0 907 T steps 7 9 N20 102 Up to date PMx User Manual version 1 0 Page 48 PMx currently provides a few options for changing filtering the data used in each of the two analyses Clicking the Edit button brings up a window of options for the table and graph to the right Both births and deaths can be filtered by sex In addition deaths can be filtered by Association Region Country and Location of death hopefully this option will be availa
180. hsonian National Zoological Park Ballou J D J Earnhardt and S Thompson 1999 MateRx user documentation Washington DC Smithsonian National Zoological Park Ballou J D J Earnhardt and S Thompson 2001 MateRx Genetic Management Software Washington DC Smithsonian National Zoological Park Ballou J D M Gilpin and T J Foose 1995 Population Management for Survival and Recovery Columbia University Press New York Ballou J D C Lees L J Faust S Long C Lynch L B Lackey and T J Foose 2010 Demographic and genetic management of captive populations Pages 219 252 in Wild Mammals in Captivity D G Kleiman K V Thompson and C K Baer eds University of Chicago Press Chicago IL Ballou J D and R C Lacy 1995 Identifying genetically important individuals for management of genetic diversity in pedigreed populations Pages 76 111 in Population Management for Survival amp Recovery Analytical Methods and Strategies in Small Population Conservation J D Ballou M Gilpin and T J Foose eds Columbia University Press New York Ballou J D R C Lacy and J P Pollak 2011 PMx Software for Demographic and Genetic Analysis and Management of Pedigreed Populations version 1 0 Chicago Zoological Society Brookfield IL Bingaman Lackey L 2010 Records Studbooks Regional Zoo Associations and ISIS Pages 504 510 in Wild Mammals in Captivity Principles and Techniques for Zoo Management 2nd Ed
181. i Europe NorthAm SAN FRAN l 0 01178 0 00148 0 00109 HONOLULU l 0 00934 0 00061 0 00027 SD WAP 0 01212 0 00133 0 00045 SEATTLE Move to EastAsi l 0 01079 0 00192 0 00013 SEATTLE l 0 00565 0 00125 8E 05 DALLAS l 0 00565 0 00125 0 00046 NZP WASH l 0 01253 0 00192 0 00012 PANAMACT Move to Austral 0 00934 0 00061 0 00023 SACRAMNTO Move to EastAsi 0 01085 0 00117 0 00017 EVANSVLLE Move to Europe 0 01031 0 00191 0 0001 TORONTO Move to SEAsia M 0 00684 0 00191 0 00013 TACOMA N Copy to Austral 0 01157 0 00147 5E 05 DALLAS Copy to EastAsi 0 01157 0 00147 0 00024 SD WAP 0 01157 0 00147 0 00013 Move button To test the transfer of individuals or groups of individuals without completing the moves use the Move button in the upper right corner of the main Management Sets window Set the Current Set to the desired source subpopulation Select an individual or group of individuals to move between subpopulations by highlighting them using Ctrl or Shift right click keys Then click the Move button A pop up window will appear Indicate the destination subpopulation Detailed results of the transfer on the source and recipient subpopulations will appear in the pop up window If the Move check box is selected the individual will be moved if the box is unchecked then the individual will be left in the source subpopulation and copied to the destination subpopulation Cli
182. ication showing the numbers or percentages of individuals in various age and sex classes in the population Fecundity Mx The average number of same sexed young born to individuals in that age class For each offspring each parent gets 0 5 of the birth attributed to him her The fecundity rates provide information on the age of first last and maximum reproduction Instantaneous Rate of Change r The intrinsic rate of increase of a population per unit time equal to the projected exponential rate of increase averaged for males and females as determined from the birth and death rates If r gt 0 the population is projected to increase if r lt 0 it is decreasing Life Expectancy Ex The average number of additional years an individual in age class x can expect to live Mean Generation Time T The average age of reproduction production of offspring averaged for males and females It is also the average time from reproduction in one generation to reproduction in the next generation T is not the age of first reproduction Mortality Rate Qx Probability that an individual of age x dies during time period Qx 1 Px This number is calculated from the number of individuals that die during an age class divided by the number of individuals that were alive at the beginning of the age class i e at risk Net Reproductive Rate Ro The rate of change per generation average number of same sex offspring that an individual will produce
183. idence interval for stochastic projections default 95 e Change the maximum number of females that breed with each breeding male default 1 PMx uses this number in stochastic projections to account for limited availability of breeding males in female biased populations e Note Changing the age class length on the Settings tab from the default 1 year also affects projections as the length of the time interval used for projections age class length For example if age class 1 month and the projections are for 20 time intervals into the future the projection will be for 20 months not 20 years in this scenario if a 20 year projection is desired then projections would need to be run for 240 time intervals See Life Tables tab and Demography Settings tab sections for more information PMx User Manual version 1 0 Page 52 Terms and Concepts Stable age distribution SAD The proportional distribution of individuals across age classes that would result from the realization of the exact life table demographic rates Px and Mx If these rates remain constant and exact the population will grow or decline at a constant rate into the future Deterministic Deterministic means predictable with no variation or determined In deterministic calculation exact values are applied to formulas that define relationships e g first year mortality will always be 24 Since there is no variation in input values the result will always
184. iduals will show Not Selected in the RecNotes column which can be modied e g to Excluded from genetic analysis This process essentially duplicates the Add Back Deselected Animals function in PM2000 PMx User Manual version 1 0 Page 121 New Features This feature is similar to the recommendations section of the templated report in PM2000 but is available upfront in PMx and can be continually modified PMx provides greater flexibility regarding the fields columns available in the table and provides the option to import sets of recommendations Helpful Hints Sort the table by UniquelD current Location Breeding or other desired order before export When manually adding a New Location it is recommended that the user enter the official ISIS mnemonic for that location when possible Be careful to avoid spelling errors Recommendations for institutions that do not currently have individuals but are recommended to receive them will be included at the end of the Export Institutional Recs file If it is difficult to get the correct list of individuals in the table using the available filtering options consider setting up a UDF or Flag for the relevant individuals that can be used as a filter For example Flag C that is Flag is not blank will return all individuals that have been marked with a flag in the Individuals tab regardless of the color of the flag Export the Recommendations table after making changes to i
185. ify a genetic goal in terms of the amount of genetic diversity GD to be retained Using the drop down menu this genetic Goal can be set as a minimum gene diversity at the END of a specific number of years or as a minimum gene diversity to be retaing DURING the entire time span of the program In the first scenario GD may drop below the target level during the program and still meet the goal as long as the minimum GD is met on the final year of the program e g by adding new founders near the end of the program The default setting is to retain 90 of the wild gene diversity at the end of 100 years Once the Goal has been set PMx will determine if this goal is achievable with the specified values for the Population Variables PMx will retrieve information from various parts of the project to provide the default values for Generation Length Maximum Potential Lambda Current N Current Effective Size Ne N and Current Gene Diversity Maximum Allowable N uses the Current N as the default setting These values can be changed from the defaut values PMx uses these values to project the change in population size and change in gene diversity over time The results in relation to the Goal are displayed in bold at the bottom left of the page and will indicate either a this genetic goal can be achieved under current variable settings and perhaps with even fewer animals or for a longer time period or b the genetic goal is not achievable in which cas
186. in its lifetime averaged for males and females Ro gt 1 for increasing populations and Ro lt 1 for declining populations Population Growth Rate Lambda A The proportional change in population size from one year to the next Lambda can be based on life table calculations the expected lambda or from observed changes in population size from year to year A lambda of 1 11 means an 11 per year increase lambda of 97 means a 3 decline in size per year Reproductive Value Vx The expected number of same sex offspring produced this year and in future years by an individual of age x Risk Qx Risk Mx The number of individuals that have lived during an age class The number at risk is used to calculate Mx and Qx by dividing the number of births and deaths that occurred during an age class by the number of individuals at risk of dying and reproducing during that age class Stable Age Distribution SAD The proportional distribution of individuals across age classes that would result from the realization of the exact life table demographic rates Px and Mx If these rates remain constant and exact the population will grow or decline at a constant rate into the future PMx User Manual version 1 0 Page 129 Survival Age Specific Px The probability that an individual that is alive at age class x will survive to age X 1 is conditional on an individual being alive at the beginning of the time period Alternatively the proportion o
187. intaining certain population goals either target N or target lambda e Be aware that these plans do not affect the genetics of the population supplementation is evaluated as an increase in numbers not as the addition of new genetic founders Likewise the removal of individuals does not lead to increased inbreeding To assess the genetic benefits of adding new founders use the Goals section of PMx Cautions e Be alert for incomplete removals due to insufficient availability when specifying numbers of individuals for removal e Remember that changes to Model Data are not saved with a project If a saved PMx project is reopened the Actua Data values will be used for the Model Data and therefore for projections Smoothing and or other desired changes to the Model Data will need to be re entered PMx User Manual version 1 0 Page 60 AVAILABILITY TAB Purpose The Availability tab allows the user to explore the number of individuals that can be removed from the population while maintaining it at constant size or growth rate The user sets the age class es and sex es from which animals are removed This tool is particularly useful in the design of release programs or other situations in which the managed population will be required to produce a harvest How to Use This Tab The Availability tab is pre filled with the current population size and growth rate These are located in the top left corner of the screen Choose a pop
188. ion 3 Demography Module Demography Summary Statistics Screen cccsessccececeseesennsaecececusecsesauaecesecsseesesaeaecesecesseseaeaeseseesseesegs 33 Demography Overview Tab ccccccccessssececccecessessnaecececssesseaeaeceseeusessesaeaeeeseceseeesaeaeceeecsseesesaeaeeeseesseeees 35 Life Tables TAD rennur EE 39 Age Distribution Tab r r sereneisesond oeenn ndes eneee niae Eee a e eee ade Ea Eea Eea EEn EEE a EERE eaS 43 CENSUS TaD seraa a a 46 SEASONALITY TaD serieen ee e eE a a E ee E EEE EEEE 48 Projections tab Mesie e a a a E a a E 50 Reproductive Planning Taberei nnsa ea EEEE E E E EAE EEEE 55 Add Renove TibDoerarecnan a en a E 58 Availability TaD ivssicccvsscccccvasscccevanccccvvasscctevsuccccevwnicccuvauicd A AEE EI ETEA EE 61 Demographic Graphs TaD isiisceccesss cccesdsctassvece cecendsncecnvdas cecuedsccacseecccedunduecessnsie ENOTEN EANET 64 Demographic Settings Tab cccccccessssececcceeessesseaececececesseaaaecesecsssesesaeaeeesecsseesesaeaeceeeceseesesasaeeeeeesseseags 67 Section 4 Genetics Module Genetics Summary Statisics SCFEEN iscsi eraio enera aE a EErEE Eanan eE E aia 70 Genetics Overview Tab scssiicccessccccteticecsaeacecesatsiecesaniceceuaticcssauccdcesadslecesauvceccssdicecasavece EEA ESES 74 Founders Tabseccciescccccsiesecedetiiecectuccaccenbbuccacsvedetedusiuavectusuacesnniuccecsbouacedsbiscuectusdaceensbucceetuedadedsbaueuecteesteeeenadee 77 MAGIA Wal Salo iicsyec cis csustean nR AE EOE ATARE 79
189. ion Management 2000 Brookfield IL Chicago Zoological Society Princ e F P G 1995 Overcoming the constraints of social structure and incomplete pedigree data through low intensity genetic management Pages 124 154 in Population management for survival and recovery J D Ballou M Gilpin and T J Foose eds Columbia University Press New York NY Princ e F P G 1998 Population Management managers as detectives The Netherlands Amsterdam National Foundation for Research in Zoological Gardens Princ e F P G 2001 Genetic management of small animal populations Lutra 44 2 103 112 Ralls K and J Ballou 1983 Extinction lessons from zoos Pages 164 184 in Genetics and conservation A reference for managing wild animal and plant populations C M Schonewald Cox S M Chambers B MacBryde amp W L Thomas eds Benjamin Cummings Menlo Park California Ralls K Ballou J D 1985 Captive breeding programs for populations with a small number of founders TREE 1 1 19 22 Ralls K J D Ballou and A Templeton 1988 Estimates of lethal equivalents and the cost of inbreeding in mammals Conservation Biology 2 185 93 Reed D H and Frankham R 2003 Correlation between fitness and genetic diversity Conservation Biology 17 230 237 Schad K Ed 2008 Amphibian population management guidelines Amphibian Ark amphibian population management workshop 10 11 December 2007 San Diego CA USA Amphibian Ark w
190. ion for each institution that is listed as a holder of the animals The format of this file is highly specific with the spacing being critical No delimiters can be used because it would be impossible to know if those delimiters might for example be included in the address information for a location These location data are used only in the labels displayed in the Recommendations reports It is not recommended that users try to edit this file The format is a line per location with the following data MNEMONIC characters 1 9 INSTCODE characters 10 18 INSTITUTION characters 19 58 ADDRESS characters 59 92 CITY characters 93 112 STATE characters 113 132 COUNTRY characters 133 152 MAILCODE characters 153 162 PHONE characters 163 182 FAX characters 183 202 EMAIL characters 203 237 CONTACT characters 238 end of line Kinships File Empirically determined kinships can be read in from a text file in which case PMx can replace the kinships calculated from the pedigree for those pairs of animals with the ones read from the file These kinships might be determined from DNA analyses or from knowledge of familial relationships or in any other way Normally the file will have extension kin but any extension is accepted The format of the file is that the initial lines list one per animal the IDs of the animals in the empirical kinship matrix Subsequent lines give the kinships although only the lower half and the diagonal of the matrix are
191. ip coefficient between an individual and all individuals including itself in the living captive born population The mean kinship of a population is equal to the proportional loss of gene diversity of the descendant captive born population relative to the founders and is also the mean inbreeding coefficient of progeny produced by random mating Mean kinship is also the reciprocal of twic the founder genome equivalents MK 1 2 FGE MK 1 GD MKb Mean kinship between two populations the mean of all pairwise kinships for all combinations of an individual from population 1 with an individual from population 2 Pedigree Certain The percentage of the living individual s pedigree that can be traced back to specific individual founders Pedigree Known Percent of an individual s genome that is traceable to known group of founders Thus if an individual has an UNK sire the Known 50 Potential Retention The proportion of genes present in a founder that have the potential to be incorporated in the descendent population If the individual is a potential founder or is still living its potential retention is 1 00 Otherwise for dead founders potential retention will be the same as the Allele Retention for that founder Prob Lost Probability that a random allele from the individual will be lost from the population in the next generation because neither this individual nor any of its relatives pass on the allele to an offspring
192. ips and related metrics e g inbreeding coefficients measures of genetic value of individuals tools for selecting individuals for pairing or culling to maximize retention of genetic diversity and means to examine the genetic effects of partitioning the population into smaller management units The Goals section integrates demographic and genetic analyses into a modeling tool for determining the combination of demographic values e g population size growth rate generation time and genetic values e g effective population size starting gene diversity that will achieve a goal for sustaining a desired level of gene diversity over time Finally a Recommendations section provides a means to record and report the breeding and transfer recommendations for each individual PMx User Manual version 1 0 Page 1 These sections provide an array of options regarding assumptions to be made about the data methods of analysis and output variables to summarize results These are described in detail in this manual This manual does not provide full documentation of the concepts behind the management of pedigreed populations nor of the algorithms employed by PMx Many of the algorithms may be described briefly in a future appendix but a complete documentation is impractical A summary of the methodologies is presented in Ballou et al 2010 and overviews of PMx and genetic methods can be found in three papers currently in press Ivy and Lacy Lac
193. irical Kinships enables a file to be imported that specifies the kinship matrix different than that calculated from the pedigree e g based on molecular data See the Kinship Matrix section for more information on this option To add a file click on the as button to browse to and open the file Then click Read Files to read in its contents Once all files have been read go to the Individuals tab and click on the Update Table button to insert the new data into the table Terms and Concepts Iteration A single stochastic simulation of the population over the specified time period For gene drop this means a simulation of which alleles randomly pass from parent to offspring through the recorded pedigree Because events in a stochastic simulation are based on probabilities the outcome of each iteration will be different therefore many iterations should be run to accurate estimate results PMx User Manual version 1 0 Page 113 DeltaGD Net change in gene diversity of the population if the pair produced one surviving offspring GV Diff Difference between the mean kinship values of the male and female in pairwise comparisons or the difference between kinship values if Kinship Value is used instead of Mean Kinship for Genetic Value Type Inbreeding Coefficient F Probability that the two alleles at a genetic locus are identical by descent from an ancestor common to both parents Unknown Percent of the male s and female s genom
194. ition D G Kleiman K V Thompson and C K Bear eds University of Chicago Press Chicago and London Boakes E H Wang J And Amos W 2007 An investigation of inbreeding depression and purging in captive pedigreed populations Heredity 98 172 182 PMx User Manual version 1 0 Page 153 Caballero A S T Rodriguez Ramilo V Avila and J Fernandez 2010 Management of genetic diversity of subdivided populations in conservation programmes Conservation Genetics 11 409 419 Caughley G 1977 Analysis of Vertebrate Populations John Wiley amp Sons New York Darwin C 1868 The variation of animals and plants under domestication John Murray London Ebert T A 1999 Plant and Animal Populations Methods in Demography Academic London Earnhardt J M Y M Bergstrom A Lin L J Faust C A Schloss and S D Thompson 2008 ZooRisk a risk assessment tool version 3 8 Lincoln Park Zoo Chicago IL Faust L J Y M Bergstrom S D Thompson and L Bier 2009 PopLink ver 2 1 Lincoln Park Zoo Chicago IL Fernandez J and A Caballero 2001 A comparison of management strategies for conservation with regard to population fitness Conservation Genetics 2 121 131 Fernandez J M A Toro and A Caballero 2004 Managing individuals contributions to maximize the allelic diversity maintained in small conserved populations Conservation Biology 18 1358 1367 Foose T J and J D Ballou 1988 Population management th
195. ject To open an existing PMx project open PMx and click Open Project PMx will automatically browse in the folder in which the last PMx project was saved Navigate to the correct location containing the PMx project that you want to open pmxproj highlight the project file and select Open Saving a Project To save a PMx project select File from the top menu bar and choose one of the following options Save Project Automatically saves the project with the name chosen when the project was created pmxproj in the folder from which the data input files were chosen Save Project As Allows the option to specify the name of the project file and or location to which it will be saved Save Only Core Project Similar to Save Project but does not include detailed genetic calculations kinship matrices these can be very large files with large studbooks If only the core project is saved PMx will need to recalculate these matrices when the project and its Genetic Details are opened The advantage to saving only the core project is to keep the size of the project file manageable and easy to email even for large studbooks Save Only Core Project As Similar to Save Project As but does not include the kinship matrices as indicated above PMx User Manual version 1 0 Page 17 PMx will also automatically ask if you want to save the project when you close the program PMx saves all files associated with a PMx project into one file called
196. jections 20time steps years r 0 078 lambda 1 081 Ro 2 079 T 8 3 N20 103 Analysis date 16 02 2011 Outdated The graph shown in the lower left corner provides deterministic projections for the population over the time frame considered Each time a new removal schedule is entered by clicking on the Go button the Total Projections are modified accordingly Clicking on the Reset button resets the harvest to zero and the population size growth rate and population total projections to those of the current population Terms and Concepts Lambda Annual growth rate the number you multiply the current population size by to project the size in one year one time interval For example lambda 1 10 would confer 10 annual growth lambda 1 00 confers zero growth and lambda 0 95 leads to 5 decline in one year PMx User Manual version 1 0 Page 62 New Features The Availability tab is a new feature and was not available in PM2000 Cautions e Note that the numbers of individuals potentially available for removal are not displayed as integers i e whole individuals Be careful if rounding up as this may lead to overharvest e PMx uses the current age structure and life tables to calculate the availability of animals for removal A change in the underlying demographic rates or a dramatic change to the age structure will alter future harvest capability e Remember that changes to Model Data are not saved with a
197. ka Replace Moves in Primary D_ Add Moves to Primary 1 00 ated UDF file Other Settings Edit Bin Detaco eo Replace UDFs Add UDFs Analysis Date mm dd yyyy 12 28 2011 v Edit how unknown pedigree affects MSI Read Files Cancel date also to Demographic Age Structure Edit Weights Save Settings Start Date mm dd yyyy 1 1 1980 v Use Defaults Read Settings petais Read Empirical Kinships Genedrop Iterations 1000 Implement changes Cancel Assumptions Dynamic Population Variables Do Not Indude Founders Unknown Weight 0 00 Change GD 0 9641 GV 0 9592 MK 0 0359 Known 100 N 125 0 Genetic Assumptions These options are also available on the Summary Statistics screen before Genetic Details is opened Parentage Assumptions Changes the assignment of parentage when there are multiple possible parents Default setting is Probabilistic parents Options are Probabilistic parents Assign a proportion of the offspring to each identified possible parent based on the probabilities given in the studbook database Most likely parents Assign parentage to the individual with the highest probability of being the parent for genetic calculations In case of ties the first one listed is used Omit uncertain parents Change any sire or dam indicated by MULT to UNK unknown individual Note that these options currently only apply to exports from SPARKS 1 6 and only when MULT parents are explici
198. known origin are likely subspecific hybrids and are being managed as a non breeding population to free up space for pedigreed tigers Projection of the rate of decline of this generic tiger population through natural mortality allows species managers to anticipate available space for expanding the managed tiger populations and to plan accordingly to meet both institutional exhibit and population needs PMx User Manual version 1 0 Page 54 REPRODUCTIVE PLANNING TAB Purpose The Reproductive Planning tab can be used to determine how many births and litters or culls are needed to reach a desired target population size or growth rate over a specified time period How to Use This Tab The upper left corner of this tab provides four variables that interact to specify a particular population goal starting population size target population size desired growth rate and time period in which to achieve this goal Modifying any one of these variables and then clicking in another field will cause PMx to recalculate the number of births needed each year to achieve this goal When recalculating PMx holds the starting population size and time period constant however if either the target population size or desired annual growth rate are modified PMx will adjust the other of these two variables to accommodate this change Birth sex ratio can also be changed default 50 50 To simply maintain population size a zero population growth management plan
199. lation Once the Total Population is created and selected as the Current Set Fst and MKb between each subpopulation and the Full Population can be determined PMx User Manual version 1 0 Page 101 GRAPHS TAB Genetics Purpose The genetics Graphs tab provides a visual representation of the genetic summaries of the project data Four different categories of graphs are available on this tab Population graphs show how the genetic status of the population has changed over time An assessment of how well founders are represented in the population can be made using the Founder graphs Individual graphs show the degree of inbreeding and kinship among selected individuals In addition the Custom graph button provides the flexibility to customize the genetic graphs for founders individuals and populations How to Use This Tab The buttons at the top left corner of the screen can be used to assess Population Founder Individual or Custom graphs Double clicking any graph opens a new window that allows the graph to be exported as a png file printed or sent to the Project Notes Population Graphs These four graphs show how Gene Diversity number of Founders Founder Genome Equivalents and Mean Inbreeding have changed over the window of time specified in the Settings tab Note These values are based only on those individuals that are included in the selected population on the Selection screen for genetic analysis This may or may not reflect the
200. lation size and resulting annual fluctuations in birth and death rates also reduce population growth these real life factors are incorporated into stochastic projections but are ignored in deterministic projections see Projection Tab section for further explanation PMx User Manual version 1 0 Page 134 When I try to plot both actual and model data on a Custom Life Table graph in Demography only the model data line shows on the graph Why doesn t the actual data show up as well If the model data have not been changed then the two lines will be the same and the model data line will overwrite plot on top of the actual data line Genetics Should remove the dead individuals from the Selected Population for the genetic analysis If the data were exported from SPARKS 1 6 then the dead individuals should be left in the selection for genetic analysis if they met the other criteria e g region or association for the population SPARKS 1 6 exports information to PMx regarding the dates on which each individual entered and or left the population based on the filter criteria so that dead individuals can be properly included in both historical and current population analyses PMx will use only living individuals to calculate the genetic status of the current living population Why are the Kinship Matrix Pairwise Info Matrix and Population Graphs sometimes blank These matrices can be very large e g the kinship matrix has about 1 milli
201. lay all individuals no filter 2 to set a single filter criterion or 3 to set multiple filter criteria In either case the variable s to be used in the filter are selected from a drop down list Click on a row under Column Name to open this dropdown list Then select the Operator gt lt etc from its drop down list In this list means not equal to Finally specify the value to be compared to the variable String variables are not case sensitive Logical variables can be compared to True or False spelled out but case insensitive When multiple criteria are set you need to specify whether Any or All of the criteria need to be met In addition to specifying comparisons as criteria you can add or remove any specific individuals from the table by highlighting those individuals in the lists at the bottom of the Filter window These individual selections will be applied after thus overriding the criteria above After specifying the desired filter criteria click OK to accept those criteria and return to the table PMx User Manual version 1 0 Page 20 ee a ne a nwo ii Do not filter the display of animals in this table 5 Only show animals where AgeClass 5 Only show animals where All of the following are true Column Name Op Value Highlight animals to add to the table Highlight animals to remove from the table 313 a 313 a Working with Graph
202. ld you like to update Demography to include your data changes Click Yes to apply these changes to the respective analyses Click the Export button to create a copy of the currently visible data as a text file txt Excel file x s or a comma delimited file csv The text file may be opened with NotePad BlocNotes WordPad Word or any other word processing software Changes made to these files will not be appear in PMx The Update Table button will import information available as a result of activity on other tabs or screens Pairing and Culling tab choices in the Genetics section Reproductive Goals and information from the Recommendations screen will accrue to the appropriate columns in the Individual table Terms and Concepts See Appendix A for a complete list of Individual Variables and definitions New Features The Individuals tab provides much more detailed information about each individual about 4x as many variables as were available in PM2000 This reduces the need to go back to the studbook data during data analysis and masterplanning as much of the commonly needed information is now exported to and is available in PMx directly Helpful Hints e This table contains a large amount of data on historical and currently living individuals i e all individuals in the export filter The sorting and filtering functionalities available in PMx can be used to quickly summarize information and answer questions about the population cu
203. le names or supply your own if you analyze your Exported file names data with pm2000 Ce Genetic Genetic EXCHANGE dbf If you are using DEMOG and GENES to analyze your data Run the Genes or Demog program accept the default names lt gt Run the program immediately Ce Do not run the program now Names should not include any Program command GENES GHLT_I N spaces or amp characters Demographic export 1 From the Reports use the Left arrow key to open the View Criteria 2 Change the Date Span dates to an interval that includes modern management and takes into account the lifespan of the species Select During the date span Geographic or Association views may be used as well as User Defined Fields 3 From the Reports menu select Analysis gt Export Data 4 While at the Demographic choice use the Space bar on the keyboard to choose Demographic Use the Down arrow key to continue down the screen The default names for the export will be M lt studbook name gt prn for males and F lt studbook name gt prn for females these can be changed Use the Down arrow key to move through the rest of the screen 5 The export will be created and stored in the studbook folder et SPARKS15 EXE E ol x Export Data File Names Report End Date Export type lt e Demographic Accept the default export lt gt Genetic file names or supply your own if you analyze your Exported file names data with pm2606 Demographic
204. les to the project by browsing to the appropriate SPARKS studbook folder If Demography Input Files are not specified then PMx will not provide any demographic analyses or modeling of goals because the Primary Input File provided by SPARKS 1 5 exchange dbf does not contain the necessary data to allow the demographic calculations to be done 5 As with data import from SPARK 1 6 additional records of moves of individuals into or out of the population can be specified either as CSV files or as Moves files and these data can optionally be applied to define also the movements of individuals in and out of the genetically managed population Any such additional demographic files would need to be created in a program other than SPARKS 6 Under Additional Optional Input Files add the exchcens txt file found in the studbook folder to the Census You may also add any of the fed files usually found in the SPARKS folder but possibly in the studbook folder to Associations and or rgn files to Regions 7 Click on Create Once PMx opens to the opening Project Notes screen select File gt Save Project PMx User Manual version 1 0 Page 9 PMx Create a new Demography Input File Required PRN Female _C ISISdosbox SPARKS NA_Mal FNA_MAL PRN 7 Male C ISISdosbox SPARKS NA_Mal mNA_MAL PRN csv Moves Apply moves to both Demographic and Genetic views Apply moves to Demographic view
205. ll rodents especially if reproduction occurs within the first year e Check the settings before and after reviewing the life tables Depending on the species alteration of the default settings may provide more accurate interpretation of the data e Remember to rerun the stochastic projections after making changes to the demographic settings PMx User Manual version 1 0 Page 69 SECTION 4 GENETICS MODULE GENETICS SUMMARY STATISTICS SCREEN Purpose The main Genetics Summary Statistics screen provides current and historical summary statistics for the selected living population as defined on the Selection tab Once the genetic analysis has been completed by going into and then closing Genetic Details this screen will display a graph that includes a historical census in red and gene diversity over time in blue How to Use This Tab The tabular information on the left side of the screen is based upon the selected population If the individuals in the selected population are changed on the Selection tab and the box Apply Updated Selection to Genetics is checked this Summary tab as well as other genetic values will be updated The following information is provided on this tab Founders PMx considers a founder to be an animal with Wild Wild parentage that has living descendants in the selected population A broader definition of the term is an individual obtained from a source population often the wild that has no known relationship
206. ll values e Check for reproduction in pre and post reproductive age classes These may be outliers e Use knowledge of the species biology husbandry and management to modify the Mx values as needed e Check for modifications that significantly change the lambda or generation length When satisfied with the life tables users can export either the Actual or Model life table to a text txt CVS csv or Excel file x s by clicking the Export button under the life table Below the Actual Data and Model Data life tables PMx also calculates the population growth rate r and lambda for a stable population under these conditions as well as net reproductive rate Ro generation time T and the projected number of males or females N for the specified projection time period default 20 years All of these values are calculated independently for males and females Default assumptions are listed at the bottom left corner of the screen in the Demographic footer These settings may all be changed on the Settings tab which includes options for handling unassigned births changing the proportion of unknown sex individuals and dealing with multiple possible parents see Demography Settings tab section for more details The Settings tab in Demography allows the user to e Change the birth flow default continuous e Change the length of the age classes default 1 year e Change the defined period to calculate early mortality defa
207. lso for other parameters such as lambda and T in the Demographic footer at the bottom of the screen The Smooth button is located below the Model Data life table with a count of the number of times the table has been smoothed Smoothing data can help to remove sharp dips and peaks within a data series Each time the life table is smoothed the Px Qx and Mx values are replaced with the median of that value the preceding value and the following value The object of smoothing is to derive a Px Qx and PMx User Manual version 1 0 Page 39 Mx curve that reflects the characteristics of the population as accurately as possible Poor data quantity small sample sizes and quality can be a problem in many studbooks The smoothing tool can provide more reasonable estimates of life table rates However care should be taken when smoothing data as smoothing can often lead to unreasonable values in the life tables Life tables should be examined for any smoothing anomalies when using this tool If the model data have been modified the Life Table tab label will indicate this with Stochastic Runs will be labeled in red as Outdated in the lower right corner in the Demographic footer see Projections tab for details Model Data can be reset to the Actual Data at any time by clicking the Reset button under the Model Data life table When altering the life tables in any way users should e Compare the Actual Data vs Mode Data life tables for a
208. lt gt 0 954 lt gt 0 965 0 061 lt gt 0 047 lt gt 0 035 1 046 7 0 years Males Females Others Send to Project Notes Demographic Details Managed N 880 Pedigree Known 99 4 Current Gene Diversity 0 975 Potential Gene Diversity 0 993 Lambda 1 006 The following information is provided on this tab Size Current size of the selected population males females unknown sex total Life Expectancy Average life expectancy at birth hatch averaged between males and females Will display if the oldest animal s ever existing is still living 30 day survival Weighted average 30 day survival of males females and unknown sex individuals where weights are the sample sizes Total sample size given in parentheses 25 live to Based on an average between males and females the age at which survivorship Lx reaches 0 25 0 10 0 05 and 0 01 respectively for 25 10 5 and 1 Some fields may display if the oldest animal s ever is still living Oldest living The oldest currently living animal displays age and UniquelD or n if more than one individual lives to that age PMx User Manual version 1 0 Page 33 Lambda A The proportional change in population size from one year to the next based on life table calculations expected lambda averaged for males and females Lambda gt 1 for increasing populations lambda lt 1 for declining populations
209. ly Updated Selection to Demography is checked and is based on the date window and any other filters such as geographic or association filters for the exported studbook data Initially deterministic values are displayed based on life table information Once stochastic projections are run several values are displayed in the center of the column and are bracketed by Confidence Intervals defaulted to 95 CI may be changed on the demographic Settings tab r Instantaneous rate of change of the population averaged for males and females If r gt 0 the population is increasing if r lt O it is decreasing Lambda A The proportional change in population size from one year to the next based on life table calculations expected lambda averaged for males and females Lambda gt 1 for increasing populations lambda lt 1 for declining populations T Mean generation time averaged for males and females which is the average age of reproduction production of offspring It is also the average time from reproduction in one generation to reproduction in the next generation T is not the age of first reproduction Ro Net reproductive rate which is the rate of change per generation average number of offspring that an individual will produce in its lifetime averaged for males and females Ro gt 1 for increasing populations and Ro lt 1 for declining populations N20 time step A projection of how many individuals will exist in 20 tim
210. male part female i e contributes to Mx of both parents or if the actual sex of each birth is used in Mx calculations i e contributes only to Mx of the same sex parent Unknown sex default 0 50 male Set the proportion of male female to attribute to individuals of unknown sex Multiple parents default Most Likely Change the assignment of parentage when there are multiple possible parents Options are Most Likely assign parentage to the individual with the highest probability of being the parent for demographic calculations Mx Treat Mult as Unknown change any sire or dam indicated by MULT to UNK unknown individual for Mx calculations Use Probabilities assign a proportion of the offspring to each identified possible parent based on the probabilities given in the studbook database Note that these options currently only apply to exports from SPARKS 1 6x and only when MULT parents are explicitly identified with probabilities assigned For other studbook exports MULTs are treated as UNKs unless the csv or ped file is manually edited to include possible parents and their probabilities This setting will be ignored by PMx if there are no MULTs in the data even if the option appears active Note Currently these three options are named differently in the Demography and Genetics Settings however they represent the same three methods of dealing with multiple parents and probabilities Future versions of PMx will use the same l
211. mended in Section 1 then only living animals may appear in the Selected Population table left side of the Selection tab screen and no historical genetic analyses will be available Using a historical date span for the genetic export is not recommended as it will include all individuals that were ever in the geographic or association filter even if they have since left the region or association but are still living or are now Lost to Follow up The historical population for demographic analysis cannot be changed in PMx when it uses prn files imported from SPARKS 1 5 or PopLink basic exports These files contain summary demographic informa tion rather than raw data and therefore limit the manipulations that can be done in PMx However it is still possible to modify the demographic selection for living individuals which affects the age distri bution and starting population for projections Such modifications will not change the life table data For maximum flexibility and analytical capability it is recommended that you use either SPARKS 1 6 or PopLink with advanced demographic exports Deciding How and Where to Create the Selection for Analysis There are several stages at which the population can be filtered for demographic and genetic analysis for the historical and current population These include setting filters in SPARKS or PopLink for exporting studbook data to PMx the main Selection screen in PMx the Selection tab within the Genetics
212. module and on the Culling tab within Genetics Each of these methods has consequences for the analysis results and the chosen selection process may differ depending upon the characteristics of the population and the analysis results desired The studbook software version used for export limits some of these options The following may be a useful sequence of events to follow when creating a project 1 Set the necessary filters in SPARKS or PopLink before exporting studbook data to PMx Set the studbook export filters to define the population that should be analyzed as closely as possible This typically involves setting a filter that restricts location e g geographic or association filter and restricts data span to that which represent current husbandry or management also see Section 1 on creating PMx projects For example All individuals in Europe geographic filter from 1 Jan 1985 to today or All individuals in JAZA Association filter from 1 Jan 1990 to 1 Jan 2009 SPARKS 1 6 combines demographic and genetic exports into one file using the same filter criteria The exported data includes information on when each individual entered and or left the data span population allowing for historical analysis of both demographic and genetic data PMx automatically determines which individuals are still living Alive true and in the Selected Population Gone false for results calculated on the current living population such as the Age Dist
213. n Assumptions Overall Statistics Stochastic Runs Age Classes are years Birth How Continuous CI 95 Iterations 500 Growth in terms of years r 0 065 lambda 1 067 Projections 20 time steps Ro 1 946 T 8 6 N20 87 Up to date i a PMx User Manual version 1 0 Page 46 New Features This feature operates in a similar manner as the Census tab in PM2000 additional new features include Ability to modify the starting year Ability to display the census as a bar graph Ability to view and graph additional events e g captures exports over time Ability to graph sex ratio for census population and at birth over time Ability to view and graph both types of lambda over time Helpful Hints SPARKS will only export census data up through the currentness date for the studbook Be sure that the currentness date is correct to get complete available census information PMx User Manual version 1 0 Page 47 SEASONALITY TAB Purpose The Seasonality tab provides seasonal birth and death data by month and a statistical evaluation regarding whether these monthly trends differ significantly from a uniform pattern across the year These data may help to inform population planning as well as suggest whether Pulse vs Continuous birth flow is a more appropriate choice on the demography Settings tab for this population How to Use This Tab The default view displays birth data on the top section of the tab and death d
214. n Variables 29 DETTE EEE TL ING IBOLT GD 0 9641 GV 0 9600 MK 0 0359 Known 100 N 141 0 The Results table on the right displays the effect of removing the individual highlighted blue row in the Current Population table The table reports the New Values for Gene Diversity Gene Value Founder Genome Equivalents FGE and Percent Known as well as the net Change in value for each variable if the individual were culled removed from the managed population PMx User Manual version 1 0 Page 93 Clicking on the Cull Animal button underneath the Results box will simulate removal of the individual from the population The culled individual will be displayed in the Selected Culls box on the bottom right side of the screen and the population s genetic statistics will be updated in the Results box and other screens under Dynamic Variables Culling will also impact the genetic values of other individuals To un cull an individual click on the individual in the Selected Culls box so that it is highlighted then click on the Reverse Cull button This will add the individual back to the list update the population s genetic statistics in the Results box and update the measures of genetic value of the other individuals in the list All Selected Culls can be reversed using the Remove All button Culled individuals can also removed from the Age Distribution Projections and other demographic screens and calculations by ch
215. n alternative method for combining the variable rankings into a composite MS value is to use quantitative weighting of the ranks for the three variables Delta GD GV Diff and F as opposed to a set of logic rules such as the Tulsa method The default Weights are equal between the three variables but can be modified by clicking the Edit Weights button in the lower center of the Settings tab This window provides similar options for editing validating and saving and resetting the values as the Edit bin windows F Edit MSI Weights Edit eMSI Weights Variable Weight Variable Weight Delta GD 1 00000 Si 1 00000 F 1 00000 F Setting the Overall MateRx Settings The center section of the genetic Settings tab provides options for changing five general settings for calculating MSI values These options are MateRx Setti F Break Point Use Average F default j Use Average MK F Break Point UseAverageF Genetic Value Type Mean Kinship Genetic Value Type Mean Kinship default Kinship Value MK Diff Method AbsoluteDiffs For Unknown Sexes ExdudeUnknowns MK Diff Method Absolute Diffs default Balanced Ranks MSI Method Tulsa Edit Bin Delta GD aco For Unknown Sexes Exclude Unknowns default Show as Male Edit how unknown pedigree affects MSI Show as Female Edit Weights Save Settings Show as Both Read Settings MSI Method Tulsa default See See Weighted Click on the Use Defaults button
216. n can be used to define the potentially breeding population i e only those animals to be included in the genetic analysis This tab operates in a similar manner as the main Selection screen located outside of Genetics module it is duplicated here for convenience to allow the user to be able to quickly modify the population for genetic analysis without having to close the Genetics module How to Use This Tab This screen operates in a very similar manner as the primary Selection screen refer to Section 2 in this manual Selection screen for detailed information There are two differences in the Selection tab located under Genetics 1 All changes in selection are automatically applied to the genetic calculations There is an option to Apply changes in Selection to Demography that can be toggled on or off but the application of changes to genetics is mandatory 2 The main Selection screen provides the option to Revert to originally imported data This option is not available here ai PMx Amur Tiger eles Overview Founders Individuals Kinship Matrix Pairwise Info Pairing Culling Management Sets Graphs Settings Selected Population Number Induded 837 Not Selected Number Not Induded 673 UniqueID Location LocalID HouseName Sex Alive AgeYears a Location LocalID HouseName Sex Alive AgeYears 69 TORONTO 3216 Pjassina Female False 19 i Female
217. n future years by an animal in age class x Cx The proportion of that sex that would be age x in a stable population r Instantaneous rate of growth calculated from the life table Lambda A or Population Growth Rate The proportional change in population size from one year to the next Net Reproductive Rate Ro Rate of change per generation Generation time T The time elapsing from reproduction in one generation to the time the next generation reproduces also the average age of reproduction New Features PMx provides greater flexibility in analyzing different species life histories such as species with particularly short or long life spans PMx provides the ability to change the length of age classes to add age classes to define the time period for early mortality calculations to model continuous or pulse reproduction and to assign the sex of births based on actual sex or a fixed proportion Several parameters Px midpoint Lx midpoint Ex Vx Cx have been added to the life tables Helpful Hints e Always review the sample sizes of the age classes If an age class has a sample size of fewer than 30 individuals these rates should be viewed with caution e Px Qx and Mx can be modified to allow other demographic characteristics to be modeled e Standard graphs in the demographic Graphs tab reflect the data in the Model Data life tables check these graphs to see if smoothing is necessary PMx User Manual version 1 0
218. ncluding by sex and by origin wild caught vs captive born individuals How to Use This Tab The left side of the Census screen provides historical data on individual counts over time based on the imported studbook data and filters Total population counts and institutions holding these individuals are given as of 31 December of each year these totals are also broken down by sex males females unknown sex and by origin wild born captive born origin unknown Yearly lambdas are provided based on census numbers Lambda from Census which includes changes in population size due to all sources e g captures imports releases exports and also lambdas based on the life tables Lambda from Reproduction which take only births and deaths into account PMx projects created using census data from SPARKS 1 6 display additional information on the number of captures births stillbirths releases deaths LTFs lost to follow up imports and exports occurring during each year Sex ratio both as males and M F is also provided These tabular data are not alterable Use the Export button under the table to save the table as a txt csv or xls file The right side of the screen displays a census graph The default graph is a line graph of the total population size The buttons below the graph allow the graph to be revised to display results by sex or by origin and as a line or bar graph The beginning date to be plotted can be change
219. nd fields are always removed Thus 123 123 and 123 will all be read as 123 Data files that can be imported PMx can read different kinds of information from a variety of data files and several of the types of data file can be provided in any of several formats The Primary Input File provides the pedigree information to PMx It is the only file that is mandatory for creating a PMx project Optional files include any of a number of forms of a Demographic Input File and files to provide Census tallies UDF data user defined fields for specifying additional information about each individual Associations lists of institutions that are members of an association or Regions lists of institutions that are within a region that is defined geographically or otherwise A Location file can provide address and contact information for each location with specimens Within PMx Genetics files can be specified to provide empirically determined kinships lists of pre determined pairings or lists of pre determined individuals to be culled Many of these files are created automatically by studbook management programs such as SPARKS and PopLink but the formats are specified below for users who wish to create or edit these files with other programs Sample files in each format are provided in the PMx Installation Primary Input File The Primary Input File can be obtained from a Genetics Export as an exchange dbf file from SPARKS 1 5
220. nd the sire is unknown then an individual would be created called MateOf123 to represent the sire and the parents of this individual would be UNK An exception to this occurs if the dam is herself wild caught In that case it is assumed that the dam was pregnant when captured and the sire MateOfxxx is given parents as WILD The Change button at the bottom center allows the user to change the genetic assumptions related to the founders of the population Checking the nclude Founders box will include the founders in all genetic analyses Normally wild caught or imported founders are not included in tallies of the genetic population status GD GV and FGE the default is for genetic calculations to include only the descendant individuals see the Genetic Settings manual section for detailed information about these options The founder table can be exported from PMx and saved as a txt csv or x s file by clicking the Export button at the bottom left of the screen New Features PMx provides greater flexibility in assigning the proportion of UNKNOWN parentage to be considered as WILD PM2000 only provided options to treat UNKNOWN parents as 100 or 0 WILD PMx also has the ability to incorporate MULT parental assumptions Helpful Hints e Sort the founder list by the Alive column in order to identify any living founders Living founders should generally be given preference in breeding over non founders that have similar or lar
221. ndividuals in the early age class es for which Mx 0 in the Model Data on the Life Table tab Breeding Age Number of breeding age individuals defined by those individuals in age classes where Mx gt 0 Post Reproductive Number of living individuals considered to be no longer capable of breeding defined by those individuals in older age classes where Mx 0 PMx User Manual version 1 0 Page 35 Proven Breeder Number of living individuals that have bred at least once in their lives regardless of whether their offspring are still living and or in the current population Of breeding age A subset of the above proven breeders that are still of breeding age i e not yet post reproductive Contracepted Number of living individuals that are listed as Contracepted in the studbook database as of the end of the export date window Sterilized Number of living individuals that are listed as permanently Sterilized in the studbook database as of the end of the export date window Fertile Number of living individuals that are presumed capable of breeding not listed as Contracepted or Sterile in the studbook database export Institutions Provides the number of institutions Locations represented by the selected living population Life Table Summary These values are based on life table calculations from demographic data of those individuals living and dead in the Selected Population on the Selection tab for which the box App
222. ndomly and all were to produce the numbers of offspring expected for animals of their age Coefficient of relatedness r The probability that at a given locus an allele sampled from one individual is identical by descent to at least one of the alleles at that locus in a second individual In a population with no inbreeding r is two times kinship Inbreeding coefficient F Probability that the two alleles at a genetic locus are identical by descent from an ancestor common to both parents New Features The ability to include empirical kinships is more streamlined than in PM2000 and the file is easier to import and integrate into the data analysis The user also has the option of using a weighted mean of the empirical kinships and the kinships originally calculated from the pedigree see Genetics Settings Helpful Hints If adding empirical data be sure that the text file is in the correct format and only includes the Unique ID or studbook number of each individual followed by the kinship matrix with no additional text or characters If the input file is incorrect an error will cause the program to close Cautions Empirical kinship data should only be included after discussions with a population management advisor Kinships and coefficients of relatedness calculated from pedigree analysis and genetic analysis will not necessarily be the same because they are based on different values and using different methods PMx User Manual ver
223. new and improved translations as they are received PMx User Manual version 1 0 Page 22 In addition any user can edit the table of translated text e g change to more local terminology or provide an entirely new translation to a new language for their own personal use The PMxStrings xls file in the PMx program folder can be opened in Excel The first three columns of the spreadsheet should not be edited Subsequent columns are the translations that a user can edit Changes can be made to an existing column for example to change Mexican Spanish to Argentinian Spanish or to correct an error in a translated term or entirely new columns can be created to add new languages to PMx The first row of each column specifies the language to appear on the PMx Language menu Do not use the same name as some prior column The second row specifies the font to be used and this can be important for languages that use alternative character sets Note that a language may not display correctly on computers that have not installed that character set Subsequent rows should be translations of the words in the English column It is best if the translated texts are not much longer than the English texts so that they will fit in the spaces on the PMx screens A number of texts are repeated in multiple rows of the PMxStrings file This is necessary because those texts are used in various places in the program and translations similarly need to be repeated If any r
224. nformation click OK to exit the window or click Add Pair to accept this pair and add additional pairs PMx does not check the sex of individuals and will allow a female x male pairing as well as same sex pairings Be careful to enter the male UniquelD first and the female second in order to have the correct UniquelDs displayed under Sire and Dam in the Selected Pairs table If this method is used to select pairs PMx may not highlight in blue the UniquelDs of selected individuals in the Male and Female tables to indicate that they have been selected for breeding already seedy EE li Enter the Sire and Dam for a pair to be added Optional additional information Success 0 6 Offspring 2 Location Notes High priority breeding for 2012 Read Pair File Click on this button at the top of the screen to import a previously created list of breeding pairs This file can be generated using the Export button in PMx or can be created manually The imported file should be a text file that can have semi colon colon or tab delimiters but not commas between fields see Appendix D for more information on input file format Auto Located above the Selected Pairs table is the Auto pair button which will automatically generate the optimal genetic pairs based on the following specifications e Pairs desired default 10 e Offspring per pair default 1 e Maximum Pairs for Males and Maximum Pairs for Females default 1 e
225. ng on management constraints reproductive success or just bad luck Click on the Accept button to add the calculated Repro Goals to the data for each individual This column can be added to many of the tables in PMx ssi TargetN 150 Max Pairs for Male 3 Max Pairs for Female 3 Limit 170 V Vx Multiplier Resulting GD 0 9598 UniqueID Sex Location Repro Goals a 5200 Female MINNESOTA 5203 Female BILLINGS 5204 Female BILLINGS 5205 Female PHILADELP 5206 Male ERIE 5207 Female BUFFALO 5219 Male GRANBY 5221 Male TORONTO 5286 Male COLO SPRG 5287 Female COLO SPRG 5341 Male SEDGWICK 5342 Female STLOUIS 5343 Female INDIANAPL uonb oOnununHnow A A A A Note Lifetime reproduction goals are NOT recommendations for pairings for next year and the optimal allocation of animals to pairings will change over time due to uncontrolled births and deaths PMx User Manual version 1 0 Page 91 Assumptions Some of the assumptions made by PMx for genetic analyses can be modified by clicking the Change button at the bottom of the screen These include parental assumptions regarding multiple possible parents proportion of WILD to assign to UNK parents including founders in the analysis assigning weights to groups and assigning weights to empirical kinships Be cautious in changing any of these settings unless the population has special analysis needs and you are very familiar with how the genetic analys
226. nown Current Gene Diversity Potential Gene Diversity and Lambda for the selected population These statistics are static and are not updated i e not dynamic if changes are made in ways other than through a new selection e g dynamic pairings or culls are not reflected This footer appears at the bottom of all primary level screens Project Notes Selection Demography Genetics Goals and Recommendations as a quick reference to the population status To open a section in PMx click on its tab It is not possible to have more than one section open ata time because often changes made in one section will change the properties and values in another section However PMx stores much of the information from each section after it is first opened so that the section can re open much more quickly updating only that information that needs to be updated The Demography and Genetics sections will first open to a Summary Statistics window from which a set of tabbed subsections are accessed from a Details button The Project Notes section is an unformatted text document or clipboard When a project is created some header information from the imported data files is transferred to the Project Notes Buttons on other tabs allow the user to send some information and graphs to the Project Notes Text can also be typed directly into the Project Notes Users are strongly encouraged to make notes about the project for example any special assumptions m
227. o not forget to rerun the stochastic projections if you change relevant data e Donot forget to change the Maximum females bred per male value on the Settings tab if males are bred to more than one female each year Cautions e The precision of stochastic projections is dependent upon the number of iterations Running only a few iterations can give misleading results e Deterministic projections do not take into account the potential limitation of mates due to a skewed sex ratio Actual growth may be lower than projected deterministically especially in monogamous species if the sex ratio is uneven or in polygamous species if there are significant fewer individuals of the limiting sex typically females e Inbreeding depression is not explicitly incorporated into projections although past inbreeding effects will be represented in the historical demographic rates Demographic rates may change if inbreeding accumulates in the population e Remember that changes to Model Data are not saved with a project If a saved PMx project is reopened the Actua Data values will be used for the Model Data and therefore for projections Smoothing and or other desired changes to the Model Data will need to be re entered Case Study Generic tigers The AZA Tiger Species Survival Plan manages tigers of known pedigree and taxonomy Amur Sumatran and Malayan tiger subspecies within limited capacity About 25 of tigers in AZA institutions however are of un
228. odern management and the lifespan of the species Geographic or Association views may be used as well as User Defined Fields The ESCape key will return you to the Reports menu Note that this is quite different than the export to PM2000 The genetic demographic and census data files are created in a single pass 3 From the Reports menu select Analysis gt Export Data To gt PMx The default name for the genetic demographic export will be exchange csv you are given the option to change it The census export is automatically named pmxcens csv If there are any available UDFs you may add them The export will run and the resulting files will be saved in the studbook folder 4 Close SPARKS Import into PMx 1 Open PMx Pick New Project and enter a project name Including the species name and a date can be helpful as projects accumulate over time 2 The Project File to Create name will automatically update to reflect this project name 3 Either manually type in the Primary Input File information or click on the eal button at the end of this field and browse to the appropriate SPARKS studbook folder Change the file type to display csv files Choose exchange csv and click on Next PMx User Manual version 1 0 Page 4 PMx Create a new project Project Name GHLT Feb2011 Project Description Intl studbook data current to Nov 2010 Project File to Create GHLT Feb2011 pmxproj coal
229. of All Living that can be selected from this drop down menu are Founders Proven Breeders Unproven Breeders Fertile Sterile Contracepted and Post Reproductive and are determined as follows Founders Displays all living genetic founders Proven Breeders Displays sexually mature individuals that have produced offspring in the past Unproven Breeders Displays sexually mature individuals that have not yet produced offspring PMx User Manual version 1 0 Page 43 Fertile Displays all individuals that are not characterized as Sterile or Contracepted in the imported studbook data Sterile Displays all individuals that are characterized as Sterile in the imported studbook data Contracepted Displays all individuals that are characterized as Contracepted in the imported studbook data Currently individuals marked as Contracepted in SPARKS may show up as of a male and of a female on the age distribution Post Reproductive Displays all sexually mature individuals in age classes for which Mx has again drop ped to 0 i e no reproductive occurs at or after this age based on Life Table Model Data for that sex The Filter drop down menu also provided the option to display age pyramids for a specific Region Association Country or Location Overview Male Life Table Female Life Table Age Distribution Census Seasonality Projections Reproductive Planning Add Remove Availabilty Graphs Settings
230. oject i e data filter set in studbook for exporting files The individual may or may not be living currently For individuals that are Lost to Follow up Alive true may or may not be living currently DeathDate Date of individual s actual death YYYY MM DD even if this occurred outside of the project date span DeathDateEst The resolution to which the DeathDate that can be estimated if it is not a known date DeathCode Codes for cause of death specifying four parameters in this order Circumstance Carcass Disposition Topographic Etiological optional Individuals that are Lost to Follow up are indicated by Ift Provided with SPARKS 1 6 exports Sire UniquelD of sire male parent if known Multiple possible sires may be listed if their Unique Ds have been exported Other options are WILD if the animal is wild caught WILDx if the animal is wild caught and has known siblings in the dataset with x being a unique or other identifier across siblings UNK if sire is unknown UNKx if sire is unknown and has known siblings MATEOF lt stud_id gt will be constructed for the unknown mate of a known parent SireProb Probabilities that the indicated sire s were indeed the actual sire s listed in the same order as under Sire Dam UniquelD of dam female parent if known See Sire above for additional options DamProb Probabilities that the indicated dam s were indeed the actual dam s listed in the same ord
231. on Breeding With offspring RecNotes 4809 BUFFALO M04040 Female 8 Hold DoNotBreed 4813 DENVER A03189 Male 8 Hold DoNotBreed 4815 LOUISVILL 102941 Female 8 Hold DoNotBreed 4825 RACINE Male 8 SendTo MINNESOTA Breed 4930 25 4826 SIOUX FAL 3872 Female 8 Hold DoNotBreed 4827 DETROIT 11141 Female 8 Hold DoNotBreed 4828 INDIANAPL 203030 Female 8 Hold Breed 5049 2 5 4831 TOLEDO 7182 Male 8 Hold DoNotBreed 4833 HOGLE u03009 Female 8 Hold DoNotBreed 4916 BRIDGEPRT 102028 Female 7 Hold Breed 4973 25 4929 SIOUX FAL 3104 Female 7 Hold DoNotBreed 4930 MINNESOTA 13238 Female 7 Hold Breed 4825 25 4965 DULUTH 100323 Male 6 Available DoNotBreed 4966 ROCHESTER 105412 Female 6 old DoNotBreed 4967 ROCHESTER 105413 Female 6 DoNotBreed 4969 GLEN OAK 1419 Female 6 SendTo DoNotBreed 4970 GLEN OAK 1418 Female 6 Export DoNotBreed 4971 COLUMBIA 8854 Female 6 ReceiveFrom DoNotBreed 4973 BRIDGEPRT 101646 Male 6 ImportFrom Breed 4916 25 4974 DENVER 08410 Female 6 Available DoNotBreed 4975 LANSING 2926 Female 6 Other DoNotBreed 4983 COLUMBUS 206006 Female Z Unknawn DoNotBreed 4984 MINNESOTA 12317 Female 7 ol DoNotBreed ba m r Export Exportinstitutionalrecs importRecs Importtist Reset from Pairs and cuts Gear all Filtered showing 125 Managed N 125 Pedigree Known 100 0 Current Gene Diversity 0 964 Potential Gene Diversity 0 975 Lambda 0 991 The Clear all button at the bottom of the screen will clear
232. on entries for a studbook with 1000 animals and the writing of the values to the tables for display can therefore be very time intensive for large studbooks To avoid very slow loading of PMx genetics the default setting is to display these tables for small to moderate sized datasets but not to show these tables if the selected set has gt 1000 individuals The user can choose to see any or all of these calculations by checking or unchecking the corresponding boxes at the bottom of the Genetics Summary Statistics page When using the Allow Pairing Dead individuals option how are MKs and GD calculated The mean kinship MK of a dead individual is the mean kinship of that individual to the living population i e does not include its kinship to itself Population GD and the MKs of living individuals are calculated as normally based on the living population and do not include dead individuals Why don t my changes e g ReproGoals Management Sets pairing and culling recommendations show up in the Individual tab You must click on the Update Table button to add any changes made on other tabs PMx User Manual version 1 0 Page 135 Do Management Sets need to be mutually exclusive and exhaustive or can individuals be in more than one management set Membership in one management set does not affect the membership in other management sets Therefore individuals can be in more than one management set e g in EEP and in Glob
233. on that is used only for education purposes that the breeding program coordinator does not need to manage that does not occupy cage space designated for the managed population and whose genetic and demographic information is not important desired in the analysis It may be easier to remove this individual from the selection in PMx rather than set export filters in the studbook software so as not to include it in the export files Another example might be that data were exported for a particular geographic region or zoo association but there may be a reason to exclude individuals from a particular institution e g private facility or dealer To remove individuals from both genetic and demographic analyses deselect the individuals in the Selection tab in PMx while both the boxes for Apply changes in Selection to Genetics and Apply changes in Selection to Demography are checked Remember to click the Update Selection button for any changes in selection to take effect For SPARKS 1 5 or PopLink basic exports the demographic selection used to calculate the life tables is determined within those programs and cannot be modified in PMx therefore any selection changes applied to demography in PMx will change the individuals in the age distribution and in the starting population for projections but will not change the data underlying the life table calculations 3 Remove individuals that can never breed again from genetic analyses It is generally re
234. on the population s long term gene diversity It is typical to start by increasing the Maximum Allowable N toa larger but reasonable number 5000 is the maximum value Click on the graph on the right or in any other field to view the updated results Changing variables such as Lambda Ne N Generation Length and Current Gene Diversity if potential gene diversity is substantially higher to other reasonable values can be explored to get a sense for what may be achievable for the population To return to the original default values click on the Reset button on the bottom left of the page The second column allows for the addition of new founders to the population the default setting is no additional founders Under Founder Related Variables enter the number of founders that will be added for each importation New Fndrs per Addition Event Next indicate the Year to Start Adding Founders the number of Years between events importations and the Year to Stop i e the last year that founders will be added The total number of founders added will be a product of the number of founders to be added each time and the number of addition events during the specified time period and intervals These additions will be reflected on the graph as increases in gene diversity The actual genetic contribution of a new founder can be indicated by the FGE per founder parameter The default for FGE per founder Founder Genome Equivalents expected to be recruited per f
235. only Additional Optional Input Files Census C ISISdosbox SPARKS NA_Mal EXCHCENS TXT UDFs Associations C ISISdosbox SPARKS AZA fed Regions DODE PMx User Manual version 1 0 Page 10 Creating a Project from PopLink 2 1 or 1 3 There are two different types of PopLink exports a Basic export and an Advanced export The Advanced export allows greater analytical power in PMx demographic analyses e g enables the user to change from yearly age classes to other divisions Basic Export from PopLink PopLink will create standard PM2000 and PMx export files the same files are usable by both versions from the studbook database Data can be exported from the true studbook e g SavTam09 or from a studbook with an analytical overlay applied e g SavTam09 Faust1 The database displayed at the top of the screen will indicate which database is being exported Select the PM2000 Export from the Export drop down menu and this screen will be displayed File Edit View Overlay Validate Reports Export Help DI O A alz Export to PM2000 If you want census data imported into PM2000 with these files run the Census Report before you click Ok below Select Options for PM2000 Export Female Demographics File Name Genetics Data File Name fSavTam09 prn SavTam09 ped Male Demographics File Name Genetics filter information will be exported mSavTam09 prn to the above file name with a
236. or example by making a selection and applying it to demography and then making a different selection and applying it to genetics Next create a new Selected Population by highlighting the individual s on the appropriate table Use the Shift or Ctrl keys to highlight several individuals within one table at the same time if desired Then use the gt and buttons to move the highlighted individuals to the other table from left to right to remove them from the Selected Population and right to left to add them to the Selected Population Once all individuals have been moved to create the desired Selected Population click on the Update Selection button at the bottom of the screen to apply the new selection to all of the relevant analyses in the Demography and or Genetics sections of PMx If this step is overlooked PMx will display the message Would you like to update to your new selection as soon as the Demography or Genetics tab whichever is affected by the change in selection is accessed NOTE The correct Apply changes box es must be checked before changes to the Selected Population are made i e before individuals are moved from one table to the other otherwise the different selections may not be saved when the PMx project is closed and reopened NOTE In contrast to genetic analysis in PM2000 for genetic analysis in PMx it is not necessary or even generally useful to restrict the selection to the currently living individuals in
237. ormation detailed information on all individuals in the selection founder information kinship matrix pairwise information similar to the MateRx software program pairing and culling options management sets similar to MetaMK and pre set and user defined genetic graphs Options are also available to customize many program settings for analyzing the genetic data and for making a new selection for genetic analysis Once the user exits the Genetics module and returns to this Summary Statistics Screen the genetic settings will be replaced with a graph depicting the population size over time red line and gene diversity over time blue line File Language Help Project Notes Selection Demography Summary Statistics Founders Living Animals Living Descendants Percent Ancestry Known Percentage of Ancestry Certain Gene Diversity Gene Value Founder Genome Equivalents Founder Genomes Surviving Mean Inbreeding 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002 2004 Year V Indude Genetic History 7 Show Kinship Matrix V Indude MateRx Allow Pairing Dead Aysuaaig 9ua5 2006 2008 2010 2012 PMx User Manual version 1 0 Page 72 After clicking on Genetic Details be patient Some of these detailed analyses can be quite time consuming to calculate and it may take awhile for the Genetics module to open The larger the dataset the longer the
238. ounder is 0 4 This value is generally considered a reasonable estimate of the average FGE that would be recruited per founder but may vary per species or population and can be changed Er PMx Sumatran Tiger GSMP 28Jul11 baa Fie Language Help Project Notes Selection Demography Genetics Goals Recommendations Goal 90 0 Gene Diversity at the END of X 100 Years 550 1 Population Variables Founder Related Variables 500 Generation Length years 7 5 New Fndrs per Addition Event 2 00 Pen Maximum Potential Lambda 1 0438 Year to Start Adding Fndrs 10 400 Current N 289 Years between events 10 u 350 m N 0 9 Current Effective Size 77 2 Year to Stop 100 300 3 e g Ne N 0 30 FGE per founder 0 40 8 250 a a a Current Gene Diversity 0 94819 z 200 z Maximum Allowable N 500 150 Solve For Nothing Use values X 100 0 8 50 Reset You can exceed goals and maintain 94 6 0 You can maintain over 90 0 for up to 221 years 0 5 Send to Project Notes Managed N 289 Pedigree Known 100 0 Current Gene Diversity 0 948 Potential Gene Diversity 0 985 Lambda 1 044 PMx User Manual version 1 0 Page 117 The Solve For drop down menu allows the user to calculate the value of variable X required to meet the Goal given the other parameter values For example Solve For K will cause PMx to calculate the population size required to meet the Goal at the top of the page The Solve For feature can be used in
239. ounder descendants Inbreeding Coefficient F Probability that the two alleles at a genetic locus are identical by descent from an ancestor common to both parents An individual s inbreeding coefficient is equal to the kinship coefficient of its parents Kinship Value KV The weighted mean kinship of an individual with the weights being the reproductive values of each of the kin An individual with mostly old nearly post reproductive kin will have a low KV while an individual with many young kin of breeding age will have a high KV Living Individuals The number of living individuals in the currently selected population Living Descendants The number of living individuals descended from population founders This may be a fractional number because PMx normally excludes all individuals with unknown parents from genetic analyses and includes only those parts of individuals that can be traced back to known founders For example an individual with a known dam but an unknown sire will be tallied as half an individual in genetic analyses unless otherwise specified under the Settings tab Mean Inbreeding Mean inbreeding is the average of the inbreeding coefficients among the living individuals The mean inbreeding coefficient of a population will be the proportional decrease in observed heterozygosity relative to the expected heterozygosity of the founder population PMx User Manual version 1 0 Page 131 Mean Kinship MK The mean kinsh
240. overrepresented i e least genetically valuable individuals in the population r a PMx Amur Tiger Overview Founders Individuals Kinship Matrix Pairwise Info Pairing Culling Management Sets Graphs Settings Selection Current Population UniquelID Sex sR KVdynamic Location Known F AgeYears ReproStatus dGD New Value Change 0 0266 0 0002 GeneDiversity 0 9639 0 0002 Female 0 0219 0 0280 PITTSBURG 1 0000 0 0000 Fertile Gene Value 0 9600 0 0000 4983 Female 0 0250 0 0249 COLUMBUS 1 0000 0 0313 7 Fertile FGE 13 8543 0 0804 4984 Female 0 0250 0 0249 MINNESOTA 1 0000 0 0313 7 Fertile Percent Known 1 0000 0 0000 5 5 5049 Male 0 0260 0 0326 INDIANAPL 1 0000 0 0000 5050 Female 0 0260 0 0321 COLUMBUS 1 0000 0 0000 Fertile 4071 Male 0 0238 0 0233 COLUMBIA 1 0000 0 0146 Fertile 4193 Male 0 0263 0 0198 MANHATTAN 1 0000 0 0078 Fertile 4194 Female 0 0263 0 0197 RACINE 1 0000 0 0078 Fertile 3640 Male 0 0270 0 0217 NY BRONX 1 0000 0 0000 Fertile 4045 Female 0 0331 0 0250 NY BRONX 1 0000 0 0000 Fertile 4195 Female 0 0281 0 0223 CHICAGOBR 1 0000 0 0078 Fertile 4319 Female 0 0318 0 0289 GRANBY 1 0000 0 0000 Fertile 4412 Female 0 0306 0 0270 MADISON 1 0000 0 0000 Fertile Fertile Selected Culls Location COLO SPRG 4074 MANHATTAN Unfiltered showing 125 Filter E Apply culls to demography Remove All Export Read Cull File Assumptions Dynamic Populatio
241. ows are untranslated the program will default to using the English term After changes are made to PMxStrings xls those changes will be used in PMx the next time that the program is opened Getting Help Support for users is not provided with the PMx software beyond the information provided in this manual PMx is free you get more than what you paid for Advisory groups of regional zoo associations such as the AZA Small Population Management Advisory Group and the EAZA European Population Management Advisory Group will likely provide assistance with PMx to their members but they are not responsible for the development and maintenance of PMx Within PMx this manual is accessible from the Help menu on the main tool bar at the top of the PMx program window In addition from any location within the program the manual can be opened at the section pertaining to the currently active part of PMx by hitting the F1 key Any reports of apparent bugs can be sent to PMx vortex9 org although no promise can be made that all such reports will receive responses or be investigated Upgrades Upgrades to PMx will likely be released from time to time either as minor fixes to bugs or as major upgrades with new features There is no user registration for PMx so users will not be notified automatically of the availability of such upgrades The PMx website will have a list of significant bug fixes and new features provided with each new version PMx will att
242. pmxproj This file contains not only all of the PMx files but also the data files used to create the project see Appendix E for more information about the files contained in the PMx project file Therefore PMx projects can be transferred easily with the transfer of this single file Note however that as PMx is revised and updated projects created with older versions may or may not be able to be opened in newer versions of PMx Also projects may not work properly when transferred to a computer with different regional settings than the computer on which the project was created Removing Temporary Files When PMx runs it creates temporary folders within the PMx program folder These folders will have a name TempNNN in which the NNN is a random number If PMx is forced to exit without closing properly e g if the program crashes with an error message then the temporary folder may be left on the computer These folders will be located within the Window TEMP location on the system and can be safely removed after PMx closes PMx User Manual version 1 0 Page 18 USING PMx Primary Components of PMx PMx has six primary sections Project Notes Selection Demography Genetics Goals and Recommendations Each of these sections is described in detail in subsequent sections of this manual Across the bottom of the screen is the Primary Population Status footer which displays the basic demographic and genetic statistics Current N Pedigree K
243. population The gene diversity of a population is 1 1 2 FGE Founder Genome Surviving The sum of allelic retentions of the individual founders i e the product of the mean allelic retention and the number of founders Founder Representation Proportion of the genes in the descendant population that derives from that founder i e proportional Founder Contribution Gene Diversity GD The proportional gene diversity as a proportion of the source population is the probability that two alleles from the same locus sampled at random from the population are not identical by descent from a common ancestor Gene diversity is calculated from allele frequencies and is the heterozygosity expected in progeny produced by random mating and if the population were in Hardy Weinberg equilibrium Gene Value GV The gene diversity of the living individuals weighted for the reproductive value of individuals Gene value is the heterozygosity expected in progeny produced by random mating if the population were in Hardy Weinberg equilibrium and if each individual were to produce the number of offspring expected from its age based reproductive value Genome Uniqueness GU Probability that an allele sampled at random from an individual is not present identical by descent in any other living individual in the population GU all is the genome uniqueness relative to the entire population GU Desc is the genome uniqueness relative to the living non f
244. pulation Initially this population includes all individuals in the left hand table Selected Population that are still alive at the end of the date span chosen for analysis minus those individuals that were exported or released or became Lost To Follow up before the end of the analysis period i e the individuals available for management at the end of the time period chosen for analysis Not Selected Number Not Included 299 UniqueID Location LocalID HouseName OtherID Sex Alive on UniqueID Location LocalID HouseName OtherID a 259 SD WAP 102949 Mokolo I Male False 22 L O Mambasa O 313 DALLAS 864685 Bambesa 1 Female False 25 mn 52 EPULU Nepoko I 157 PARISZOO Z61079 Pablo WW Male False 30 155 DALLAS 001051 Viviane 11451 249 ANTWERP M5758 Paprika 1n Female False 20 154 DALLAS 600074 Kopo 11461 I 108 ROTTERDAM 101465 Mambuti 1 Female False 30 216 SD WAP 102950 Kamina 10 194 ROTTERDAM 101470 Lindi 0 Female False 24 153 SANDIEGOZ 160217 Lisette 10 219 BERLINZOO 900036 Aburo 0 Male False 27 152 SANDIEGOZ 004435 Kitambala m 283 DALLAS 823502 Fons n Male False 25 68 SANDIEGOZ 004434 Bayahu 10 478 DISNEYAK 000211 Zenzelle 0001DB Female True 14 172 COLO SPRG 74M012 Baruti I 160 CHICAGOBR 21064 Fredricka 1 Female False 29 69 PARIS ZOO 755165 Irumu EN 253 CHICAGOBR 22530 Mufuh ii Female False 27 35 PARISZOO Z4911C Dolo 1 214 CHICAGOBR 22694 Uhuru 1688 Male False 18 z 123 PARIS ZOO 75714
245. pulation if optimal reproduction of potential founders were to be achieved calculated as 1 1 2FGE potential Where FGE potential is the population s potential founder genome equivalent Gene value of the current living population and is the gene diversity of the population weighted for the reproductive value of individuals Average mean kinship value of individuals in the current living population Number of unrelated individuals founders that would represent the same amount of gene diversity as does the population of currently living individuals PMx gives FGEs calculated from the kinship matrix and also gene drop simulations Maximum FGE that can be attained if all founder allele retentions are set to their potential retention Provides an upper limit to what might be achieved through perfect genetic management but is not usually realistically achievable Sum of allelic retentions of the individual founders i e the product of the mean allelic retention and the number of founders Mean Inbreeding The average of the inbreeding coefficients among the living individuals Mean Ne Current Ne Ne N Average effective population size of the selected population over the analysis time span Given in relation to the number of Generations over which Ne is calculated Effective population size of the selected living population based on the number of living males and females that have produced offspring Ratio of the effective
246. r by year counts of number of and PopLink Census Report This file will males females unknown sex and automatically be created and reside in number of wild born captive born the SPARKS studbook folder and origin uncertain individuals In PopLink run Census Report under Reports File will be created in the PopLink Database folder PMxCensus csv SPARKS 1 6 In SPARKS This file is created auto Like exchcens txt from SPARKS matically along with the primary input 1 56 but with additional content field exchange csv under Analysis Export to PMx and will reside in the SPARKS studbook folder The formats of these file types follow Exchcens txt format Starts with a blank line Here represents spaces The variables just need to be separated by spaces the number of spaces does not matter Spaces before the first column are expected The exact name of the variables in the header line actually line 3 can vary but there can be no spaces within a variable name The order must be maintained as PMx User Manual version 1 0 Page 147 Order Content 1 Year 2 Total alive 3 Male alive 4 Female alive 5 Unknown Sex alive 6 Total alive 7 Wildborn alive 8 Captive born alive 9 Origin unknown alive Note that Total_Alive is repeated twice that is the format output by SPARKS 1 56 and PopLink Sample file blank HUMBOLDT PENGUIN SPHENISCUS HUMBOLDTI Year Tot_sex
247. rategy is to penalize individuals with high levels of partially unknown parentage PMx prorates the MSI value for varying levels of partially unknown parentage in the following way The default settings are as follows If the offspring of the pair has If unknown genome is lt 6 25 there is no penalty on the MSI If unknown genome is gt 6 25 the MSI pairing is 4 unless MSI is already 5 or 6 If unknown genome is gt 12 5 the MSI pairing is 5 unless MSI is already a 6 If unknown genome is gt 25 the MSI pairing is 6 If unknown genome is gt 50 the MS pairing is No Way These rules for how unknown parentage affects the final MS value can be revised by clicking the Edit how unknown pedigree affects MSI button This opens a new window that allows the definitions to be modified for each bin in terms of Genome Unknown and the Impact value of that bin designation On the right is a choice of four methods for incorporating pedigree uncertainty into the MS calculation e MSI Minimum MSI values will be at least the Impact value default method e MSI Incremented Impact value is added to the current MSI e MSI Assigned MSI is changed to the Impact value e No Effect MSI is calculated ignoring the Impact of unknowns As with the Edit bin click Validate and Save Changes after changed the settings clicking Reset will return the values and method to the default settings PMx User Manual version 1 0 Page 111 Weighted method A
248. rds as described above for the ped file format except that the leading MOVE tag does not start with an e g MOVE 2 19790101 Y capture 19810520 death PMx User Manual version 1 0 Page 143 5 Lineage pedigree format PMx can read the Primary Input File as a Lineage reference pedigree file with the extension txt The first few lines are skipped headers lines starting with or Record format ID Dam Sire Sex Selected Living Age Vx Location Generation Known Progeny Inbreeding MK KV GU_all GU_desc PrLoss UDFs Note that females are coded as 1 males as 0 Opposite from SPARKS and ped coding of the sexes The data fields after Location and Vx are not actually read by PMx and only they need to be there at all if optional UDFs are added to the end of the line PMx will allow DAM SIRE UDF and MOVE lines in the Lineage file just as it does with the ped file see above Demography Input Files The table below shows the types of input files that can be imported for demographic components of PMx the software that creates them how they are created and their content File Type Created Using Created by Contents Uses prn SPARKS 1 56 1 6 or PopLink In SPARKS Under Analysis Exporting a Demography Export for a given filter condition In PopLink by Exporting to PM2000 for a given filter condition Both prn files male female will be in either the SPARKS folder or
249. ribution or current Gene Diversity PMx User Manual version 1 0 Page 28 SPARKS 1 5 and PopLink currently do not export information on when individuals enter and leave the population if other than by birth capture and death Therefore it is necessary to set export filters for genetic analysis separately in these studbook programs to include only those individuals currently living in the population In this case PMx will not report historical genetic results see Section 1 of the manual for information on setting export filters Setting the proper filters when exporting data from the studbook will result in a table of selected individuals in PMx left table comprised of all individuals exported for genetic analysis which is either all individuals that were ever in the defined population anytime during the defined data span SPARKS 1 6 or all living individuals in the defined population SPARKS 1 5 or PopLink The user then needs to decide if particular individuals institutions should further be removed from the demographic and or genetic analyses for other reasons 2 In PMx deselect any additional individuals that need to be removed from all analyses BOTH genetic and demographic analyses SPARKS 1 6 and PopLink advanced export only There may be a number of reasons why the user may want to remove additional individuals from both the genetic and demographic analyses For example there may be a particular individual in an instituti
250. ring Culling Management Sets Graphs Settings Population Founder Individual Custom Founder Representation Founder Descendants 12019689 8066 67152824256 36 3434234875747 1 74192238628 52255514052 44 RIND 16 120194898056 67152824256 36 3434348757471 74192238 28 542555140524544 8RMENS 16 Founder Contribution Founder Retention i 514052444368 1 3120296 89 8066 671 52824256 36 3434348757471 74192238628 522555140524544 8AOEINS 1 quell Uniquell Assumptions Dynamic Population Variables Do Not Include Founders Unknown Weight 0 00 GD 0 9526 GV 0 9485 MK 0 0474 Known 96 N 47 0 Individual Graphs Histograms are given for Mean Kinship and Inbreeding for each individual in the selected living population Use the Filter button to specify the individuals to be graphed without affecting other genetic analyses or graphs El PMx tapir_UNK Genetics Selection Summary Founders Individuals Kinship Matrix Pairwise Info Pairing Culling Management Sets Graphs Settings Population Founder Individual Custom Mean Kinship Inbreeding 3 DAIIRO RDBB ROME OE ats WV PREV EIB B 3 DG BABA BEBO AD EID 3E P ni li PSY ZS EIBISE IREN 4 Assumptions Dynamic Population Variables Do Not Include Founders Unknown Weight 0 00 GD 0 9526 GV 0 9485 MK 0 0474 Known 96 N 47 0 PMx User Manual version 1 0 Page 103 Custom Graphs The Custom graphs menu pro
251. rives from that founder i e proportional Founder Contribution Number of copies of a founder s genome that are present in the living descendants Each offspring contributes 0 5 each grand offspring contributes 0 25 etc Probability that a random gene in a founder individual exists in at least one individual in the living descendant population Proportion of genes present in a founder that have the potential to be incorporated in the descendant population If the individual is a potential founder or is still living its potential retention is 1 00 For dead founders potential retention will be the same as the Allele Retention for that founder Number of descendants in the selected living population PMx User Manual version 1 0 Page 77 If UNKnown parents are to be considered as WILD at least in part see Genetics Settings then the founders who have UNK x UNK for their parents will be tagged with a U after their UniquelD in the table If UNK parents are to be excluded from calculations then individuals with UNK x UNK parents will not be listed in the founder table Founders with a Unique ID of MateOfxxx in which xxx is the Unique ID of another individual are hypothetical or pseudo individuals that were created by PMx in order to complete the pedigree These individuals are the UNKNOWN parents of individuals whose other parent is xxx For example if an individual has the following parents dam with Unique ID 123 a
252. rom genetic analyses in this way count toward the historical genetic analyses over their entire lifetime even if they are already non reproductive for a number of years e The Ne and Ne N calculations will accurately reflect the number of past breeders in the population even if the individuals are no longer capable of breeding in the future Terms and Concepts Selected Population Those individuals that are included in a particular analysis The Selected Population for genetic analyses may be the same or different as the Selected Population for demographic analyses Managed N Number of living individuals in the Selected Population for genetic analyses This may or may not represent all living individuals in the population that need to be managed in terms of space social groups and other non breeding considerations New Features e PMx provides the option to exclude individuals from demographic analyses as well as genetic analyses with SPARKS 1 6 and PopLink advanced exports PM2000 only offered a selection screen in the genetics section e The selection screen in the genetic section of PM2000 only showed individuals living on the day chosen for genetic analysis The PMx selection shows both living and relevant dead individuals for SPARKS 1 6 and PopLink advanced exports which allows PMx to conduct more precise historical calculations for both demographics and genetic analyses Helpful Hints e Sorting the table first by Gone and th
253. rovided on this tab see Appendix B Glossary for detailed definitions Founders Potential fdrs N Individuals L Descendants Anc Known Anc Certain Gene Diversity Kinship Matrix Gene Drop Potential GD Gene Value Pop Mean Kinship Founder Genome Equivalents Potential FGE FG Surviving Number of founders that have contributed to the selected living population Number of potential founders living individuals that have no living relatives in the population but have the potential to reproduce and contribute to the population Number of living animals in the currently selected population for genetic analysis Number of living animals descended from founders Percent of the living individuals pedigree that can be traced to a group of founders Percent of the living individuals pedigree that can be traced back to specific founders Gene diversity GD in the current living population as a proportion of the source population PMx calculates GD in two ways Gene diversity calculated from the kinship matrix as 1 mk where mk is the average mean kinship in the population Gene diversity GD calculated from gene drop simulations Each founder is assigned two unique alleles that pass stochastically through the pedigree Final GD is calculated from the final distribution of alleles and is based on the number of alleles and the evenness of allele frequencies Potential GD of the po
254. rows The resulting F for this pair is 0 0718 and MSI is 4 as seen in the blue columns on these rows and also in the Results table The values for F and MSI in the blue columns for other females give the F and MSI for each of those respective females when paired with male 4193 allowing a quick at a glance assessment of the range of values across potential mates Likewise the F and MSI values given for the other males are in relation to pairing with female 4074 Individuals Kinship Matrix is ring Culling Management Sets Graphs Settings Selection Males Specify Pairs Read Pair Fie Females Pairwise data to display E Do not show Paired UniqueID MKdy Rank KVdynd Location AgeY F Result MSI a UniqueID MKdys Rank KVdynai Location AgeYe F Result MSI C GGU 0 0718 4 3178 f New Value Change 4203 0 0240 1 0 0283 OMAHA 15 i 4407 0 0215 1 0 0277 PITTSBURG 13 ai Jenin enon IE 4983 0 0247 0 0247 COLUMBUS Gene Value 0 9605 0 0003 0 0270 0 0233 COLUMBIA 4984 0 0247 0 0247 MINNESOTA FGE 14 1414 0 0438 0 0272 0 0223 NY BRONX 0 0259 0 0215 COLO SPRG Percent Known 1 0000 0 0000 0 0276 0 0203 DES MOINE 0 0262 0 0244 SYRACUSE 0 0276 0 0203 DETROIT 0 0264 0 0330 COLUMBUS 0 0276 0 0208 CHICAGOLP 0 0265 0 0237 INDIANAPL 0 0283 0 0280 LOUISVILL 0 0270 0 0260 BRIDGEPRT Sire Dam F Success Offspring Location Notes 0 0292 0 0370 COLO SPRG 0 0270 0 0198 RACI
255. rrent and historical and to identify subsets of individuals with specific characteristics of interest Cautions e The ability to edit data within PMx is a double edged sword Greater flexibility and convenience also come with increased opportunities for error so edit with caution Remember that changes made in PMx will not translate back to the original studbook data Any revisions in the true data also need to be made directly in the studbook data e g within SPARKS or PopLink PMx User Manual version 1 0 Page 80 KINSHIP MATRIX TAB Purpose The Kinship Matrix tab displays the kinship values between every pair of living individuals in the selected population The kinship value between any two individuals is also equal to the inbreeding coefficient of any offspring that are produced by mating between these two individuals Most of the additional genetic analyses can be calculated from this table of kinship values How to Use This Tab To quickly calculate the kinship between any two individuals enter the two Unique IDs in the open boxes on the left of the screen and click Calculate This will return the Kinship value between the pair EE PMx Crowned lemur Genetics adividuals Kinship Matrix Pairwise Info Pairing Culling Management Sets Graphs Settings 29 38 48 49 54 55 61l 65 68 Location DUKEPRIM DUKEPRIM DUKEPRIM DUKEPRIM DUKEPRIM CHEHAW CINCINNAT CINCINNAT DUKEPRIM CHEF Enter the IDs of two animals in th
256. rt Filtered showing 49 Assumptions Dynamic Population Variables Do Not Indude Founders Unknown Weight 0 00 0 0203 DETROIT S050 0 0264 0 0330 COLUMBUS 0 0208 CHICAGOLP 4828 0 0265 0 0237 INDIANAPL Selected Pairs 3 5 0 0276 6 0 0203 DES MOINE 4542 0 0262 0 0244 SYRACUSE 7 8 9 Change GD 0 9645 GV 0 9601 MK 0 0359 Known 100 N 144 1 The Remove button below the Selected Pairs table will unpair the highlight pair remove their hypothetical offspring recalculate all genetic values and remove the pairing from the Selected Pairs table Remove All will remove all pairs In both instances the genetic calculations will reflect these changes Due to programming limitations PMx may not remove the blue highlighting from the UniquelD even though an individual no longer is recommended to breed The Export buttons below the Males and Females tables and the Selected Pairs table can be used to save these tables as txt and in some cases also csv or x s files PMx User Manual version 1 0 Page 88 Other Options on the Pairing Tab Specify Pairs This button at the top of the screen allows the user to type in specific pairs recommended for breeding as an alternative to selecting them from the tables This method also allows the pairing of dead animals even if the Allowing Pairing Dead option is not checked on the main Genetics Summary Statistics screen After entering the pertinent i
257. s Graphs displayed in PMx generally follow a common style with some exceptions such as the age pyramid graph More details about using specific graphs are given in later sections of this manual but a few words can be said here regarding the common features of PMx graphs When a graph is displayed ona PMx tab window it can be viewed larger and accessed for export by double clicking on the graph to open a Graph window Buttons on that window include options to Export to File the graph to a png file a format that can then be imported into other documents to Send to Project Notes the graph from where it can be copied and pasted into other documents or to Print the graph Exporting a graph will also recreate a csv file containing the data used to create the graph which can be imported into Excel Males Females PMx User Manual version 1 0 Page 21 Double clicking on the graph in the Graph window will open up the Chart Properties window where the features of the graph and even the data points in it can be edited before it is exported or printed vr Chart Properties i Gallery Data QD Binding Ei DataTable AxisX Gridlines AxisY X Y chart lines z Click here to update sample data Language Options and Regional Settings PMx was first developed in English with USA regional settings for data format It is expected that the program will work correctly with
258. s Options are also available to customize many program settings for analyzing the demographic data Helpful Hints e Be sure to indicate a Census File when creating the project in order to display a census graph PMx User Manual version 1 0 Page 34 DEMOGRAPHY OVERVIEW TAB Purpose The Demography Overview tab provides more detailed demographic information for the current population as defined on the Selection tab when the box Apply Updated Selection to Demography is checked This includes total number of individuals by sex and reproductive status population growth parameters mortality rates survival data reproduction data stochastic projection results and impact of current age sex structure How to Use This Tab This tab is accessed from the Demographic Details button on the Demography Summary Statistics screen The table on the left side of the screen provides a number of demographic statistics pertaining to the population Values are provided for the Total population and also by sex when appropriate The four graphs on the right are repeated from the Age Distribution Census Projections and Graphs tabs see the manual sections for these tabs for further explanation If individuals are added to or removed from the Selected Population on the Selection tab and the box Apply Updated Selection to Demography is checked these statistics will be updated to reflect the new selection PMx Demography Overview Male Life Table F
259. s C and Wilcken J 2009 Sustaining the Ark the challenges faced by zoos in maintaining viable populations International Zoo Yearbook 3 6 18 Leus K and R C Lacy 2010 Genetic and demographic management of conservation breeding programs oriented towards reintroduction Pages 74 84 in Iberian Lynx Ex Situ Conservation An Interdisciplinary Approach A Vargas C Breitenmoser amp U Breitenmoser eds Fundacion Biodiversidad IUCN Cat Specialist Group Madrid Spain Leus K K Traylor Holzer and R C Lacy 2011 Genetic and demographic population management in zoos and aquariums recent developments future challenges and opportunities for scientific research International Zoo Yearbook 45 213 225 PMx User Manual version 1 0 Page 155 Malo A F F Martinez Pastor G Alaks J Dubach and R C Lacy 2010 Effects of genetic captive breeding protocols on sperm quality and fertility in the white footed mouse Biology of Reproduction 83 540 548 Miller P S and P W Hedrick 1993 Inbreeding and fitness in captive populations Lessons from Drosophila Zoo Biology 12 333 351 Montgomery M E Ballou J D Nurthen R K England P R Briscoe D A and Frankham R 1997 Minimizing kinship in captive breeding programs Zoo Biology 16 377 389 Odum R A and B R Smith 2001 The effects of prorating risk in the development of life tables Zoo Biology 20 279 291 Pollak J P R C Lacy and J D Ballou 2000 Populat
260. s animals or to identify individuals that are not valuable in this population but may be good for use in release programs or for export to other regional populations The Culling tab may also be used to deselect individuals from the genetic analysis that for whatever reason can never breed again and should therefore be removed from the mean kinship calculations before pairing decisions are made See the Section 2 of the manual for a description of the consequences of removing non reproductive individuals using the Culling tab rather than the Selection screens How to Use This Tab All living individuals in the selected population for genetic analyses are listed in the Current Population table on the left side of the screen As with other PMx tables clicking on the appropriate column heading will sort the individuals by that variable and right clicking on the header opens the full list of variables that can be added to or deleted from the table The dGD column in blue shows the change in the population s gene diversity that would result if that individual were removed from the population A negative value for GD means that the population s overall gene diversity would decrease if that individual were to be removed indicating a genetically valuable individual a positive dGD indicates a genetically overrepresented individual whose removal would increase the gene diversity of the population This column can be sorted to quickly identify the most
261. s szccssececcessenccesssceccessacnvcvsecexeuvaccudebsssceecesseandesssecaeeveonsutebssneceeetsndedateaved 151 Appendix F References on Management of Pedigreed Populations cc cccccssccceessceceesseceeeesteeeeeees 152 PMx User Manual version 1 0 SECTION 1 USING PMx INTRODUCTION TO PMx Overview and Purpose PMx provides a suite of tools to support the genetic and demographic management of pedigreed animal populations through analysis of data typically recorded in a studbook Most such populations will be captive ex situ but PMx can also be used for managing wild populations for which intensive monitoring allows for at least a partial pedigree to be determined PMx was designed to guide primarily the management of populations for which there is a desire to maintain the genetic diversity as close as possible to the source population such as is often the case for conservation breeding programs for wildlife species However it can also be useful for management of domesticated livestock such as rare breeds or closed populations for which a primary concern is the protection of diversity PMx provides no guidance on selective breeding for augmenting phenotypic characteristics and the genetic methods provided in PMx are designed specifically to minimize genetic change due to either selection or drift PMx was derived from pedigree analysis programs that assume sexual reproduction with two discrete sexes Some of its calculations ar
262. s this is not achievable and other goals lower 90 and or shorter time period may be considered For some populations it might be reasonable to set the goal higher than 90 for 100 years A large well managed population with long generation length and or with periodic addition of new founders may be able to retain 95 GD for 200 years Cautions Remember to model only what is reasonable for the population For example it may not be possible to import founders on a regular basis a higher growth rate may not be feasible for a highly male biased population or it may not be feasible to increase generation length if reproduction in older individuals is unreliable PMx User Manual version 1 0 Page 118 SECTION 6 RECOMMENDATIONS SCREEN Purpose The Recommendations section provides a table in which recommendations for individuals can be recorded and exported for reporting purposes Recommendations can be generated automatically from selected pairs and culls in other parts of the program and or can be entered manually and can be exported as a table of recommendations for all individuals or a table with recommendations for each institution How to Use This Section Typically the Recommendations section is used after demographic and genetic analyses have been completed Click on the Recommendations section tab to view the recommendations table Each individual represents a row in the table Basic information such as Location Local ID Sex and
263. s within a reintroduction program How to Use This Tab Upon opening this tab a list of management sets is displayed on the left and a list of individuals on the right under Current Set Above the list of management sets PMx provides access to the Full Population which includes all individuals in the population as selected in the Selection tab ES PMx testmeta Genetics iol x Current Set es mat Ee e 1 0000 SANDIEGOZ 1 0000 MILWAUKEE 1 0000 PORTLAND 1 0000 SAN ANTON 1 0000 MILL MOUN 1 0000 TOLEDO 1 0000 MILWAUKEE 1 0000 FRANKLINP 1 0000 PORTLAND 1 0000 PORTLAND 1 0000 CINCINNAT 1 0000 CINCINNAT f r 1 0000 LOUISVILL mat overs cow 0 0000 mn 1 0000 Mo 1 0000 Ft Nan Beat Filtered shoning 120 Fiter Assumptions Dynamic Population Variables Eoo Change co asnan or osram onas on aH a Management sets can be created by the user as subpopulations Certain types of sub populations can be automatically created using the button This option can create subpopulations based on Location Association Region Country Social Group or a management set that includes the Full Population Association or Region files must have been imported into PMx when the project was created or can be added using the Genetic Settings tab Regions and Countries based on Location are automatically imported from SPARKS 1 6 exported data see Section 1 on Using PMx for more information on Regions
264. se in that order Sex Options are Female Male Hermaphrodite Abnormal Asexual Unknown Group terms to be determined at a later date Known Proportion of an individual s genome that is traceable to known founders either through positive identification of all ancestors or all possible ancestors Thus 100 known individuals can have completely identified ancestors or can have MULTs multiple possible parents in their pedigree provided that the identity of all possible parents is specified in the Sire and or Dam fields in the database Certainty Proportion of an individual s genome that is completely identified exact identity of both parents are known and traceable to known founders Individuals that are 100 Certain do not have any MULTs or UNKs in their pedigree Certainty represents a higher degree of knowledge than Known and therefore is always less than or equal to Known Wild caught founders i e parents are WILD x WILD or WILD x WILD are 100 known and certain any UNK is unknown and uncertain To illustrate the distinction between Known and Certainty 0 ej O 204 204 Known 100 Known 100 Known 50 Certain 100 Certain 50 Certain 50 PMx User Manual version 1 0 Page 123 BirthDate Date of birth YYYY MM DD BirthDateEst The resolution to which the BirthDate that can be estimated if it is not a known date Alive True if the individual is alive at the end of the date span defined by the pr
265. sion fractional value after the integer DeltaGD Net change in gene diversity of the population if the pair produced one surviving offspring MKDiff Net difference in the mean kinship MK values for the male and female PMx User Manual version 1 0 Page 85 New Features The Pairwise tab is a new feature and was not available in PM2000 It essentially incorporates the DOS based software program MateRx functionality into PMx Helpful Hints Filters can only be used for the variables in the row and column headers i e UniquelD and Addl Data variable Once the table is filtered the Addl Data variable can be changed without affecting the filter For example to get a table for only reproductive age individuals with their locations set Addl Data to AgeYears use the Filter button to restrict the table to only breeding age individuals and then change Addl Data to Location Sorting the rows and columns by MK will position the most genetically valuable individuals in the upper left of the table and the most detrimental in the lower right Import the matrix into Excel or similar program and use the Autofilter or other Excel functions to quick identify the range of MS options and best potential mates for females If the table on the Pairwise Info tab is empty be sure that the Include MateRx box is checked on the Genetics Summary Statistics screen PMx applies a threshold level of inbreeding to determine MSI do not breed
266. sion 1 0 Page 83 PAIRWISE INFO TAB Purpose The Pairwise Info tab provides information about all possible male female pairs in the selected living population This information can be used to categorize the relative suitability of pairs for breeding This tab incorporates much of the functionality available in the MateRx DOS based software program How to Use This Tab This tab displays a matrix of Males rows and Females columns for the selected living population Numerous variables can be displayed in the table which can be sorted filtered and exported About the Mate Suitability Index MSI The default value in the table is the MSI Mate Suitability Index value for each male female pair MSI is a composite score that integrates four genetic components into a single index 1 Delta GD dGD Change in gene diversity GD of the population if one offspring is produced by the pair Positive dGD increases the GD of the population while negative dGD decreases GD 2 Differences in MK values MKDiff Difference in the genetic value mean kinship value of the male and female Breeding a pair with a large MKDiff is detrimental because it combines under represented and over represented genetic lines 3 Inbreeding coefficient F Inbreeding coefficient of any offspring resulting from the pair i e the kinship value for the pair Inbreeding is considered to be detrimental to the fitness of the resulting offspring 4 Unknown ancestry
267. sl ote marts Reia tf coe Culling Management Sets Graphs Settings See et nee te Lae See iquelD Sex n Eas 804 Fearn IGTN Female SEASS E 996 gle 0 0654 1 0000 BEERWAH 997 Male 998 Male 0 0644 1 0000 DUBBO 1009 Female 0 0765 1 0000 MOGO 1011 Male 0 0735 1 0000 WELLINGTN 1012 Male 0 0686 1 0000 MAREEBA 1085 Male 0 0669 1 0000 ADELAIDE 1120 Female 0 0761 1 0000 ADELAIDE 1153 Female 0 0744 1 0000 AUCKLAND 1154 Female 0 0735 1 0000 HAMILTON 1155 Male 0 0735 1 0000 HAMILTON 1164 Female 0 0665 1 0000 PERTH 1166 Male 0 0654 1 0000 YARRALUML 1194 Female 0 0697 1 0000 MOGO Overall GDw 0 8972 MKw 0 1028 MKb 0 0353 Fst 0 0535 Fitered showing 346 Dynamic Population Variables Assumptions WeDo GD 0 9478 GV 0 9443 MK 0 0522 Known 100 N 346 0 Summary information for each subpopulation N GD Mean F is given in the table on the left along with information on the relationships of these subpopulations MKb Fst to the one selected as the Current Set Summary statistics describing the average relationships among all subpopulations GDw Mkw MKb Fst are displayed in the lower left of the window under the list of Management Sets Click the Comparisons button to show a matrix indicating the Fst in blue and MKb in pink between each pair of subpopulations This table can be saved as a txt csv or x s file using the Export button PMx User Manual version
268. stochastic projections with these new settings Clicking Defaults will return the settings to the default values Male E hil PMx Demography Overview Male Life Table Female Life Table Age Distribution Census l Projections Reproductive Planning Add Remove Availability l Graphs Settings 1 i Birth Flow is Pulse Continous Age Classes are 1 years MA Report results using time unit as years Z i For early mortality use 30 days Project for 20 time steps Distribute Unassigned Mx i In prop to known Exclude Number of Iterations for simulations 500 Select Confidence Interval Add 2 age Classes to life tables 95 90 75 68 Assign sex to births in Life Table Use actual a TE Stochastic Projections Treat each birth as male Maximum Females bred per Male 1 Ratio of Male Female Mx 1 12 l When calculating Life Table Unknown sex 0 50 male For projections births are treated 0 50 male Multiple Parents Most Likely v Defauts ok Assumptions Overall Statistics Stochastic Runs Age Classes are years Birth Flow Continuous CI 95 Iterations 500 Growth in terms of years r 0 065 lambda 1 067 Projections 20 time steps Ro 1 946 T 8 6 N20 87 Up to date Setting options are listed below Birth flow default continuous Select birth flow as Continuous reproduction throughout the year or Pulse seasonal breeders Continuous birth flow applies the Mx val
269. sumptions Overall Statistics Stochastic Runs Age Classes are years Birth Flow Continuous CI 95 Iterations 500 Projections 20 time Growth in terms of years r 0 071 lambda 1 073 Ro 1 695 T steps 7 3 N20 112 Up to date Custom Graphs Census This screen allows the user to create custom graphs from census data Available options will be dependent upon the data exported from the studbook program currently many options are only available via exports from SPARKS 1 6 e Select Census in the upper left box e Next select at least one of the 16 variables under Variable s to Plot in the two center left boxes Multiple boxes can be checked however some variables cannot be plotted together as they require different y axes Most variables are based on counts and can be plotted together Exceptions are Sex Ratio males and Birth Sex Ratio which can be plotted together but not in combination with other variables and the two measures of Lambda which can be plotted together but not in combination with other variables e Select whether to plot data for Total all individuals Males Females and or Sex unsexed in the lower left box These boxes are ignored for the following variables institutions Sex Ratio Birth Sex Ratio Lambda N and Lambda Repro e Select whether to plot as a Line or Bar graph under the graph Sex Ratio and Lambda are more logical as line graphs e Revise the earliest date to plot if d
270. t to save it intact In some cases making changes in PMx can cause the Recommendations table to also change causing some individuals and or recommendations to be deleted If this occurs the exported text file can be used to recreate the recommendations using Import Recs PMx User Manual version 1 0 Page 122 APPENDIX A LIST AND DESCRIPTION OF INDIVIDUAL VARIABLES Variables are listed in the default order that they appear on the Individual tab in the Genetics section Although the variable descriptions below may refer to an individual for convenience many of these variables can be applied to a group as well Not all variables are exported by all studbook software versions columns for unused varaiables are omitted in PMx UniquelD The identifier used for a single individual or group throughout the project typically the studbook number Location The last location of the individual within the scope of the project Usually the current or last location indicated by the institution s ISIS mnemonic If an individual left the scope of the project e g was transferred outside the region or association then Location may not reflect the current location LocallD Identification number used by the institution indicated in the Location field LocallD must be referenced in conjunction with Location HouseName Often a familiar name used for an individual OtherID Various identifiers such as Transponder Tag Band Tattoo and ColorPha
271. terval 5 Females Males Females Males Females Males Females Males Fer 0 0 oo 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 r Age Unit years Birth Flow Continuous CI is95 Iterations 500 Projections 20time steps Analysis date 14 02 2011 m Overall Statistics years r 0 078 lambda 1 081 Ro 2 079 T 8 3 N20 112 Stochastic Runs Outdated Next go to the table labeled Enter what proportion of removals will be available from each age sex class Each sex should sum to 1 0 Decide which sexes and age classes are available and or preferred for removal and what proportion of the total removals should be made up of each available sex age class Enter these figures into the table PMx User Manual version 1 0 Page 61 making sure that each column i e proportions for each sex sums to 1 0 It is possible to set removals for only one sex in that case leave the proportions in the column for the other sex at 0 00 Click on the Go button The table on the far right will show the number of individuals that are projected to be available for removal in each of the specified sex age classes at each interval e g each year for the time period considered same as the setting for all projections while meeting the goals set at the upper left side of the screen The total number of individuals across age classes of each sex available for removal are shown in the blue row at the top of the table This tabl
272. the export files PopLink can also export census data for graphing in PMx To use this option run the Census Report Reports gt Census Report with the desired filters Running the report automatically creates an Exchcens txt file no need to click on the Export button on the report PopLink places the PMx export files ped prn and Exchcens txt in the studbook folder e g C Documents and Settings User Name My Documents PopLink 2 1 PopLink Databases Studbook name in PopLink 2 1 C Program Files PopLink 1 3 PopLink Databases Studbook name in PopLink 1 3 PMx User Manual version 1 0 Page 11 Basic Import into PMx Open PMx select New Project and name it The Primary Input File will be the ped file in the studbook folder My Documents PopLink 2 1 PopLink Databases Studbook Name Studbook Name ped chimpanzee_test testing PopLink basic export C Users faust Documents PMx projects chimpanzee_basicexport pmxproj C Users faust Documents PopLink 2 1 PopLink Databases CHIMPANZEE CHIMPANZEE ped Ea Cancel Next gt gt Click Next On the next PMx import screen enter the prn files from the studbook folder and also the Exchcens csv file optional note screen format may be slightly different than shown below PMx Create a new project X Demography Input File Required Moves Female C Users faust Documents PopLink 2 1 PopLink Databases CHIMPANZEEYCHIMPAN _ Male C Users faust
273. them from one table to the other If individuals are moved and then different boxes are checked before clicking Update Selection this new selection will not be saved e When making changes in selections it is recommended to carefully check the total Number Included above the Selected Population table the Managed N in the footer and other variables to confirm that the correct subset of individuals is being used PMx User Manual version 1 0 Page 32 SECTION 3 DEMOGRAPHY MODULE DEMOGRAPHY SUMMARY STATISTICS SCREEN Purpose The main Demography Summary Statistics screen provides basic summary statistics for the population as defined on the Selection tab It includes a census graph for males females and individuals of unknown sex as well as population demographic values How to Use This Tab The tabular information on the left side of the screen is based upon the selected population If the individuals in the selected population are changed on the Selection tab and the box Apply Updated Selection to Demography is checked this Summary tab as well as other demography values will be updated Fie Language Help Project Notes Selection Demography Genetics Goals Recommendations Summary Statistics Values Size 416 464 0 880 Census Life Expectancy from birth years 30 day survival 0 38 2554 25 live to 15 9 vears 10 live to 21 0 years 5 live to years 1 live to years Oldest livina 25 0 ID 2905 vears 0 940
274. thin the age sex class see below for further discussion Check Effect Reproductive Planning to incorporate the plan into the calculations on the Reproductive Planning tab to estimate the number of births needed to meet population goals The Enable box is checked by default uncheck this box to disable the plan 10 Click Save to save the plan and close this window or Clear to return to the default values of zero PMx User Manual version 1 0 Page 58 r Define a Supplement or Removal Plan Enter Numbers or Proportions values imply Supplementation values imply Removals years Available Available Add Remove Add Remove lt Name Required Age Class Males Females Males Females J Plan 2 0 0 0 0 0 1 z 2 0 0 ime mee te 2 4 0 0 0 Start time 5 gt 3 s im _ e 4 0 0 2 2 5 5 2 0 0 0 Every 5 time interval 6 2 1 0 0 z 7 P 5 Values are 8 1 2 0 0 LE 9 1 1 0 0 1 Proportions 4 3 0 0 J 3 0 0 E Effect Reproductive Planning i 3 0 0 0 7 Enable 1 0 0 0 0 2 0 0 Each created plan will be displayed as a row in the table on the left side of the Add Remove tab Check boxes are provided here to easily apply or not apply the plan to reproductive planning Affect RP or to enable or disable the plan Enable Other modifications to the plan can be made by clicking Edit to open the Define a Supplementation or Removal Plan window Individual plans can also be deleted at th
275. tion Management Center Colleen Lynch Lincoln Park Zoo Jennifer Mickelberg Smithsonian Institution National Zoological Park Kanako Nishimoto ISIS Paul Pearce Kelly Zoological Society of London Kristine Schad AZA Population Management Center Karin Schwartz Kathy Traylor Holzer IUCN SSC Conservation Breeding Specialist Group CBSG and others PMx was developed with support from the Institute of Museum and Library Services USA Association of Zoos and Aquariums AZA Chicago Zoological Society and Smithsonian Institution National Zoological Park with a substantial amount of time and expertise of collaborators who were supported by their institutions and or their own personal time PMx is copyrighted by the Chicago Zoological Society but it is distributed as freeware for use by anyone who has a need for it It is illegal for anyone to sell in whole or in part PMx without prior permission from the Chicago Zoological Society or to represent it as the work of another References Ballou J D 1999 MetaMK Metapopulation Mean Kinship Analysis Washington DC Smithsonian National Zoological Park Ballou J D J Earnhardt and S Thompson 2001 MateRx Genetic Management Software Washington DC Smithsonian National Zoological Park Ballou J D C Lees L J Faust S Long C Lynch L B Lackey and T J Foose 2010 Demographic and genetic management of captive populations Pages 219 252 in Wild Mammals in Captivity D G
276. tion of the total genetic variance in the combined set Note that genetic variance is proportional to GD so Fst GDb GDt and since GD 1 MK for any population Fst 1 MKb 1 MKt See cautions below Full Population The selected living population Full Population statistics GDw The weighted mean GD within subpopulations with each within subpopulation GD being obtained as 1 MK including only kinships between individuals in that subpopulation and the mean across subpopulations being weighted by the number pairwise kinships within each subpopulation N in which N is the number of living captive born animals in the subpopulation Mkw The overall mean of all kinships between two individuals that are in the same subpopulation This will be the same as a weighted mean of the MKw values for the subpopulations with the weightings being the number of pairwise kinships in the subpopulations Mkb The overall mean of all pairwise kinships between individuals in different subpopulations This will be the same as the weighted mean of all the pairwise MKb values with the weights being the number of kinships included in the MKb value for each pair of subpopulations Fst A measure of the overall amount of genetic divergence among subpopulations Measured as the proportion of the GD of the total population GDt the sum of all defined subpopulations that consists of variance between subpopulations Defined as Fst GDb
277. tly identified with probabilities assigned For other data exports MULTs are treated as UNKs unless the csv or ped file is manually edited to include possible parents and their probabilities PMx User Manual version 1 0 Page 105 Value proportion WILD to assign to Unknown parents Assigns a portion of the pedigree of an unknown UNK individual as being an unrelated founder WILD Default value is zero This option is available only if there are UNKnown parents in the database O do not include individuals with unknown parents in genetic calculations 0 5 treat individuals with unknown parents as unknown and wild 1 0 treat all animals with unknown parents as having wild parents The optimal value to use here depends on the amount of unknownness in the population s pedigree If the population has a mostly unknown pedigree then it may be better to use a higher value here If the population has only a small amount of unknownness in the pedigree then it may be better to use a lower value here The appropriate value may also be influenced by how likely it is that the unknown individuals are related to the rest of the population or not Include Founders Choose whether or not to include the founders in the genetic summaries of population genetic status and measures of genetic value of individuals The default setting for genetic statistics is to include only the descendent individuals but to exclude wild caught founders Note that by incl
278. to further refine the list of individuals that should be included in either demographic analyses genetic analyses or both Using the Selection Screen The following information describes the Selection screen view when data are exported from SPARKS 1 6 or from PopLink using the advanced Analytical Survival Statistics option see subsequent information on differences using other studbook software exports and filters When the PMx project is first created the left hand table shows the individuals in the Selected Population that will be included in the population analyses based on the data exported from the studbook In the right hand table are those individuals Not Selected to be in the analyses The total number of selected or unselected individuals Number Included Not Included is displayed above each table Individuals within each table can be sorted by any column by clicking on the column heading Click again to sort in the reverse order As with other tables in PMx the table can be customized by changing the width and order of the columns and by adding or deleting columns by right clicking on the header Many columns can be helpful in identifying individuals that should be excluded for either demographic and or genetic analyses PM2000 users will notice an important difference between PM2000 and PMx imports PM2000 only allows selection in the genetics section and only displays individuals living on the day chosen for genetic analysis The PM
279. to reset all MateRx Settings to the default values and settings The Save Settings and Read Settings buttons are not currently active but are intended for future use After making any changes under the Genetic Assumptions Other Setting or MateRx Settings click on the Implement changes button to apply these new settings PMx User Manual version 1 0 Page 112 Additional Data Files These settings provide the option to import additional data files for use in the project Multiple files can be added serially Associations are fed files that are text files that contain a list of institutional mnemonics representing the members of a particular regional zoo association These are distributed with SPARKS and PopLink and reside in those program folders however these association lists are time sensitive as association membership changes and so these files should be updated regularly It is possible to modify or create new association lists by editing an existing fed file or creating a new one Once imported the variable Association can be added to most PMx data tables and can be used to automatically create Management Sets on the Management Sets tab PMx will assign associations to individuals based on its current last location not based on historical association membership also see Section 1 of the manual Regions are rgn files that are text files that contain a list of institutional mnemonics representing institutions that resid
280. uals in each age and sex class Two columns are provided one for Males one for Females to specify the individuals to add or remove for each interval in which the plan will be applied Values can be entered as the Number of individuals in each age and sex class to add or remove or as the Proportion of each age and sex class to add or remove Enter positive numbers to Add numbers and negative numbers to Remove individuals Next move to the right side of the screen to define the application of these additions and removals Begin by entering a Name for the plan Enter the specific year time interval at which the plan should start Start time This is the first time interval at which the first individuals will be added or removed Enter the specific year time interval at which the plan should end End time This is the last time interval during which individuals will be added or removed Enter the time interval at which individuals will be added or removed The above three values Start time End time and every X time interval determine those time intervals during which individuals will be added and or removed from the population For example if Start time 2 End time 20 and time interval 5 then individuals specified in the table will be added and or removed in time intervals 2 7 12 and 17 Specify whether the values entered in the table on the left are given in terms of Numbers of individuals or Proportions of individuals wi
281. uding the founders the kinship calculations are not affected Weight Groups Allows large groups to be weighted when calculating the population statistics Group data must be entered into a ped file or possibly a file from ZIMS in the future Do not use this tool unless you are familiar with it Weight to assign to empirical Kinships Provides the option to integrate empirical data with estimated kinships among founders e g molecular data into PMx and to specify how much to weight these empirical data Weighting depends on the level of confidence in the molecular results and can be done by entering a value between 0 and 1 in which O donot use empirical data use only original pedigree calculations 0 5 use a split between empirical and pedigree data e g if empirical data says kinship 0 3 and pedigree data says kinship 0 1 then PMx will use 0 2 1 0 use empirical data for those kinships entered by importing a file of empirical kinships rather than a kinship calculated from the pedigree default value The optimal value to use here depends on the uncertainty standard error around the empirical data If there is a smaller standard of error then higher weight should be given to the data If there is a larger standard of error then a lower weight should be given to the data However more research is needed on this This box will only be accessible if empirical kinships have been imported Other Settings Analysis Date Date that
282. ues to the number of individuals in the age class after 50 of the mortality for that age class has occurred Pulse birth flow applies Mx values to all individuals entering the age class essentially simulating all births occurring on the same day each year PMx User Manual version 1 0 Page 67 Age class length default 1 year Change the length of the age class in the life tables This can be changed to a particular number of days weeks months years or decades and may be useful for species with particularly short or long lifespans Changing the age class length also affects projections as the length of the time interval used for projections age class length see Projects tab for more information Early mortality definition default 30 days Change the length of time used to calculate early mortality displayed on the demography Overview tab Unassigned Mx default in proportion to known Determine if births to unknown age parents contribute to Mx in proportion to the Mx rates of individuals of known age default or are excluded from the life table calculations Add age classes Add additional age classes to the bottom of the life tables for both sexes Additional age classes will be of the same length as the original ones This is useful for example when the oldest recorded individual is still living Assign sex to births default each birth is 0 5 male 0 5 female Determine if each birth is considered as part
283. ulation goal by setting either a constant population size OR a constant growth rate Click the relevant button and adjust the number in the corresponding box to match the population goal For example to grow the population by 10 each year in addition to any individuals that are removed click the Maintaining Lambda at button and enter 1 10 in the box To have the population remain at its current size click the Keeping Pop at size button and enter the current population size in the adjacent box note that you can also achieve this result by clicking the Maintaining Lambda at button and entering 1 00 in the adjacent box GB PMx NA MAL test projections Demography How Many Animals Can Be Removed Time Intervals 1 year that can be removed while 55 1 081 Keeping Pop at size Maintaining Lambda at 30 25 Go Reset Epor Total Projections Assumptions Numbers and ages of animals that could be removed ter what proportion of movals will be available n each age sex dass sex should sum to 1 0 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 years Interval 0 Age Males Females Males Total Interval 1 Interval 2 Interval 3 Interval 4 In
284. ult 30 days e Change the distribution of Unassigned Mx default in proportion to known e Add additional age classes to the bottom of the life table e Change the sex assignments to births default each birth is 0 5 male and 0 5 female e Change the sex assignment of unknown sex individuals default 0 5 male e Change the assignment of multiple parents default most likely parent is used for calculations if UniquelDs have been exported otherwise MULT is treated as Unknown e Change the time interval for reporting results default years to days weeks months or decades This changes only how population growth lambda r and generation length T are reported these rates are relative to the interval chosen here This setting does not change age class length See Projections tab and Settings tab sections for more information e Change the birth sex ratio for projections default 0 50 male PMx User Manual version 1 0 Page 40 Terms and Concepts see Appendix B for complete definitions Survival Rate Px The probability that an animal that is alive at age class x will survive to age x 1 Mid Px The probability that an individual survives to the mid point of age class x Mortality Rate Qx The proportion of individuals that die during an age class This number is calculated from the number of animals that die during an age class divided by the number of animals that were alive at the beginning of that age class th
285. vides the capability to plot almost any data from the PMx project analyses To create a graph choose the graph category Population Founder Individual and the variable or genetic summary to graph These variables may be plotted against another genetic variable against individuals Unique IDs as a frequency histogram or as a cumulative frequency The Frequency Histogram and the Cumulative Frequency options allow the user to specify the interval for which data are combined and displayed The Filter Individuals button can be used to change the specified individuals to be graphed The Sort on and Sort Founders on pull down menus can be used to change the order of the individuals on the x axis when Unique IDs are used For definitions of Custom graph variables see the Summary Overview Founders and Individuals tab sections of the manual and the Appendix B Glossary EE PMx tapir_UNK Genetics Selection Summary Founders Individuals Kinship Matrix Pairwise Info Pairing Culling Management Sets Graphs Settings Population Founder Individual Custom Choose a variable Plot against Founder AgeYears a Frequency of AgeYears Founder Certainty UniquelD Founder Contribution A Founder Descendants Frequency Histogram Founder F Founder FOKE Founder Gen Founder GUAI Founder GUDescend Founder Known Founder KV Founder MK Founder MKRank Founder NLivingOffspring w Interval 5
286. vidual data as can be viewed on the Individual tab of Genetics and a pop file that has a smaller set of core information about each individual These files are semi colon delimited so they can be easily opened in Excel or other programs e A rep file that contains as a formatted text file a table of the founder contributions to each individual in the descendant population e The Project Notes saved as a Report rtf file so that they can be imported into Word or other text editing programs e The Recommendations table saved as a tab delimited RecFile txt file that can be imported into Excel or other programs e A PMxProject xml file that contains in xml format readable by Internet Explorer and other programs the core information that defines the project It is highly recommended that the files within the original pmxproj file as opposed to a copy not be edited because the formats of some of the files are highly specific and any changes might make the PMx project unreadable by PMx Because all of the files needed by PMx are included within the omxproj file a project can be transferred to another folder or to another computer by simply copying the pmxproj file Moreover because copies of all input files that were used to create a Project are stored within the pmxproj file those original data are archived with the project and can be used to revert to the originally imported data via a button on the Selection tab if it becomes necessar
287. wise specified Apply date also to Demographic Age Structure Checkbox to apply the above Analysis Date to the demographic analysis as well as genetic analysis default is yes Start Date Starting date of the analysis Default is the starting date of the export filter window Gene drop Iterations Number of iterations that the gene drop simulation is run Default 1000 PMx User Manual version 1 0 Page 71 Current Living Animals Living Descendants Percent Ancestry Known Percentage of Ancestry Certain Gene Diversity Gene Value Founder Genome Equivalents Founder Genomes Surviving Mean Inbreeding Genetic Details V Indude MateRx Genetic Assumptions Parentage Assumptions Probabilistic parents hd Value proportion WILD to assign to Unknown parents 0 00 Indude Founders Weight Groups 100 Weight to assign to empirical Kinships Other Settings Analysis Date mm dd yyyy 1228 2011 By V Apply date also to Demographic Age Structure Genedrop Iterations 1000 Start Date mm dd yyyy Indude Genetic History Show Kinship Matrix Allow Pairing Dead Managed N 125 Pedigree Known 100 0 Current Gene Diversity 0 964 Potential Gene Diversity 0 975 Lambda 0 991 Click on the Genetic Details tab to open the full Genetic section of PMx an expansive genetics module that includes tabs for more complex genetic overview inf
288. ww amphibianark org Soul M M Gilpin W Conway and T Foose 1986 The Millennium Ark how long a voyage how many staterooms how many passengers Zoo Biology 5 101 113 Wilcken J and C Lees eds 1998 Managing zoo populations compiling and analysing studbook data Sydney Australia Australian Regional Association of Zoological Parks and Aquaria Willis K 1993 Use of animals with unknown ancestries in scientifically managed breeding programs Zoo Biology 12 161 172 Willis K 2001 Unpedigreed populations and worst case scenarios Zoo Biology 20 305 314 Willis K and R E Willis 2010 How many founders how large a population Zoo Biology 28 1 9 PMx User Manual version 1 0 Page 156
289. x selection screen on the other hand allows selection for both demographic and PMx User Manual version 1 0 Page 25 genetic analyses and shows both living and dead individuals which allows PMx to conduct historical demographic and genetic calculations In PMx the left hand table with the Selected Population will contain the following individuals 1 Individuals already living in the population at the start of the date span selected for analysis including those individuals that may have left the population before the end of the analysis period by Death Lost To Follow up LTF Release or Export These individuals contribute to the analyses from the start of the analysis date span to the end of the selected date span or up until the date that they leave the population if they do so before the analysis end date 2 Individuals that enter the population at some point during the date span selected for analysis either by Birth Capture or Import including those individuals that leave the population before the end of the date span These individuals contribute to the analyses beginning on the date they enter the population until the end date for analysis or until they leave the population if this happens before the analysis end date The Managed N in the footer at the bottom of the screen represents the number of living individuals in the population currently selected for genetic analysis along with a summary of the genetic status of this po
290. y Lacy et a Be aware however that PMx provides some new approaches and uses new algorithms that are not yet fully documented in any published reference History of PMx PMx was derived from the PM2000 software package Pollak et al 2000 incorporating all analyses of PM2000 and adding a substantial number of new analyses and options PMx also incoporates the analyses of MateRx Ballou et al 2001 and MetaMK Ballou 1999 PM2000 was itself a combination of the capabilities of the programs GENES written by Robert Lacy DEMOG written by Laurie Bingaman Lackey and Jonathan Ballou and CAPACITY written by Jonathan Ballou as well as adding some new features Many people especially including members of the AZA Small Population Management Advisory Group SPMAG the EAZA European Population Management Advisory Group EPMAG and the IUCN SSC Conservation Breeding Specialist Group CBSG were involved in developing the algorithms used in these various programs and provided assistance with software design and testing PMx like its predecessor programs was designed to work with pedigree data maintained by the SPARKS studbook software that was developed and is distributed by the International Species Information System ISIS 2011 More so than PM2000 however PMx is designed also to accept pedigree data from a variety of database programs as long as the data can be transferred in specified formats In particular the developers of PopLink stud
291. y to discard all modifications made within PMx to the selected population PMx User Manual version 1 0 Page 152 APPENDIX F REFERENCES ON MANAGEMENT OF PEDIGREED POPULATIONS Albers K B M 2005 Demography of breeding programmes The Netherlands National Federation for Research in Zoological Gardens Allendorf F W 1986 Genetic drift and the loss of alleles versus heterozygosity Zoo Biology 5 181 190 Allendorf F W and G Luikart 2007 Conservation and the Genetics of Populations Blackwell Publishing Ltd Malden MA Asa C S K Traylor Holzer and R C Lacy 2011 Can conservation breeding programmes be improved by incorporating mate choice International Zoo Yearbook 45 203 212 Avila V J Fernandez H Quesada and A Caballero 2011 An experimental evaluation with Drosophila melanogaster of a novel dynamic system for the management of subdivided populations in conservation programs Heredity 106 765 774 Ballou J D 1983 Calculating inbreeding coefficients from pedigrees Pages 509 520 in Genetics and Conservation A Reference for Managing Wild Animal and Plant Populations C M Schonewald Cox S M Chambers B MacBryde and W L Thomas eds Benjamin Cummings Menlo Park California Ballou J D 1987 Small populations genetic diversity and captive carrying capacities Proceedings 1987 AAZPA Annual Conference 1987 33 47 Ballou J D 1999 MetaMK Metapopulation Mean Kinship Analysis Washington DC Smit

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