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Chapter 1 - Lincoln Park Zoo

1. First Location SONGKHLAZ Pedigree Unknown 100 Current Location SONGKHLAZ Dam Current Age Current Sex 785 850 3 734 Female Version 2 3 February 10 2012 1699 1660 3 496 Female SURABAYA SURABAYA 50 UNK 1865 2 825 Unknown PEACE RV PEACE RV 68 56 UNK 1946 2 7 1 Male PEACE RY PEACE RY 57 39 UNK 1556 2 7 1 Male PEACE RV PEACE RV 71 5 UNK UNK 2 768 Female PEACE RV PEACE RV 100 UNK 1851 2 757 Unknown PEACE RV PEACE RV 57 71 UNK UNK 2 727 Female CHIANGMAI CHIANGMAI 100 117 PopLink User s Manual This report lists all the living individuals with an UNK or MULT ancestors anywhere in their pedigree e g sire dam grandparent great grandparent etc Typically these individuals might not be used to make breeding pairs because of the unknowness in their pedigree and this report can be used to start to investigate which individuals may need further research on pedigree or analytical assumptions For more details see Chapter 9 on making analytical assumptions for unknown pedigree animals ANTECEDENT LIST REPORT and DIAGRAM The Antecedent report gives a list of all the ancestors for a given focal specimen Sunbittern 225 Antecedents Antecedents For 225 Antecedants Diagram Select Fitters No Filters Applied Ee Dam lec Birth Date GE Geheit Current Age Current Sex Se SE pace 6 WILD WILD 3 7 1 1960 Unknown Dead
2. Tala Gazlay NOTES Studbook Keeper Institution Lincoln Park Zoo Studbook Keeper Email Species Type Egg Laying Studbook Scope Incubation Period In Days Regional 28 Maximum Hatch Date Range For Clutch Mates Class In Days AVES 3 Order Currentness Date GRUIFORMES 3 22 2010 Family MM DD YYYY EN Scientific Name Studbook Description EURYPYGA HELIAS Common Name SUNBITTERN Cancel In the Studbook Overview Table you can edit any of the general fields associated with your studbook and add details about studbook wide conventions in the Species Notes field Note that changing the Species Type field i e Egg Laying or Live Bearing after studbook creation has studbook wide consequences When Species Type is switched the display language throughout PopLink e g column headers data labels on data entry forms etc will change to match the new Species Type Egg Laying or Live Bearing The language within all existing specimen records also updates as appropriate e g a Birth event is changed to a Hatch event and any future records conform to the current Species Type When edited the Species Type does not save a data history for the change or any of the subsequent language changes Version 2 3 February 10 2012 69 PopLink User s Manual OTHER GENERAL COMMENTS ON EDITING SPECIMENS DELETED DATA If for some reason you want to delete an entire specimen from your database you can do so using the menu op
3. Studbook Sire Dam Sex SE Notes ID Location HYP3 WILD WILD Female UNKNOWN ANALYTICAL DATA FOR TRUE SPECIMENS A Haei Table Field True Overlay Notes E 485 Master Dam UNK WILD Sire UNK WILD 467 Sex Sex Unknown Female Master Analytical Notes UNKs made WILD based on parsimonious assesment Events Transaction Code Hatch Transfer Location PITTS CA CHICAGOLP J Transaction Code Transfer Location SD VVAP Local ID 467 v 2 Importing Overlay Data Users have the option to import overlay data from a different version of the same studbook To use this option open the studbook without the overlay the one which you d like to import the overlay into Select File gt Import Overlay Data and a window is displayed listing the existing studbooks the Overlay column indicates whether those existing studbooks have one or more overlays attached By double clicking on the studbook with the desired overlay the overlay is imported into the studbook and can be opened by selecting View gt Overlays If you are trying to import an overlay that has the same title as an overlay currently in your studbook a window will pop up asking you to re name the imported overlay You should use caution when using this option PopLink does not check whether the studbooks are the same species or if any changes have been made to individuals that overlay data are being applied for in the newer version of the studbook As long as a studbook ID matches between the
4. Female Female f Male The left hand table lists all specimens in the studbook living and dead Clicking on their studbook ID will bring up their specimen report the right hand table lists all of the Related Specimen s that will be involved in the social event Move individuals back and forth between the tables by selecting them and using the Right and Left arrow buttons All of the columns in both tables are sortable by clicking on the column headers You can choose multiple individuals at once by holding the Shift key to select consecutively listed individuals or the Ctrl key to select non consecutively listed individuals Once all of the desired individuals are listed on the right press Ok and the Related Specimen field will be filled in with the Studbook ID Numbers selected NOTE All individuals entered in the studbook living or deceased are eligible for entry into Ze asocial event at any point in time There is no check to determine whether an individual was D alive during an event or whether the Related Specimens are in the same Location as the RA focal individual Be careful with which individuals you select to make sure that these data are entered accurately Version 2 3 February 10 2012 58 PopLink User s Manual 5 Comment The Comment field is important to documenting and understanding the details of a Social Event This field allows free text of unlimited length and can be used to document deta
5. Female TOLEDO S AMERICA 8 WILD WILD 3 7 1 1961 Unknown Dead Male CLEVELAND S AMERICA 10 WILD WILD 3 7 1 1964 Unknown Dead Male TOLEDO S AMERICA 16 WILD WILD 3 7 1 1964 Unknown Dead Female CLEVELAND S AMERICA 18 WILD WILD 2 7 1 1965 Unknown Dead Male SAN ANTON S AMERICA 29 WILD WILD 3 7 1 1962 Unknown Dead Male PITTS CA BAHBLANCA 30 WILD WILD 3 7 1 1962 Unknown Dead Female PITTS CA BAHBLANCA 44 8 16 2 2 7 1975 None Dead 14 483 Female SAN ANTON NZP WASH 66 10 6 2 3 26 1981 None LTF LTF Male CHICAGOLP CHICAGOLP 68 29 30 2 9 1 1982 None Dead 15 414 Female CHICAGOLP PITTS CA 88 18 44 1 11 11 1983 None Living 23 009 Male FRANKLINP SAN ANTON 158 66 68 1 10 24 1988 None Living 18 056 Female FRANKLINP CHICAGOLP In this case specimen 225 has 12 antecedents in the studbook The Generations Removed column lists how many generations a given specimen is from the focal individual Thus individuals with generations removed of 1 would be the specimen s parents 2 would be grandparents etc If you click on the Antecedents Diagram button next to the report or select the Antecedents Diagram report from the Pedigree Reports section you can get a quick visual diagram of the relationships of the individuals in the Antecedents table Sunbittern 225 Antecedents Sele Antecedents For 225 Export Select Highlight No Highlights Selected N BU Q e 8 e e ee e e e ee e e e ee ov wv e e wv a Cm et lw lt e e ee e
6. Version 2 3 February 10 2012 152 PopLink User s Manual Significance is determined by comparing whether the 84 confidence intervals Z 1 386 around each median overlap 84 Cls are used rather than 95 Cls because comparisons of overlapping Cls using 95 are extremely conservative Schenker and Gentleman 2001 Payton Greenstone and Schenker 2003 determined that 83 84 confidence intervals produce the appropriate type error rate of a 0 05 Note that these comparisons using the simplifying assumption that the standard errors of the two medians are approximately equal Payton et al 2003 this should be true for the majority of populations but results should be interpreted carefully if the standard errors of the medians have large differences If the 84 Cls overlapped and the null hypothesis that male and female median life expectancies are not different is supported the data are pooled for further analyses If the Cls do not overlap and the null hypothesis is rejected medians are reported for males and females separately Comparison of survival curves using the log rank test For the Analytical and Expert reports the log rank test is used to compare survival curves between data subsets In the Analytical tool male and female survival probabilities incorporating unknown sex individuals as described above are compared The log rank test is based on the number of observed and expected deaths at each survival interval Klein and
7. Current Previous EL O01 Studbook ID is temporary i 0 T1052 Version 2 3 February 10 2012 T PopLink User s Manual In the Main tab summary information about the studbook previous validation runs and the current run are displayed at the top of the report PopLink prioritizes errors based on their effect on demographic and genetic analyses e High Priority errors indicate that the record has major logical inconsistencies or is missing necessary data These errors may also have a large impact on genetic or demographic analyses e Medium Priority errors indicate possible logical inconsistencies or missing data but the data will likely have a less dramatic effect on genetic or demographic analyses e Low Priority errors indicate areas of records that should be reviewed or clarified but will be unlikely to have a large effect on analyses In the Detailed Error List by Studbook ID tab the report lists all studbook errors sorted by ascending Studbook ID number PopLink checks your studbook for 57 common errors Table 2 but the on screen validation report table will only display errors that occur in your studbook ranked by priority or by studbook ID The Help button next to each error gives details on how to resolve the error The Previous column displays the number of errors of each type you had on your last validation and the Current column displays the number of errors of each type you have in this run Note t
8. Databases File Edit Window Community Help folder in order to view the databases created by H gen Ouen D GG AJO pa PopLink 2 3 Object Explorer gt e i X a E E L LFAUST NB6730S SQLEXPRESS SQL Server 9 0 3042 LPZ_DOMAIN 4 View Tools as 2 Expand a particular database folder to display its database objects G Gay Databases 4 La System Databases 3 To display the list of tables in the database suis i D Database Diagrams expand the tables folder as shown in the figure to E Ga Tables the right The studbook s main data are stored in i System Tables dbo Master dbo Event dbo Reproductive 2 dbo DeletedEvent ES dbo DeletedHistory dbo Sex dbo SpecimenNote and dbo Overview EEN Other data tables store Deleted data Overlay E dbo DeletedReproductive data and data related to UDFs and User Defined SE dbo DeletedSpecimenNote Institutions H CH dbo DeletedUserDefinedFieldValue E ES dbo Event 4 In order to display the data contained in a table 3 3 dbo History All ES dbo Master right click on the table to display and select Open m eee oe Table ES dbo OverlayHistory 9 CH dbo OverlayInformation 9 CH dbo OverlayMaster 5 The window on the right of the Object Explorer will display all the data in the table in a grid like view as in the example below E dbo OverlayReproductive E dbo OverlaySex E dbo OverlaySpecimenNote E dbo OverlayUserDefine
9. Name Location d oun CHICAGOLP South Outdoor Yard OUT ICHICAGOLP North Outdoor Yard 1 our CHICAGOLP East Outdoor Yard MED CHICAGOLP Medical Holding QUAR CHICAGOLP Quarantine Holding Night House CHICAGOLP West Indoor Housing H d UI gt Enclosure Name Location Description OUT CHICAGOLP A South Outdoor Yard Add Delete Close ee sees The User Defined Enclosures pop up has a table listing all entered enclosures across all institutions Below that table is an area to edit add new or delete enclosures You can define enclosures from many different institutions or several enclosures at the same institution To track that the User Defined Enclosures table lists the Enclosure Name required Location required Description optional and Date Edited auto filled for each enclosure Since Enclosure Name and Location uniquely define each Enclosure you can have the same name for Enclosures existing in multiple locations i e there can be an Exhibit A at CHICAGOLP MYSTIC and CHICAGOBR without any conflict Creating New Enclosures To create a new Enclosure enter the Enclosure Name unlimited characters free text Location institutional mnemonic and Description free text Once the required fields are completed click Add and a new line will be added to the User Defined Enclosures table Editing Existing Enclosures To edit an existing enclosure highlight th
10. Unknown NULL NULL NULL 16 16 WILD WILD 1 1 1929 12 00 Unknown NULL NULL NULL 17 17 WILD WILD 1 1 1929 12 00 Unknown NULL NULL NULL 18 18 WILD WILD 1 1 1930 12 00 Unknown NULL NULL NULL 19 19 WILD WILD 1 1 1931 12 00 Unknown NULL NULL NULL 20 20 WILD WILD 1 1 1931 12 00 Unknown NULL NULL NULL 21 21 WILD WILD 1 1 1931 12 00 Unknown NULL NULL NULL 22 22 WILD WILD 1 1 1931 12 00 Unknown NULL NULL NULL 23 23 WILD WILD 1 1 1933 12 00 Unknown NULL NULL NULL 24 24 WILD WILD 1 1 1936 12 00 Unknown NULL NULL NULL 25 25 WILD WILD 1 1 1937 12 00 Month NULL NULL NULL Version 2 3 February 10 2012 155 PopLink User s Manual Custom Database Queries Custom database queries can be run to pull only database information that you re interested in This could also include joining multiple tables with a single query in order to pull data from multiple tables into one grid of information To run a custom query 1 Select a database from the expanded database list in Object Explorer 2 Click the New Query button usually above the Object Explorer window Lis Microsoft SQL Server Management Studio File Edit View Project Tools Window Community EL New Query iy fi Gi fa GS Go of bd a E Object Explorer ECK 2 E F RANDYMARSHSOLEXPRESS SQL Server 9 0 3042 E Databases Q System Databases Connect 3 A New Query Editor window will open in the right
11. without further analytical assumptions this type of parental notation is not useful for genetic analyses with the current software Under current software MULT parentage does not assign relationships between individual animals so that in the genetic analyses MULT parents provide the same amount of pedigree information as UNK parents i e no information Information from MULT notes and other research should be used to develop parentage assumption in the analytical overlay CONCEPTS BEHIND MAKING SOUND ANALYTICAL ASSUMPTIONS Assumptions for animals with unknown origin and or unknown parentage Although creating assumptions to replace unknown data is best done on a case by case basis there are some general principles that may apply to many populations The most common types of unknowns that affect genetic analyses are unknown parentage and unknown origin so assumptions for these will be addressed here More specific unknown data issues that do not fit into these categories can be discussed with your SPMAG PMC advisor There are two possible options for an animal of unknown origin and unknown parentage it is either related to individuals in the living population or it is unrelated and represents a unique genetic lineage To determine the likelihood of each option one must consider the details about the anima s record birthdate location of first event and weigh the completeness and accuracy of this data for each decision Use the outline bel
12. 2 Sire Dam Use the Sire Dam fields to enter parentage information either using the pull down list or typing directly into the field The Sire pull down list includes all males in the studbook as well as generics WILD UNK MULT If entering an option that is not in the list double check that the studbook ID is included in the studbook and is a Male The Dam field is identical to Sire except the pull down lists all females in the studbook IS j Guidelines Note 6 How to Enter Dam and Sire B Dam and Sire Known In the simplest case the dam and sire are known are already in the studbook and can be entered by typing in the correct studbook ID for each Wild Caught Specimens If a specimen is wild caught and nothing further is known about its ancestors then enter WILD for dam ID and WILD for sire ID If there is specific information about the parents in a managed wild population perhaps then wild caught specimens might be added to the studbook for completion of the pedigree Genetic analyses on the studbook assume that any Version 2 3 February 10 2012 36 PopLink User s Manual parent recorded as WILD is unique it is the parent of that specimen only and is unrelated to all specimens in the studbook except those who descend from that one offspring Dam and or Sire Are Known But Not In Studbook Things are more difficult if the parents are known but are not yet in the studbook This can happen if the parents are in the i
13. Filters can be used to search through studbook databases that are too large to search manually to ask specific questions that may be helpful in data cleanup data entry and studbook updates and in generally increasing your familiarity with your studbook dataset for example you can set filters to limit the data to all the living individuals in North America who have bred before or all the males at a particular institution born since 1980 Filtering is also an important way of restricting your data to an appropriate subset for demographic and genetic analysis PopLink has two methods for applying filters If you are looking at the studbook viewer or a report and would like to filter the data you can set filters for that individual screen report by clicking on the Select Filters button located directly above the data You can also set filters that will apply to all reports you run by going to the Reports drop down menu and selecting Default filters from the Options area Note that these Default filters will not apply to the studbook viewer only to any reports run subsequently It might be appropriate to set default filters if you have a subset that you consistently want to see e g living in North America or within AZA or filters can be set for an individual screen report if you frequently change the data subset you d like to see Choosing either filter option will open a pop up screen in which to select the desired filters Each filter fie
14. ceccecececeseeeeeeseseseeeeeeeeneneeeeenenaenenes 39 Guidelines Note 8 Estimated birth dates occ ceeeeceeceececeeceseeceeneceeneseeeeeneseees 40 De WC ANING RE 40 Guidelines Note 9 Rearing Type 41 6 INO 41 7 NOOS oasa E tes E EE 42 More Guidance on Entering New Specimens cccceececseeeeeeeeeeeaeeeeseeeeesaeeeesaees 42 Guidelines Note 10 How to Enter a Wild Born Gpecmen 42 Guidelines Note 11 How to Enter a Captive Born Specimen s nssennsnnnennnennnenns 43 Guidelines Note 12 How to Enter an Unknown Origin Gpecimen 43 ENTERING EDITING SEX DATA 44 Gilidelines Note EN 45 ENTERING EDITING REPRODUCTIVE DATA 45 ENTERING EDITING EVENT DATA 46 1 WSUS ACT OMG ee TEE 47 Guidelines Note 142 EVENS eieiei 47 2 PEO A OU EE 47 3 PS IR EE 48 Guidelines NOE 15 LOCA De eg de eee tt sg hl et he td tht pt tas 48 4 Transaction Date Transaction Date Estimate i ccccseeeeceseeeeeeveeeeeenes 48 Guidelines Note 16 Transaction Dates 48 D Klee 49 6 In Depth Lost to Follow Up Events 49 Guidelines Note 17 Lost to Folow Up 50 Version 2 3 February 10 2012 PopLink User s Manual 7 InDepth Death Events and Death Codes n0nnnnannnennnnnnnnennnennnnnrnnenrennnn 51 Tablets Sparks Death GOGCS E 51 ENTERING EDIMING SPECIMEN Cen 52 Table 2 The Following Note Types Are Included In The Drop Down Menu Or You Can Enter Your Own Type If Deered essisdsesc a a A 53 ENTERING EDITING UDF DAT
15. 00 00 000 Unknown NULL NULL NULL Wild Bom Parent NULL Not Reported AB121 E dbo OverlaySex a 3 3 WILD WILD 1898 01 01 00 00 00 000 Unknown NULL NULL NULL Wild Bom Parent NULL Not Reported 010FD Segoe ugin roca id 4 4 4 WILD WILD 1907 01 01 00 00 00 000 Unknown NULL NULL NULL Wild Bom Parent NULL Not Reported AC9EE a a e pie aSa 5 5 WILD WILD 1907 01 01 00 00 00 000 Unknown NULL NULL NULL Wild Bom Parent NULL Not Reported E3123 o E dbo Overview 6 6 6 WILD WILD 1913 01 01 00 00 00 000 Unknown NULL NULL NULL Wild Bom Parent NULL Not Reported 4215F a E dbo Reproductive 7 7 7 WILD WILD 1913 01 01 00 00 00 000 Unknown NULL NULL NULL Wild Bom Parent NULL Not Reported 7022 a E dbo Sex 8 8 8 WILD WILD 1916 01 01 00 00 00 000 Unknown NULL NULL NULL Wild Bom Parent NULL Not Reported 1391 e 9 9 9 WILD WILD 1920 01 01 00 00 00 000 Unknown NULL NULL NULL Wild Bom Parent NULL Not Reported 405DC ee pep 10 10 10 WILD WILD 1921 01 01 00 00 00 000 Unknown NULL NULL NULL Wild Bom Parent NULL Not Reported C3642 a 5 don Larsen ickNtekie A 11 WILD WILD 1921 01 01 00 00 00 000 Unknown NULL NULL NULL Wild Bom Parent NULL Not Reported 0D804 a E dbo UserDefinedinstitution 12 12 12 WILD WILD 1925 01 01 00 00 00 000 Unknown NULL NULL NULL Wild Bom Parent NULL Not Reported 9669EI y EN A Views lt gt Synonyms w lt m Query executed successfully LFAUST NB6730S SGLEXPRESS 9 0 SP2 LPZ_DOMAIN LFaust 53 ANTEATER 00 00 00 285 rows Ready Ln3 Co
16. 1399 Mail Code Mail Code Seles Export Phone 508 222 304 Phone 336 879 760 410 576 385 205 879 040 708 485 026 513 569 822 This report lists the historic and current institutions that any individuals in the studbook have been held at Current institutions include institutions that are currently housing living individuals Historical institutions include any institution that are not currently holding any individuals in the studbook but have done so in the past Both recognized mnemonics and user defined mnemonics are included in this report LOST TO FOLLOW UP REPORT E Sunbittern Lost To Follow Up Report Lost To Follow Up Report No Filters Applied Current Location ANTWERP Select Filters Studbook Current Transaction Date Est Transaction Date 6 19 1990 LTF CHICAGOLP d 25 1991 None 9 834 os Era Si eg 47 1999 aaa aa ae ee Tora 5 21 1997 Sch T o Stee D 5 29 1997 Ek ee T mee FRANCINE a 5 1 1975 hee Der S ier eg E ieee 5 11 9000 BEE Seege a Version 2 3 February 10 2012 115 PopLink User s Manual This report lists all the soecimens whose current final status is lost to follow up i e their last event is Go LTF as well as the location date and age when they went LTF You can use this report as a quick reference list for individuals whose final status you may want to research further LIFE TABLE REPORT Sunbi
17. 2 3 February 10 2012 85 PopLink User s Manual li Use the Delete button to delete a row of data that is in your PRIMARY database and not in the SECONDARY database note that there should be no data with this option based on 5a above iii Leave the data in the PRIMARY studbook as is by clicking Next to move onto the next specimen 7 Although the Database Comparison Tool will show you differences between the Studbook Overview data in your original and new databases it will not automatically update any fields in the Studbook Overview table using the Resolve Differences editing tool If there are changes you need to make edit the studbook overview for your original database by hand through the studbook viewer Although this process may be time consuming you should only need to import analytical data into your overlay once after this point you can create and maintain any new assumptions directly in the PopLink overlay If this process is confusing consult your SPMAG or PMC advisor as he she is the expert in working with analytical data and can assist you with your initial import CLEAN UP MNEMONICS TOOL After initial importation of your studbook there may be some mnemonics in your dataset that are unrecognized i e not in the standard ISIS library of institutional names and mnemonics In the Validate pull down menu selecting Clean Up Mnemonics will open a pop up that assists you in determining whether these mn
18. 21 1998 None Dead 0 03 Unknown SANTA ANA SANTA ANA 506 108 369 i 8 16 2002 None Living 4 246 Female SANTA ANA SANTA ANA 507 108 369 i 9 21 2002 None Living 4 148 Female SANTA ANA SANTA ANA S Sunbittern 369 Descendants Descendants For 369 Export Select Highlight hp Highlights Selected ES ain i 369 153 195 A TF D 446 ae 507 EE 108 369 ee S Leier 369 Dee oe 108 369 fo LIVING DESCENDANT LIST REPORT This Living Descendant List report gives a subset of only the living descendants for any specimen JE Sunbittern 369 Living Descendants Living Descendants For 369 Descendants Diagram Select Filters No Filters Applied Studbook Generations n Birth Date Current Current First ID Removed Birth Date Status Current Age Current Sex Location Location 108 369 1 6 19 1997 None Living 9 405 Male BALTIM AQ SANTA ANA 108 369 1 8 16 2002 None Living 4 246 Female SANTA ANA SANTA ANA 108 369 1 9 21 2002 None Living 4 148 Female SANTA ANA SANTA ANA Version 2 3 February 10 2012 119 PopLink User s Manual SOCIAL COMPATIBILITY REPORT Wed superbbirdofparadise Social Compatibility Report This matrix represents the outcome of the most recent interaction recorded between two individuals green reflects a positive interaction red reflects a negative interaction 0 blue reflects a neutral interaction and a blank cell signifies that no social interaction has been recorded between the
19. A Ok Cancel If User Defined Fields UDFs already exist in your database you can edit an existing specimen s values for the defined UDFs or enter values for a new specimen under the UDF tab in the specimen editor Select the desired UDF from the drop down menu on the left and the desired value for the UDF from the drop down menu on the right You can also type into the Value box if desired Version 2 3 February 10 2012 54 PopLink User s Manual Entering New UDFs for a Specimen If you would like to create a new UDF to be used for specimens throughout your studbook you can do so by going to the Edit drop down menu and selecting User Defined Columns which will pop up the following dialogue box User Defined Fields Use this tool to alter the UDFs for your studbook To adda new LDF type inte the fields below and click Add Da Description Date Edited U Studbook ID KEY Studboak Number 11 21 2006 SSPANIMAL Masterplan animals H 11 21 2006 SP SUBSPECIES Subspecies 11 21 2006 SP ST oan cS CONTACT Free Protected F F 11 21 2006 SP DOCUMENTED Documentation on file ON 11 21 2006 als w UDF Name Description SUBSPECIES Subspecies Add Delete Clase This table will display all of the existing UDFs in your studbook To create a new UDF name the field in the UDF Name field enter a description and click Add This new UDF column will then be added to all specimens in your studbook and you will
20. Concepton Date SEx Reproductive Events Local ID House Mame Addl Fields Notes UDF Sort By Filter By Do Not Include Estimated Canc Do Mot Include House Mame Mo Fields Selected No Motes Selected Mo LIDFs Selected Studbook ID hi No Filters Applied After choosing the Studbook Report Ok Cancel For the Sex Reproductive Events Local ID and House Name fields you have the option of including all events information or the current or last if the specimen is dead released LTF value for each of the fields In the Addl Fields Notes UDF boxes you can select specific specimen notes UDF fields and fields like rearing ownership and birth hatch type for display on the report You also have the option of sorting the report by Studbook ID birth date or current location You can select filters for the report by clicking on the Filter By button Selecting current for all the fields will produce a table with a single line per specimen e g E Sunbittern File Edit D o A Bal ve View Validate Reports Export Help STUDBOOK REPORT 158 154 231 543 Export Select Filters No Filters Applied H A PSE Hatch Date deiere Sire Dam Sex eege Event Location Local ID 1 7 1 1948 Unknown WILD WILD Female Uncontracept Death PHILADELP NHN e 7 1 1948 Unknown WILD WILD Female Uncontracept Death PHILADELP NHN 3 7 1 1954 Unknown WILD WILD Female Uncontracept
21. Do With MULT Parentage ccccccccceeecseeceeeceeeceeeeceeeseeeseueeseeenseesees 135 CONCEPTS BEHIND MAKING SOUND ANALYTICAL ASSUMPTIONS 135 Assumptions for animals with unknown origin and or unknown parentage 135 Evidence to consider when making assumptions about birth origin or parentage 135 Table 4 Basic assumptions about animals with UNK or MULT parentage and the consequences Of those ASSUMPTIONS ccccsecceeecceeeceeeceeeecseeceeeseueeneeesseeseeens 137 My POtneliCal ANGCSIONS ananasen tint eee ed end edad ei 137 Groups and black hole aesumpions ssns ierni E 137 Version 2 3 February 10 2012 PopLink User s Manual Genetic CONSEQUENCES Of ASSUMPTIONS ccccceecccceececeeececeeececseeeesseseesseeeeneaes 138 Table 5 Genetic consequences of two potential errors that can occur when animals with unknown ancestry are included or excluded in a breeding program Modified from Wilis o072 ea eE AE EAEE Ee 139 BIBLIOGRAPHY E 140 APPENDIX 1 POPLINK SURVIVAL TOOL cccssssccseseeseeneesenseesenneesenseeseneesees 141 INTRODUG MON ME 141 TERMINOLOGY EE 141 HOW TO RUN AN ANALYSIS IN THE SURVIVAL TOOL cceeeeeeeeeeeeee eee 142 GENERAL METHODOLOGY USED IN THE SURVIVAL TOOL eee 143 DESCRIPTIVE SURVIVAL STATISTICS REPOR Pirinioa auena 144 ANALYTICAL SURVIVAL SGSIATIISTIGGSRERORT 146 EXPERT SURVIVAL STATISTICS REPOR Tirran 147 COMPARAT
22. Double check PopLink s assumed dates of contraception for any contracepted neutered individuals See manual section on the Reproductive Data Table in Chapter 3 11 Double check whether any specimens have Sexing Notes in the Specimen Notes table see manual section on the Sex Data Table if they do edit soecimen s Sex Data Table data to reflect the sex change date see manual section on Entering Editing Sex Data in Chapter 4 12 Check the Studbook Overview Table see manual section on Studbook Overview in Chapter 3 and edit any fields that did not import appropriately some fields may have extra characters because of importation issues and sometimes data are not imported in for some fields because of the format of the SPARKS file that these data are based on 13 If you have an analytical xxstudbookname dataset discuss with your SPMAG or PMC advisor about appropriately importing those data see Chapter 9 14 Contact the studbook analyst at the Population Management Center for more assistance studbook lpzoo org Version 2 3 February 10 2012 oe 19 PopLink User s Manual Chapter 3 VIEWING AND MANAGING DATA IN POPLINK ORIENTATION Once a database has been created and opened PopLink will open its main program window important program functions can be found in the upper left hand corner Fel sunbittern Fle Edt View Overay Valldate Reports Export Help Dio e Sr PopLink displays the studbook name in the blue b
23. Ee eege 24 EY Aes HERR RE E 25 SPECIMEN NOTES DATA TABL Bircssuesssssssussoteusmnedensansadenmessedeumeuretanmenvedouseenessuaeaedes 26 USER DEFINED FIELDS DATA TABLE circ ccterigostcerbsestderidariderddenidecddastlenidesiosidatdacde 26 Guidelines Note 2 UDFS ccccccccccsecceceeeeeceeeeeceeceeseeeesseeeesseeesseeeesseseesseeeesaaeees 27 SOCIAL DATA TABLE ascona 27 ENCEOSURES DATA E 28 Version 2 3 February 10 2012 PopLink User s Manual MEDICAL DATA WA BL E 29 STUDBOOK OVERVIEW sess ecpeverccecevees toceveseecuuees tesnceeeunsuereesaeeeresuesaeeseenvesseeeaee 30 Guidelines INOTE 3 ee 31 OTHER DATA TABLES STORED IN ROBIN 31 1 HASHMI OLMIS EE 31 2 User Defined Institutions Table 31 3 Deleted Translated Data Table 31 4 User Defined Enclosures Data Table 31 Chapter 4 ENTERING and EDITING DATA IN POPLINK ccsecsssseeceeseeeeaes 32 OVER VEV eegen 32 BASIC CONCEPTS HOW TO ENTER DATES AND DATE ESTIMATES 32 Guidelines Note 4 How to Enter Transaction Uaies cc cccececceseeceseeseeeeseeeeees 32 HOw to Esimate REN 33 EDITING AN INDIVIDUAL SPECIMEN S DATA 34 ENTERING A NEW GSPRECHMEN 34 ENTERING EDITING MASTER DATA 35 1 SIMO OOK D KEE 35 Guidelines Note 5 Studbook Number 35 2 SEDAN a SnC rT OS NOt TRE aren ag cent nw ee eee gO Set OTT 36 Guidelines Note 6 How to Enter Dam and Ge 36 3 BS US kel 39 Guidelines Note 7 How to Enter Birth Tvpe 39 4 Birth Date Birth Date Estimate 2 0 0
24. Letters can be used to designate temporary studbook numbers regional studbooks should use T to designate temporary studbook numbers The T numbers should be unique and never reused even after they have been changed to a permanent number When T numbers are replaced with permanent numbers the former T number should always be entered into the Specimen Notes table as an Old Studbook Number note this is not done automatically by PopLink Leading zeros should not be used because much of the existing software e SPARKS ARKS and ISIS recognize 001 01 and 1 as different studbook IDs lf a regional studbook is started when an international studbook already exists the regional studbook should use the international studbook numbers While waiting for the international studbook keeper to assign permanent studbook numbers the regional studbook keeper should assign unique temporary i e T numbers When an international studbook is started after one or more regional studbooks have already been published a regional studbook keeper should continue with the existing regional numbering system The regional studbook keeper should cross reference the international studbook number with a Specimen Note If a regional or international studbook already exists the permanent studbook numbers must be retained Permanent studbook numbers should never be changed However in the future numbers should be as simple and sequential as possible
25. Moeschberger 1997 Skalski et al 2005 To conduct the test PopLink calculates Omale the sum of male deaths observed Oremale the sum of female deaths observed Emaie the sum of male deaths expected Fremale the sum of female deaths expected Where expected deaths are calculated using the number of individuals male or female at risk at a survival interval multiplied by the pooled mortality rate i e the mortality rate expected if there was no difference between male and female mortality rates These calculations exclude any extrapolated values that are used because the oldest individual in a data subset is censored e g values that are displayed in red at the end of the Kaplan Meier table Then ZooRisk calculates the log rank test statistic as 2 Ilan Enare Ornate E penare E E This is compared to the chi square distribution with 1 degree of freedom to test for significance male female REFERENCES Klein JP Moeschberger ML 1997 Survival Analysis Techniques for Censored and Truncated Data Springer New York 502 pages Payton ME Greenstone MH Schenker N 2003 Overlapping confidence intervals or standard error intervals What do they mean in terms of statistical significance Journal of Insect Science 3 34 1 6 Schenker N Gentleman JF 2001 On judging the significance of differences by examining the overlap between confidence intervals The American Statistician 55 3 182 186 Skalski JR Ryding KE
26. REPORT Species Type Egg Laying Incubation Period 28 Days Maximum Hatch Date Range For Clutch Mates 3 Days 45 reported dams with 132 123 174 429 offspring not including 33 offspring of UNK MULT dams 45 reported sires with 130 123 172 425 offspring All ages are at dam conception Select Filters ies applied to parents No Filters Applied Sire Age At First Estimated Conception Sire Age At All Estimated Conceptions Number Of Offspring Per Sire Clutch Size Ser 2 a e ID Offspring gt 123 32 66 25 18 24 29 EI o 23 108 22 65 22 5 22 The Reproductive Report can be exported using the Export button in the upper right corner When the Reproductive Report is exported the PopLink HTML export which resembles the SPARKS Reproduction Report differs from the PopLink Reproductive Report displayed on the screen in the following ways e Dam Age at First Birth is simplified into two tables that list 1 the 10 youngest dams at first reproduction by ascending age and 2 the 10 oldest dams at first reproduction by descending age Dams with UNK birthdate estimates are excluded from these tables Version 2 3 February 10 2012 113 PopLink User s Manual e Dam Age for All Births is simplified into one table that lists the 10 reproductive events single births or litters of offspring of the oldest females listed in descending order of age at reproduction Note that a female may be listed more than once in
27. STUDBOOK KEEPERS IMPORTING FOR THE FIRST TIME When you start using PopLink to maintain your studbook dataset there are a few important steps to ensure that your studbook is translated and maintained appropriately Later manual sections will describe in more detail how to carry out some of these steps 1 Discuss with your SPMAG or PMC advisor before you decide to maintain your database in PopLink 2 Run a SPARKS data validation before importation into PopLink If you have any non physical birth events coarse validation error T 22 in SPARKS you should fix this error in your SPARKS studbook before importation PopLink strips non physical events out of the event stream see page 25 for more details Import dataset into PopLink 4 Double check that you have the same number of historic and living specimens as in your SPARKS dataset Run clean up mnemonics see manual section in Chapter 6 6 Run clean up UDF casing see manual section in Chapter 6 this is optional it does not impact your data but is mostly for aesthetics Run delete empty UDF see manual section in Chapter 6 Run PopLink data validation and address errors as appropriate see manual section in Chapter 6 Look at the Specimen Notes table sort by name and look at the PopLink Assumptions notes these document any changes PopLink made on importation and can be a useful guide to the changes many of which are referred to in the rest of the items on this list 10
28. Sex Reproductive Events Specimen Notes User Defined Fields UDFs and the Studbook Overview In addition if you opted to show them using the Settings pop up you will also see the Social Enclosure and Medical tables These tables can be returned to from any other screen by selecting Translated Data from the View drop down menu or clicking on View Data shortcut button Version 2 3 February 10 2012 20 PopLink User s Manual Above the data PopLink reports 1 what filters are being applied to the data see Chapter 5 for more details on filters 2 the total numbers of individuals in the viewer denoted as Males Females Unknown Abnormals Total 3 the total number of current institutions for animals in the viewer 4 whether the table has been sorted from its original order 5 which specimens have been edited in the current session and 6 the currentness date for the studbook NOTE In any data table and many reports double clicking on a specimen s Studbook ID will pop up a specimen report which displays the entire record for that individual Edits can be made to a specimen s record by clicking on the Edit button directly to the a G y right of its Studbook ID button for more details see Chapter 4 A 7 e In most data tables including those displayed in reports you can right click anywhere in the table and select Export to Excel which will automatically pop up a spreadsheet version of the table
29. The section Background on Studbooks is adapted from information from the Studbook Guidelines and from the AZA s Studbook Factsheet AZA 2006 Version 2 3 February 10 2012 10 PopLink User s Manual The quality and consistency of data in studbooks are critical to the effectiveness of cooperative programs for species management Genetic and demographic recommendations for population management are only as good as the data upon which they are based thus inconsistencies and errors in studbooks can compromise the desired effects of even the best management plans What is a Studbook Keeper A studbook keeper is the individual who compiles and maintains a population s studbook researching and tracking the pedigree and demographic data on a group of animals usually a specific species in captivity Much of this job involves ferreting out the truth from multiple versions of a specimen s record and the studbook keeper is the only person focused on this pursuit from a population level focus rather than an institution level focus The studbook keeper is often also the species expert who knows the data history the history of a species in captivity the species biology in captivity and where possible in the wild and the necessary information for appropriate population management What Data Are Included in a Studbook A studbook tracks the movement of each specimen for its entire life starting with the date of capture
30. _ Verify that the correct sire has been identified Make sure that event i Sire s status is not Living on i dates are entered correctly for the sire and offspring Note that this i EH 24 estimated conception date error will be displayed if offspring were produced via artificial l insemination using sperm from a dead sire Note that this validation es check is only run for captive born origin individuals emma _ Make sure that the correct sire and dam are recorded Check locations 2 _ and event dates for sire and dam Verify that the offspring s birth date FH 25 i Sire and Dam locations differ i is entered correctly Note that this error will be displayed if offspring on estimated conception date were produced via artificial insemination using sperm from sire at _ another location Note that this validation check is only run for captive ee porn origin individuals l e Dame status is not Living on Verify that the correct dam has been identified Make sure that event EH 26 estimated conception date for dates are entered correctly for the dam and offspring Note that this Determine if any of these specimens are duplicate records If they are _ different specimens verify the Local IDs If they are the same EM 01 Local ID is not unique specimen consolidate the information into one record Include a note _ in the specimen s record explaining the Studbook ID change Verify the parental ID for the sp
31. after the date window and the date window is bracketed by known dates the individual is included e g KUKABKK or KABKU b If all unknown event dates are bracketed between two known event dates and within the date window the individual is included e g AKUKB c If the individual has an known event date that falls within the window and has no unknown event dates after that point the individual is included from that known event date until the window closes e g KAUKB individual s lifespan is only included from the last K to B Version 2 3 February 10 2012 150 PopLink User s Manual d If there is an unknown date within the window but there is a known date that falls within the window before the unknown date the individual will be censored at the last known date e g KAKUB individuals lifespan is only included from A to K e Inall other cases of unknown known event combinations the entire individual is excluded from the analysis 3 When individuals have events at unknown unrecognized institutions for which the event date is not UNK it will be treated as a transfer out of the geographic window e g the individual will be censored on that date If they have an event at an institution within the geographic window after that and before the window close date an additional survival record will be created for them in the table e g in this rare case an individual will have two separate survival records one from entry
32. and 3 months old then for the 6 7 age class that individual would be tallied as 3 12 0 25 c An individual that dies in a given age class is tallied as 1 for that age class regardless of how long it lived in the age class d Males are attributed to male risk tallies females to female risk tallies Unknown sex individuals are tallied 0 5 to male age class tallies and 0 5 to females 3 Calculate each age specific mortality rate as the number of deaths per age class number of individuals at risk for Q Fecundity Rate Calculation No individuals with unknown birthdates are used in fecundity rate calculations All birth date estimates are ignored the entered birth date is used in all calculations 1 Tally the number of births that occurred to parents in each age class during the demographic window a For captive births of known sex individuals with known age parents the birth is split between parents and assigned to the parent s age class e g 0 5 of the birth is assigned to the dame age class and 0 5 of the birth is assigned to the sire s age class b For captive births of unknown sex individuals with known age parents the birth is split between parents and assigned to the parent s age class e g 0 5 of the birth is assigned to the dame age class and 0 5 of the birth is assigned to the sire s age class c For captive births of known or unknown sex individuals with unknown parent s or parents with unknown age the birth is spli
33. as the middle of the estimated interval Le year or month For example a birth occurring sometime in 1988 should be entered as 1 July 1988 with a 1 Y in the Date Estimate field 1 January 1988 or another date should not be entered for a date estimated to calendar year Seasonal breeders should be estimated to the middle date of the breeding season When making date estimates the studbook keeper should use a scenario that is realistic with regard to the species biology and husbandry 5 Rearing In this field use the pull down menu to select whether the specimen was Hand Parent Foster Colony Group Peer Supplemental Unknown or Not Reared you should not enter free text into this field Version 2 3 February 10 2012 40 PopLink User s Manual D Guidelines Note 9 Rearing Type When relevant for the taxon rearing data should be collected for all specimens in the studbook Rearing data are often essential because whether a specimen was hand or parent reared may determine population and or specimen management strategies Life history characteristics socialization and reproduction are potentially influenced by the type of rearing For example a SPMAG advisor or species manager may want to correlate the effect of hand rearing on subsequent reproductive success Also in nonseasonal breeders birth intervals can decrease for dams with hand reared offspring so hand rearing information is a potentially important part of a
34. assumptions for already existing specimens This is accessed via the Overlay drop down menu and the Analytical Data for True Specimens option which displays a table of all the existing analytical data in your overlay Sunbittern Faust File Edit View Overlay Validate Reports Export Help D o A a al v Analytical Data For True Specimens This table displays which specimens have analytical assumptions indicated by text or in the fields To add analytical data for a specimen that is not in the table enter the studbook number in the box below and click Add To edit analytical data for a specimen in the table click on the edit button eo Edit Sire Dam Sex Geen TN Events Notes 485 WILD WILD 485 Add Delete You can edit analytical data for an already existing specimen in this table by clicking on the Edit button Typing a specimen number in to the box in the lower left of the screen and clicking Add will allow you to add analytical data for a specimen not already in the table an Analytical Data specimen editor will pop up Version 2 3 February 10 2012 129 PopLink User s Manual Edit Analytical Data 467 Master ex Reproductive Events Specimen Mates Event Date Est True Data Unknown 5 26 2000 None Analytical Changes Female g Event Date Add Hypothetical Delete Tex Female 10 10 2006 LFaust Notes Additonal Options Specimen R
35. be used to correctly sort events If events have the same transaction date e g a transfer and a death you can use the Move Up Down buttons to reorder them How to Estimate Death Dates Death dates should only be estimated with great caution Estimating death dates requires information that can generally fix the time and location of death Specimens that have disappeared from an institution should be listed as lost to follow up Under no circumstances should a specimen be assumed dead or assigned a death date just to remove it from reports or analyses If some evidence exists to support a specimen s death but the exact death date is not known death dates should be estimated to the midpoint of the estimated unit e g 1 July 19 for an estimate to calendar year see page 32 for more on date estimates When the birth date and death date for a specimen are estimated to the same calendar year the dates should be entered as splitting the year into thirds 2 May 19 and the death date should be entered as 1 September 19 _ Version 2 3 February 10 2012 48 PopLink User s Manual 5 Notes The Event data table has a Notes button at the bottom left of the data entry screen Clicking on this will open a text box which you can use to document any necessary facts about the fields you have just edited or entered such as sources discrepancies with institutional records etc When you enter notes closing the box saves the notes the
36. births are attributed to known parents with a known age 93 births are attributed to known parents with an unknown age 20 births are attributed to unknown parents This means that 25 of the total births are attributed to unknown parents or parents with unknown ages Would you like these births proportionally factored into the Fecundity Yes No Note that when you run a SPARKS MxQx report similar statistics pop up but the numbers of births and the s of unknown births may be different For this pop up PopLink counts the number of births that are attributed to unknown parents and to unknown age parents an individual with both parents unknown counts as 1 an individual with only 1 parent unknown counts at 0 5 The percentage is based on the percentage of total births that have some type of unknownness e g in this example 20 93 3324 20 93 The last line of text in the pop up asks Would you like these births attributed to Known parents with an unknown age or unknown parents proportionally factored into the fecundity For most species it is a good idea to say Yes to this question as it adds additional fecundity data to your dataset However if a large proportion of your data is attributed to unknown age or unknown parents then your fecundity data will not necessarily be a realistic representation of potential fecundity for your species and you and or your SPMAG or PMC advisor should use it with caution PM2000
37. complete physical barriers still in place Introduction physical restricted Also known as a protected contact introduction this step involves partially protected exposure to a new individual and can vary greatly from species to species Generally this involves giving the individuals being introduced access to the same space but with limited physical access to each other In aquatic species this can involve sharing the same water system but still separated by a physical barrier In terrestrial species this often involves introduction across a barrier that allows for some tactile auditory and or olfactory exposure Introduction full This final step to introduction removes all barriers between individuals and allows full physical and sensory contact Altercation This event type can occur during the introduction process or in an established pair or group of individuals This category is intended to capture major agonistic events this includes one individual being aggressive towards group mates or 2 sided altercations On a species by species Version 2 3 February 10 2012 56 PopLink User s Manual basis the severity or frequency of the events may be considered when deciding what to record as an Altercation Use the Comment field to provide details on the severity of the event Prosocial Intended to capture any important positive interaction indicating social compatibility Breeding Interaction This event t
38. complete statistical analysis software TERMINOLOGY Median life expectancy the age to which half the individuals in the analysis survive This can also be thought of as the typical life expectancy for a population or how long the typical individual in a population can be expected to live Median life expectancy is a standard measure used by human and animal demographers to compare life expectancies within and between populations or species For humans for example median life expectancy for individuals in the United States that survive to their first birthday is approximately 77 5 years The correct interpretation of these statistics is that if he she survives the first year of life the typical American will live to be around 77 that half of all Americans can be expected to die before they reach 77 and half will live longer than 77 Maximum longevity the age of the oldest observed individual for a population whether censored still living at the analysis end date transferred out of the window or lost to follow up LTF or dead It is not necessarily the biologically possible maximum age but only reflects the individuals included in the analysis For humans for example the maximum longevity documented is 122 years Lifespan the time from birth or hatching until death for an individual animal Species do not have lifespans Survivorship L the probability that a newborn individual will be alive at age x Survivo
39. darn conception Select Filters ies applied to parents No Filters Applied 7 Sire Age At First Estimated Conception This tab lists all sires with offspring their age at the time of their first offspring s estimated conception date their birth date and estimate and the ID of their first offspring by ascending order of sire s age at first birth You can view the Specimen Report of any sire by double clicking on the Studbook ID or of any offspring by clicking on the Offspring s ID Sunbittern Reproductive Report REPRODUCTIVE REPORT Export Species Type Egg Laying Incubation Period 28 Days Maximum Hatch Date Range For Clutch Mates 3 Days 45 reported dams with 132 123 174 429 offspring not including 33 offspring of UNK MULT dams 45 reported sires with 130 123 172 425 offspring All ages are at dam conception Select Filters Fiters applied to parents No Filters Applied Median age 3 8575 Mean age 4 57 Studbook ID Sire s Hatch Date Age At Estimated Conception 6 20 1994 None 102 1 489 8 2 1985 None 123 544 1 563 5 1 2004 None 546 511 1 752 6 16 2002 None Sai 441 178 6 23 1998 None 477 213 1 856 10 24 1991 None 277 211 2 012 8 14 1991 None 275 123 2 073 2 25 1987 None 162 1 ee ier Ais ee SS E EE t Version 2 3 February 10 2012 112 PopLink User s Manual 8 Sire Age at All Estimated Conceptions This tab lists all sires with offspring their age at the time of
40. date to censor date and a second from re entry date to close date This creation of a double record also occurs if an individual is transferred out of and back into the region and all institutions are known In addition individuals are excluded for specific analyses based on the starting age used in the analysis 1 Inthe Descriptive Survival Statistics Report the starting age day 365 individuals that die before their first birthday are excluded from the analysis 2 Inthe Analytical Survival Statistics Report the starting age day 0 all individuals are included in the analyses 3 Inthe Expert Survival Statistics Report the starting age is user defined and individuals that died at an age less than the starting age are excluded from the analyses Calculations of Kaplan Meier survival probabilities Using the individual records in the Included Individuals table survival statistics are calculated following methodology described in Klein and Moeschberger 1997 PopLink constructs the Kaplan Meier Statistics table with a survival probability L at every time t that an individual in the sample dies or is censored The resulting table has a row for each survival time and columns for age number of deaths observed the number at risk e g the number surviving to that age the mortality rate Qx for that age class of deaths divided by at risk and the Kaplan Meier estimate L L Ob ai Klein amp Moeschberger equation 4 6 1 mo
41. descendants social dominance genetic connections etc Consider the relative that incorporates the most lineages to cover all genetic bases e g if the potential parents are animals A and B where A is the parent of B choosing the offspring B as the assumed parent is more genetically conservative because it incorporates another lineage animal B s other parent The potential sires dams are not related or their relationships are not known a One potential sire dam produced far more living descendants Assume most prolific male female is the sire dam b Two potential sires dams produced an equivalent number of living descendants Make no assumptions or construct a hypothetical parent that is a genetic combination of the two potential parents Many potential sires dams produced or are assumed to have produced many living descendants Number of founders at institution not Known Make no assumptions or construct hypotheticals to make everyone at the institution related to some degree to avoid inbreeding Many potential sires dams produced many living descendants and number of founders at institution is known Construct hypothetical parents to make everyone at the institution equivalently related to some degree Determine hypotheticals and relationships using Equation 9 in Willis 2001 see Black Hole section below If you have any questions developing assumptions consult a SPMAG PMC advisor Always have other species
42. each offspring s estimated conception date their birth date and estimate and the ID of each of their offspring A sire with more than one offspring will be listed more than once You can view the Specimen Report of any sire by double clicking on the Studbook ID or any offspring by clicking on the Offspring s ID Sunbittern Reproductive Report REPRODUCTIVE REPORT Export Species Type Egg Laying Incubation Period 28 Days Maximum Hatch Date Range For Clutch Mates 3 Days 45 reported dams with 132 123 174 429 offspring not including 33 offspring of UNK MULT dams 45 reported sires with 130 123 172 425 offspring All ages are at darn conception Select Filters ies applied to parents No Filters Applied seeeeeeccsscnssceucnsecesscesssescessessusesssessesceeesenesseeusnssenssenssseseassesesessseesenseussenessneusnscaneseesssessssessesenes Sire s Hatch Offspring s Estimate ID Date ID 7 31 1976 309 52 17 922 7 31 1976 None 306 52 17 662 7 31 1976 None 300 52 17 213 7 31 1976 None 280 56 16 561 5 17 1978 None 372 56 16 55 5 17 1978 None 371 108 16 219 6 5 1986 None mz 108 16 12 6 5 1986 None 505 ba sce mania E ae S t 9 Number of Offspring Per Sire The Number of Offspring Per Sire tab lists the number of offspring born to each sire throughout the sire s life This list is ordered in descending number of offspring Sunbittern Reproductive Report REPRODUCTIVE
43. experts and a SPMAG PMC advisor review your assumptions before creating or using an overlay in any analyses Version 2 3 February 10 2012 136 PopLink User s Manual Table 4 Basic assumptions about animals with UNK or MULT parentage and the consequences of those assumptions Animal most likely is captive born and Sire UNK Dam UNK probably related to others in population captive born and probably Sire MULT Dam MULT Choose the most probable parents at the time and institution of animals origin to be the sire and dam Example Choose potential sire or dam with the most living descendants Sire HYP Dam HYP Unknown animal becomes a relative in an existing family Unknown animal becomes the offspring Genetic consequence for the individual and the population Animal has an estimated genetic value now Estimates of GD may increase or decrease depending on whether family was previously under or overrepresented Choosing the most probable parents may help avoid potential inbreeding Animal becomes valuable genetically unrelated to rest of hypothetical Estimates of GD increase founders of population Sire WILD Unknown animal Dam WILD becomes a new not really wild in this founder case just unrelated Animal becomes very valuable genetically Estimates of GD increase wild born and Sire WILD Unknown animal unrelated to Dam WILD becomes a new
44. export files are placed within the specific studbook database folder from which the export was created e g C Documents and Settings User Name My Documents PopLink PopLink Databases Studbook name When you open PM2000 you can navigate to this folder to import the data When a PM2000 project is created with data imported from PopLink there will be a pop up message that warns you that data validation has not been performed PM2000 does not recognize PopLink data validation even if validation has been run Click No to proceed without running data validation Version 2 3 February 10 2012 90 PopLink User s Manual PMx EXPORT PopLink will create standard PMx export files for your studbook database You can export from your true studbook e g Sunbittern or from your studbook with an analytical overlay applied e g Sunbittern Faust1 The database displayed at the top of the screen will indicate which database is being exported When you select the PMx export from the Export drop down menu this screen will be displayed Export to PMx Select Options for PMx Export Select Census Parameters Female Demographics File Name fSunbittern1 prn Male Demographics File Name Genetics Data File Name imSunbittern1 pm Sunbittern1 ped All Individuals Demographics File Name Genetics institution information will be Sunbitternidemog csv exported to location txt Click on the Select Filters buttons to set your demographic and g
45. facilitates tracking inter subspecific crosses Subspecific crosses should be included in the studbook because many populations are managed at the species level as genetic variation is lost through time more populations may be managed at this level If data for different subspecies are kept in separate databases it will not be possible to manage at the species level without reentering all of the data into a combined subspecies database 2 Geographic Scope AZA studbooks are approved at either the North American regional or international level An international studbook should include all soecimens of the species held in captivity anywhere in the world AZA regional studbooks must include specimens that are being or have been held in the North American region and all ancestors of those specimens regardless of whether they have ever been in the North American region It is important that every regional and every international studbook trace and record each specimen s pedigree back to wild caught specimens This means that a regional studbook keeper does not stop at the regional boundaries when collecting data The regional studbook keeper should enter all captive ancestors of specimens that have lived or are living in the region regardless of where those ancestors now live or have ever lived Complete pedigrees are essential to reliable genetic analyses incomplete pedigrees hamper genetic analyses and must be completed via hypothetical ancestors and
46. henna each Offspring s birth date is correct le f Assign a permanent Studbook ID before studbook publication or 5 Eo a eee Geptlation planning _ These Dam IDs should be entered as MULT e g MULT1 If two EL 02 Dam ID is MULT _ specimens have the same possible dams they should have the same TEE MULT for the Dam Specimens with MULT dam should have a Parent ID Assumptions EL 03 _ No parental ID assumptions _ note stating the Studbook IDs of the possible dams Specimens with _ recorded _ WILD dam should have a Parent ID Assumptions note stating the e Eeer These Sire IDs should be entered as MULT e g MULT1 If two EL 04 Sire ID is MULT _ specimens have the same possible sires they should have the same a Ee _ Specimens with MULT sire should have a Parent ID Assumptions note EL 05 _ No parental ID assumptions _ stating the Studbook IDs of the possible sires Specimens with WILD _ recorded _ sire should have a Parent ID Assumptions note stating the Studbook Geer ee EL 06 alc Birth Type incompatible See Manual page 36 for more assistance pong MEN first eent EE EL 07 Birth Date in the future Geer this specimen s history and correct the Birth Date and EL 08 Birth Date Estimate is invalid ia this specimen s history and correct the Birth Date and EL 09 Sex Date in the future GE this specimen s history and correct the Sex Date and EL 10 Sex Date Estimate is invalid Ge this specimen s history and correct t
47. information about how long the specimen lived there or where the specimen was transferred subsequently In this situation the specimen should be recorded as lost to follow up the day it was sent to the new location The second situation can occur when there is a failure to link a soecimen s move between two institutions To link the sending and receiving institutions must submit a record to ISIS and or the studbook keeper When the link is not made there are two records one that ends in lost to follow up on the day the specimen was sent and one that starts with unknown birth date parentage etc The third situation can occur when a specimen is lost within an institution s record system For example a specimen remains on the institution s inventory for an extended period after the specimen had actually been transferred or died Here the specimen should be recorded as lost to follow up around the last time the specimen was known to have been at the institution Thefts and escapes should be entered as lost to follow up with an explanatory note entered in the Specimen Notes It is not appropriate to enter thefts or escapes as transfers to unknown or fictional locations In particular soecimens should not be transferred to creative locations such as STOLEN THEFT or ESCAPED Version 2 3 February 10 2012 50 PopLink User s Manual 7 In Depth Death Events and Death Codes In SPARKS studbook keepers were given the option of adding death c
48. information bar at the top of the report iA NOTE When you import or open your dataset for the first time PopLink automatically filters ey the data in the main viewer to include only the L VING individuals This was done because it e d is a very common view and it significantly reduces the loading time of large studbooks with L d many dead individuals This filter can easily be changed or removed in either the default N filters pull down or in the individual filters pop up DESCRIPTIONS OF SPECIFIC FILTERS Institution The Institution tab allows you to filter in two ways 1 by geographic area which allows you to enter one or more individual institutional mnemonics e g CHICAGOLP SD WAP and or geographic mnemonics e g N AMERICA EUROPE FLORIDA or 2 by association using a FED file These filters will limit your selected report or dataset to individuals who have ever been at an institution that falls into the filter using the filter in combination with other filters can further limit the dataset e g setting Status Living would limit it to individuals who are currently living at an institution within the filter When filtering by geographic area you can enter multiple mnemonics identical to those mnemonics used in SPARKS use the FIND button to lookup mnemonics if you are uncertain about spelling Selected mnemonics will be listed in the geographic area filter box When you have selected all the desired mnemonics use the App
49. living during the fourth year age class During this period it is at risk for reproduction measured in the age specific fecundity Mx and death measured in the age specific mortality Qx Mx and Qx are the variables that constitute a life table the basis for population size projections Genetic and demographic analyses often use Filters see Chapter 5 that include a range of dates This is why entering transaction dates is very important for population demography If a transaction date is entered as unknown analytical software cannot assign that portion of a specimen s life to the life table Studbook keepers are commonly confronted with date information of low precision the exact date for an event transaction is uncertain Often the reporting institution can only establish that a specimen arrived or died during a period such as a month or year For some long lived species event dates may only be reported to the nearest decade or a broad range of years PopLink allows the studbook keeper to enter dates that are less precise than the exact date There are four different levels of date precision that require different standards for PopLink data entry EXACT DATES The most precise date precision level is obviously the exact date This is used when the specific date for a transaction is reported to the studbook keeper The precise date is entered in the Transaction Date field and NONE is entered in the Date Estimate field NEAREST UNIT ESTIMA
50. need to edit each specimen to give it a UDF value It is important to enter the UDF for each specimen you would like to select or filter using that UDF in the future Version 2 3 February 10 2012 55 PopLink User s Manual ENTERING EDITING SOCIAL DATA y Edit True Data 966 e eco C2 etm Master Sex Reproductive Events Specimen Notes UDFs Social Enclosures Medical Event Event Date Date Est Outcome Comment 8 31 2011 None Delete Event Type Event Date Event Date Estimate Introduction full 8 31 2011 None E MM DD YYYY Outcome Related Specimen 1246 1217 1208 977 Comment Mesh removed introduction went well with no agonistic Instructions behavior reported Apply Changes l Batch Input Re Ok Cancel Under the Social tab you may edit or delete pre existing Social events add new events and reorder events that occur on the same day in an animal s record 1 Event Type There are six options to choose from as Social Event Types What constitutes each event type is likely species or even institution specific so the studbook keeper should carefully define what types of events fit into each category and document them in Species Notes Specifics could also be detailed in the Comment field associated with the note Introduction visual Often the first step in an introduction process is to give individuals only visual access to one another with
51. next social group change end date Version 2 3 February 10 2012 123 PopLink User s Manual Male Female Unknown The number of individuals of each sex residing in each enclosure during the date span Enclosure Size The number of individuals in the enclosure Group Male Female Age Range at Start End The sex specific age ranges of all animals in the social group at the start and end dates Born Hatched Died In Out These fields list the Studbook IDs of animals that enter exit an enclosure or social group via being born hatched into the enclosure being transferred in or out of the enclosure or dying Even if an individual is entered into exited out of an enclosure on their birth death date there must be a comment added by PopLink to count as a born died in an enclosure Enclosure Members The Studbook IDs of all the individuals in the enclosure NOTE If you select a During date span that starts before or ends after there are any p individuals in the enclosure voure showing there will still be a row in the report but there TE ho will be O individuals listed in the row If the As Of filter is applied the born hatched died in and out columns will be empty as this reflects the enclosure group composition p on a single day When Show All Enclosures filters are applied note that if there s an e j enclosure listed in the User Defined Enclosures tab that has never had any animals in it i it will still show u
52. not include two events previously tracked in SPARKS ownership nonphysical transactions and Management Group In Out these transactions were excluded because they are irregularly used difficult to maintain and not recommended for tracking in the Studbook Guidelines If a specific specimen had these types of transactions upon studbook importation the transactions are stripped out of the events data table When this occurs PopLink automatically makes note of it for that soecimen in the Specimen Notes Table Note that although not recommended for tracking in the guidelines PopLink does allow you to enter current owner see page 41 if necessary in your studbook Note that when data are filtered see Chapter 5 if a specimen fits into a given filter e g living in between 1 1 1990 and 1 1 2006 all of that specimen s events will be displayed in this table even if the events occurred outside the filter date range Version 2 3 February 10 2012 25 PopLink User s Manual SPECIMEN NOTES DATA TABLE Sunbittern File Edit view Validate Reports Export Help D S 4 all Select Filters As of 9 21 2009 AND Status Living Totals 59 47 12 118 at 51 Insttutions Mo Sort Order Applied No Edits Currentness Date 6 2 2001 eee Edit Description Comment Note Date User Edited 2 56 Breeder Num NZP3 9 24 1987 SPARKS 122 a Breeder Num DENVER 10 3 9 1988 SPARKS 122 Egg Lay Date infertle eggs 12 5 1992 SPAR
53. of entry are referred to as left truncated data Individuals exit the analysis by 1 dying within the analysis window 2 being transferred out of the geographic window before the end date or 3 being alive in the geographic window on the end date the last two types of exit are referred to as right censored data If an individual enters exits and reenters the analysis window e g if the window is North America and an animal is transferred to Europe and then back to North America the individual will have multiple survival records in the Included Individuals table The number of specimens affected by this is reported in the Advanced tab of each report if this number is very high or a substantial proportion of your specimens this violates one of the assumptions of survival analysis and you may want to read further on how it impacts your analytical results Klein and Moeschberger 1997 Inclusion of an individual is straightforward if all of its event dates are known and the institutions at which it was housed are recognized and fall within the geographic window If an individual has estimated event dates e g date estimator D M Y etc date estimators are ignored and the actual event date is used in analyses When individuals have unknown event dates date estimator U and or have an event at an unrecognized location all or a portion of their life may be excluded from the analyses 1 All individuals with unknown birthdates birthd
54. of the unpedigreed individuals For example if A 7 28 and there are 10 unpedigreed animals coming out of the black hole the estimated relatedness would be closest to first cousins Once a relationship among the unpedigreed animals has been estimated then a hypothetical pedigree can be constructed to create that relationship in the analytical studbook Miau 2353 25 2 553 2 581 2 667 018755 PGP LA 4571 48 4923 5 333 um Hatsis s5 6154 see 6957 8 mm tap a se 16 126 s2 be None n a P parent GP grandparent Some group living populations are too complicated for the black hole solution presented here If a population has always lived in groups and parentage has never been tracked and will continue to not be tracked in the future then a non pedigree based genetic management strategy will be required A pure group management strategy does not require parentage assumptions and is beyond the scope and purpose of this monograph Genetic consequences of assumptions The dangers of unknown or missing data in a pedigree lie in the risk of either underestimating or overestimating gene diversity Estimations of gene diversity will differ based on whether unknown ancestry animals are included or excluded from the breeding population Table 4 Animals with unknown pedigrees could be potential new founders or descendants of lineages not yet represented in the population If we completely exclude such unknow
55. on Create My New Database Now to proceed a NOTE If a studbook is currently in use in SPARKS an error message will pop up and R IJ PopLink cannot open the studbook Closing your studbook in SPARKS will allow PopLink to vif create your database TA N Version 2 3 February 10 2012 15 PopLink User s Manual At this point your newly created studbook database will be opened in the Studbook Viewer in the main PopLink window This studbook database is referred to as translated data it is based on the SPARKS dataset but includes modifications and special features unique to PopLink These modifications will be pointed out throughout the manual When you create a PopLink database from a SPARKS studbook a zipped copy of your SPARKS studbook is archived in the PopLink database folder e g in C Documents and Settings User Name My Documents PopLink PopLink Databases PopLink Studbook Name SPARKS backup SPARKS Studbook Name This folder the SPARKS studbook name folder can be unzipped and moved into your SPARKS directory if you wish to view the original studbook in SPARKS OPENING AN EXISTING POPLINK DATABASE Any studbooks that you ve previously created in PopLink are accessible through the Open an Existing Database dialogue box that pops up at the PopLink startup This window includes a list of all databases that have been created to date To select a database highlight it and then select Open Database at the bottom If you wis
56. or assumptions that are often little more than good guesses see page 125 on assumptions in studbooks Version 2 3 February 10 2012 11 PopLink User s Manual 3 Temporal Scope Zoo records for some species go back into the last century Although many specimens do not reproduce successfully when a population is first initiated in captivity their records may be valuable for demographic analyses e age specific mortality Thus every effort should be made to include as many specimens as possible Historic records may be added gradually with successive versions of the entire historical studbook Studbook keepers should not limit temporal scope because of perceived or real changes in husbandry or management No specimen should be excluded from a studbook because it lived under outmoded management and husbandry regimes There are a few cases in which entering all specimens within the scope given above may be unrealistic and represent an inordinate amount of work without a corresponding benefit These cases are rare and should be determined by the appropriate Taxon Advisory Group TAG in consultation with the SPMAG advisor and the studbook keeper 4 Institutional Scope Any and all institutions that can be verified as holding or having held specimens should be included in the studbook Inclusion of data from an institution should not be contingent on whether it is a member or affiliate of AZA if an institution provides data to the stud
57. or date of birth if born in captivity and ending with the date of death or the date at which the specimen leaves the region or managed population or is lost to follow up Every event and location should be included in the database In addition to the date and location of each event the studbook should also include information on parentage sex origin cause of death if Known house name transponder number band or tattoo number and any other information that will assist in tracking individual specimens Studbooks are limited in scope in several ways 1 Taxonomic Scope In general the taxonomic scope of a studbook is a species genus or a group of closely related species or genera with relatively small population sizes Interspecific hybrids are usually not listed in the studbooks for either species If the combined living and historical population size is large separate databases can be created for each subspecies However if all subspecies are included in a single database each subspecies can be identified with a User Defined field UDF see page 54 on how to use and create UDFs Because a UDF allows sorting and selection of specimens for reports and analyses in most cases it is best to create a single database for all subspecies For species with uncertain taxonomy i e they might change as more information is accumulated a single database will accommodate addition or loss of taxa Combining all subspecies in a single database also
58. or leave an enclosure With an As of date the report shows group composition in an enclosure as of that date All Enclosures as of 9 15 7011 Enclosure Name Location Start Date End Date Male Female Unkne Outdoor1 HOUSTON 9 15 2011 9 15 2011 0 0 0 aes muon A CC a pa gone oe a aa a sn aoe a e Geesen eer SEN emeng EE a EE ee aa vn ovina Cen TTT TTT TTT TTT TTT When the Enclosure Report is selected from the Report menu a pop up gives you the option to view the history of an enclosure during a span of time or as of a certain date It also allows you to specify which enclosure you are interested in either Show All or select a particular enclosure from the drop down Once the appropriate information is entered the Enclosure Report is generated see above right Select Date During ASOf 9 15 2011 9 15 2011 Select Endosure In the report each row is a record of each social group within an enclosure Each new row indicates that an animal has moved in out of that enclosure thus changing the group composition in the enclosure The report s columns are Enclosure Name Name of the Enclosure as defined in the User Defined Enclosures list Location The institutional mnemonic describing the site of an Enclosure as defined in the User Defined Enclosures list Start End Date The date an individual entered the focal enclosure or that the group situation changed start date until the day before the
59. others in the founder population Animal becomes very valuable genetically Estimates of GD increase Sire UNK Dam UNK Sire WILD Dam WILD Unknown animal Animals become valuable becomes the offspring genetically of wild founders Estimates of GD increase wild born and related to others in the population sibs or clutch mates Hypothetical ancestors Hypothetical ancestors can be created to deal with unknown or uncertain portions of an animal s pedigree These hypothetical specimens are often created to be the ancestors of living specimens that Originated at the same institution but whose parents cannot be identified Create records for each hypothetical parent as needed and give these hypothetical parents WILD WILD parents of their own Capture locations and dates for the hypothetical animals can be based on assumptions or conventions e g average age at which animals of this species are caught or logical age of hypothetical animal at the time of the real animal s birth date and are not relevant if the analytical studbook is only used for genetic and not demographic analyses The true studbook should be used for demographic analyses Groups and black hole assumptions Pedigree assumptions for group living animals are more complicated than the cases previously mentioned A simple and resolvable case of group unknownness is a group of presumably interrelated animals at a single institution where parentage wa
60. recognized institution Unknown Sex Although there is no automatic report to generate a list of unknown sex individuals these can be easily identified by filtering your dataset to Status Living using the appropriate geographic or FED file filters and sorting the Master Data Table by the Current Sex column These individuals can also be seen in the Age Pyramid report See page 103 for more details on that report In addition running Data Validation can indicate data errors that may cause data to be interpreted as UNKNOWN such as blank sire or dam fields or sire or dam fields filled with studbook IDs that are not found in the dataset How to Determine if UNKNOWN Parentage is Really Unknowable 1 Focus on animals with living descendants in the managed population Unknowns that are dead LTF released with no living descendants in the population are not important for genetic management though they may be relevant to other analyses Begin by investigating the animals with the most impact on the population i e those with the most living descendants in the managed population The Specimens with UNK MULT Parentage and Descendants report is sorted by this criterion so start at the top of the list and work down Research the unknown parents of animals by contacting each institution that reported having the specific animal in question The first holding institution may be the best source of information about the origin of an animal a
61. row and click Add Analytical Changes and then add the data by filling in the appropriate Version 2 3 February 10 2012 130 PopLink User s Manual fields If you needed to create a third transfer for this specimen you would click Add Hypothetical and could then transfer the specimen to SD WAP Edit Analytical Data 467 DAR Master Sex Reproductive Events Specimen Notes Transaction Location Local ID Transaction Transaction Code Date Date Eer True Data Hatch PITTS CA 5508 5 26 2000 Mone True Data Transfer VOKATYH 9 1 2000 Unknown Add Analytical Changes Add Hypothetical Master Sex Reproductive Events Specimen Notes Transaction estore ees lana Transaction Transaction Code Date Date Est True Data Hatch PITTS CA 5508 5 26 2000 None Analytical Changes Transfer CHICAGOLP True Data Transter VORKATY H 9 1 2000 Unknown Transfer SD WAP 467 11 17 2006 None 2 Making hypothetical specimens to create pedigree relationships for already existing specimens If you have an existing specimen with UNK pedigree and need to create hypothetical pedigree relationships for that soecimen see the second half of this chapter for more details on how to do that you could create an entirely hypothetical specimen in your analytical overlay In the Overlay drop down menu select Hypothetical Specimen which will display a table of all existing hypothetical specimens you can use the Add box in
62. that are frequent across multiple individuals use a standard description for these in at least part of the comment box e g LETHARGY NOTED at the beginning of the note this will allow you to easily search for individuals with that note using the Filter options see chapter 5 or sort the Medical Notes table to quickly see affected individuals Record these conventions in the Studbook Overview s Notes Section 5 Medical Alert Note Category Type Medical Alert v Temporary v Start Date 10 4 2011 Observer tg pregnancy due date estimated 4 1 2012 Instructions Apply Changes The Medical Alert category is intended to alert staff to a health condition allergy or disease that is important in providing appropriate care for an individual In this category the Type and Start Date are the only required fields but the details on the alert should be provided in a Comment The Type field provides three options Permanent Temporary or Other The Type assigned to a Medical Alert describes how long it is applicable e g arthritis would be considered a Permanent condition pregnancy would be considered Temporary and Other would be defined as an unknown period of time or as an intermittent condition Use the Comment text box to detail the type of condition and if or when it ends Version 2 3 February 10 2012 66 PopLink User s Manual 6 Medical Procedure Note Category Type Medical Procedure D
63. the Databases folder to include all your studbook databases opened with PopLink 2 3 2 Right click on the database you want to delete and click Delete 3 The Delete Object dialog box will open Click Ok and it will delete the database SS Script UN Help Object Explorer IX Li ect 2 Object to be deleted Connect S Fl Object Type Owner Status Message E L RANDYMARSH SOLEXPRESS SQL Server 9 0 3042 C Database aA Lg Databases ES System Databases m 17 _03GORILLA New Database New Query Script Database as Connection Tasks Server RANDYMARSH SQLEXPRESS Reports RR Rb RR amp Connection CLARITYINTERNAL ngudnritz View connection properties i Progress FH bal p Delete Rename Ready v Delete backup and restore history information for databases Close existing connections Refresh Properties Replication Management AHHH Version 2 3 February 10 2012 157
64. the event s Transaction Code Research this specimen s history and enter the Transaction Date and i Estimate 2 RER EE EE EE CEECECEOT CEC CCCECECLEEECUCCOEECECECECC CCC CEE CE CEO CECE EO EECECEE EE EOL ECE SECEDE CE CEE COC ECE CUCCCCECECECCOCUCCCCCCECEECECCCECLECCCEECECECECT EE ECCECCEY LCE EE EECECEE EE CELE CEE EE EC TEL CEC EEC ECCT CCE EC CCE EEETCEETTECECETTECECCETCECECCLECECECTECCCEEEETECTCCE TEPC TECCEEEEELEEETTETCETTETEEEEPTCCLCLETCCEEEELECECCEEPEETT ELT CLEPPE CETTE CT CCETTETTCLETE CEC ETLEECEECECTECTCECTETECT ETT CETTE LECECTETCCTEEPCEEE CTCL ECTETCUTCLELTECETET TERETE TTCECEETTCEC EC ETT i Research this specimen s history and correct the Transaction Date and i eer cme ea et ee Eetmate S _ This check is only performed for live bearing species The dam s _ location does not match the offspring s location on the offspring s birth EH 22 i Birth location conflicts with i date Verify that the offspring s dam birth date and birth location are i dam s location all entered correctly Check the dam s transfer records and locations i _ Note that this validation check is only run for captive born origin rr e AdividualS _ Dam s status is not Living on _ Verify that the correct dam has been identified Make sure that event EH 23 _ birth date for live bearing _ dates are entered correctly for the dam and offspring Note that this aaa Species only __validation check is only run for captive born origin individuals
65. the left hand corner to add individuals to this table just as in the Analytical Data table above Sunbittern Faust1 File Edit View Overlay Validate Reports Export Help D o Z a se Hypothetical Specimens This table displays specimens that are entirely hypothetical To add an entirely hypothetical specimen that is not in the table enter a new hypothetical studbook number HYP in the box below and click Add To edit the hypothetical specimen in the table click on the edit button eee Edit Sire Dam Sex Soccer Events Notes HYP3 WILD WILD ik ik HOOK By convention hypothetical specimens have unknown birth and other event dates so they are not used for demographic analyses and go LTF so they are not counted as living individuals within the studbook Version 2 3 February 10 2012 131 PopLink User s Manual Generating Overlay Reports You can see a quick summary of all analytical changes in your overlay by running an Overlay Report in the Overlay drop down menu The Overlay report is split into two tables 1 Hypothetical Specimens and 2 Analytical Data for True Specimens For each specimen with analytical data this report summarizes what data table and data field the change was made in what the True data are and what the Overlay data are E Sunbittern Faust File Edit View Overlay Validate Reports Export Help D o A al al kl OVERLAY REPORT Export HYPOTHETICAL SPECIMENS
66. two studbooks PopLink will apply overlay data even if it is nonsensical PopLink will drop analytical data for true specimens not tied to a studbook ID in the current studbook Version 2 3 February 10 2012 132 PopLink User s Manual Batch editing in an Overlay By selecting the Overlay gt Batch Edits menu item PopLink allows you to rapidly assign analytical parentage to specimens with unknown or MULT parentage Use the Overlay Sire and Overlay Dam columns to easily assign alternate parents Use the Notes box to document background on your assumptions Caution You should not use this window to edit true sire or dam information that should be done following the procedures in Chapter 4 AfricanSpoonbill Overlay Overlay Batch Edit DER SPECIMENS WITH UNK MULT PARENTAGE AND DESCENDANTS acz UNK Notes UNK UNK Notes LINK LINK Notes UNK UNE hd Notes LINK Lk Notes LINK LINK Notes LINK UNK h Notes LINK Lk Motes LINK 103 h Notes UNK UNE h Notes LINK Lk Notes LINK LINK h Notes Lk UNK S Notes K Cancel keck keck ZS TD bech bech keck md OT Ga ho ill VW a Where to Document Assumptions should always be carefully documented so that any future studbook keeper or data analyst who uses your studbook will understand what information is true and what information is assumed fiction Notes on assumptions why and how the assumptions were made shou
67. way to create analytical assumptions is to utilize SPARK plug software Thompson and Willis 2001 SPARK plug can import a SPARKS database apply previous and or new assumptions create a record of all assumptions that can be used from year to year and create a new analytical SPARKS database while leaving the true studbook unaltered this analytical database can be used to export data to PM2000 ZooRisk or PMx ISIS is working to develop a new centralized real time online record keeping system that will accept institutional records and eliminate the need to maintain studbook datasets in SPARKS the Zoological Information Management System ZIMS is expected to be released in 2010 PopLink is designed to complement ZIMS Creation of PopLink was motivated to 1 replace SPARK plug folding the program functions into a program written in modern computer language and thereby eliminating many bugs and run errors with changing operating systems 2 enhance the ability of studbook keepers and population biologists to maintain and edit data used in population management 3 give users new tools to clean up and make analytical changes to studbook datasets PopLink was designed to give users the ability to Version 2 3 February 10 2012 12 PopLink User s Manual e Import a species studbook from SPARKS and manage its data within PopLink e Assist with data management and manipulation fixing errors appropriately documenting studbook changes p
68. window end date 1722 2008 Institution window All Institutions Additional filters No Filters Applied of years in window Zi Total population size on end date 312 DATASET INFORMATION Total number of specimens of males of females of other sex specimens of wild origin specimens of captive origin specimens of unknown origin specimens s The Advanced tab lists all Expert Survival Statistics results in an easy to extract via copy and paste into Excel format See the Comparative Advanced Results section for more details on results included in this tab The Included Individuals table shows the partial or full lifespans of each individual included in the survival analyses see the Detailed Methodology section on page 150 for more on how this table is constructed The Expert Survival Statistics Report excludes any individuals whose age at death is less than the start age entered at the beginning of the analysis The Data Quality table which reports data quality test results for the Pooled Male and Female datasets The Kaplan Meier Survival Statistics Table and the Kaplan Meier Graph reports and displays the survival rates by age at death note that the start age entered at the beginning of the analysis is the day in which the Kaplan Meier Survival Probability is 1 0 If this table is blank it means that data quality tests were failed Version 2 3 February 10 2012 148 PopLink User s Manual COMPARA
69. with a large portion of the population it can be a wealth of useful information This module is optional and can be hidden using the Settings option from the Edit menu Information in the Enclosure Data Table includes the Enclosure Name which is pre defined using the User Defined Enclosures functionality see page 60 Enter dates Exit dates Date Estimates and any desired Comments on the specifics of the move into the enclosure Each individual can have multiple Enclosure records over its lifetime Version 2 3 February 10 2012 28 PopLink User s Manual MEDICAL DATA TABLE SSS we m Vebdete Reports Export Help fie Lat View Ojo Zia olz Select Fiters As of 9 15 2011 AND Status Living Totals 15 12 1 28 at 7 Institutions No Sort Order Acched Edges 55 Cusrertness Date 1 19 2010 Master Sex Reprockactive Everts Specmen Notes UDFs Socal Enclosures Medcal Sudbook Overview Studbook e Unit of ID Edit Lategeg Type Value Measureme Start SEN End Date Observer i Comment ss Medcal Proce Visual Assess L 7 7205 tg post hatch exam seems heakhy and alert eating wel 55 _ Weir 50 Grands WI A to post hatch wieght San Ge eng Se Carhopuinon fe 14 2006 to Sigk wheezing with mouth open 55 Ckagnostics Cuture 14 2005 tg diosca swab culture 24hrs results postive for Strept e 55 Medication Antibiotic 25 M oandi 5 15 2005 Sa tg admin every 2 hours
70. with meals for 2 weeks see KG 55 dt Geran a Mead S Z 2005 tg Where Gone cating more repni and more kee 55 E Weitz la 75 Gasdai SI to wot gan normal SS a Medcaton VYocane 25 M oants 6 17 2009 tg Brd flu vcore geg The Medical Data Table is new in PopLink 2 2 2 3 and allows you to track important medical records for individuals This is not meant to be a replacement for a full medical record keeping system e g MedARKs but can be a useful tool in tracking major events in an animal s health as well as medical information relevant to population management and daily care Having this type of information easily accessible can facilitate timely answers for health related questions and medical emergencies This module is optional and can be hidden using the Settings option from the Edit menu Information in the Medical Data Table is organized by Category which describes one of eight different kinds of medical notes Clinical Sign Diagnostics Disease Status General Medical Note Medical Alert Medical Procedure Medication and Weight The Type field gives more details specific to each Category The Value Unit of Measurement and End Date only appears for specific note Categories and only appear as options when appropriate The Start Date Observer and Comment appear for every note Category and Type Each individual can have multiple Medical records over its lifetime Version 2 3 February 10 2012 29 PopLink User
71. xv wv e sw wv e e ev wv le lw n ee e e e ee o ev wv wv sw wv e e e wv wv a ee e e e e e e e ev e e DN ENEE EEGENEN e CEET ENEE EEN EENEG NEE NENNEN NEEN a NEE EENEG ENEE ENEE NEE E ENEE E EEN a a O S ee ica e te Ae 18 44 ee WE ee EE 225 EE Es ne Ee Version 2 3 February 10 2012 118 PopLink User s Manual In this diagram males are blue females are pink and unknown abnormal sexes are grey Each individual s parents are listed below their ID in parentheses sire dam Double clicking on a box will open up that individual s specimen report Using the hand tool in the upper right hand corner of the report allows you to grab and move the diagram Selecting the magnifying class tool in the upper right hand corner allows you to zoom in on an area of the diagram by left clicking your mouse and zoom out on an area by right clicking your mouse DESCENDANT LIST REPORT and DIAGRAM This report is identical to the Antecedents List report except that it focuses on all the Descendants for a focal individual Sunbittern 369 Descendants Descendants For 369 Descendants Diagram Select Filters No Filters Applied Studbook Sire Dam Generations Birth Date Birth Date Current EE ENEE Current First ID Removed Est Status Location Location 446 108 369 1 6 19 1997 None Living 9 405 Male BALTIM AQ SANTA ANA 454 108 369 i 4 9 1998 None Dead 0 079 Male SANTA ANA SANTA ANA 459 ue 369 1 9
72. year because it could not have happened eg the birth could only have happened before the transfer on 12 August In these situations the Version 2 3 February 10 2012 33 PopLink User s Manual estimate must be adjusted to the midpoint of the uncertain period e g the midpoint of 1 January to 12 August in the current example EDITING AN INDIVIDUAL SPECIMEN S DATA To edit an existing specimen use the Edit button located to the right of a specimen s Studbook ID or the Edit Specimen option in the Edit pull down menu Using either of these options will result in a specimen editor pop up window with tabs for editing relevant information from each data table For existing specimens the existing data will be displayed at the top of the screen and the editable fields will be displayed below When editing an existing specimen s record you may be adding entirely new data e g new events or editing data that already exists in the record PopLink uses variable histories to track the editing history on a field that is changed that is after editing data that already exists you will still be able to see the previous values for that field For example in the specimen below the sire was changed from specimen 8 to WILD using the specimen editor When looking at that specimen in the studbook viewer the Sire field will have a drop down arrow which when clicked on will display a table with all the old values for the field
73. you re viewing Sorting Data in the Studbook Viewer can be sorted by clicking on the column headers at the top of any field By default entries are displayed in ascending numerical order of Studbook ID Clicking once on a column header will sort the entries in ascending order clicking again will sort the entries in descending order Fields with both numeric and alphabetic entries will sort numeric entries before alphabetic entries When a field is selected for sorting its button will have an arrow indicating whether the sorting is in ascending or descending order Note that data can only be sorted by one column at a time no double sorting occurs DATA TABLES MASTER DATA TABLE Sunbittern Fie Edit view Validate Reports Export Help Dlelelalalzl Select Filters As of 9 21 2009 AND Status Living Totals 59 47 12 118 at 51 Insttutions Ho Sort Order Applied Mo Edits Currentness Date 6 2 2001 Master Reproductive Sex Events Specimen Notes LIDFs Studbook Overview Studbook Current Current Hatcl ID Edit Current Sex Location Local ID Sire Dam Hatch Date 8 8 Mae CLEVELAND 920543 WILD WILD 7A196861 Unkno 29 a hale PITTS CA 132 WILD WILD F f1 1962 L ko 52 Male DENVER 960096 1i 12 7 31 1976 None 56 a Male NZP AWASH 205380 zi 16 of 17 1978 None 66 Male CHICAGOLP B138 10 6 3 26 1981 None 76 Female MILWAUKEE B3688 242 246 1 5 1982 None Ti w Male SAN ANTON 960334 8 16 S
74. you should not change the extensions pm for demography files ped for genetics files The Demography filters chosen will limit your studbook database to a specific population that will be used to calculate life table parameters M Q Lx etc The chosen filters will be displayed in the filter box you should change the default filters to your desired demographic window which is generally the period of modern management for your species You can also set other filters in addition to date and geographic windows The Genetic filters are used to create the list of individuals that will be considered living individuals in your current population PopLink exports this list of specimens and their pedigree information to PM2000 If desired you can change the default filters using the Select Filters button PopLink can also export census data for graphing in PM2000 to do this run the Census Report with desired filters before exporting from this screen Version 2 3 February 10 2012 89 PopLink User s Manual When you click OK on the export screen you may see a pop up message about demography calculations for specimens with unknown data specimens born to unknown parents or to unknown age parents Please note that the Following numbers are calculated slightly differently than SPARES For each offspring each parent gets 0 5 of the birth attributed to him her There are 445 total births in the demographic window 332
75. 0 12 2001 None CHICAGOLP 21309 10 20 2004 None User Defined Fields flighted color phase Tag Band RED GREEN BLUE 10 20 z Transponder ID T8743 10 20 2 The Specimen Report is a one page version of all the studbook data for a particular specimen Clicking on the Go buttons next to Sire and Dam will pop up their individual specimen reports Clicking on the Show Descendants button will display a list of all descendants for the selected individual If the individual is dead the information displayed in the top left reflects that soecimen s last data e g last institution age at death last sex If still living these data reflect the specimen s current status Version 2 3 February 10 2012 98 PopLink User s Manual Main Tab Main Secondary Sex Reproductive Sex Event Date Event Date Est Reproductive Event Date Event 1 Female 12 20 2000 None 1 Not Contracepted 12 20 2000 None Events _ Transaction Code Location Local ID Transaction Date Transaction Date Est 1 Hatch CHICAGOBR 397 12 20 2000 None 2 Transfer LOWRY 204765 10 12 2001 None 3 Transfer CHICAGOLP 21309 10 20 2004 None Specimen Notes User Defined Fields Description Comment Note flighted_ color phase 1 Tag Band RED GREEN BLUE 10 20 2 1 lyes brown 2 Transponder ID 18743 10 20 2 tt 5 The Main tab in the Specimen Report displays the Sex Reproductive Events Specimen Notes and User D
76. 0 AND EndDate 1 31 2009 PopLink Version 2 2 I REPORT OVERVIEW Ju Based on this analysis if a SAVAGE TAMARIN survives to its first birthday its median life expectancy is 4 5 years 76 3 of SAVAGE TAMARIN survive to theirfirst birthday The maximum longevity observed for SAVAGE TAMARIN is 28 0 years Please see the body of the report for more details BACKGROUND ON ANALYSES These analyses were conducted using animals that lived during the period 31 January 1980 to 31 January 2009 at all institutions in the studbook The analyses mainly focus on survival statistics from 1 year e g excluding any individuals that did not survive past their first birthday These statistics most accurately reflect typical survival Jl for animals which can be seen on exhibit in Zoos and aquariums This report summarizes survival records of individuals housed at zoological facilities for a specific geographic range and time period these records trace an individual s i history from birth or entry into the population to death exit out of the population or the end of the time period As such this history only reflects standard practices including management husbandry and acquisition disposition practices for the specified time period and geographic range Thus the report contents should be viewed with some caution as they may not reflect current zoo and aquarium management techniques or practices Moreover for long lived species these paramete
77. 000 1 000 last 5 years 3 0 104 1 000 1 000 2003 53 44 10 0 107 1 000 1 000 last 6 years 3 0 104 1 000 1 000 2002 53 44 10 0 107 1 029 1 004 last 7 years 3 0 104 1 030 1 004 2001 51 43 10 0 104 1 020 1 006 last 8 years 3 0 101 1 020 1 006 The Census Report lists the number of living individuals in your selected geographic region or the entire studbook by sex and birth type The annual growth rate lambda is calculated for the total population as Annual lambda Population size last year Population size this year Lambda gt 1 0 indicates a growing population Lambda lt 1 0 indicates a declining population and Lambda 1 0 indicates a stable population Lambdas can fluctuate widely from year to year so a more appropriate average growth rate is the geometric mean lambda which is also displayed in the table for different time frames For example in this population over the past 5 years the total population has been growing on average at 1 014 or 1 4 per year Note that the left hand lambdas are growth rates for the Total population size and the right hand lambdas are growth rates for the captive born portion of the population These statistics are calculated for the captive born portion of the population because population managers are frequently interested in the population s rate of growth from captive reproduction Note that for the results on origin the numbers of individuals should not be interpreted as the numbers of i
78. 117 ANTECEDENT LIST REPORT and DIAGRAM usekinsenna n a 118 DESCENDANT LIST REPORT and DIAGRAM ssssssssessssnnesnnssenensnresrrrnsrrrsrrrerrresnn 119 LIVING DESCENDANT LIST REP OR WV RE 119 SOCIAL COMPATIBILITY REPORT 3454epicetecctests ospeetectiusi teaser a 120 FOCAL INDIVIDUAL ENCLOSURE REPORT naassonssnssnnsennssrenssnrenrnnrsnrsnrresrersnnrennne 122 ENCLOSURE REPOR WE 123 MEDICAENOTE SREPOR RE 124 Chapter 9 ANALYTICAL DATA AND OVERLAYS IN POPLINK 0000 125 BACKGROUND CONGEP RE 125 True Data VSi AMANV UCM Dala E 125 Guidelines Note 18 Assumptions ANd Conventions ssssssssersesrresrreerrrrsrrenn 125 Why Do We Need Analytical Data 126 ANALY TIGALIDATALINGPOPRLING ans A A 127 Background and ISON EE 127 How to Create and Document Analytical Assumptions in Pop mk 128 POPLINK OVERLAYS General Features 128 Editing Analytical Data and Creating Hypothetical Specimens cceeeeeees 129 1 Making analytical assumptions for already existing specimens sesssensennnn 129 2 Making hypothetical specimens to create pedigree relationships for already EXISTING SPECIMENS EE 131 Generating Overlay REDONIS E 132 Importing Overlay RE 132 ES AUG Ih SAILING NYA seat VOY aka et a ahead eae 133 WNETE e HR ee ln EE 133 How to Identify When Analytical Assumptions are Necessary cceeeeeeeeees 133 How to Determine if UNKNOWN Parentage is Really Unknowable aannnannnaan 134 What to
79. 5 None 368 10 6 1995 None 30 16 9 14 1986 None 116 9 30 1986 None 87 18 4 25 1991 None 204 5 13 1991 None 443 18 5 24 2002 None 516 6 11 2002 None 30 19 9 30 1986 None 118 10 19 1986 None 195 19 1 5 1998 None 438 1 24 1998 None 168 20 1 23 1995 None 350 2 12 1995 None an 20 ink 15 7 1986 None an7 15 27 1986 None 3 Birth Seasonality The Birth Seasonality tab lists both the number and percentage of litters that occur in each month Only litters with birth date estimates of None Day or Month are displayed Sunbittern Reproductive Report REPRODUCTIVE REPORT Export Species Type Egg Laying Incubation Period 28 Days Maximum Hatch Date Range For Clutch Mates 3 Days 45 reported dams with 132 123 174 429 offspring not including 33 offspring of UNK MULT dams 45 reported sires with 130 123 172 425 offspring All ages are at darn conception Select Filters ies applied to parents No Filters Applied Sire Age At First Estimated Conception Sire Age At All Estimated Conceptions Number Of Offspring Per Sire Month bierg Percentage January 23 5 52 February 30 7 19 March 33 7 91 April 41 9 83 May 26 13 43 June 39 9 35 July 48 11 51 August 42 10 07 September 42 10 07 October 27 6 47 November 16 3 84 December 20 4 80 Total 417 99 99 Version 2 3 February 10 2012 110 PopLink User s Manual d Dam Age at First Birth This tab lists all dams with offspring their age at the time of their fir
80. 976 None FRANKLINP YULEE YULEE 21 59 1068 1447 H 1261 UNK UNK Day i Dead 7 19 1953 JAKARTA MUNICH MUNICH 19 80 sajd lt WJ SPECIMENS WITH MULT PARENTAGE Studbook Current Current AZA Location Living Desc BULVERDE 0 Second Location GULF BREZ Birth Date Est None First Location YULEE Birth Date 6 17 1997 LTF 1024 MULT 1 This report lists all individuals living and dead that have an UNK or MULT sire or dam or have one or both parents that are not in the studbook The table displays the number of living descendants the individual has as well as the number of living descendants in AZA institutions based on the AZA FED file On the right hand side of the table the individual specimen numbers of the living descendants are listed and can be used to open up specimen reports for the descendent This report can be used to help investigate which individuals may need further research on pedigree or analytical assumptions clean up can be prioritized based on the number of living descendants e g individuals who may currently be eligible for breeding For more details see Chapter 9 on making analytical assumptions for unknown pedigree animals LIVING SPECIMENS WITH UNK MULT IN PEDIGREE REPORT File Edit View olesia al ve Validate Reports Export Help Living Specimens With UNK MULT In Pedigree No Filters Applied Select Filters Studbook ID
81. 984 None 102 Ge Hot Contrace 8 2 1985 None 108 a Not Contrace 6 5 1986 None The Reproductive Data table can be used to track changes in the reproductive status of individual specimens It displays all reproductive status events of each specimen including the Reproductive Status the Event Date for when reproductive status was assessed and the Event Date Estimate PopLink recognizes three different possibilities for Reproductive status Not Contracepted Contracepted and Neutered Sterile Like Sex reproductive status is treated as an event stream rather than a constant state in PopLink because it can change throughout a specimen s life Most specimens will be entered with a not contracepted status at birth but throughout their lives could be placed on and removed from contraception multiple times Version 2 3 February 10 2012 23 PopLink User s Manual Upon importation from SPARKS PopLink creates a reproductive event for each individual as of their birthdate Reproductive Status Not Contracepted Event date specimen birthdate Event Date Estimate any birthdate estimate that may exist Any additional changes in Reproductive Status are taken from the SPARKS sex field For example if a SPARKS specimen was designated as a contracepted or neutered male or female PopLink creates a second Reproductive Event changing the Reproductive Status as of the date the studbook was imported into PopLink e g Reproductive Status Contra
82. A EG 54 Editing Existing UDES for a SOCCIMG ME 54 Entering New UDFS for a SPECIMEN cceecccceececeeeeeceeeeesseeeesaeeeeseeeeesaaeeesaaeeeeas 55 SON SEA Le SE BR CEET BR RRE 56 igs ECT I e vastusesucwencutetunnaunadutsiusaiuesanteiciauepsiusoautedanewnacuimausesusnauneiuepaneiusdausaiul 56 2 Event Date amp Event Date Estimate ccccccccecccscceeeceeeseeeseeeceeeseeeeeeeaees 57 GE euer EE 57 A Related SPCCIME Ms ege 58 SCH ei in EE 59 Deleting Individuals From Events And Deleting Entire Events c eeceeeeee 59 More Ideas On How To Use The Social Datafable cc eecccecceceeceeeeeeeeeenees 59 ENTERING EDITING ENCLOSURES DATA EE 60 User Defined RS ee GE 60 Hate ENCO ie 60 EANO EXISUNG ae EE 60 Bizet 60 Creating IEMCIOSUKG FE CORCS EE 62 Auto Adding Birth and Death Information from Events Record ccscceeeeeeees 63 ENTERING EDITING MEDICAL EECHER 64 Ps eeler Ee TE 64 IAGO SUGCS egerne Nee 65 3 DISCASE Eege 65 4 General Medical Note cccccsecccesceceeeeceseetececeeeeteu cess eeseueeteneessneesaeetas 66 5 Medical AlE ssena nso ed ee eee ered Meveaea awed Seems 66 6 Medical PROC COUN Coa ict ait ht see ist at iat at tt eet ait ites aes death 67 Ce ele EE 67 Oe WV GIOIA EE 68 ENTERING EDITING DATA IN THE STUDBOOK OVERVIEW TABLE 69 OTHER GENERAL COMMENTS ON EDITING SPECIMENS ce eeceeeeeeeees 70 DELE TEO DATA enero er ine tne ne ee eee ae 70 RE
83. AGOL NHN 4 13 15 248 8 17 19 None 66 68 Unkno 8 17 198 None Uncont 8 17 198 None Hatch CHICAGOL B8590 8 17 15 Death CHICAGOL NHN 9 22 1 249 9 29 19 None 66 68 Unkno 9 29 198 None Uncont 9 29 198 None Hatch CHICAGOB 89035 SESCH lt gt Note that if you select to include UDFs in your studbook report and you have specimens that have multiple UDF rows you will receive this error when running the report PL_test An unhandled exception has occurred in your application If you click Continue the application will ignore this error and attempt to continue lf you click Quit the application will be shut down immediately Specified argument was out of the range of valid values Parameter name rowlndex This is the result of a data error in your studbook each specimen should only have a single UDF row in the UDF table see manual section on Entering Editing UDF data for more information You can clean up specimens that happen to have an extra blank UDF row using the Validate gt Delete Empty UDF Rows If the error persists you will need to identify which specimens have two or more UDF rows and consolidate their UDF records into a single UDF row Version 2 3 February 10 2012 101 PopLink User s Manual SUMMARY COUNTS REPORT Sunbittern Summary Counts Report SUMMARY COUNTS REPORT Percentages may not add to 100 due to rounding Select Filters No Filters Applied Name Count Percent Description SEX REPR
84. Age Report Unknown Age Report 24 29 43 96 unknown age specimens out of 158 154 231 543 total specimens Select Filters No Filters Applied Studbook Minimum py ee Current First Current Tee pee Hatch Date ID Age Location Location Status Est 1 7 151 Female PHILADELP S AMERICA Dead 7 1 1948 Unknown 2 29 142 Female PHILADELP S AMERICA Dead 7 1 1948 Unknown 3 7 047 Female PHILADELP S AMERICA Dead 7 1 1954 Unknown 4 31 493 Male PHILADELP S AMERICA Dead 7 1 1954 Unknown 5 45 875 Male SANDIEGOZ S AMERICA Dead 7 1 1951 Unknown 6 25 112 Female TOLEDO S AMERICA Dead 7 1 1960 Unknown 7 119 581 Male DENVER S AMERICA Dead 7 1 1962 Unknown This report lists all individuals in your population with birth date estimates of UNKNOWN Because their birth date is unknown these individuals cannot be assigned to an age class and cannot be used in any of your demographic analyses mortality and fecundity rate calculations The minimum age in this report is the time from the specimen s first known transaction date to the present or the specimen s death Because it is based on the first known transaction date you know that the specimen in question is at least that old you can use this information to make an analytical assumption about the specimen s age if you would like the specimen included in your demographic analyses See Chapter 9 for more details on making analytical assumptions AGE OUTLIERS REPORT LI Sunbittern Age
85. Although the Database Comparison Tool will show you differences between the Studbook Overview data in your primary and secondary databases it will not automatically update any fields in the Studbook Overview table using the Resolve Differences editing tool If there are changes you need to make edit the studbook overview for your primary database by hand through the studbook viewer After you ve made any edits or changes you d like you can re run the Database Comparison Tool to double check that you have resolved everything you wish to change Importing analytical assumptions into PopLink from an analytical studbook option 2 above ci Create PopLink databases for the true studbook and the analytical xxspecies studbook you want to compare via the Open Create New dialogue box when the program is launched or the File drop down menu Open your true studbook database and open or create the overlay for your true studbook which will store all of your analytical data see page 128 for details Open the overlay through the Overlay drop down menu you will then see your database name displayed as studbook overlay e g LSNGuenon Faust1 Under the File pull down menu select Compare Databases and when prompted select the PopLink dataset you created for your analytical SPARKS studbook A screen like this will be displayed Version 2 3 February 10 2012 84 PopLink User s Manual LSNGuenon Faust File Edit View O
86. DUCTION Kee EC 9 How to Use This Manual 9 Beieleit llelde te RE 9 SV SIS m FROGUING Ta CN 10 ceting Ve 0 WA POO NN EEN 10 BACKGROUND ON STUDBOOKS G zerresi E 10 Whati aeo DOOK aasan NAN 10 de e ee 10 What lS a Studbook Keeper siissiissiesdeiieninn 11 What Data Are Included in a Studbook 00 0 0 ecccccecceeceeeeeeeeeeseeeeesseeeeseeeeesaeeeeeas 11 FISTOLY OF SIUGD OOK SOWA Ganse 12 Chapter 2 GETTING STARTED IN POPLINK 0 cccccssssseesseeseeseesseseeeneessoeaes 14 INSTALLA TON OF POP EC EE 14 Software requirements for running Pop mk cece cccceeeeeeeeeeeeeeeesaeeeesaeeeesaeess 14 TO WASTAUIN A OD A csr a a E 14 Optional program functions for power users sssnsennsennsennsnrrsrrnerrsrrrsnrrerererennee gt 14 LAUNCHING POPEINK USER LOGIN EE 15 CREATING A NEW POPLINK DATADAGE 15 OPENING AN EXISTING POPLINK DATADAGE 16 SEH Dee 17 PopLink Files and Databases Storage Location 17 Changing File Storage Location E 17 MOGUIE WISIDINEY EE 18 SAVING BACKING UP MOVING DELETING AND ACCESSING POPLINK BY AVR EE 19 CHECKLIST FOR STUDBOOK KEEPERS IMPORTING FOR THE FIRST TIME 19 Chapter 3 VIEWING AND MANAGING DATA IN POPLINK ccsccssssseeseeees 20 ORIENTATION Soe 20 ST WDBOOK EA 20 ELA ANE TEE E T E E AE E E E EO a ee E eines 21 BEE 21 MASTER DATA RE 21 EStimMaled Maler del RE 22 PA Cunen EE 22 STEE 22 Guidelines Note 1 OWNerSNiD eresuresirenun a a 22 REPRODUCTIVE DAT A T Eeer eer aere 23 SEX
87. Death PHILADELP NHN 4 7 1 1954 Unknown WILD WILD Male Uncontracept Death PHILADELP NHN l kel sees e e ss ATi Ta ArT rs RAs ee ee se Ae Fa ott MAK IDS TIAN ASW Ku II ra UE Fa 4 Version 2 3 February 10 2012 100 PopLink User s Manual Selecting all will display a table more like the traditional SPARKS Studbook Report with all events listed all Sex Events listed etc Sees Sunbittern File Edit View Dlcleiglelzz Validate Reports Export Help STUDBOOK REPORT 159 155 227 541 Export Select Filters No Filters Applied a B Sire Dam Sex Date Ge Geer Date Gees Event Location pte Da Death AMSTERDA NHN 9 24 1 243 7 1 1956 Unknown WILD WILD Mae 7 1 1965 Unknown Unecont 7 1 1965 Unknown Wild Capture S AMERICA NONE 7 1 19 Transfer CHASE FRAK Transfer FORTWOR 66010 1 18 15 Death FORTWOR NHN 10 3 15 244 7 1 1956 Unknown WILD WILD Mae 7 1 1969 Unknown Uncont 7 1 1969 Unknown Wild Capture S AMERICA NONE 1 1 197 Transfer CHASE _ MAg Transfer DENYER 10429 9 1 19 Death DENVER NHN 12 4 15 245 1 6 197 None 243 12 Unkno 1 6 1972 None Uneont 1 6 1972 None Hatch FORTWOR 72010 1 6 197 Death FORTWOR NHN 1 6 197 246 7 1 197 Unknown WILD WILD Female 7 1 1975 Unknown Uncont 7 1 1975 Unknown Wild Capture S AMERICA NONE 1 1 197 Transfer WASSENAA ss 1f1 197 Transfer AMSTERDA B7601 8 26 15 247 3 31 19 None 66 68 Unkno 3 31 198 None Uncont 3 31 198 None Hatch CHICAGOL B8416 3 31 15 Death CHIC
88. E None The Master data table summarizes basic information on the specimens in the studbook database Some of the fields in this table Studbook ID Sire Dam Birth Type Birth Date Birth Date Estimate Rearing Owner are based on data entered directly into the Master table all other fields Estimated Conception Date Current Sex Current Reproductive Current Status Current Location Current Age Current Age Est Current House Name Current Local ID and Current Enclosure are based on data entered into the Version 2 3 February 10 2012 21 PopLink User s Manual eight other tables in the translated data tables in your PopLink dataset e g the Sex table the Events table and the Enclosures table if it is shown etc For more details on how to enter data into specific Master Data Table fields see page 35 A few notes on how PopLink fills in specific fields Estimated Conception Date PopLink reports the estimated conception date in order to aid population managers in their attempt to identify unknown parentage The conception date of a given specimen is calculated based on that specimen s birthdate and estimate and the gestation period entered during studbook creation which can be edited in the Studbook Overview Data Table This date should be viewed as a general guide of when conception may have taken place and will have the same date estimator i e the same level of certainty as the birthdate s estimator All Curre
89. GIONAL Studbook Studbook data current as of 11 30 2006 Compiled by Steve Foss ross lpzo0 org PopLink Studbook filename ChimpUb PopLink User Who Exported Report Lisa Faust Date of Esport 1 22 2008 No Filters Applied PopLink Version 1 25 REPORT SETTINGS Date Window 22 January 1980 to 22 January 2008 Institution Filter All Institutions Additional Filters Hone SUMMARY OF ANALYSES DATASET DESCRIPTION see the Included Individuals tab for a complete list of individuals in the analysis Pooled Data H of individuals with partial or full lifespans in analysis 25 of als Which had died by 22 January 2008 analysis end datel267 AE 1 The Summary tab displays the Analytical Survival Statistics Report including statistical results data quality results and summary details of the most important survival parameters To produce the results included in these tabs PopLink a Calculates Kaplan Meier survival probabilities and median life expectancies for the Pooled data and the Male and Female subsets as described in the Detailed Methodology section b Determines whether Pooled Male and Female subsets pass the five data quality tests and produces the Data Quality Table Version 2 3 February 10 2012 146 PopLink User s Manual c Compares the survival curves of males and females using the log rank test see Detailed Methodology If the curves are not significantly different the data are pooled for further anal
90. HYP002 etc c Any differences between the databases displayed in the bottom table should be only analytical changes modifying unknown parentage unknown dates unknown sexes etc 5 When you click on the Resolve differences button any changes you make will be considered analytical changes and will be added to your overlay not your true data If there are any data differences that appear to be due to updates to the true data e g you should have updated them in your main primary database not in the xxstudbook database you should not resolve these differences with this tool as they will be put into your overlay 6 To resolve differences between the two datasets start with the Master table Note that you can also simply use the database comparison tool to generate a list of potential changes and then edit existing specimens enter new specimens by hand through the Edit drop down menu a A pop up editor will take you specimen by specimen through potential edits The pop up has each of the 6 data tables in order from top to bottom Master Sex Reproductive Events Specimen Notes and UDFs If discrepancies exist between the records in the two studbooks you are comparing those discrepancies will be shown and you have three options i Use the Accept button to apply what is in the SECONDARY xxstudbook database to the OVERLAY in the PRIMARY database e g moving data from the SECONDARY to the PRIMARY Version
91. ING EDITING MASTER DATA Edit True Data 8 Master Sex Reproductive Events Specimen Notes LUDFs SE Sire Dam Hatch Type Hatch Date Geier Hearing Owner 8 WILD WILD Wild Hatch 7 1 1961 Unknown Parent Not Reported To edit a piece of data for this specimen alter any of the following fields and click Apply Changes ID Sire Dam WILD WILD Hatch Type Hatch Date Hatch Date Estimate Wild Hatch 7 1 1961 Unknown ai MM DDAYYYY Rearing Type Owner Institutional Mnemonic Parent Not Reported Optional Click here to add change notes Notes T Batch Input i Ok Cancel Under the Master tab you may use pull down boxes or directly enter text to edit information in the following fields 1 Studbook ID When editing an existing specimen the studbook ID will not be editable If an existing studbook specimen needs to be renumbered for some reason e g a specimen with a temporary number needs to be assigned a permanent number that can be done via the Edit gt Renumber Specimen menu option see page 70 for more details When adding a new specimen PopLink will automatically find the highest studbook number in your studbook and assign the next sequential studbook number to the new specimen You should only alter this pre assigned number under specific circumstances e g if the soecimen needs a temporary number If you need to see the highest studbook or temporary number yo
92. IVE ADVANCED RESUE eege ei eee eet ese 149 DETAILED METHODOLOGY USED IN THE SURVIVAL ANALYSEG 150 INcIUSION EXGCIUSION Of dee Te E EE 150 Calculations of Kaplan Meier survival probabilities cccceeccseeesseeeeeeeeeeeeeens 151 Calculations of Age based Life Table ceccccccccccseceeceeeeseeeeesseeeesseeeeseeeeeseaes 152 Calculations of Confidence Intervals around Median Life Expectancy 152 Statistical Comparisons of Male and Female Survival Statistics 0000000000000 152 Comparisons of median life expectancies using confidence intervals 152 Comparison of survival curves using the log rank fest 153 KI sd e EN 153 APPENDIX 2 ACCESSING POPLINK DATA IN MICROSOFT SQL SERVER MANAGEMENT STUDIO EXPRESS ees euegee eg EeEE ENEE ee Ee 154 Starting and Connecting to SQL Server 2005 Express don 154 Displaying Data IMMA TAINS EE 155 Custom Database EE 156 XDONINO Dal arn anebngeaiuld aud eres eta See Ue eae 157 Radek RE e 157 Version 2 3 February 10 2012 PopLink User s Manual Chapter 1 INTRODUCTION and OVERVIEW INTRODUCTION TO POPLINK PopLink is a computer program designed to help maintain analyze and export the data of a captive population that are relevant to its genetic and demographic management This software can be useful to studbook keepers the individuals responsible for tracking and maintaining the data relevant to an individual species wit
93. KS 122 EggLay Date infertile eggs 9 1 1993 SPARKS 122 Egg Lay Date infertile eggs 12 10 1903 SPARKS 122 a Note Imprinted bir 8 17 2001 SPARES 153 Breeder Num SAN AN 10 1 4 1989 SPARKS 153 fote Imprinted bir 8 17 2001 SPARES 88 Breeder Num SANAN3 4 19 1984 SPARKS The Specimen Notes Table is used to record important text information about specific specimens as text notes A given specimen may have no Notes and will therefore not show up in this table or single multiple Notes The Description displays the type of note based on SPARKS note types and additional PopLink note types The Comment field is a text box of unlimited length The Note Date field can be edited by the user to reflect the relevant date for each specimen note and the User Edited field gives the source of the comment SPARKS for any imported comments and whoever is logged into PopLink for any new comments For changes PopLink makes to the data during translation e g separating sex and reproductive status the description will display PopLink Assumption Note comments will explain the changes in the translated data and the user will be whomever was logged into PopLink when the database was created USER DEFINED FIELDS DATA TABLE Fie Edit View Validate Reports Export Help Di alz Salect Fiters Me Filters Applied Totals 145 152 2 299 at 75 Institutions Ho Sort Order Applied Edits 19 18 17 15 Currentness Date 1 3 2006 Master
94. Link doesn t crosscheck location and enclosure location validity i e if the rest of the record says this specimen is in CHICAGOLP but the enclosure location is in CHICAGOBR Be sure to select the correct enclosure for your individual Also there are no move up down buttons for this table be cognizant to enter events in the same day in chronological order Auto Adding Birth and Death Information from Events Record If you are tracking Enclosures in your database PopLink may offer to assist you in adding enclosures records as you are entering birth and death event data for a specimen 1 Births When a new specimen is created if the Dam of a specimen has a current enclosure record PopLink will ask if you want to add an enclosure event into the same enclosure for the birth of the offspring the newly created individual with a pop up If No is selected no further action is taken If Yes is selected an Enclosure event will be added to the new specimen s Enclosures record with its birth date as the Start Date and a comment auto added saying Born Hatched in enclosure Even if an individual is entered into an enclosure on their birth date there needs to be a comment auto added by PopLink through this pop up to count as a birth hatch in an enclosure in the Enclosure Reports PopLink PopLink has detected that this specimen s mother was in enclosure Aviary HOUSTON at the time of its birth Would you like PopL
95. Millspaugh JJ 2005 Wildlife Demography Analysis of Sex Age and Count Data Elsevier Inc Massachusetts 636 pages Version 2 3 February 10 2012 153 PopLink User s Manual APPENDIX 2 ACCESSING POPLINK DATA IN MICROSOFT SQL SERVER MANAGEMENT STUDIO EXPRESS The underlying studbook database storage system for PopLink 2 3 has been changed from the binary file data bin used in version 1 3 and before to a SQL database You won t see this difference when you re looking at your database in PopLink but the under the hood change means that your studbook data are stored in a way that is more permanent secure and accessible With a SQL database power users can use a different program SQL Server Management Express to view and export data and write custom queries for more detailed analyses To utilize these features there is one additional installation procedure complete this step after PopLink has been installed To install 1 Go to http Awww microsoft com downloads details aspx Familyld C243A5AE 4BD1 4E3D 94B8 5A0F62BF7796 amp displaylang en 2 If you have a 32 bit operating system download the SQLServer2005 SSMSEE msi file 3 If you have a 64 bit operating system download the SQLServer2005_SSMSEE _x64 msi file 4 Run your downloaded SSMSEE file In the dialogue boxes a Accept licensing terms of installation b Enter your name and company c Use the default selection on feature selection Click Finish and installat
96. NUMBERING SPECIMENS wcosdricncedsancsatdanmctsantiedddeaties saeahdedGiaatewibaeatesarteatieds 70 ERR R EUREN 71 Chapter 5 FILTERING DATA IN POPLINK 0 ccecesceceneeeeenseeeeneeeenseesenseesenneesenes 72 INTRODUCTION OVER VIEW EE 72 DESCRIPTIONS OF SPEOIRIG FIGCTE EE 73 WA STU OM EE 13 BE 74 Ae 74 e 74 PCD FOCUICUV EE 74 SE E 74 Version 2 3 February 10 2012 PopLink User s Manual IKEA Klee 19 SE Anen 19 Srel te ere te E ee er eee ee 19 TC COM EH 75 e EE 75 D ener ere ert ee ee ee E ee ee eee eee ee ee eee eee ee 75 Rip E 75 SEARCH NOTES was Specimen Notes filter in PopLink 2 1 and before 76 Chapter 6 DATA VALIDATION AND CLEAN UP IN POPLINK ssseeseees 77 DATA NVALIDA FON REPOR WEE 77 Table 3 57 Errors Used in PopLink Data Validation cc eceeeeeeeeeeneeeeeeeeeeees 78 DATABASE COMPARISON TOOL aannnannnnnnnnennnnnnnnrnnnnnrrnenrnsnrrnnrnrsnersnrrnnnrrsnrreeneee 82 Comparing two versions of the Same studbook nnannnannnennnnnnnnnnnnnnennsnnrnnenennnne 82 Importing analytical assumptions into PopLink from an analytical studbook 84 CLEAN UP de due ent e TE 86 UDF CASING CLEAN UP TOO stint a a aa 88 DELETE EMPTY UDF ROW TOOL anene deeg 88 Chapter 7 EXPORTING DATA FROM POPLINK ccccccsssseeseeeseeeeeneeseeeneeesneaes 89 els 280 10 hed ws me perme ere een ere ne raat reer er Ua ne RT nee ee ee 89 FV APOR EE 91 TECHNICAL NOTES ON EX
97. OBR 890017 1 20 1989 None 66 Transfer CHICAGOLP B8138 1 25 1991 None To edit the existing event s for this specimen highlight the desired event and alter any of the fields below To add a new transaction event click Add and alter the fields To change the order of events occurring on the same day use the Move Up Move Down buttons When completed click Apply Changes Transaction Code Location Local ID Hatch v ICHICAGOLP g i B8138 v Transaction Date Transaction Date Estimate 3 26 1981 si bone MM DD YY YYY Click here to add change notes Notes Batch Input Ei Ok Cancel Under the Events tab you may edit or delete pre existing events add new events and reorder events that occur on the same day in a specimen s record Version 2 3 February 10 2012 46 PopLink User s Manual 1 Transaction Code PopLink recognizes eight different Event types Captive Birth Wild Capture Transfer to another institution Release into the wild Recapture from the wild Death Go LTF Lost to Follow Up and Return From LTF PopLink does not track three types of events previously tracked in SPARKS ownership nonphysical transactions management group in out and social group in out B Guidelines Note 14 Events Events or transactions should provide a continuous record of a specimen s history in time and space The terms transaction and event are often used interchangeably
98. ODUCTIVE 142 14 214 e 204 LA Bi e Oo GA FA specimens listed as Fernale Not Contracepted specimens listed as Male Not Contracepted specimens listed as Unknown Not Contracepted specimens listed as Other Not Contracepted Tatal specimens with rearing Hand specimens with rearing Parent specimens with rearing Foster specimens with rearing Unknown Tatal specimens have Dam ID as UNK specimens have Dam ID as WILD specimens have Dam ID as studbook number Total LA LI specimens have Sire ID as UNK REARING DAMS SIRES Wa specimens have Sire ID as WILD The Summary Counts Report gives basic details on the types of specimens within your dataset You can set filters for the report using the Select Filters button and export using the Export button Note that the report tallies all relevant states for a category but does not report any states that have no individuals For example in the screen above this studbook had no individuals with Colony Group rearing type so the line for that rearing type is not shown in the report Version 2 3 February 10 2012 102 PopLink User s Manual AGE PYRAMID REPORT The Age Pyramid Report includes three separate tabs with detailed information about specimens in the studbook this report can be limited using the Select Filters button The default filters that are applied are STATUS living and DATE as of today s date These default filters
99. OPLINK There are several routines and tools within PopLink that can be used to assist in data clean up and validation This chapter describes how you can use these tools to improve the data quality of your studbook database The tools it covers are Data Validation Report Database Comparison Tool Reports useful in data clean up Clean up Mnemonics Tool UDF Casing Clean Up Tool Delete Empty UDFs Tool GE E eg DATA VALIDATION REPORT Under the Validation pull down menu you can select Run Data Validation to produce a prioritized list of potential errors within your studbook HE Sunbittern BEIR File Edit View Validate Reports Export Help olesia al ve VALIDATION REPORT Export Species Type Egg Laying Incubation Period 28 Days Maximum Hatch Date Range For Clutch Mates 3 Days 29 out of 544 specimens have errors Main Detailed Error List by Studbook ID Current Validation Previous Validation a Date of Validation 11 20 2006 E Total Number of Errors 32 a D Coe meme ge a HIGH PRIORITY ERRORS Description Help Current Previous EH 08 Sire ID is not a male EH 12 Sex record is missing EH 17 Event record is missina 1 0 T1052 S lt MEDIUM PRIORITY ERRORS Description Help Current Previous EMOL Local ID is not unique 0 EM 10 Reproductive record is missing 1 0 T1052 383 535 536 LOW PRIORITY ERRORS Code Description Help
100. Outliers Report AGE OUTLIERS REPORT 10 Oldest Dead Females 10 Oldest Dead Males 10 Oldest Dead Other Sex 10 Oldest Living Females 10 Oldest Living Males 10 Oldest Living Other Sex SE Current Sex Hatch Type Current Age gie SC EE cabot 76 Female Captve Hatch 26 962 Mone AME TERDAM MILVYSLUEKEE ZE Female Captive Hatch 25 892 Mone HOS Tor SANDTEGOS 95 Female Captve Hatch 25 095 None NZP CRC ASHEBORO 110 Female Captive Hatch 23 195 None PITTS CA LOWRY 171 Female Captive Hatch 22 658 None DENVER DENVER 122 Female Captve Hatch 22 598 None DENVER BALTIM AQ 140 Female Captive Hatch 21 325 None DENVER SANDIEGO 158 Female Captve Hatch 20 909 Mone CAICAGOLP FRANELINP 16 7 Female Captive Hatch 20 304 Mone PHILADELP SEATTLE 172 Female Captive Hatch 19 932 None SAN ANTON FRESNO Version 2 3 February 10 2012 106 PopLink User s Manual This report lists separate tables with the 10 oldest living and dead individuals of each sex This report can be useful to look for age outliers individuals that are exceptionally old and may affect your mortality and life table analyses Current ages or ages at death may be accurate for these individuals but if an individual has an exceptionally old age and is at an institution you haven t received a studbook update from recently or the individual is historic and data might not be accurate you should consider whether the individual is really still living or should be made lost to follow up in
101. PORTS TO PM2000 amp PMnx 92 Ihe Tabe ee EE 92 Mortality Rate E ere 92 FECUNGITY ate Calculati OMi A NTT 93 Genc UC E ee EE 94 ZOORISK EXPOR eegener 94 SPARKS me nl Renee eee eee eee ee eee ee ee eee ere 95 Chapter 8 POPLINK REPORTS grussen ee Eege gees Eeu ee Ge EeNE EE nnmnnn 97 SPECIMEN REPORT EE 98 VETE E 99 SS CONIA Ee DEE 99 STUDBOOR EE 100 SUNMARY COUNTS REPOR E 102 AGE PY RAMID REP OR E 103 1 Age Pyramid for Known Age Known Sex Specimens nannnoannnennnne1nna 103 2 Detaled Age Pyramid BEE 104 Ss Fales DY BIN TypEnsesesenesen 105 WINKNOW NAGE REPORT EE 106 AGE OUTLIERS RE EE 106 CENSUS REFOR E 107 CEN US DETAIES REPOR EE 108 SURVIVAL TOOLE REFOR gegen 108 REPRODUCTIVE tegen 109 E But 109 Se ET elt fl Un 110 EE eg 110 Version 2 3 February 10 2012 PopLink User s Manual A DAM AGS ALF ISL BI E 111 5 DAMAGE EE enee 111 6 Number Of ONnSDMINGi Cl eege eege 111 7 Sire Age At First Estimated Conception ccccccccceceeceeseeeeeeeeeesaeeeesaeeeeeeees 112 8 Sire Age at All Estimated Conceptons 113 E INUMDEF Of OPSDMING Per SIN Catach attended de geheegt eege 113 CURRENT INSTITUTIONAL HOLDINGS REPORT a ssesessnennnsnnssensnsnrsrrenrrrnsrenn 113 Alo TORIC CURRENT INSTT TU TIONG LIS EE 115 LOST TO FOLLOW UP REPOR LE RE 115 LIFE TABLE REPOR E 116 SPECIMENS WITH UNK MULT PARENTAGE AND DESCENDENTS REPORT 117 LIVING SPECIMENS WITH UNK MULT IN PEDIGREE REPORT 08
102. PopLink User s Manual Welcome To PopLink St INSTITUTE of ee Museum Ubrarg line oln P irk 7 00 VICES PopLink Version 2 3 User s Manual Lisa Faust Louise Bier Kate Schowe Talia Gazlay February 10 2012 Version 2 3 February 10 2012 PopLink User s Manual PopLink 2 3 Release Date February 10 2012 Programmers Yee Man Bergstrom Lincoln Park Zoo Adrian Lin Lincoln Park Zoo Clarity Consulting Nathan Gudritz Joy Pak Brendan McNutt Nathan Gonzales Guillermo Gomez and Jerry Brunning Development Team Lisa Faust Ph D Lincoln Park Zoo Steve Thompson Ph D Lincoln Park Zoo Louise Bier AZA Population Management Center and Lincoln Park Zoo Design Team sarah Long M S AZA PMC and Lincoln Park Zoo Kristine Schad M S AZA PMC and Lincoln Park Zoo Rachel Low AZA PMC and Lincoln Park Zoo Cara Groome AZA PMC and Lincoln Park Zoo Katelyn Marti AZA PMC and Lincoln Park Zoo Kate Schowe Lincoln Park Zoo Joanne Earnhardt Ph D Lincoln Park Zoo Kevin Willis M S Minnesota Zoological Gardens Colleen Lynch M S AZA PMC Bob Wiese Ph D San Diego Zoo Carrie Schloss Lincoln Park Zoo Amanda Kamradt Lincoln Park Zoo Talia Gazlay Lincoln Park Zoo PopLink development was supported by Institute of Museum and Library Services Conservation Project IC 05 04 0416 04 Lincoln Park Zoo American Zoo and Aquarium Association AZA Minnesota Zoological Gardens Fort Worth Zoo United Airlin
103. RKS any associated dates with when the event changes occurred are lost Data histories that are created when data are edited within PopLink are lost Current owner if it was entered tracked within the PopLink master table is lost Unrecognized mnemonics mnemonics that are not included in the ISIS institution list e g mnemonics that were unrecognized by PopLink including ones that were imported or new ones that were entered will still be unrecognized when sent to SPARKS If you entered information into the User Defined Institutions table e g address contact information etc those data cannot be sent to SPARKS Institution List any edits made to the Institution List within PopLink will not be sent to SPARKS 6 Removal dates removal date estimates these are not stored in PopLink and none are sent to SPARKS with the exception of LTF events see below 7 Go LTF events SPARKS does not have this transaction code These events are translated as follows a Upon importation PopLink creates two events out of any original SPARKS LTF event see Chapter 4 Lost to follow Up Events section When exporting back to SPARKS PopLink translates this back to a single event a transfer event to the event location on the event date with LTF U in removal date estimate field D when the go LTF event is a single event e g it s not a transfer to a certain location and then a go LTF at that location it is translated as a transfer event with a U in t
104. Reproductive Sex Events Specimen Notes UDFs Studbook Overview SE Edit SSPANIMAL EE NAME PHYS_PRO RECTAL UL BLOOD PROGE B T 15 Yy no subsp Alice n y i Pk no subsp Gerry I Sissy mm 18 RR ee ee ee ee ee eg a i ES EE pg st babai E e a Version 2 3 February 10 2012 26 PopLink User s Manual The User Defined Fields UDF Table contains any UDFs created in SPARKS for your imported studbook population UDFs can be used to define subpopulations within your studbook BA Guidelines Note 2 UDFs UDFs allow the studbook keeper great flexibility when defining the population that is to be managed UDFs can be used to identify subspecies color phases hybrids chromosome type common defects proven breeder in the SSP other management plans etc With a UDF the user can define a specific subset of the data for analysis For example once identified with a UDF the studbook keeper can analyze just one subspecies out of the entire studbook database Use of several UDFs simultaneously will allow a creative studbook keeper to divide the database into a wide range of subsets for analysis Some UDFs will remain constant over a specimen s entire lifespan Subspecies would usually be such a UDF unless the specimen was misidentified or the subspecies definition was to change However some UDFs may change with time e g nonproven parent to proven parent When using UDFs it is extremely important to keep them up t
105. SB2509 283 263 2 9 2000 None 6 7 1 Nor CG ORLANDO SB2510 283 263 4 1 2000 None 6 628 Nor 485 a Female OMAHA 11823 WILD WILD 7 18 2000 None 6 333 Nor 499 Unknown DALLAS WA 140098 sA 140 7 3 2001 None Se Nor 500 a Male CENTRALPK C01106 165 99 4 5 2001 None 5 618 Nor 503 Female Ra H 101617 SE 182 10 6 2001 None Biel Nor 505 Male FRESNO 230007 165 99 4 8 2002 None 4 611 Nor m D 1 mA 8 m ian Za sr n a fier T n n n n Sp a Version 2 3 February 10 2012 128 PopLink User s Manual When opened and applied to a studbook overlay data will be used in all reports and analyses e g data exports all reports in the report menu data validation etc To close an overlay use the Remove Overlay menu option in the Overlay drop down menu Editing Analytical Data and Creating Hypothetical Specimens Once an overlay has been created you can start to add analytical assumptions about parentage sex birth or death dates or other unknown data for more information on how to make assumptions see the second half of this chapter All analytical data will be stored in your overlay and all editing of analytical data will occur through the overlay drop down menu Note that if you click on the edit button in the main studbook viewer the pop up specimen editor always indicates that you are editing true data Edit True Data 472 There are two types of analytical edits you can make within PopLink 1 Making analytical
106. Settings pop up also provides the option to toggle the Social enclosure and medical data modules new in PopLink 2 2 2 3 on and off The Settings box is not studbook specific any settings you specify are applied across any studbook you might open PopLink Files and Databases Storage Location This location specifies where the PopLink folder located by default in My Documents is stored on a users computer Libraries a B Gazlay Talia E Contacts gt k Desktop NM Downloads P Favorites JB Links 4 My Documents U My BloWue Viewer Views gt P My Dropbox os gt SPARKS Make New Folder Changing File Storage Locations Changing file storage locations should not be done frequently the simplest setup for you as a studbook keeper and us when we need to assist you is to leave your PopLink files stored in the default location of Version 2 3 February 10 2012 17 PopLink User s Manual C Documents and Settings User Name My Documents PopLink which can also be described with the address C Users User Name Documents PopLink depending on your Operating System Changing this default location will typically not be necessary unless your My Documents folder is mapped to a network drive instead of a location on your hard drive If that is the case you can use this option Settings option to store it elsewhere on your C drive we suggest creating a new folder called C PopLink and browsing to that in the address
107. TES The next level of date precision is an estimate to the nearest unit of time either day month or year These estimates range in precision from within a few days during a month or during a year This option was included in PopLink to allow the studbook keeper to establish a Version 2 3 February 10 2012 32 PopLink User s Manual degree of precision for date data Although this is a nice feature for showing precision it does not affect analyses When an analysis is performed on the studbook PopLink ignores the estimator and treats the date as an exact value This is a key concept that must be considered whenever date information is entered into PopLink The correct way to treat this level of precision is to enter the midpoint of the range of the date and the appropriate estimator AS an example if it is Known that a specimen arrived at an institution during a specific month the mean date for that period a month is the 16th of the month for months with 31 days This is the appropriate date to enter into the Transaction Date field In the Date Estimate field Month is entered If a specimen arrived sometime during a calendar year the mean date for the year e g 1 July 19 _ is entered into the Transaction Date field and Year is entered into the Date Estimate field When the birth date and death date for a specimen are estimated to the same calendar year the birth date should be entered as splitting the year into thirds 2 May 10 an
108. TIVE ADVANCED RESULTS 7 PM2_SavTam09 Comparative Advanced Results Ee COMPARATIVE ADVANCED RESULTS Note that all results are displayed in this table regardless of whether data quality criteria are failed Please see the PopLink manual for more details Descriptive Analytical Expert Description Pooled ANALYSIS WINDOW BACKGROUND Type of analysis Descriptive Analysis start age days 365 Analysis window start date 1 31 1980 Analysis window end date 1 31 2012 Institution window All Institutions Additional filters No Filters Applied of years in window Total population size on end date of specimens with birth date death date DATASET INFORMATION Total number of specimens of males of females of other sex specimens of wild origin specimens of captive origin specimens of unknown origin specimens of left truncated specimens of specimens that entered after window start date of specimens that were alive at start of window of right censored specimens of specimens that were still alive in geographic region at end of window 4 Hl A Comparative Advanced Results table is created if you selected the option at the beginning of your analysis It will produce a concise set of results for pooled male and female data subsets for all reports that you selected including the descriptive report This table was designed so that
109. The first event for each specimen should be either a birth or capture see pages 42 43 on entering wild caught captive born or unknown origin specimens In the past some studbooks have used a transfer as the first event usually for specimens that were either wild caught or of unknown origin Transfers should not be used as the first event for any specimen When the first event is a transfer the specimen s origin is unclear and must be inferred from data in other fields A transfer as the first event is ambiguous and implies that the information for that specimen is incomplete e g where was the transfer from Did the studbook keeper intentionally make the first event a transfer or was capture or birth mistakenly omitted Poplink s Data Validation page 77 will check whether your studbook has transfers as first events The data for each specimen should include all known and unknown locations and events When necessary PopLink and other analytical programs can exclude specific events and locations from reports and analyses using Filters Thus a studbook keeper should not exclude any data on location in order to create a geographic subset of their population The benefit of including all locations could be great Analyses and reports could be run only on specimens that had passed through a specific albeit obscure location this might be required to assess a common factor such as disease or behavioral problems Moreover most Filters see C
110. User s Manual ENTERING EDITING SEX DATA Edit True Data 8 Studbook Event Date ID Sex Event Date Est 8 Male 7 1 1961 Unknown Add Delete To edit the existing sex event s for this specirnen highlight the desired event and alter any of the fields below To add a new sex event click Add and alter the fields When completed click Apply Changes Sex Male MM Event Date Event Date Estmate 7 1 1961 Unknown al MM DD YYYY Click here to add change notes Notes anges Batch Input ji Ok Cancel Remember that sex data are tracked as a data stream and an individual may be a single sex for its entire life or switch sexes e g from unknown sex at birth to male or female To edit existing sex event s highlight the desired event and edit the data in the fields to enter a new sex event use the Add button To delete an existing sex event highlight the desired event and use the Delete button For an individual with known sex at birth use the Sex pull down menu to designate whether the individual was male female or abnormal sex When entering a new individual PopLink will autofill the Event Date and Event Date Estimate using the birth date and birth date estimate you still need to fill in the sex for your new individual For specimens where the sex is known at birth these fields should be identical For an individual that is unsexed at birth use the Sex pull down menu to designate t
111. Version 2 3 February 10 2012 125 PopLink User s Manual species they are usually applied to the population at large Most conventions combine common sense logic and biology into a simple rule to be used when data are unknown or unclear One common example is a species that breeds once per year and can only be imported from the wild as juveniles e g older than 6 months younger than 18 months A convention might be developed to set the birth date for all wild caught specimens with unknown birth dates as January estimated to month of the previous year Another example might deal with specimens of unknown origin wild caught or captive born that enter the population before the first reported captive birth A convention could be established that all specimens entering the population before the first reported captive birth are wild caught Conventions should be outlined in the Species Notes in the Studbook Overview Table and noted in the Specimen Notes whenever they are applied to a given specimen One of the most common types of conventions is the method for back dating births from the date young are first observed or heard Marsupials bears cavity nesting birds and other species whose young are not likely to be noticed until sometime after birth will have conventions for estimating date of birth These should be carefully documented in the Species Notes and Specimen Notes Most minor assumptions are guided by information provide
112. able is blank it means that data quality tests were failed The estimates in this life table can be used in population management software such as PM2000 and ZooRisk note that at the moment they need to be entered by hand into the software Note that Life Table estimates calculated by the Survival Tool may be different than those calculated by SPARKS PM2000 or ZooRisk but they should be more precise estimates because they are based on finer time units days vs tenths of years in SPARKS PM2000 If this table is blank it means that data quality tests were failed 7 The Advanced tab lists all Analytical Survival Statistics results in an easy to extract via copy and paste into Excel format See the Comparative Advanced Results section page 149 for more details on results included in this tab You can use the EXPORT button to send the Report and the Included Individuals table to files in your studbook databases folder The Report is exported as ANALYTICAL SURVIVAL STATISTICS REPORT htm and can be opened in your default web browser by double clicking on the file or in Word by right clicking on the file and choosing Open With Microsoft Word The Included Individuals table is exported to ANALYTICAL SURVIVAL STATISTICS INCLUDED INDIVIDUALS TABLE csv and double clicking will open the table in Excel EXPERT SURVIVAL STATISTICS REPORT The Expert Survival Statistics Report allows the user to define the starting age for survival analyses This m
113. after each Note filter Use the AND OR pull down to describe how to combine the filters Note that when you apply the NOT CONTAINS or NOT filter it will retum specimens that have atleast one note that does not contain match the text other note types for that specimen might contain match the text so review filter results carefully This filter will search ALL note and comment fields throughout an animal s records including Specimen Notes Medical Notes and comment fields in Social and Enclosure Enter Search Text AND lon lban Dete _ Clear All Filters Ok Cancel NOTE The Search Notes function filters the comments slightly differently in the Social table f vr in comparison to other tables because its table records are connected to multiple individuals j RK When a phrase is entered in Search Notes records are limited to only those Social events Gel J with that search text in the comment field rather than showing all the Social events related to a specimen that has that note This way you can clearly see which specimens listed in the Related Specimens field have a given social note For any specimens that meet the criteria you set up in the Search Notes tab PopLink will show all of their records in the rest of the tables Master Sex Reproductive Events Soecimen Notes UDFs Enclosures and Medical Version 2 3 February 10 2012 76 PopLink User s Manual Chapter 6 DATA VALIDATION AND CLEAN UP IN P
114. al In the right hand case there was no recognized mnemonic real or synonym in the ISIS institution list This may be because 1 you have created a new spelling for an existing institution but that spelling is not yet a synonym or 2 the institution is not in the ISIS list at all Double check the institution list if you have simply created a new spelling you should enter the Correct Mnemonic in the box if the institution is truly a unique institution you should add it to your studbook as a User Defined Institution To do so leave the Unrecognized Mnemonic in the box and click Add which will pop up this box Add a User Defined Institution to the Current Database Seles Mnemonic OODWARD Name Pe Address S City Pe State L Country KC Mail Code E Phone E Fax S Emal Liaison D General Location UNKNOWN A 2 9 H AMERICA Notes Ok Cancel Enter as much as you know about this institution in these fields including any notes about the institution For the General Location field you can enter a regional designation so that the institution will show up in a given Filter view such as N AMERICA or EUROPE add these using the accepted mnemonic for that region which you can look up using the find button You can view and edit all your user defined institutions through the View drop down menu Selecting User Defined Institutions will pop up this box Version 2 3 February 10 2012 87 PopLink User
115. aler s location lengthy intervals between capture and arrival at the first institution require verification Version 2 3 February 10 2012 42 PopLink User s Manual Captive Born Specimens D Guidelines Note 11 How to Enter a Captive Born Specimen Captive born specimens are identified by several coordinated data entry procedures Usually the exact date of birth is known and can be entered without an estimate If only the month or year of birth is Known it should be entered with a MONTH or YEAR in the Date Estimate field see page 32 on estimating dates Usually one or both parents are known and their studbook numbers can be entered as the dam and sire see page 36 on how to enter dam and sire However for some specimens one or both parent identities will be unknown Every effort should be made to identify the parents unknown parentage has profound effects on genetic analyses If parentage cannot be established either one or both parent studbook numbers should be entered as UNK The first event for a captive born specimen should be a captive birth at the birth location The Birth Type of the specimen should be entered as CAPTIVE BORN Eggs collected from the wild should have Captive Hatch as the first event with both parents entered as WILD or W ILD when parents or siblings have been individually identified Rearing method should be entered if known see page 41 on how to enter rearing type Specimens Of U
116. anchor animals from the Related Specimens field you can simply make a new selection without that individual If you need to delete the original anchored specimen open up the edit window for one of the other Related Specimens and make a new selection of Related Specimens through their record If you delete an entire Social event its connections to all the individuals involved will be deleted More Ideas On How To Use The Social Data Table If you can t or don t want to track social interactions in detail you can still use this table to record major behavioral compatibilities or incompatibilities of animals For example if you know that one individual in your population has been introduced to another with continued negative results e g they are socially incompatible you can use this table to enter a single event reflecting those collective interactions and then use the Social Compatibility Report see Chapter 8 to check and compare which individuals are compatible Version 2 3 February 10 2012 59 PopLink User s Manual ENTERING EDITING ENCLOSURES DATA Before you can create enclosure events in the Enclosures Data Table you must develop a list of User Defined Enclosures for your studbook by going to Edit gt User Defined Enclosures User Defined Enclosures wi User Defined Enclosures o Je X Use this tool to alter the Enclosures for your studbook To add a new Enclosure type into the fields below and click Add
117. anual a If user selects option to include offspring attributed to unknown parents these births are proportionally assigned in proportion to the M values that have already been observed Note that in the PMx export the more detailed demographic export file All Individuals Demographics File a csv file contains the raw data on individual animals and PMx calculates life table statistics rather than using PopLink calculated life table statistics See the PMx manual for more information Genetic Export PopLink does not perform genetic calculations during the export to PM2000 or PMx PopLink compiles information on pedigree status location and identification to export to PM2000 or PMx in ped files which are then used by PM2000 or PMx for genetic calculations See the PM2000 or PMx manual for more information on genetic calculations in PM2000 Lacy and Ballou 2002 or PMx Ballou et al 2011 ZOORISK EXPORT PopLink will create standard ZooRisk export files for your studbook database these files are compatible with ZooRisk version 3 8 You can export from your true studbook e g sunbittern or your studbook with an analytical overlay applied e g sunbittern Faust1 The database displayed at the top of the screen will indicate which database is being exported When you select the ZooRisk export from the Export drop down menu this screen will be displayed File Edit View Overlay Validate Reports Export Help B S Al al al
118. ar at the top of the window The eight pull down menus directly below the blue bar can be used to navigate throughout the program The shortcut buttons below the menu functions can be used to in order from left to right Create a New Studbook Open an Existing Studbook Edit a Specimen s Record View Data i e jump to the studbook viewer Run Data Validation or View a Specimen Report STUDBOOK VIEWER Once a database has been created and opened PopLink will display the Master data table of the Translated Data i e your studbook data from SPARKS translated into PopLink format in the Studbook Viewer window File Edit View Overlay Validate Reports Export Help D o Z a l Select Filters As of 9 30 2011 AND Status Living Totals 62 49 8 119 at 53 Institutions No Sort Order Applied No Edits o Ka Currentness Date 3 22 2010 gt Master Sex Reproductive Events Specimen Notes UDFs Social Enclosures Medical Studbook Overview See Edit Current Sex Current Current Sire Dam Hatch Date Hat Location Local ID 56 ma EEN 122 Female ALT AQ 980307 77 36 2 15 1987 Mom 139 Male RIO GRAND 821782 77 36 4 25 1988 None 140 Female us ee e 5 25 1988 We 153 Male BIRMINGHM 1770 18 44 8 16 1988 None 158 pese Den mam ee we 10 24 1988 None 170 Male DALLAS 906764 57 80 8 17 1989 None The PopLink Translated Data contains a total of six different data tables accessible via tabs Master
119. ars D e WE FIZ 62 a d J gt ge E i A Or eei Di OO Or Chr Chr Chr Chr Chr Chr Chr Ch CH fetten testen testen ies tie ee ee eS eS 2 LJ On tt A kA Ba kk PF FA P Re P tu 1 BALTIM AQ V CENTRALPK CHICAGOLP 1 CLEVELAND DALLAS 0 DALLAS WA 2 CH NOM AZA INSTITUTIONS 6 3 2 11 at 6 Institutons 1 j i d J Institution Male Female Unknown er ca U mT A P i ei eiei This report gives a quick summary of the number of living individuals in AZA and non AZA institutions based on the AZA FED file in the Federations folder Version 2 3 February 10 2012 114 PopLink User s Manual HISTORIC CURRENT INSTITUTION LIST Sunbittern File Edit view Overlay Validate Reports Export Help Dol el ve Historic Current Institution List HISTORIC INSTITUTIONS Mnemonic Name Address City State ATTLEBORO Capron Park 201 County S Attleboro USA Country 02703 BARTELSH Mr Henry Ba 84 Cortlandt New York USA BRITGUIAN CHASE lt CURRENT INSTITUTIONS Mnemonic Name Address City ASHEBORO North Carolin 4401 Zoo Par Asheboro USA BALTIM AQ National Aqu 501E Pratt S Baltimore USA BLRIVILINGH hed Birmingham Country 27205 9416 21202 3194 2630 Cahaba Birmingham USA 35223 ZC Chicago Zool 3300 Golf Rd Brookfield USA 60513 CINCINNAT Cincinnati Zo 3400 Vine St Cincinnati USA 45220
120. ase see the Appendix at the end of the manual Version 2 3 February 10 2012 108 PopLink User s Manual REPRODUCTIVE REPORT Sunbittern Reproductive Report REPRODUCTIVE REPORT Export Species Type Egg Laying Incubation Period 28 Days Maximum Hatch Date Range For Clutch Mates 3 Days 45 reported dams with 132 123 174 429 offspring not including 33 offspring of UNK MULT dams 45 reported sires with 130 123 172 425 offspring All ages are at dam conception Select Filters Filters applied to parents No Filters Applied Sire Age At First Estimated Conception Sire Age At All Estimated Conceptions Number Of Offspring Per Sire TTT Clutch Size Dam Age At First Hatch Dam Age At All Hatches Number Of Offspring Per Dam Interhatch Intervals Hatch Seasonality TTT na b The Reproductive Report displays general reproductive information pertaining to your population and includes nine separate tabs with detailed reproductive information The general information at the top of the report includes the reproductive information that you entered when you first created your studbook e g species type and incubation period The reproductive report can be limited using the Select Filters button In the reproductive report all filters are applied to the parents NOT the offspring There are no default filters for this report i e default is No Restriction All reported ages of sires are ages at dam conception s
121. ata quality tests that affect how results are displayed c If male and female data are of sufficient quality compares the confidence intervals around median life expectancies to determine whether male and female median life expectancies are statistically different see Detailed Methodology section page 152 If the medians are not statistically different i e Cl s overlap pooled results are displayed if the medians are statistically different i e Cls do not overlap medians are reported for males and females separately 2 The Included Individuals Table shows the partial or full lifesoans of each individual included in the survival analyses see the Detailed Methodology section page 152 for more on how this table is constructed In addition to excluding individuals with unknownness in their record as described in the Detailed Methodology Section the Descriptive Survival Statistics Report excludes any individual which has died before their first birthday from the analysis These individuals are excluded because the report is focused on providing an estimate of median life expectancy of individuals which survive the vulnerable 1 year of life If desired users can run the Analytical Survival Statistics Report which does not exclude these individuals for comparison 3 The Data Quality Table displays results of the five data quality tests for males females and the overall pooled sample If a subset of data fails any of the 5 tests no r
122. ate estimator U are excluded from the Survival Tool analyses because age at death or censoring cannot be calculated for such individuals If your population has a large number of specimens with unknown birthdates and or if there are few specimens with known birth dates to base your survival analyses on you may consider making analytical assumptions for these specimens so they can be used in analyses The Unknown Age Report will be a good starting point for finding and making assumptions about these individuals 2 For individuals with other unknown event dates death transfers etc that make it difficult to determine whether they are in the analytical window or not the Tool attempts to include as much of their lifespan as possible in the analyses In cases where there is too much uncertainty in whether or when an individual entered or exited the analytical window the individual is excluded from all Survival Tool analyses These cases are complex to summarize them we use the following notation U unknown event date K known event date A window start date B window close date Event streams go from left to right in time so a sequence KUAKKB can be interpreted as an event with a known date then an event with an unknown date then the window start date known date known date window close date The summarized rules for exclusion of part or all of an individual s lifespan from the analyses are a If all unknown event dates are before or
123. atus event use the Add button When entering a new individual in PopLink a reproductive event of Not Contracepted on the individual s birthdate entered in the Master table will be autofilled Remember that for individuals already existing in your studbook e g imported from SPARKS PopLink assumes that individuals are not contracepted at birth for more information on PopLink translation of reproductive status see page 24 Any individuals that were not neutered or contracepted in SPARKS upon importation will have a single event Reproductive Status not contracepted Event Date Estimate specimen s birth date estimate lf you get information that a specimen has been contracepted or neutered enter an additional event with the relevant information and use the Notes box to enter supporting information about the event Use the Notes button to document any necessary facts about the fields you have just edited or entered such as source of information about contraceptive discrepancies with institutional records etc When you enter notes closing the box saves the notes the notes are transferred to the Specimen Notes table for the specimen you re entering with a description of Reproductive Table Notes and the date of entry ENTERING EDITING EVENT DATA Edit True Data 66 Studbook Transaction Location Local TD Transaction Transaction ID Code Date Date Est 66 Hatch CHICAGOLP B8138 3 26 1981 None 66 Transfer CHICAG
124. bers transponder numbers and other types of useful identification like three toes on the left hind foot should be listed in Specimen Notes not as local ID 4 Transaction Date Transaction Date Estimate Transaction dates should be entered as MM DD YYYY To express uncertainty about the transaction dates date estimates can be entered by using the edit button next to any Date Estimate data entry field For more information about entering dates and date estimates see page 32 Note that in keeping with the Studbook Guidelines recommendation that studbook keepers not track removal dates PopLink has eliminated the removal date fields BJ Guidelines Note 16 Transaction Dates The Sequence of Transactions The sequence of transactions events is sorted by the Transaction Date field This means that an event with an earlier transaction date will be listed before an event with a later transaction date This seems logical for a transaction with some known transaction date For transactions with unknown dates but a known sequence e g a transfer occurred between a known birth date and death date but the date of the transfer is unknown a date that is between the transaction date of the previous transaction and the transaction date of the next transaction should be used to place the transaction appropriately in sequence and an Unknown date estimate should be entered This date will be ignored by any analysis performed by PopLink but will
125. book Choose the desired field and enter the value you wish to filter by in the space next to it Version 2 3 February 10 2012 75 PopLink User s Manual SEARCH NOTES was Specimen Notes filter in PopLink 2 1 and before The Search Notes function allows searching of any note or comment field anywhere in a specimen s record including Specimen Notes Social Enclosure and Medical Data Tables The search function allows filtering of individuals in the following ways e Not restrict to individuals that have a note that does does not contain the full exact text in the search box the entire note must match e Contains Not Contain restrict to individuals that contain a specific word or phrase somewhere within a note Search terms are not case sensitive You can add multiple filter conditions at once using AND or OR Note that when using Not or Not Contains it will return any specimens that have at least one note that does not contain or match the text other note types MAY contain or match the text so review filter results carefully Also note that the Search Notes function will return all the Specimens with a particular note not restrict down any of the relevant notes tables to only those notes Amen E el Breeder Rearing Reproductive Event ID Status Date Parent Age Institution SEARCH NOTES Hatch Type UDF Sex GC Restriction Contains m Fil in the fields below and click Add
126. book keeper it should be included in the studbook provided it can be verified When a reliable source reports a specimen s transfer to an institution that does not respond to the studbook keepers requests for information the transfer should be accepted and the specimen should be denoted as lost to follow up at the receiving institution see page 49 on how to enter lost to follow up History of Studbook Software Computerized studbook datasets for AZA managed programs and many international programs are maintained in the Small Population Analysis and Record Keeping System SPARKS ISIS 2002 SPARKS has been used to enter and edit data validate the data to check for errors query the data for management and research purposes and export data to the analytical software used for population management including Population Management 2000 PM2000 Pollack et al 2002 ZooRisk Earnhardt et al 2008 and PMx Ballou et al 2011 The data maintained in SPARKS are supposed to represent the truth as represented in the respective records of each contributing institution or other source However for many species some studbook data are ambiguous e g unknown origins ages parentages and studbook keepers upon the advice of their PMC or SPMAG advisor often make plausible assumptions that facilitate use of studbook data for breeding and iransfer plans These assumptions are imposed before the data are exported to PM2000 ZooRisk and PMx One
127. box For more details see the installation instructions in Chapter 2 Getting Started in PopLink NOTE When changing the location of your PopLink folder all the associated files will be d yy moved and then the files in the previous location will be deleted Consequently if you ve ZC e Yi changed the location in the past but want to set it back to the default of My Documents you ll need to manually create a new folder titled PopLink in your My Documents folder hit Browse and then use the Make New Folder option and select that folder as your new location When creating a new folder highlight the desired location i e My Documents before selecting Make New Folder option Module Visibility The Module Visibility feature allows you to show or hide any or all of the optional modules only the Social Enclosures and Medical modules When selected the module s data tables will be visible and editable within PopLink and the associated reports will show up in the Reports menu When unchecked the module and its reports are hidden No data are deleted or lost when a module is hidden when toggled back on all the data previously entered will still be present As a default the three new modules are unselected and not shown Once selected and shown they will remain that way until you unselect them Settings PopLink Files and Databases Location C Users igazlay Documents Pop Link Module Visibility Show Socia
128. cepted Event date date of importation into PopLink Event Date Estimate None For individuals that were designated as contracepted neutered in SPARKS there may be further details on the date of that event if they were entered into SPARKS as a Contraception Note In PopLink these are stored in the Specimen Notes table Contraception Note they can be used to edit the Event date for the contraception event from the PopLink default date SEX DATA TABLE Sunbittern File Edit view Validate Reports Export Help D 4 el al k Select Filters As of 9 21 2009 AND Status Living Totals 59 47 12 118 at 51 Institutions No Sort Order Applied No Edits Currentness Date 6 2 2001 Studbook Edit Sey Event Date Event Date ID Est 438 a Mae 1 24 1998 None 441 Mae 6 23 1998 None 442 C Female 2 1 1998 None o 443 Female 8 6 1998 None AAA Unknown 7 10 1998 Nene o 446 a Mae 6 19 1997 None The Sex data table displays all sex events of each specimen including the recorded Sex the Event Date for when sex was determined and the Event Date Estimate PopLink recognizes five different possibilities for Sex status Female Male Unknown Abnormal and Hermaphrodite Unlike in SPARKS the sex of a specimen in PopLink is treated as an event stream rather than a constant state since the sex status of an individual can change during its life Many specimens may only have a single entry in the Sex Data Table i e specimens coul
129. cimen s Reproductive Status ns EM 12 Reproductive Status is invalid Research and correct the specimen s Reproductive Status l EM 13 Reproductive Date is blank EE this specimen s history and enter the Reproductive Date and EM 14 Reproductive Date is invalid 3 Research this specimen s history and correct the Reproductive Date ne Plas EE EE _ Enter the mnemonic for this event s location If the location is unknown Sas ee enter UNKNOWN e A specimen s first event must be either Birth Hatch or Wild Capture If _ Eeer atch _ the specimen is of unknown origin enter the first event as Birth Hatch EM 16 araid caou i at an unknown location using the best estimate possible for the H l _ Birth Hatch date The next event in the specimen s record should be a E T transfer to a known location ummm A specimen that has Go LTF or Release must have Return From LTF VT E E Te Or or Recapture prior to any subsequent event Return from LTF and EM 17 Balance even _ Recapture are new events added to PopLink that are not in SPARKS i Note that they are not automatically entered by PopLink and must be E eer entered manually mmm No events should occur after death Make sure all events and dates E TT DE after death oe entered correctly CIE eebe _ This check is only performed for live bearing species Review this EM 19 eae _ specimen s offspring and verify that the dam is correct Check that eg cone
130. cimen Notes tab can be used to add notes to a specific specimen s record You may either choose a Note Type from the drop down menu or enter your own description and enter your note into the Comment box You may also enter a date the note was edited If you wish to delete a comment highlight that comment and click the Delete button Version 2 3 February 10 2012 52 PopLink User s Manual Table 2 The Following Note Types Are Included In The Drop Down Menu Or You Can Enter Your Own Type If Desired Acquisition note Adult adult behavior Adult infant behavior Age estimate Aggression Animal management note Antlers horns Artificial insemination Behavior note Birth note Breeder Number Breeding encounter Breeding management note Breeding separation Broker Carcass note Carcass recipient Collection data Color phase Contraception Copulatory behavior Dam taxon Dam Sire Id s elsewhere Death note Death number Diet Disposition note Donor s name Egg information Egg lay date Electro ejaculation Environment Event Table Notes Fecal check worming Feeding Fledge date Foot management Fostering note Freezebnd General activity Genetic information Gestation behavior Grooming Group behavior Growth stage Handrearing note House name Version 2 3 February 10 2012 Human interactio
131. cimens with UNK MULT in pedigree Report page 117 This report includes individuals with unknownness anywhere in their pedigree e g for some specimens the parents may be known but there may be an ancestor with unknown parentage further back in the pedigree This report can quickly help you identify individuals in the current population that have any amount of unknownness in their pedigree Specimens with UNK MULT parentage and descendants Report page 117 This report includes all living and dead individuals with UNK or MULT for one or both of their parents This report includes columns for each individual that indicate the number of descendants they have in the living population both in the AZA population and in the total population helping you to prioritize individuals for pedigree research i e those individuals with the greatest number of descendants in the managed population should be prioritized first Unknown Age Report page 106 This report returns all living and dead individuals with a birth date estimate of UNK in your studbook database If these individuals make up a large proportion of your population you can check by looking in your Summary Counts Report page 102 or if many of these individuals are still alive it may be important to create birth date assumptions for the individuals in the table The table includes each individual s minimum age calculated as the minimum amount of time the individual has been living in a
132. could check the Specimen Notes Data Table for any specimens with Sexing Notes and edit the Sex Data Table to reflect these different sex events for more details on how to make these edits see page 44 EVENTS DATA TABLE Sunbittern E E File Edit view Validate Reports Export Help pelr alaz seert Bikers As of 9 21 2009 AND Status Living Totals 59 47 12 118 at 51 Insttutions Me Sort Order Applied Ne Edits Currentness Date 6 2 2001 Master Reproductive Sex Events Specimen Notes LE Studbook Overview SE Edit e ere Local ID a Tona a 8 Wild Capture S AMERICA NONE 1 1 1962 Year E o Transfer MAMIRARE Inge Yea E g Transfer NYBRONS o O 35 923 None e E E E 8 Transfer CLEVELAND 920543 5 28 1992 None 29 o Wid Capire BAHBLANCA NONE 14 193 en 29 Transfer CHASE Lion Year ee 52 Hatch HOUSTON 7974 7 21 1976 None The Events Data Table lists in chronological order by specimen all events that have occurred for each specimen in the dataset Information in the Events data table includes Transaction Code i e Event type Location of the transaction Local ID of the animal when included Transaction Date and Transaction Date Estimate PopLink recognizes eight different Event types Captive Birth Wild Capture Transfer to another institution Release into the wild Recapture from the wild Death Go LTF Lost to Follow Up and Return From LTF PopLink does
133. d Sex Female on 4 13 2004 shown in the User Interface Results Specimen 441 is included in the filter result set because although the specimen was not designated as female on 1 13 2004 it was female at some point in its lifespan and it was living as of 1 13 2004 Reproductive The Reproductive filter allows filtering of studbook data by three different reproductive types Not Contracepted Contracepted and Neutered Sterile select one or more of these types to set Reproductive filters PopLink will return all specimens that fit at least one of the criteria Like Sex data an individual can have multiple reproductive statuses throughout its lifetime this filter returns any individuals that have ever been a specific reproductive status Event The Event filter allows filtering of studbook data by eight different event types Birth Wild Capture Transfer Release Recapture Death Go LTF and Return from LTF To select Event filters check the box next to the desired option s PopLink will return all specimens that fit one or more of the criteria When combined with an As Of date filter PopLink will return all soecimens with the event on the as of date when combined with a During date filter PopLink will return all soecimens with the event occurring during the date span When combined with the Location filter PopLink will return all specimens that have Version 2 3 February 10 2012 74 PopLink User s Manual a giv
134. d be reliably sexed from birth however specimens that are not sexually dimorphic or where sex is not easily identifiable at birth could initially be classified as Unknown Sex until genetic testing or until reproductive maturity confirms the sex In a case where a specimen s sex is initially unknown or misidentified a specimen would have multiple entries in the sex data table For example in the table above specimen 485 was unsexed at birth its birthdate was the sex event date 7 18 2000 and was determined to be female after genetic testing on 10 2 2006 Upon importation from SPARKS PopLink takes each individual s SPARKS sex and creates a sex event for that individual as of their birthdate e g Sex Male Event date specimen birthdate Event Date Estimate any birthdate estimate that may exist Reproductive status e g Neutered or Contracepted is stripped out of these data fields in PopLink and thus males in PopLink include individuals designated as male contracepted male or neutered male in SPARKS females in PopLink include individuals designated as female contracepted female or neutered female from SPARKS There is no difference in translation of Unknown and Abnormal sex Version 2 3 February 10 2012 24 PopLink User s Manual In some versions of SPARKS when sex is edited for an individual specimen a note is automatically added to the SPECIALS file a Sexing Note with the date the change was made If desired you
135. d by reliable sources they fill the gap between partial information hints innuendos and suspicions on the part of individuals and institutions reporting to the studbook keeper Assumptions are usually specific to a single specimen or to group of specimens held at the same institution For example estimates of age to particular calendar years e g 1993 or 1994 would usually be considered minor assumptions It is difficult to generalize about what might be considered a minor assumption In most cases inclusion of minor assumptions in the studbook is dependent on the studbook keeper s good judgment Any assumption should be documented in the Specimen Notes for that specimen It is essential that all assumptions and conventions be documented in the database conventions should be discussed with the SPMAG advisor before they are applied to the studbook or analytical database Why Do We Need Analytical Data One of the main goals in creating analytical data is to fill in unknown data in a pedigree allowing us to more accurately estimate inbreeding and genetic variation within the population For a captive population the amount of genetic variation or more specifically gene diversity is typically estimated from the number of founding animals and the relationships among the founders living descendants Inbreeding which reduces gene diversity in a population and often creates health problems in individual animals is determined from the degre
136. d in your Primary studbook database folder When you double click on the report it will open in your default web browser such as Internet Explorer You can then save the reports as Word documents File gt Save As or by clicking on the Edit in Word shortcut button and edit as desired Comparing two versions of the same studbook option 1 above 1 Create PopLink databases for both studbooks you want to compare via the Open Create New dialogue box when the program is launched or the File drop down menu 2 Open your main studbook database this will be referred to as your primary database and would be the database you want to add any changes to 3 Under the File pull down menu select Compare Databases and when prompted select the secondary PopLink studbook to which you want to compare your main studbook A screen like this will be displayed Sunbittern File Edit View Validate Reports Export Help D O A ve DIFFERENCES BETWEEN PRIMARY SUNBITTERN AND SECONDARY TRUESUNO6 Export Master Sex Reproductive Events Specimen Notes Lt Studbook Overview The following records are in the primary database only Studbook Hatch Date ID Sire Dam Hatch Type Hatch Date Est Rearing Owner The following records are in the secondary database only gt Hatch Date Est Hatch Date Captive Hate 2 19 2006 Parent Not Reported 293 358 Captive Hate 5 15 2005 Day Parent Not Reported e L
137. d the death date should be entered as 1 September 19__ the Date Estimate for both these entries should be Year TIME RANGE ESTIMATES The next lower level of precision is a range i e plus or minus several months or years This level of precision denotes that an event took place within a range of months or years As an example if a transfer took place in 1991 or 1992 the mean date for that period e 1 January 1992 would be entered in the Transaction Date field and 1 YEAR in the Date Estimate field To estimate an event within a decade the mean date for the decade 1 January 19 D would be entered in the Transaction Date field and A 5 YEARS indicating a date range of plus or minus five years in the Date Estimate field PopLink will use the date entered in the Transaction Date field for demographic analysis this date must be the mean of the range of the date precision UNKNOWN DATE The lowest level of precision is an unknown date Unknown dates are created by selecting UNKNOWN in the Date Estimate field The UNKNOWN instructs PopLink to ignore any date entered into the Transaction Date field during analysis This removes these specimens from demographic analyses Specimens with unknown dates are still important and should be entered into the database because they are often necessary to establish genetic pedigrees How to Estimate Dates The use of date estimations by PopLink demonstrates the contradiction between the information in a s
138. dField E dbo OverlayUserDefinedFieldValue Es dbo Overview E dbo Reproductive ES dbo Sex E E E m E E 6 IMPORTANT NOTE Unless absolutely necessary do not manipulate the data displayed in the grid This will change the H E data in your database viewed through SQL E Server or through PopLink without tracking S i dias ei E changes within PopLink 2 3 E dbo UserDefinedFieldValue E dbo UserDefinedInstitution press v Community Help 15 Ke mability SR Table dbo Master Summary UniqueID i StudbookID Sire Dam BirthDate BDateEst LastAge LastStatus LastHouseN z t 1 1 WILD WILD 1 1 1879 12 00 Unknown NULL NULL NULL 23 2 2 WILD WILD 1 1 1881 12 00 Unknown NULL NULL NULL gt 3 3 WILD WILD Unknown NULL NULL NULL 4 WILD WILD 1 1 1907 12 00 Unknown NULL NULL NULL 5 5 WILD WILD 1 1 1907 12 00 Unknown NULL NULL NULL E 6 6 WILD WILD 1 1 1913 12 00 Unknown MULL NULL NULL yt 7 7 WILD WILD 1 1 1913 12 00 Unknown NULL NULL NULL ii y 8 8 WILD WILD 1 1 1916 12 00 Unknown NULL NULL NULL 9 9 WILD WILD 1 1 1920 12 00 Unknown NULL NULL NULL 10 10 WILD WILD 1 1 1921 12 00 Unknown NULL NULL NULL 11 11 WILD WILD 1 1 1921 12 00 Unknown NULL NULL NULL 12 12 WILD WILD 1 1 1925 12 00 Unknown NULL NULL NULL 13 13 WILD WILD 1 1 1926 12 00 Unknown NULL NULL NULL 14 14 WILD WILD 1 1 1927 12 00 Unknown NULL NULL NULL 15 15 WILD WILD 1 1 1928 12 00
139. dbook IDs that are temporary This list returns any non numerical Studbook Dst including hypotheticals Re number any temporary IDs to permanent Studbook numbers Leave any hypothetical specimen IDs as is Once the IDs are made permanent they may no longer be changed by this utility Non numerical IDs New ID T1052 Apply Close You can select any given non numerical ID and type in a permanent studobook number to change the specimen s ID permanently Unlike SPARKS PopLink will not prompt you with the next available numerical studbook ID You should look up the next available numerical ID before using the Re number Specimen tool Version 2 3 February 10 2012 70 PopLink User s Manual BATCH ENTERING DATA Users have the option to enter a batch of similar individuals which is especially useful when entering large litters or clutches This function can only be used when Entering a New Specimen e g selecting the New Specimen option from the Edit pull down menu To duplicate a new specimen 1 Click on the box next to Batch Input in the bottom of the specimen editor pop up window Enter the total number of duplicate individuals you want to create from the batch editor including the individual you are currently editing Enter all relevant information sex reproductive events social enclosures medical etc for the main specimen you ll be duplicating and select OK The Batch Editor Form
140. dified for clarity p116 t St i where d is the number of deaths and N is the number at risk and each age s survival probability is multiplied together By definition at the starting age for the analysis survivorship is 1 0 note that in the Descriptive report start age day 365 for the Analytical report start age day 0 for the Export report start age user defined Estimates in the table are made until the maximum longevity of the dataset if this is estimated based on user entry values are extrapolated from the oldest age at death in the sample to the estimated maximum longevity using an exponential decay function Klein and Moeschberger 1997 To calculate the exact median life expectancy where L 0 5 PopLink uses linear interpolation unless one of the Kaplan Meier estimates falls exactly on 0 5 If Xo Lo is the smallest survival time in days survival probability pair gt 0 5 x L is the largest pair lt 0 5 and x 0 5 is the pair of interest 7 La 0 5 x Xo l 8 l EE E K amp M equation 5 4 8 modified for clarity p116 Lo E L PopLink makes these calculations for pooled male and female data subsets For analyses that require separation by sex individuals with other sex codes including unknown sex abnormal sex hermaphrodite etc are distributed proportionally by sex ratio and infant mortality between males and females D deaths N number of individuals M males F females U
141. dividual s health This type of information can be helpful to query when looking for symptomatic trends in an individual or across a population of individuals In this category the Type and Start Date are the only required fields The End Date field can be used to reflect the duration of a Clinical Sign select the check box to be able to edit the End Date field Version 2 3 February 10 2012 64 PopLink User s Manual 2 Diagnostics Note Category Type Diagnostics v Urinalysis v Start Date 10 4 2011 Observer Comment g 1na urine sample collected voluntarily 10 4 2011 in the AM testing for signs of diabetes Instructions Apply Changes The Diagnostics category is intended to allow users to track any medical tests for an individual The Diagnostics can be specified by Type Chemistry Panel Culture Hemogram Imaging Serology TB Test Urinalysis Pathology Biopsy or Other For any Diagnostics type the Start Date should be the date the diagnostics were sampled or taken the note should be updated later in the Comment section to report the test results In this category the Type and Start Date are the only required fields NOTE The Diagnostics note type can be a useful tool in documenting medical tests and their N4 results Be sure to use complete and standard accepted veterinary language and avoid using d D shorthand think about how others would interpret the note and maintain standards ove
142. e Dam ID UNK _ Research the parentage of the specimen If the sire is already in the _ studbook use the sire s correct Studbook ID as the Sire ID If the sire _ is not in the studbook create a new specimen record for the sire and ee use that Studbook ID as the Gre _ Research this specimen s history and enter the Birth Date and RE ee eek A Estimate EH 11 Birth Date is invalid Geer this specimen s history and correct the Birth Date and Version 2 3 February 10 2012 78 PopLink User s Manual GAN ERROR DESCRIPTION HELP ASSISTANCE FOR ERROR e ei S Sex record is missing Enter sex information for this specimen aaa __EH 13 Sexis blank Research and enter the specimen s Sex EH 14 Sex is invalid Research and correct the specimen s Sex CeE __EH 14 Sexisinaid esea and coreci he Ee EH 15 Sex Date is blank _ Date is the date the specimen was identified as a given sex e g its _ Research this specimen s history and correct the Sex Date and EH 16 Sex Date is invalid _ Estimate The Sex Date is the date the specimen was identified as a _ This specimen has no Event records Research the specimen s history EH 17 Event record is missing and enter a first event for this specimen First event must be either ee _birth hatch or wild Capture mannan _FH 18 Transaction Code is blank Enter the event s Transaction Code EH 19 Transaction Code is invalid Correct
143. e desired row and alter any of the three fields in the data entry fields below and click Apply When an enclosure is edited in any of the three fields a dropdown history is visible in the User Defined Enclosures table Note that editing an existing enclosure s name will change all related data records in the Enclosures data table in individual specimen records Deleting Enclosures To delete an existing enclosure highlight the desired row from the User Defined Enclosures table and click Delete Note that once deleted there is no way to view deleted enclosures You will be prevented from deleting enclosures that are referenced in a specimen s record in the Enclosure Data Table even if there isn t anyone in the enclosure currently If an enclosure is extinct e g torn down or no longer used make note of it in the enclosure description instead of deleting the enclosure It may be helpful to rename Version 2 3 February 10 2012 60 PopLink User s Manual the enclosure in a manner that signifies that it is extinct e start it with a capitol X in front of the name to easily see that enclosure doesn t exist anymore i e XexhibitA NOTE Tracking Changing Enclosure Names Enclosures names evolve and change over time To capture and track that information edit the original enclosure name to reflect the newer name The old name will still be visible in the form of a drop down data history in the User Defined Enclo
144. e of relatedness between an individual s parents A complete and accurate pedigree is necessary to accurately assess both gene diversity and inbreeding and is therefore important in maintaining the genetic health of a captive population In addition to the benefits to population wide genetic analysis creating analytical assumptions to resolve an individual specimen s pedigree can ensure that that individual and or its offspring are included in a breeding and transfer plan Population managers don t typically make breeding recommendations for individuals with unknownness in their pedigree unless it is demographically necessary creating analytical assumptions for these specimens can allow them to be added to the breeding population Although there are costs to consider when making assumptions in an analytical studbook the genetic costs of leaving data true and accurate but unknown are generally greater than the cost of mistaken or incorrect assumptions Willis 1993 Analytical assumptions can also be important to demographic analyses For example if a large proportion of a population is wild caught with unknown birth dates those specimens cannot be used in Version 2 3 February 10 2012 126 PopLink User s Manual calculations of mortality or fecundity rates Although the specimens true birthdates can never be known it may be possible to make an analytical assumption based on the import history e g assume that all wild caught anima
145. e population s genetic and demographic identity When studbooks are published by studbook keepers these data are the primary focus of the document though the studbook keeper may also include information on the species biology and ecology the status and distribution of wild populations a bibliography of relevant publications etc Why Keep Studbooks Studbooks are primarily used for monitoring and managing populations in zoos and aquariums without studbooks it would be virtually impossible to manage populations scientifically In the Association of Zoos and Aquariums AZA the Species Survival Plans SSP and any other AZA managed programs use studbooks to manage specimens of a particular species at participating institutions as a single population Computerized studbook datasets provide accurate up to date information in a standardized format this standardized format enables detailed genetic and demographic analyses For example studbooks can be used to gain basic information about the current status of a population numbers of individuals genetic health etc to help make decisions about which specimens to breed based on the best genetic pairings and to help assess whether a population is stable increasing or decreasing in numbers Within AZA these decisions are generally made with the assistance of a population biologist from the Population Management Center PMC and or the Small Population Management Advisory Group SPMAG 1
146. e primary database The following records are in the secondary database only Studbook Event Date ID Event Date Est 548 Unknown 2 19 2006 None 549 Unknown 5 15 2005 Day EE labaa ZIAD o a a Me The folowing records differ in the two databases b For the bottom table on each tab you will be able to see the specific data field that is different between the two datasets e g in the above example specimen 1 has a rearing type of hand in the primary database and parent in the secondary database c Note that this data comparison does not compare the data in the Social Enclosures or Medical Data Tables 5 To resolve differences between the two datasets start with the Master table and click on the button at the bottom of the screen note that you can also simply use the database comparison tool to generate a list of potential changes and then edit existing specimens enter new specimens by hand through the Edit drop down menu A pop up editor will take you specimen by specimen through potential edits The pop up has each of the 6 data tables in order from top to bottom Master Sex Reproductive Events Specimen Notes and UDFs If discrepancies exist between the records in the two studbooks you are comparing those discrepancies will be shown and you have three options a Use the Accept button to apply what is in the SECONDARY database to the PRIMARY database e g moving data from the SECONDARY to t
147. ecimen s offspring _EM 02 Hatch Birth Type is blank Research and enter the specimen s Hatch Birth Type _ EM 03 Hatch Birth Type is invalid Research and correct the specimen s Hatch Birth Type EM 04 Hatch Birth Type incompatible If the first Location is known the Hatch Birth Type should not be _ with first Location unknown GE EERERRERERESEERERESEE REESEN EES EE EEC CEE EERE CECE EE EES Eee ere EEE ECE EES EEE CECE EEE SEE EES EEE EEE EEE EEE EE EES EE ITAA CEE TEES EEE TESTE EE CEC ER ET EEC ET ET CEC ERLE EEC EEEEEEC ET EE CEC EE EE CERECETEEEECECEETECECEECEEECEECECETEECECECEE CER EC EEE EE CELE EE EECEEEEEECEEEEEEEE EE TITEI ETETETT EE _ Hatch Birth Type incompatible EM 05 with parental 1D E E M 06 Rearing is blank Research and enter the specimen s Rearing type P EM 07 _ Rearingis invalid Research and correct the specimen s Rearing type EM 08 Birth Dates differ in Master and Review the dates and estimates and make sure they are exactly the _ Events table same i l _ Verify that these dates are entered correctly making sure no event EM 09 First event is before birth date occurs prior to the birth date Version 2 3 February 10 2012 79 PopLink User s Manual PRROR ERROR DESCRIPTION HELP ASSISTANCE FOR ERROR _ EM 10___ Reproductive record is missing Enter reproductive status information for this specimen l EI Reproductive Status is blank Research and enter the spe
148. ed e g pouch or nest cavity emergence to estimate the date of birth this can be based on the species biology or perhaps an observed change in the parents behavior Species Notes should describe how dates are back calculated The date when the young are first observed should be provided in Special Data Other conventions have been developed for species with multiple life stages and high fecundity eg some anurans In some cases especially with wild caught adult specimens or adult specimens from the private sector the studbook keeper may not have specific information on the individual specimens that would allow precise estimates However it is still important to estimate the birth date these estimates are important for demographic analyses In some cases a generic estimate may be appropriate conventions should be developed for generic birth date estimates see page 125 on conventions Dates should always be estimated to the smallest time unit possible If a standard estimated birth date convention is developed for the species it should be described in the Species Notes Although the studbook keeper may enter the birth date as an estimate all demographic analyses programs SPARKS PopLink PM2000 ZooRisk use the date entered as an exact date to calculate age specific demographic parameters Thus there are some specific rules to follow when making date estimates so that demographic parameters are less biased All dates should be entered
149. ed with a parent would be W LD BORN while a specimen born to a pregnant female collected from the wild would be CAPTIVE BORN CAPTIVE BORN should be used when it is known that the specimen was born in captivity whether or not the parents of the specimen are Known Fertilized eggs or gametes which were collected in the wild but which were born in captivity should be entered as CAPTIVE BORN but with W LD dam and sire UNKNOWN birth type should be used when the birth type is unknown and although there are some rare exceptions unknown birth type will usually be associated with unknown parentage unknown birth date and unknown birth location There is an important difference between captive born specimens with unknown parents and specimens with both unknown birth type and unknown parents In the former case it is more likely that the alleles carried by the specimen are carried by other specimens in the population In other words captive born specimens of unknown parentage are not considered possible founders under usual circumstances On the other hand specimens of unknown birth type and unknown parentage may be considered possible founders for analysis purposes only if it is determined that a wild caught origin is possible or likely given information in other data fields e g date of birth location of birth 4 Birth Date Birth Date Estimate The birth date should be entered as MM DD YYYY To express uncertainty about the date of birth bi
150. ee page 22 for calculation of estimated conception date All tables can be exported to Excel by right clicking on the table and selecting Export to Excel Note that for informational purposes dams and sires with Unknown birth estimates are displayed in the nine tables in the Reproductive Report in PopLink Ages at birth for these individuals are not used to calculate any of the mean median statistics displayed at the top of some tables In addition to the nine tabs the reproductive report displays the number of reported dams with offspring the number of offspring Male Female Unknown Abnormal Total born to those dams the total number of offspring born to UNK MULT dams the number of reported sires and the number of offspring Male Female Unknown Abnormal Total born to those sires The nine tabs display 1 Litter Size The litter size tab lists all observed litter sizes and the frequency and percentage of each litter size within your studbook and filter restrictions Note that litters are defined based on the Maximum Birth Hatch Date Range defined in the Studbook Overview table Sunbittern Reproductive Report REPRODUCTIVE REPORT Si Species Type Egg Laying Incubation Period 28 Days Maxirnum Hatch Date Range For Clutch Mates 3 Days 45 reported dams with 132 123 174 429 offspring not including 33 offspring of UNK MLLT dams 45 reported sires with 130 123 172 425 offspring All ages are at dam conception Select Fi
151. eeder that likely got his or her specimens from the wild or another source that is unrelated to the rest of the population and probably from the wild or 2 UNK if they probably are or were specimens in the studbook population but there is no information on who they were If names or ID numbers exist for the dam and or sire but nothing else is known about them it is tempting and easy to enter those names in the Dam and Sire fields because this would avoid creating studbook records for the newly discovered dam and sire Any Dams Sires without their own individual studbook record are treated as Unknown parents Therefore a studbook record should be created for each parent making it explicit what is and is not known about them Every entry in the dam or sire field should either match the studbook number of a specimen in the studbook or be WILD or WILD1 WILD2 etc UNK or UNK1 UNK2 etc or MULT or MULT1 MULT2 etc Dam and Sire Are Unknown If truly nothing is known about the parents of a specimen then dam and sire should be entered as UNK This would be the case if the specimen might be either wild caught or captive born If parents are unknown but the specimen came from the wild then the specimen is wild caught see above Dam and sire would also be entered as UNK if the specimen was born in captivity but there is no information on who the parents could have been One parent might be known but the other parent is unknown perha
152. efine the population of individuals at risk for events So if a demographic window of N America 1 1 1980 1 1 2006 is selected the data in the life table would include e For individuals born in North America after 1 1 1980 and before 1 1 2006 all data on their life from birth to the point when they leave the risk window e g die or are transferred out of N America or it closes e g they are living in North America on 1 1 2006 e For individuals living in North America on 1 1 1980 all data on their life from 1 1 1980 until they leave the risk window or it closes e For individuals living outside of North America on 1 1 1980 but transferred into North America after that date all data on their life from their date of transfer until they leave the risk window or it closes Data on individuals with unknown birthdate estimates are not used in any life table calculations because the specimen s age cannot be calculated The Life Table tabulates age and sex specific probabilities of death and birth based on the historical data derived from the studbook Separate life tables are constructed for males and females The life table PopLink exports to PM2000 and PMx has the following variables e Age Class x e Number Alive per Age Class e Age Specific Mortality Rate Qx the probability of dying during a specific age class e g between the ages of 0 1 or 5 6 years of age Calculated for each sex as the number of deaths per age class
153. efined Fields tables for an individual Secondary Tab Main Secondary Social Events l Event _ Event Date Date Est Outcome Comment Related Specimen i Introduction visual 10 7 2011 None 56 123 139 473 R Introduction full 10 7 2011 None 0 473 570 Enclosures Enclosure Name Enter Date Enter Date Est Exit Date Exit Date Est Comme 1 OUT 3 CHICAGOLP 1 1 2011 None 10 7 2011 None 2 INDOOR CHICAGOLP 10 7 2011 None None Medical Notes Category Type Value Unit of Measurement Start Date End Date Obsern 1 Diagnostics Culture 10 7 2011 tg 3 Medication Anti parasitical 25 Milligram s 10 7 2011 tg ili The Secondary tab displays the data recorded in the optional Social Enclosures and Medical modules This tab is only shown when at least one of the three modules is shown in the Settings options Long comment fields in Specimen Notes Social Events Enclosures and Medical Notes may be difficult to view within the Specimen Report To view the entire specimen note description double click on the Note number A Notes text box will pop up that displays the specimen note in its entirety Version 2 3 February 10 2012 99 PopLink User s Manual STUDBOOK REPORT The Studbook Report produces a formatted table of specimens option you will be prompted to set specific options for the report Studbook Report Parameters Select setup options for this report below Estmated
154. emonics are simply incorrect e g a real mnemonic and institution exists and you may have mistyped the mnemonic or not known what the correct mnemonic was or if the mnemonics are truly unique e g the institution does not yet exist in the standard ISIS list of institutional names The pop up window has two cases of unrecognized mnemonics CB Clean Up Mnemonics CH Val Clean Up Mnemonics PopLink found a recognized mnemonic for PopLink could not find a recognized your unrecognized one mnemonic for your unrecognized one Double check if this is the correct institution and If this institution is not in the institution list click click Apply if it is Add to create it as a user defined institution If it is correct the speling of the mnemonic and click Apply Unrecognized Corrected Mnemonic Unrecognized Corrected Mnemonic Close In the left hand case PopLink has matched your unrecognized mnemonic to an existing ISIS synonym mnemonic synonyms are used to link different versions of the same institution such as CHICAGOLP the true mnemonic with LINCOLN LINCOLNPK LPZS The Corrected Mnemonic will be the institution s true ISIS mnemonic You can use the find button to open the Institution List and double check whether the Corrected Mnemonic is what you meant with the unrecognized mnemonic and click Apply to correct your unrecognized mnemonic Version 2 3 February 10 2012 86 PopLink User s Manu
155. en event occurring at a given institution For example you may filter for all individuals born at a given institution Birth Type The Birth Type filter allows filtering of studbook data by three different birth types Captive Born Wild Born and Unknown these are based on the birth type field in the Master data table To select Birth Type filters check the box next to one or two options If two options are checked PopLink will return all specimens that fit either criterion Parent The Parent filter allows filtering of studbook data by ten different parent types individuals for which Either or Both parent s are Wild Unknown MULT Hypothetical or Blank To select Parent filters check the box next to at least one and no more than nine options PopLink will return all specimens that fit at least one of the criteria Rearing The Rearing filter allows filtering of studbook data by six different rearing types Hand Parent Foster Colony Group Unknown and Not Reared To select Rearing filters check the box next to at least one and no more than five options PopLink will return all soecimens that fit one of the criteria Breeder The Breeder filter allows filtering of studbook data by two breeding histories Has Bred and Has Not Bred The breeder non breeder designation is based on whether an individual is indicated as a parent in another individual s sire or dam column Individuals that are possible parents as
156. enetic views for export The filters displayed in the boxes are defaults Demographics Genetics Select Filters Select Filters The following are defaut fiters e The following are defaut fiters Locations N AMERICA AND During Locations N AMERICA AND As of 1 1 1900 10 7 2011 AND Status 10 7 2011 AND Status Living Living Ok The file names are defaults that are chosen based on your database name you can change the file names if you desire but you should not change the extensions prn and csv for demography files ped for genetics files For demography PMx can import either prn files or a more detailed file All Individuals Demographics File a csv file For both the Demography filters chosen will limit your studbook database to a specific population that will be used to calculate life table parameters M Qx Lx etc for the prn files or which individuals are included in the csv file The chosen filters will be displayed in the filter box you should change the default filters to your desired demographic window which is generally the period of modern management for your species You can also set other filters in addition to date and geographic windows The Genetic filters are used to create the list of individuals that will be considered living individuals in your current population PopLink exports this list of specimens and their pedigree information to PMx If desired you can change the default filters usi
157. ent after Go LTF or Release Event if your database has death events directly after Go LTF events the individual s age at death is not usable in the Survival Analyses Removing the Go LTF event or having the individual Return from LTF before death will ensure that the data are included See the Validation section of the manual for more details EM 18 Events after Death this error like EM 17 signals some uncertainty around the terminal events for an individual the death events which the Survival Tool is trying to analyze The PopLink Age Outliers report check for data errors and impossibly old individuals if there are undead individuals in your studbook that are no longer tracked but have likely died these individuals may skew your Survival statistics Once you ve evaluated data quality issues in your studbook select the Survival Tool option in the Reports menu You are prompted to select which type s of analysis you d like to run Survival Tool Selection Sele Select the types of survival analyses to conduct below y Descriptive Survival Statistics for communication purposes Analytical Survival Statistics for populaton management Expert Survival Statistics Customize my M analyses by using Olas the starting age in days where Lx 1 Generate a Comparative Advanced Results table for the analyses selected above Ok Cancel You can run single or multiple reports at once For the Expert Survival Statistic
158. eport Ok Cancel This editor displays the True data for the specimen and any Analytical Changes that may have been made for the specimen rows of Analytical data will always apply to the True data row directly above them e g in the Events table where there may be multiple True data rows The five tabs allow analytical edits on specific fields most relevant to analytical assumptions parentage sex reproductive status and types and locations of transactions Where relevant PopLink fills in other fields with data that will not affect analyses or that does not require analytical assumptions clicking the Additional Options button shows those fields You can use the Specimen Notes tab or the Notes buttons on individual editing screens to enter comments about the assumptions you re making Any notes will be stored in the overlay only not in the True data and will be stored with codes indicating that they refer to Analytical data Master Sex Reproductive Events Specimen Notes Description Comment ld Studbook Number T1112 Master Analytical Notes UNKs made WILD based on parsimonious parentage ass True Data Hypothetical For Sex Reproductive and Event data you can 1 modify an existing event by creating analytical assumptions or 2 add a new completely hypothetical event For example on the Events tab if the final transfer for specimen 467 was actually to CHICAGOLP you would highlight the True Data
159. er transfer back to an institution that does report to a studbook keeper Return from LTF or if the studbook keeper receives information about an event e g a specimen death after a long period of non reporting An individual is considered lost to follow up during the period time when its status is unaccounted for Specimens that have gone to a non reporting institution and may have or probably have died should never be killed off in the studbook they should be considered lost to follow up unless a record of death can be provided Presumptions of deaths that are entered into the studbook may severely bias demographic analyses lost to follow up removes the specimen from the life table without the presumption of death Under no circumstances should a death date be assumed or arbitrarily assigned for any specimen There are three general situations in which a specimen can become lost to follow up 1 Transfer from a known location on a known date to a known location eg out of the region for a regional studbook and subsequently not tracked 2 Transfer from a known location on a known date to an unknown location and 3 Disappearance death or transfer from a known location on an unknown date if transfer to an unknown location An example of the first situation is a transfer of a specimen to a location that does not or historically did not keep records Therefore although it is known when and where the specimen was seni there is no
160. es AZA Conservation Endowment Fund International Species Information System ISIS Zoological Society of San Diego Arcus Foundation PopLink is shareware distributed free of charge by the Lincoln Park Zoo The software and the manual are not guaranteed to be free of bugs and errors and the user is responsible for insuring that the application of PopLink is appropriate to the problem at hand PopLink is owned and copyrighted by Lincoln Park Zoo but not copy protected Individuals can hereby make unlimited copies of PopLink for the purposes of population management research and education Manual citation Faust LJ Bier L Schowe K Gazlay T 2012 PopLink 2 3 User s Manual Lincoln Park Zoo Chicago IL Software citation Faust LU Bergstrom YM Thompson SD and Bier L 2012 PopLink Version 2 3 Lincoln Park Zoo Chicago IL ACKNOWLEDGEMENTS This manual was written with editing help and text from many people including Kristine Schad Carrie Schloss Sarah Long Steve Thompson Kate Schowe Nathan Gudritz Amanda Kamradt and Talia Gazlay Sections of the manual are based on Thompson S D Earnhardt J M and Turner Erfort G 1997 Guidelines for Data Entry and Maintenance of North American Regional Studbooks Lincoln Park Zoo Chicago Illinois Version 2 3 February 10 2012 PopLink User s Manual Table of Contents Chapter 1 INTRODUCTION and OVERVIEW cccsssseessssseescssseessenseessenneees 9 INTRO
161. estimates of key survival parameters 1 Can the median life expectancy be calculated The median life expectancy cannot be calculated if there are not enough deaths relative to the size of the living population in your subset of data 2 Is sample size number of individuals at risk greater than 20 individuals at the median 3 Is the 95 Confidence Interval Cl bounded That is are both limits to the 95 Confidence Interval defined 4 Is the sample size in the first age class of analysis e g the first day of analysis greater than 30 individuals 5 Is the length of the 95 Cl lt 33 of the maximum longevity lf a data subset pooled male or female fail any of these tests results for that data subset are viewed as unreliable and are not reported Statistical comparisons of male and female survival statistics are used to determine whether data can be pooled together or need to be separated by sex If male and female survival patterns are not found to Version 2 3 February 10 2012 143 PopLink User s Manual be statistically significantly different PopLink reports results for a pooled dataset in which sex is ignored this has the benefits of increasing sample size and therefore reliability of estimates if there are no true differences in survival between males and females If significant differences are found PopLink reports information for males and females separately in this case unknown sex individuals in the sample are propo
162. esults for either that subset or pooled data will be displayed You can see why the subset failed by looking at the results of the five data quality tests in the Data Quality Table You can use the EXPORT button to send the Report and the Included Individuals table to files in your studbook databases folder The Report is exported as DESCRIPTIVE SURVIVAL STATISTICS REPORT htm and can be opened in your default web browser by double clicking on the file or in Word by right clicking on the file and choosing Open With Microsoft Word The Included Individuals table is exported to DESCRIPTIVE SURVIVAL STATISTICS INCLUDED INDIVIDUALS TABLE csv and double clicking will open the table in Excel Version 2 3 February 10 2012 145 PopLink User s Manual ANALYTICAL SURVIVAL STATISTICS REPORT The Analytical Survival Statistics Report calculates its statistics based on a starting age of 0 days all animals in the window are included in the analysis After selecting the Analytical Survival Statistics Report option and setting your demographic window PopLink produces a report with multiple tabs Summary Included Individuals Table Data Quality Table Kaplan Meier Statistics Table Kaplan Meier Graph 30 Day Mortality Graph Age Based Life Table and Advanced Chimp06 Analytical Survival Statistics Report ANALYTICAL SURVIVAL STATISTICS REPORT ANALYTICAL SURVIVAL STATISTICS REPORT CHIMPANZEE Studbook FAN TROGLODYTES NORTH AMERICAN RE
163. even wiet Zoe ba vc LI nbn 2 fon AMAL Lef TN Th ae e wb blot PI anwacten a Rearing L Hatch Type Hatch Date eeu Wild Hatch 7 1 1948 Unknown Hand Not Reported WILD WILD Wild Hatch 7 1 1948 Unknown Parent Not Reported WILD WILD Wild Hatch 7 1 1954 Unknown Foster Not Reported WILD WILD Wild Hatch 7 1 1954 Unknown Parent Not Reported vi Studbook ID Rearing Resolve Differences In True Database 4 Each tab shows specimen by specimen differences between your two studbooks for each PopLink data table The top two tables on each tab will show specimens that are either unique to the primary database or unique to the secondary database the final table will display specimens that are in both databases but have differences in particular fields A few key points Version 2 3 February 10 2012 82 PopLink User s Manual a On the Master tab the top two tables will display entire individuals unique to either database The other tabs Sex Reproductive etc will display individual events sex events reproductive status events transaction events that are different between the two datasets For example specimen 548 above is in the secondary database and not the primary it appears that the secondary dataset may be more up to date than the primary one When you look at the Sex table you see that in the specimen s Sex events as well as they would also not be found in th
164. for STATUS and DATE cannot be changed for the age report however additional filters for other fields may be selected The three tabs display 1 Age Pyramid for Known Age Known Sex Specimens Sunbittern Age Pyramid Report Age Pyramid Report Known Age 56 46 12 114 Unknown Age 3 1 0 4 Sala Pas As of Sf21 2009 AND Status Living Age Pyramid Known Age Known Sex Detailed Age Pyramid Talies By Birth Hatch Type 40 hJ CH Age Class Ech CH 5 0 Number of Specimens This figure will give a general picture of the population s age structure Note that any unknown sex and unknown age individuals are not included in this pyramid you can see how many individuals are excluded by looking at the Known Age and Unknown Age totals directly below the report title Version 2 3 February 10 2012 103 PopLink User s Manual 2 Detailed Age Pyramid HE Sunbittern File Edit View Validate Reports Export Help D F El vel Age Pyramid Report Known Age 55 43 12 110 Unknown Age 0 1 0 1 Select Filters ke of 11 14 2006 AND Status Living gecccoceccocccsccsccecsoccesocccseccscecsscecssococceccseccsocesseecssecsssecssceeg Age Pyramid Known Age Known Sex Detailed Age Pyramid Tallies By Birth Hatch Type SE IEE SES EE Color By Sex Male Female Unknown and Abnormal 472 482 468 et hg 3 pee ey Cag ey A The detailed age pyramid lists specific soecimen numbers for individuals i
165. h to delete a database highlight it and select Delete Database at the bottom of the window To escape from this window at any time you may click on the Cancel button on the bottom right of the window Studbook databases created in previous versions of PopLink can be read by PopLink 2 3 Your 1 3 2 1 and 2 2 databases will automatically be moved into 2 3 upon installation See the following section about moving studbooks if your databases are not automatically moved If your studbooks from previous versions of PopLink violate any of PopLink 2 3 s naming restrictions including starting with numbers or incorporating spaces dashes slashes or other restricted characters the program will prompt you that your studbook name is invalid If this error message pops up use Windows Explorer to navigate to C Documents and Settings User Name My Documents PopLink PopLink Databases and rename the studbook folder with a name that does not violate SQL naming restrictions You can then open the studbook through the Open Databases dialogue box Version 2 3 February 10 2012 16 PopLink User s Manual SETTINGS PopLink Files and Databases Location C Users tgazlay Documents Pop Link Module Visibility V Show Social Events module Iw Show Enclosure module Jk Show Medical Notes module The Settings pop up allows you to specify where you want your PopLink files and databases as well as their exports and reports to be stored The
166. hapter 5 include a geographic criterion e g North America and a date criterion so it is important that the studbook record where each specimen was located at every point in its history 2 Location Locations in PopLink should be entered as the institutional mnemonics the letter codes used in SPARKS e g CHICAGOLP for Lincoln Park Zoo AUDUBON for Audubon Park and Zoological Gardens Use the Find button to lookup an institutional mnemonic when necessary you can also use the Institution list xls file in My Documents PopLink to quickly look up mnemonics and institutions If you have an institution that does not have an institutional mnemonic in the PopLink institution file you can create your own see page 86 for more details on that process If you attempt to enter an unrecognized mnemonic one that is not in the Institution List or the User Defined Institutions List as a location in your Event data entry a pop up window will be displayed allowing you to add information about that institution After you click OK the new institution is added to the User Defined Institution list Version 2 3 February 10 2012 47 PopLink User s Manual 3 Local ID B Guidelines Note 15 Local ID The institutional accession number entered into the Local ID field is a unique number used to identify the specimen in the institution s collection inventory If the accession number is unknown enter UNK House names band numbers tattoo num
167. hat if you found an error on a previous validation and fixed it it will not be displayed in the list PopLink does not run any validation tests for the Social Enclosures or Medical Data Tables The columns to the right of the Current column display the specimens which have a given error and clicking on them links to that specimen s Specimen Report Table 3 57 Errors Used in PopLink Data Validation Gone ERROR DESCRIPTION HELP ASSISTANCE FOR ERROR _ Double check your currentness date in the Studbook Overview Table TE E E ihan _ If the currentness date is out of date please update it The currentness EH 01 date is the last date you did a complete update of your studbook i e one se _ solicited taxon reports from all holding institutions and entered those data into SPARKS or PopLink _ Determine if these are two different specimens If they are different specimens assign a new Studbook ID to one If they are the same EH 03 Studbook ID is not unique specimen consolidate the information into one record Include a note _ in the specimen s record explaining the Studbook ID change Verify _ that the parental ID is correct for the specimen s offspring _ Research the parentage of the specimen If the dam is already in the _ studbook use the dam s correct Studbook ID as the Dam ID If the dam is not in the studbook create a new specimen record for the dam and use that Studbook ID as th
168. he PRIMARY b Use the Delete button to delete a row of data that is in your PRIMARY database and not in the SECONDARY database c Leave the data in the primary studbook as is by clicking Next to move onto the next specimen Version 2 3 February 10 2012 83 PopLink User s Manual Resolve Differences Between Primary Sunbittern And Secondary Truesun06 Specimen 1 Studbook Hatch Date ID Est 1 WILD WILD Wild Hatch 7 1 1948 Unknown Hand Not Reported 1 WILD WILD Wild Hatch 7 1 1948 Unknown Parent Not Reported Accept Rearing Owner True Sire Dam Hatch Type Hatch Date Studbook a ee Date Event Date True ID Est Studbook Reproductiv Event Date Event Date True ID e Est Studbook Transaction ID Code SE Description Comment True 1 Breeder Number 12 Delete Studbook ID Transaction Transaction Location Local m Date Date Est True NOTE Be extremely careful as you are deleting or adding data to your Primary dataset there is no UNDO option in PopLink Make sure you consider which data are valid before the Studbook IDs for each type of data e g clicking on one of the white 4s and the purple 3 ur Sh Ji clicking accept You can compare specimen reports from each studbook by clicking on oi E 6 f 4 in the screen above You can see a complete set of differences between datasets by exporting a report Be careful
169. he Sex Date and oe Reproductive Daie ue Research this specimens history and correct the Reproductive Daie aan ue 89 Estimate nn EL 12 Reproductive Date is invalid Research this specimen s history and correct the Reproductive Date e ANd EstiMa e cnn ela EE ER E EE Ge this specimen s history and correct the Transaction Date and GE EE EE E Er _ Research this specimen s history and correct the Transaction Date and _ Estimate Version 2 3 February 10 2012 PopLink User s Manual After running data validation you should use this report to clean up any errors that can be resolved Errors that cannot be resolved or are not true errors should be noted in your Specimen Notes so that next time you run Data Validation and start to clean up that specimen you know that you already attempted to resolve their data error Version 2 3 February 10 2012 81 PopLink User s Manual DATABASE COMPARISON TOOL This tool highlights all differences between two studbook databases You can use the Database Comparison Tool for 1 Comparing two versions of the same studbook and resolve differences between the two 2 Importing analytical assumptions into PopLink from an existing analytical studbook for more information on analytical assumptions see Chapter 9 Note that clicking Export will produce a report listing all of the identified differences this report will automatically be displayed in HTML format and also save
170. he individual as unknown sex Again the Event Date and Event Date Estimate are autofilled with the birth date and birth date estimate when entering a new individual If the sex is identified later in the specimen s life e g at sexual maturity or through genetic testing add an additional sex event for the specimen with the appropriate Sex and the date which the individual was officially sexed in the Event Date Event Date Estimate fields If an individual is initially misidentified as one sex and then determined to be the opposite sex it is important to enter two separate sex events For example if an individual is misidentified as a female at birth it will have a first sex event female on its birthdate if it is later found to be male the studbook keeper should enter a second sex event with an event date of the date the new sex was determined Tracking changes with multiple events in this way will show population managers that this specimen may have originally been managed as a female and may help with interpretation of reproductive success e g if the individual did not reproduce because it was paired for breeding with a male An existing sex event should only be directly edited in the event of a data entry error In all other cases sex should be recorded as a data stream i e changing the sex by adding a new sex event rather than editing the current sex Version 2 3 February 10 2012 44 PopLink User s Manual Use the Notes b
171. he removal date estimate field 8 Return from LTF events Recapture events SPARKS does not have these transaction codes These events are translated as TRANSFER events to the event location on the event date This means that a A return from LTF will trigger SPARKS Error T 08 Embedded Lost To Follow Up b A recapture event may trigger SPARKS Error T 06 Transfer after release 9 UDF field types PopLink stores all UDF fields as character fields while SPARKS allows character numeric date fields etc When exporting all UDFs are exported as character fields even if the data held within them are of another format 10 Because PopLink does not track some specific events allowed in SPARKS non physical events ownership events management group in out surplus and social in out events all events in the PopLink export are translated as physical events in which no loan is involved in the Moves dbf file Physical True Owner True 11 ID character lengths Because SPARKS limits the length of ID fields any individual in PopLink with a studbook ID Dam or Sire ID of more than 6 characters will be displayed in the SPARKS Export Errors report and given a new default value of EX1 EX2 and so on You should reassign other studbook numbers in SPARKS to fix these default values 12 Unrecognized codes you should run PopLink data validation before you do your SPARKS export and check for any errors associated with invalid data types including
172. hin zoos and to population biologists the individuals responsible for editing the data for use in genetic and demographic analyses upon which management decisions are based How to Use This Manual PopLink was designed with on screen clarification and help in the user interface to make using the program as easy as possible This manual contains additional background and explanation on PopLink s features as well as information on how to appropriately enter specimens based on the Guidelines for Data Entry and Maintenance of North American Regional Studbooks Thompson et al 1997 Although this manual includes details on management of Association of Zoo and Aquarium AZA managed programs and studbook guidelines PopLink is a program that can be used with studbook data from any region A couple of special aids will help orient you throughout the manual Ur NOTE There will be special reminders here that will alert you to important points or Y explain confusing concepts STUDBOOK GUIDELINES INFO This icon will indicate information that has been adapted from the 1997 Guidelines for Data Entry and Maintenance of North American Regional Studbooks Thompson Earnhardt and Erfort 1997 POPLINK CHANGE This icon will indicate specific alterations to a studbook s data made by PopLink These alterations may change the way that data are stored displayed or recorded compared to how they were entered in SPARKS Although PopLink contain
173. his was due to SPARKS data entry methods for ownership nonphysical and other physical events This issue is eliminated in PopLink because current owner if tracked is a state in the Master record rather than an event in the Event record For some species ownership information may be useful to the operation of cooperative management plans When there is a special reason to track ownership it is possible to do so in SPARKS However the studbook keeper should only track ownership when 1 it has been discussed and requested by a management group or population manager 2 complete ownership data are available for every living specimen and 3 ownership data are carefully verified upon entry into the database to avoid mistakes Ownership issues concerning SSP or other recommended moves require communication directly between the institutions involved the Species Coordinator is not responsible for tracking ownership per se REPRODUCTIVE DATA TABLE Sunbittern File Edit view Validate Reports Export Help D S 4 al se Glas El Rare As of 9 21 2009 AND Status Living Totals 59 47 12 118 at 51 Insttutions Ho Sort Order Applied Meo Edits Currentness Date 6 2 2001 SE Edit Reproductiv Event Date Event Date a e Est 66 Not Contrace 3 26 1981 None 76 a Not Contrace 10 5 1982 Nome 77 a Not Contrace 2 2 1983 Here 87 Not Contrace 10 31 1983 None J 88 Not Contrace 11 11 1983 None 95 a Not Contrace 8 17 1
174. iagnostic Sampling Start Date 10 4 2011 Observer Comment tg biopsy of growth on right thigh Instructions Apply Changes The Medical Procedure category is intended to track any physical procedure or medically related event with Types Diagnostic Sampling Medical Exam Sedation Surgical Procedure Visual Assessment Prescription or Other Use the optional Comment text box to detail the Type of Medical Procedure and any accompanying follow up In this category the Type and Start Date are the only required fields 7 Medication Note Category Type Medication v Anti fungal v Value Unit of Measurement Start Date End Date 5 Ounce s 10 4 2011 iv 10 18 2011 Observer Comment g na topical preparation applied to affected area 2x daily during morning and evening feed sessions for 14 days Instructions Apply Changes The Medication Note category is intended to document the Type of medication Analgesic Antibiotic Anti fungal Anti Inflammatory Anti Parasitical Behavioral Modifier Cardiac Modulator Contraceptive Gastric Motility Gastroprotectant Hormone Nutraceutical Respiratory Product Topical Preparation Vaccine or Other Value numerical amount administered in one dose Unit of Measurement Microgram s Milligram s Gram s Kilogram s Pound s or Ounce s and the Start End Dates for a medication In this category the Type Value Unit of Measurement and Start Da
175. ial interactions enclosure social group history and medical notes INSTALLATION OF POPLINK PopLink is available for download at www l pzoo org poplink To obtain a copy on CD email software Ipzoo org Software requirements for running PopLink e net framework 1 1 e nei framework 2 0 SQL Server Express 2005 Note that if you are installing on a machine with Windows Vista or 7 you must have administrator privileges to proceed with installation If you don t have administrative privileges have an administrator install for you see instructions in the InstallReadMe file in the PopLink 2 3 download folder To install PopLink 1 Download the current zipped version of the program and save it to your computer 2 Unzip the downloaded file PopLink 2 3 zip into a folder you designate on your computer 3 Open the InstallReadMe file and follow the instructions to install PopLink 2 3 and SQL Server Express 2005 Once you ve completed these steps the installation automatically puts a PopLink shortcut on your desktop and you re ready to start PopLink 2 3 If you have a previously installed version of PopLink 1 3 2 1 or 2 2 PopLink 2 3 will automatically move your studbook folders into PopLink 2 3 for you If you have an earlier version PopLink 1 0 1 2 you can move your studbooks between the two versions by copying and pasting studbooks into C Documents and Settings User Name My Documents PopLink PopLink Databases See the manua
176. ight be appropriate if you are interested in determining survival parameters from a specific point in a species life history For example for bird populations it might be appropriate to look at survival from fledging rather than from starting at 365 days the first birthday the methodology used in the Descriptive report For bear populations it might be appropriate to look at survival from emergence from the den as the quality of studbook data may be questionable e g institutions may inconsistently report how many individuals were born be unable to estimate how many were born and died before emergence etc For species in which most individuals are wild caught and few births are recorded sample sizes may not be appropriate in the early ages The decision on the starting age for analysis should be made by those who understand how to interpret the patterns in mortality After selecting the Expert Survival Statistics Report option and setting your demographic window PopLink produces a report with multiple tabs Advanced Included Individuals Table Data Quality Table Kaplan Meier Statistics Table Kaplan Meier Graph Version 2 3 February 10 2012 147 PopLink User s Manual E ChimpO6 Expert Survival Statistics Report A i Sele EXPERT SURVIVAL STATISTICS REPORT Data Quality Table Kaplan Meier Statistics Table Description Pooled ANALYSIS WINDOW BACKGROUND Type of analysis Expert Analysis window start date 1 22 1980 Analysis
177. ils like the enclosure s the event took place in possible precursors or warning signs leading up to an event details of the interaction and justification for the assigned outcome For example a Comment for a Breeding Interaction could say OS o e Master Sex Reproductive Events Specimen Notes UDFs Social Enclosures Medical Related 56 83 Breeding Interaction 9 28 2011 None 56 Kiana and 83 Yaki Event Event Date Date Est Outcome Delete Event Type Event Date __ Event Date Estimate Breeding Interacton 9 28 2011 None Feed MM DD YYYY Outcome Related Specimen Comment 56 Kiana and 83 Y aku copulated for the first witnessed tme Instructions This occurred around noon n the off exhbt holing area directi after a feed For the last few days Yaku had been showing increased folow time with Kiana and she had presented to Yaku earber today l Batch Input Ko Ok Cancel The Comment section is completely optional no information is required As a studbook keeper it is your responsibility to determine the type and level of information recorded and to enter that information consistently Deleting Individuals From Events And Deleting Entire Events When a social event is created in a specimen s record the event is anchored to the individual it was first created in that individual will be listed first in the Related Specimens field If you want to delete one of the non
178. in both studbooks was simplified with SPARK plug software which introduced the concept of an overlay a record which allows changes to specimen records without altering the original studbook After analytical changes are completed within the SPARK plug overlay SPARK plug uses the overlay and a copy of the original studbook to create a new separate analytical studbook The overlay with assumptions and other changes existed as a separate file that could be applied to an updated version of the studbook each year removing the need to maintain two separate studbooks Although this system made maintenance of analytical data simpler it was still a confusing and clumsy process due to the complicated user interface in SPARK plug PopLink was designed to simplify the process of creating and applying analytical data In PopLink your true data is maintained in your main studbook database Like in SPARK plug analytical data is maintained in overlays in PopLink However unlike SPARK plug you do not need to create an analytical studbook XXNAME or a second database to use your analytical data Instead you can simply add your overlay to your main studbook database before exporting it to analytical software e g PM2000 PMx or ZooRisk Also your overlays are stored with your studbook ensuring that the true and analytical data will never get disassociated PopLink simplifies the storage of your data but the same philosophy of what you keep in yo
179. in PopLink There are three mechanisms to provide assistance while you re working with PopLink 1 You can refer to your printed or electronic version of this manual The electronic version can be downloaded from the website or opened through the Help menu in the software 2 While in the program help text is provided on the screen If you hover over icons tool tips will appear describing the function of a particular icon 3 If you have specific questions that are not addressed in the manual you can contact the software developers at software lpzoo org or the Studbook Analyst in AZA s Population Management Center at studbook lpzZoo org BACKGROUND ON STUDBOOKS What is a Studbook A studbook is a true record of the history of a captive population and can exist as both a computerized dataset and as a paper and or electronic printed version The population in question includes all or some of the individuals of a given species in a defined geographic area usually either regional e g North American regional studbook or international and is defined when the studbook is initiated The studbook includes pedigrees of animals a listing of the various locations in which animals have been held and any other relevant information about the specimens e g house names behavioral notes etc The entire history of each individual is traced in a studbook Taken together these collective histories in the computerized dataset describe th
180. indicated with MULT are not considered breeders To select a Breeder filter highlight one of the options Status The Status filter allows filtering of studbook data by four different Status options Living Dead Lost To Follow Up LTF and Released To select a Status filter highlight one of the options Only one Status filter may be selected at a time The Status filter is commonly used with a date filter setting the Status filter with an as of date filters the data to the individuals that may have been Living Dead LTF or Released as of a certain date regardless of their current status Setting this filter with a during date filters the data to the individuals that were ever Living Dead LTF or Released during a particular date window Setting this filter without specifying a date filter is the same as setting the no restriction date filter ID The ID filter allows filtering of studbook data by two different ID types Numerical and Not Numerical This filter is useful to indicate the presence of temporary IDs usually T as well as hypothetical individuals in a studbook To select an ID filter highlight one of the options Because this filter allows only two mutually exclusive options only one may be selected at a time UDF If the studbook you are using has user defined fields you may filter based on those fields Under the UDF tab is a drop down menu with the user defined fields specific to that stud
181. ing breeding behaviors This module is optional and can be hidden by using the Settings option from the Edit menu Information in the Social Data Table includes the Event which includes six event types Introduction visual physical restricted and full Altercation Breeding Interaction Prosocial and Other For each event you also track the Event Date Date Estimate Outcome or O for neutral and any desired Version 2 3 February 10 2012 27 PopLink User s Manual Comment on the specifics of the event In addition it lists the Related Specimens who were involved in the event Clicking on each Related Specimen will pop up an individual s Specimen Report The way event types are used may vary from studbook to studbook depending on the important social interactions and behaviors of a species if tracking and analyzing these data be sure to be consistent within your studbook and record your conventions in the Studbook Overview Notes section NOTE Because social events by definition involve multiple individuals the Social table is event based rather than individual based like the rest of the data tables In the Social data table there is no Studbook ID on the far left of the table instead each row represents a unique social event that encompasses multiple animals Each event is anchored in the individual animal s record in which the event was originally created When you hit the edit button for a specific social event fro
182. ink can export your studbook back to SPARKS format an exported studbook will lose some of the richer data allowable in PopLink but the SPARKS format will be readable by SPARKS and ZIMS when available To export your studbook into SPARKS you should 1 Run PopLink data validation and check that you do not have any invalid code errors e g blank IDs invalid formats such as error EH 11 EH 14 etc correct these errors in PopLink before exporting 2 On the SPARKS export screen you can name the export file As a default the SPARKS export location is in C Documents and Settings User Name My Documents PopLink PopLink Databases Studbook Name SPARKS Export Studbook Name You can also filter the exported data if desired e g to all individuals in North America or with a specific UDF 3 Review the SPARKS Export Errors report that will pop up upon export it is also saved in your species studbook folder in SPARKS The errors identified in this report are fields from PopLink that SPARKS does not have the capabilities to read e g long studbook IDs or dam sire IDs To ensure that all individuals in your studbook are exported to SPARKS the PopLink export routines choose DEFAULT values for unacceptable field values The SPARKS Export Errors report contains a list of errors and the New Default Values PopLink has assigned You should go and edit your data in SPARKS to correct or change these default values where appropriate l L Da
183. ink to atternpt to insert an enclosure record for it s birth date Deaths When a death event is added to an individual s Events record and the individual is currently in an enclosure PopLink will prompt you with a pop up offering to create a death event in their current enclosure If No is selected no further action is taken If Yes is selected adds the Death Event Date as an End Date to the individual s current Enclosure record and adds a comment Died in enclosure There needs to be a comment auto added by PopLink through this pop up to count as a death in an enclosure in the Enclosure Reports PopLink e D x PopLink has detected that this specimen is currently in enclosure Aviary HOUSTON Would you like PopLink to close this record at this death date Examples of auto added events Master Sex Reproductive Events Specimen Notes UDFs Social Enclosures Medical Studbook Overview Studbook ID Edit S 9 6 2011 None Aviary HOUSTON 9 6 2011 None None Born Hatched in enclosure Version 2 3 February 10 2012 63 PopLink User s Manual ENTERING EDITING MEDICAL DATA The medical module was designed to keep track of important medical information essential to daily care or population management Eight different categories of medical notes can be recorded here Each Note Category displays a different data entry configuration with required and optional fie
184. invalid Sex Birth Type Birth Date Estimate Rearing and all Dates If an individual has invalid codes for any of these fields the individual will be given a new default value as displayed in the SPARKS Export Errors report The default value will need to be corrected in the SPARKS studbook 13 Dates before 1753 because of database translation issues any dates that occur before the year 1753 cannot be translated appropriately into SPARKS format these dates will be left blank in the exported SPARKS file and the user will need to reenter the dates So Version 2 3 February 10 2012 96 PopLink User s Manual Chapter 8 POPLINK REPORTS In the Reports pull down menu you have the option to run 26 reports 1 Specimen Report 2 Studbook Report 3 Summary Counts Report 4 Age Pyramid Report 5 Unknown Age Report 6 Age Outliers Report 7 Census Report 8 Census Details Report 9 Survival Tool 10 Reproductive Report 11 Current Institutional Holdings Report 12 Historic Current Institution List 13 Lost to Follow Up Report 14 Life Table 15 Pedigree Reports 16 Specimens with UNK MULT parentage and descendants 17 Living specimens with UNK MULT in Pedigree 18 Antecedent List 19 Antecedent Diagram 20 Descendant List 21 Descendant Diagram 22 Living Descendant List 23 Social Compatibility Report Only visible if selected in Settings 24 Focal Individual Enclosure Report Only visible if selected i
185. iology of the species with an eye toward how rearing might affect management practices Conventions for rearing types should be described in Species Notes see page 31 on species notes Rearing data may be difficult to collect Rearing categories are not listed on ARKS taxon reports so the studbook keeper may have to make a special request for this information In addition because some zoos do not routinely record rearing types in ARKS this information may be difficult to obtain if it is only available from daily keeper records Also rearing categories are often open to interpretation a studbook keeper may want to solicit exact dates of rearing and categorize the information to fit the husbandry and management plan For many species or even particular situations it may be advisable to record rearing dates and information as text in Special Data However notes in Special Data should be in addition to the rearing or UDF field because it is not possible to analyze i e sort on text in Special Data 6 Owner This field is optional but can be used to track the current Owner for a specimen if desired enter the institutional mnemonic of the owner As a studbook keeper you can choose to enter the current owner in this field if it is important to management of your species Because PopLink has removed these data from the EVENTS records some of the original motivations for not tracking ownership in SPARKS have been eliminated but you should stil
186. ion is complete If you have trouble downloading the msi file or have questions about how to install please email us at software pzoo org We recommend reviewing SQL Server Management Studio Express Tutorial under the Help menu in the program and other Help features as needed However we re including assistance with some of the basic features of SQL Server Express to assist you in exploring your studbook data Starting and Connecting to SQL Server 2005 Express Edition 1 Run SQL Server Management Studio Start gt Program Files gt Microsoft SQL Server 2 When you open the program a dialog will open up asking where to connect a Connect to Server Microsoft iat Windows Server System SQL Server 2005 Server type Database Engine e Server name RANDYMARSH SGLEXPRESS Authentication Windows Authentication e CLARITYINTERNAL ngudnitz Connect Cancel Help Options gt gt 3 Leave Server Type as Database Engine 4 Leave Authentication as Windows Authentication 5 For Server name Replace the RANDYMARSH part of the name above with your Computers name and then click Connect Version 2 3 February 10 2012 154 PopLink User s Manual Displaying Data In A Table 1 Once the program connects to your local SQL service you should see an Object Explorer Ea Microsoft SOL Server Management Studio Express window on the left side Expand the
187. ions history and status Version 2 3 February 10 2012 30 PopLink User s Manual Guidelines Note 3 Species Notes IR CH Species Notes provide an important means of attaching explanations and Ge documentation directly to the studbook database As more studbooks are distributed primarily or solely as electronic databases the use and importance of Species Notes will increase substantially Soecies Notes allows the studbook keeper to annotate and or document conventions problems and major assumptions The format of Species Notes is text which allows for complex and detailed explanations Because the information in Species Notes travels with the studbook database it helps interpretation of the data by population managers SPMAG members and successive studbook keepers Every major assumption and every convention should be documented in this section In addition changes made during the creation of analytical studbooks should be documented in Species Notes OTHER DATA TABLES STORED IN POPLINK In addition to the main data tables Translated Data that comprise your studbook database PopLink stores some additional Data Tables 1 Institution List In the File pull down Menu you can select the option to look at the complete Institution List which is based on the most recent institution list from ISIS current as of July 2011 It contains names addresses and contact information for all institutions with ISIS recognized mnemonics cha
188. l specimens whose sire and dam are both wild such as when an egg is collected from the wild and hatched in captivity some fields have the option of selecting multiple filters within that field for example in the Parent filter you could select Either Parent Wild AND Either Parent Unknown If multiple filters are selected within the same field PopLink will return specimens that meet at least one of the criteria e g if both Either Parent Wild AND Either Parent Unknown are selected in the Parent field PopLink will return specimens that have at least one parent Wild or at least one parent Unknown specimens do not necessarily have to have both a Wild and Unknown parent to qualify These multi option filters have a check box to the left of each filter option whereas fields in which only a single option can be selected are chosen by highlighting Every filter field has a No Restriction option Each filter is set to this when PopLink is first opened except for the Status filter which is set as Living and the Date filter which is set as As of End Date with today s date Once filters have been set the No Restriction option can be used to clear existing filters within that field To clear all filters in all fields select the Clear All button on the filter pop up window PopLink will always display whether filters are set for a given report or the studbook viewer in the
189. l 25 Ch 25 INS 5 For more information on query syntax please go here htip www w8schools com sql default asp This resource contains very useful information regarding properly querying a database The information ranges from basic to advanced Version 2 3 February 10 2012 156 PopLink User s Manual Exporting Data Data can be exported from SQL to a number of different formats Any table either a database table or a table created by a query can be copied and pasted into Excel 1 Once the table you wish to export is in the right hand viewer highlight the rows you wish to export 2 Right click on the highlighted area and select Copy 3 Open Excel and hit Control V or select Edit gt Paste 4 Note that the data will be pasted in without column headers which you will have to enter by hand Deleting a Database In previous versions of PopLink you could delete databases in two ways 1 through the program in the Open Database dialogue box File gt Open Database highlighting the database you want to delete and selecting Delete Database or 2 via windows explorer by deleting the studbook folder in My Documents PopLink PopLink Databases In PopLink 2 3 if you delete the studbook folder using windows explorer you must also delete the database through SQL server Deleting a studbook through PopLink option 1 above is best because it avoids this step To delete the database within SQL server 1 In the Object Explorer window expand
190. l Events module Iw Show Enclosure module IV Show Medical Notes module Note that the Settings functionality can also be accessed from the Edit dropdown menu although you cannot change the file storage location while you have a database in PopLink open Version 2 3 February 10 2012 18 PopLink User s Manual SAVING BACKING UP MOVING DELETING AND ACCESSING POPLINK DATABASES When you create a new studbook database PopLink automatically saves that database you never have to formally save your studbook while you are working on it or before exiting The easiest way to create a backup e g a copy of your database is to use the Backup Database menu option under the File drop down menu The default backup location places the database in a folder on your desktop this folder can then be zipped and emailed backed up to a flash drive moved to a network folder etc You can move your PopLink databases using Windows Explorer by locating the studbook you want to move in C Documents and Settings User Name My Documents PopLink PopLink Databases To move the studbook s copy and paste the studbook s folder between one computer s PopLink Databases folder and the others To delete a database use the Delete function in the Open Database dialogue box If you end up deleting a database through Windows Explorer follow the instructions in Appendix 2 Deleting a Database to remove it from SQL Server as well CHECKLIST FOR
191. l carefully consider the implications of tracking ownership in your dataset You can also leave this field as not recorded as it does not impact any analyses See Guidelines Note 1 page 22 for more information Version 2 3 February 10 2012 41 PopLink User s Manual 7 Notes The master data table has a Notes button at the bottom left of the data entry screen Clicking on this will open a text box which you can use to document any necessary facts about the fields you have just edited or entered such as sources discrepancies with institutional records etc When you enter notes closing the box saves the notes the notes are transferred to the Specimen Notes table for the specimen you re entering with a description of Master Table Notes and the date of entry More Guidance on Entering New Specimens Wild Born Specimens BJ Guidelines Note 10 How to Enter a Wild Born Specimen IAA When recording the vital statistics of a new wild born specimen the specimen s parents should be entered as WILD For birth date many specimens are captured when young and their likely year or month of birth can only be estimated based on the specimen s size at the time of arrival to the first location Dates of birth estimated to the nearest calendar year should be entered as 1 July 109 and YEAR to indicate an estimated year of birth For species that breed seasonally a more precise date e g May or June would be more accurate In situation
192. l section Changing File Storage Locations for more information page 17 Optional program functions for power users PopLink stores data in a SQL database and power users who are interested in accessing and analyzing their data outside of PopLink can do so using SQL server Management Studio Express which can be used to view export and run customized queries on the underlying database tables created by PopLink Version 2 3 February 10 2012 14 PopLink User s Manual For instructions on how to install SQL Server Management Studio Express and interact with PopLink in this way please see Appendix 2 LAUNCHING POPLINK USER LOGIN You can start the program by clicking on the PopLink shortcut placed on your desktop during installation As the program starts up it will prompt you to login with a User ID You can enter any desired identifier here your full name your initials etc and PopLink will remember this user ID the next time you log into the program This ID is used to track the user who made changes to the studbook database exported data ran reports etc After logging in you have three options to choose from Create A New Database Open An Existing Database Settings CREATING A NEW POPLINK DATABASE After logging in to PopLink you will have the option to open an existing database or create a new database New databases are created in PopLink in three ways 1 importing the desired data f
193. ld SparksExportErrors Microsoft Excel cay Home E Insert Page Layout Formulas Data Review View PDF e Cut Sale de Cu Calibri e LU Age Ee p Wrap Text General MV F BC Past SE A a d H D Conditi l Format k Format Painter IE pe ate P A Ki d eet as Table Styl Clipboard E Font Ia Alignment Ia Number E Styles A B E D E F D H l J Sparks errors for Sunbittern These PopLink fields have data that cannot be exported to SPARKS Default values have been chosen You should correct these default values 1234567 Studbook ID 1234567 EX1 13665325 Studbook ID 13665325 EX2 1 2 3 4 StudbookID Field Name with Invalid Data Old Value New Default Value 5 D T 133 Location ID 1234567 BLANK B 4 Immediately after exporting your SPARKS dataset from PopLink you should run clean up routines within SPARKS within the menu system Data Quality gt Clean Up This re indexes the SPARKS files ensuring that SPARKS can read them appropriately Version 2 3 February 10 2012 95 PopLink User s Manual The SPARKS export creates MASTER dbf MOVES dbf SPECIALS dbf and UDF dbf files to the named studbook folder as well as a VARS MEM METAFILE dbf SPARKSRC dbf and CONTACT dbf A few caveats about PopLink Data that are lost in the export 1 Reproductive state and sex these two event streams are transformed back into a single field in SPARKS with the last state for both being what is sent to SPA
194. ld also be placed in 3 the Species Notes section of a studbook for general assumptions and conventions that may affect many animals in a population 4 the Specimen Notes section see page 52 of an individual specimen record for changes or assumptions affecting a specific individual How to Identify When Analytical Assumptions are Necessary In order to construct a useful analytical studbook one must first learn exactly what information is unknown or missing in the true studbook Data may fall into several categories of unknownness 1 truly unknowable e g origins of specimens obtained in the early 1900s when records were not kept as consistently 2 missing or not yet available e g sex of newborns or origin of specimens obtained by institutions known to have good records and 3 not yet investigated i e pertinent institutions and sources haven t been asked yet With enough work on the part of the studbook keeper all unknown or missing studbook data should eventually fall into the first two categories unknowable or missing although this may be an ongoing process Version 2 3 February 10 2012 133 PopLink User s Manual PopLink includes several features to identify the unknown or missing data in your studbook that are relevant to population management These are briefly mentioned here and are discussed in detail in the reports chapter the relevant page numbers are included after each report name 1 Living spe
195. ld has its own tab which can be selected to add filters within that field A tab name in bold font indicates that filters within that field are currently selected Once any desired filters have been selected click the OK button at the bottom of the pop up screen to apply the filters All selected filters will be displayed at the top of the screen below the Select Filters button wo Select Filters Breeder Rearing Reproductive Event ID Status Date Parent Age Institution SEARCH NOTES Hatch 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 the desired association file No Restriction Geographic Area Association Clear All Filters Ok Cancel Most filters can be used alone or in combination When filters in multiple fields are applied the filters will be compounded To qualify for a selected filter combination an individual will need to qualify for both all filters together For example if Captive Born is selected for Birth Type and Hand is selected for Rearing PopLink will return only captive born specimens who were also hand reared If Captive Birth is selected for Event and Both Parents Wild for Parent PopLink will return only captive born Version 2 3 February 10 2012 72 PopLink User s Manua
196. lds All the notes types are specialized for a specific type of medical data except for the General Medical Note category which can be used for any type of medical information that does not fit in the other seven categories With all note categories you can record the Observer optional which will typically be the person observing the issue and not necessarily the studbook keeper recording the issue in the studbook and a Comment field NOTE Once a medical event is created everything in the event is editable EXCEPT the VG rz Category If the wrong category is selected and Apply Changes is pressed the event will 5 j need to be deleted and re entered with the correct Note Category selected If the mistake is d caught before Apply Changes is selected the Note Category can still be changed The following figures systematically list and explain the purpose of each Note Category 1 Clinical Sign Note Category Type Clinical Sign Integument Start Date End Date 10 4 2011 E Observer tg small lesions observed on bottom of left foot Instructions Apply Changes The Clinical Sign category allows you to track any unusual signs symptoms being displayed by an individual The Type field describes the body system Cardiopulmonary Endocrine Gastrointestinal Integument Lymphatic Musculoskeletal Nervous Reproductive Urinary or Other This functionality is somewhat equivalent to a red flag for an in
197. ls were captured as infants and import date e g all individuals are estimated to be two years old at import and birth date is estimated as two years before recorded import date Creating an analytical assumption in such cases allows the specimens with unknown birth dates to be utilized in demographic analyses NOTE Replacing unknown data with assumptions is a procedure that has Ei serious implications for population management and should be undertaken with LV JN extreme caution While assumptions can be developed by knowledgeable studbook keepers and population managers any changes to be made in an W Ji analytical studbook should be discussed with a Small Population Management e Advisory Group SPMAG or Population Management Center PMC advisor prior N to any population analyses or management decisions ANALYTICAL DATA IN POPLINK Background and History In the past studbook keepers and population biologists wanting to use analytical data and assumptions had to maintain two studbook databases in SPARKS a true studbook and an analytical studbook which by convention was called XXNAME where NAME is the name of the true studbook The analytical studbook should have had all analytical data denoted as such within the SPARKS Special Data and in the Species Notes This complicated system which required time consuming and error prone maintenance of two separate studbooks i e new births deaths and other events had to be entered
198. lters Filters applied to parents Mo Filters Applied Sire Age At First Estimated Conception Sire Age At All Estimated Conceptions Number Of Offspring Per Sire Clutch Size Dam Age At First Hatch Dam Age At All Hatches Number Of Offspring Per Dam Interhatch Intervals Hatch Seasonality 1 97 12 P 2 88 Total 100 00 Version 2 3 February 10 2012 109 PopLink User s Manual 2 Interbirth Intervals The Interbirth Interval tab lists all interbirth intervals in days for each dam s consecutive offspring Intervals are calculated from the date of birth of the last offspring of one litter to the date of birth of the first offspring of the next consecutive litter The report is ordered by increasing interbirth interval and both dams and offspring may be listed more than once Sunbittern Reproductive Report REPRODUCTIVE REPORT Species Type Egg Laying Incubation Period 28 Days Maximum Hatch Date Range For Clutch Mates 3 Days 45 reported dams with 132 123 174 429 offspring not including 33 offspring of UNK MULT dams 45 reported sires with 130 123 172 425 offspring All ages are at dam conception Select Filters lee applied to parents No Filters Applied Intervals are calculated from the last of a clutch to the first of the next clutch oe SEET Offspring1 Hatch Date Hatch Date Offspring2 Hatch Date so eme S 80 4 371 1 1 1995 None 372 1 5 1995 None 158 5 et 1998 None 457 6 7 1998 None 68 1i 9 25 199
199. lthough subsequent holding institutions may have better historic records Also it may be helpful to request records on all other specimens of the same species present at the institution within several years of the birth of the specimen in question i e a historic taxon report to help identify possible parents If no new information surfaces from researching any of the institutions involved in a specimen s history check ISIS data from the ISIS website www isis org for any additional pertinent data For specimens that have passed through dealers or importers consult the Dealer List a list of people and private facilities maintained by Alan Shoemaker Riverbanks Zoo for more information that may lead to clues about a specimen s origin Version 2 3 February 10 2012 134 PopLink User s Manual 6 If you have extra time and energy internet searches government quarantine records and talking with people who have been in the zoo community for a long time may help uncover useful information about institutions or facilities related to the specimen in question T If you cannot resolve unknownness leave the unknowns in the true studbook and develop assumptions to incorporate into an analytical overlay What to Do With MULT Parentage While careful documentation of MULT parentage where more than one known individual could be the possible parent is appropriate and important for record keeping within the true studbook database
200. ly button to set your filters When filtering by association you will be given the option of choosing a FED file e g AZA EAZA FED files are simply a list of institutional mnemonics The FED files pre loaded in PopLink are based on the most recent versions of each regional FED file The AZA FED file is current as of September 2009 These FED files can be altered by opening them using Windows Notepad or similar text editing software and adding or deleting mnemonics New FED files can be created by saving a list of mnemonics FED files are stored in your My Documents PopLink folder in the Federation Files subfolder Note that as FED files are not stored within your studbook database if you would like to use your customized FED files on a different computer you will need to manually move them Version 2 3 February 10 2012 73 PopLink User s Manual Date The Date filter can be used in conjunction with any other filter to confine the dataset to a certain time period either during a date span or as of an end date To add a date filter highlight one of the options and windows will appear that allow entry of the appropriate dates Dates should be entered in an American date format MM DD YYYY When as of or during date filters are set without any other filters PopLink assumes that the desired status of individuals is Living and automatically applies this filter condition Age The Age filter all
201. m the Social data table the edit data screen that appears will be for the anchor specimen The event can also be edited through any of the Related Specimens records When edited a Social event will be updated in all Related Specimens records ENCLOSURES DATA TABLE File Edit View Overlay Validate Reports Export Help D o Z al al Select Filters As of 9 27 2011 AND Status Living Totals 2 4 1 7 at 2 Institutions No Sort Order Applied Currentness Date 9 7 2010 Master Sex Reproductive Events Specimen Notes UDFs Social Enclosures Medical Studbook Overview Studbook Edit Enclosure Name Enter Date Enter Date ID Est 64 Holding 1 CHICAGOLP 1 1 2005 None Exhibit B CHICAGOLP 3 23 2009 None None moved for breeding intro Holding 2 CHICAGOLP 1 1 2010 None 5 12 2010 None The Enclosure Data Table is new in PopLink 2 2 2 3 and allows you to track the enclosure and thus social group history of the animals within your studbook These data help to answer questions such as what enclosures has Studbook 23 lived in over their life who have they lived with and who are they living with now The implications of these data are far reaching from gauging the social aptitude of an individual to tracing possible disease contacts If maintained consistently for a studbook or even a subset of a studbook e g a single institution
202. n Identification Identity description Immobilization Incubation note Individual behavior Litter Clutch Master Table Notes Medical diagnosis Medical note Medical observation Medical procedure Medical treatment Missing escaped Multiple clutching Museum number Necropsy results Neonatal behavior Neutering Notching mark Note Old Accession Number Old Studbook Number Parent ID Assumptions Parturition behavior Permit Physical condition Physical legal arrival Possible parents Pre copulatory behavior Regional Studbook Number Reproductive behavior Reproductive Table Notes Research observation Sex Table Notes Sexing note Shed molt Sire Taxon Stereotypic behavior Tag Band Tattoo Territoriality Transponder ID Vendor Taxon Vocalization Weight Length 53 PopLink User s Manual ENTERING EDITING UDF DATA Editing Existing UDFs for a Specimen Edit True Data 15 no subsp Alice gt Add Delete In general a specimen should only have one row of UDF values If this specimen has multiple rows you should combine them into a single row To edit the existing user defined fields for this specimen highlight the desired row select the desired UDF and select an existing value or enter your own To add a new UDF column go to the Edit pull down menu and select User Defined Fields When completed click Apply Changes Existing User Defined Fields Value SSPANIMAL y M Batch Input
203. n Settings 25 Enclosure Report Only visible if selected in Settings 26 Medical Notes Report Only visible if selected in Settings We will describe each of these reports in detail Note that in the Options section of the Report pull down menu you have two options 1 Run Reports In New Window which will pop up a new window with each report you subsequently run rather than running them all in the main viewer window and 2 Select Default Filters which will set filters that will apply to all the Reports run through this menu see page 72 for more details Many reports contain an EXPORT button in the upper right corner By clicking on this button a formatted report is automatically displayed on the screen and saved in your studbook folder The default format for these reports is HTML e g they will pop up in your default web browser If you want the reports to regularly be displayed in another format by default you navigate to your studbook folder find a report right click on the HTML report select Open With and Choose Program The dialogue box displayed to the right will pop up and you can select the Always use this program option which will change the default file format reports are displayed in You can also keep your default format as HTML and save the reports from within your browser with alternate formats File gt Save As In addition you are able to export the tables in most reports di
204. n each age class clicking on the specimen numbers will pop up a Specimen Report for that individual Within this report you have several ways of looking at subsets of your specimens a Highlights You can highlight based on any of the standard filter criteria highlighted individuals will be displayed in yellow on your pyramid For example you could highlight based on a UDF field or if you wanted to see where the individuals in your collection were in the age pyramid you could highlight based on your location Select Highlight Locations CHICAGOLP AND Status Living Color By Sex X Male Female Unknown and Abnormal Un in erd teal fel fea 2 Version 2 3 February 10 2012 104 PopLink User s Manual b Color Coding using the pull down menu There are also some pre defined ways of color coding the age pyramid I Sex This is the default highlighting with males on the left in blue females on the right in red and unknown sex individuals in the middle section of the pyramid in gray ll Parent 1 2 3 Selecting this option will code your individuals as Individuals with WILD WILD parents green Mixed orange individuals with one or both parents born in captivity i e have studbook numbers note that individuals in this group may have one parent that is WILD or UNK Individuals UNK MULT or some combination e g dam UNK sire MULT or dam UNK sire 23 pink iii Breeder selecting this op
205. n individual animal Each row indicates that the focal animal moved between enclosures or that the group composition within its current enclosure changed i e another animal moved in out For more information on any specific enclosure event refer to data in the focal individual s Enclosures data table SE Location Start Date End Date Group Size roger na Indoorl HOUSTON 8 2 2008 8 30 2008 3 1 829 1 829 Outdoor HOUSTON 8 30 2008 9 15 2009 1 1 829 1 829 Aviary HOUSTON 9 15 2009 7 15 2010 1 1 829 1 829 Free Flight LOWRY 7 15 2010 11 2 2010 2 1 829 1 829 Aviary HOUSTON 11 2 2010 9 5 2011 1 1 829 1 829 Aviary HOUSTON 9 5 2011 9 6 2011 2 1 829 1 829 Aviary HOUSTON 9 6 2011 10 19 2011 3 1 829 1 829 To generate a Focal Individual Enclosure Report enter the Studbook ID for the desired specimen and select Go In this report each row indicates that the focal individual has either 1 moved enclosures or 2 that the group composition within its current enclosure has changed i e another individual has moved in out The report s columns are Enclosure Name Name of the Enclosure as defined in the User Defined Enclosures list Location The institutional mnemonic describing the site of an Enclosure as defined in the User Defined Enclosures list Start End Date The date the individual entered a new enclosure or that the group situation changed start date until the day of the next
206. n pedigree animals from the genetic analysis we may be underestimating gene diversity of the captive population and throwing out rare or unique alleles On the other hand if we include unknown animals in the breeding population based on the assumption that they are completely unrelated to all others in the population then we may be overestimating gene diversity in the population Furthermore we risk inadvertently inbreeding animals because the relationship between an unknown pedigree animal and any other animal in the population is completely unknown a potential mate could be a close relative or entirely unrelated Version 2 3 February 10 2012 138 PopLink User s Manual Table 5 Genetic consequences of two potential errors that can occur when animals with unknown ancestry are included or excluded in a breeding program modified from Willis 1993 Truth Unrelated wild Related Breed as INCORRECT INCLUSION unrelated CORRECT Risk inbreeding Underestimate F wild Overestimate GD Decision INCORRECT EXCLUSION Lose alleles CORRECT Underestimate GD Version 2 3 February 10 2012 139 PopLink User s Manual BIBLIOGRAPHY Association of Zoos and Aquariums AZA 2006 Studbook Fact Sheet Accessed August 22 2006 http www aza org ConScience ConScienceStudFact Ballou J D Lacy R C Pollak J P 2011 PMx Software for demographic and genetic analysis and management of pedigreed populations Ver
207. n studbook database should always contain your true data In PopLink you can also create an overlay that you can use to enter and store any analytical changes to your dataset Before explaining the technical details of creating and maintaining analytical data in PopLink we ll provide some background on the differences between true and analytical data and why creating analytical data is necessary True Data vs Analytical Data A studbook is the best possible representation of the truth as it is currently known Each studbook must contain an unambiguous representation of what is Known and what is not known about every specimen in the population Although studbooks may contain minor assumptions or estimates such as birth dates estimated to the month or year information that is truly unknown should be entered as such This is important because what is known and factual should never be confused with what has been assumed in case new information emerges in the future Analytical studbooks in contrast are constructed to facilitate population management by including assumptions half truths and necessary fictions They may contain significant assumptions about variables such as dates of birth transfer death parentage and origin eg captive born or wild caught In some cases analytical studbooks contain hypothetical specimens ancestors created to complete the pedigree and facilitate genetic analyses In effect an analytical studbook fills in
208. nclosure at a time it is best to create new enclosures to encompass each combination in one entry e g if exhibits A B and C exist and can be managed in any combination to form a single or multiple exhibits also have AB AC BC and ABC as options Use the Description section to explain what each represents Only create combinations of Enclosures that are concurrently possible Name Location Description pee OUT2 CHICAGOLP North Outdoor Yard 9 28 2011 OUT3 CHICAGOLP East Outdoor Yard 9 28 2011 MED CHICAGOLP Medical Holding 9 28 2011 QUAR CHICAGOLP Quarantine Holding 9 28 2011 INDOOR1 CHICAGOLP West Indoor Housing 9 28 2011 OUT2 3 _ CHICAGOLP OUT2 OUT3 10 19 2011 Version 2 3 February 10 2012 61 PopLink User s Manual Creating Enclosure Records Once you ve created User Defined Enclosures you can add data into the Enclosures data table To edit existing Enclosure event s highlight the desired event and edit the data in the fields to enter a new Enclosure event use the Add button To delete an existing Enclosure event highlight the desired event and use the Delete button If creating an event for an individual that is currently in an enclosure specify the Enclosure Name Enter Date Enter Date Estimate and a Comment optional and select Apply Changes Leave the Exit Date blank to indicate that the individual is currently in the enclosure ot Add True Data Master Sex Reprod
209. ndividuals that were wild born captive born etc during the census year These tallies are based on the specified origin of the individuals who are living on the census date in the selected set of institutions In the example above 96 individuals are living within the AZA FED file as of 31 December 2004 of those 96 individuals 95 were captive hatched and 1 was wild hatched Version 2 3 February 10 2012 107 PopLink User s Manual CENSUS DETAILS REPORT The Census Details report tallies the number of various events that occur during each year for your population When run the report displays a pop up identical to the Census Report pop up You will be asked to enter a month and day each annual census will be started on The default is to run the report starting on January 17 e g PopLink will count all events that occur between January 17 and December 31 in a year but for some species e g seasonal breeders populations where individuals are reintroduced at a certain time of year etc it may be more informative to select an alternate date on which to start the census Generally you should leave the year at the default last year but you can enter an earlier year if you don t want certain years data displayed You will then be given the option of limiting your data geographically either to a region or set of institutional mnemonics or by using a FED file and or by User Defined Field If there are any individuals with imp
210. ng the Select Filters button Version 2 3 February 10 2012 91 PopLink User s Manual PopLink can also export census data for graphing in PMx Use the Select Census Parameters button to determine the desired filters PMx export files are placed in a Folder titled PMx Exports within the specific studbook database folder from which the export was created e g C Documents and Settings User Name My Documents PopLink PopLink Databases Studbook name PMx Export When you open PMx you can navigate to this folder to import the data TECHNICAL NOTES ON EXPORTS TO PM2000 amp PMx Life Table Calculations PopLink life table calculations for the PM2000 and PMx export were programmed to replicate SPARKS MxQx table calculations which are exported in prn files for each sex The programming team validated PopLink algorithms and occasionally found slight differences between SPARKS output and PopLink Output but generally both programs output the same life tables Differences when seen could sometimes be traced to inaccuracies in how SPARKS appeared to be counting individuals at risk or how it rounded but sometimes the cause of the differences could not be determined For transparency we will provide detailed technical documentation of how PopLink life tables are calculated Documentation assistance with how specific algorithms which are based on SPARKS methods operate was provided by Jon Ballou The Demographic Window is used to d
211. nknown Origin B Guidelines Note 12 How to Enter an Unknown Origin Specimen Lake Many studbooks include specimens with unknown origins Every effort must be made to ascertain the true origin of every specimen in the studbook For some of these specimens thorough investigation will eventually identify origin as either wild caught or captive born For other specimens assumptions or conventions may be invoked to resolve uncertain origins see page 125 on assumptions and conventions Despite a studbook keeper s best efforts a few specimens will probably have origins that are truly unknowable Such specimens are a problem for genetic analyses because they will eventually require a decision to treat them as wild caught or to exclude them from analyses The first event for specimens of unknown origin should be entered as a birth at an unknown location UNKNOWN with unknown birth type UNKNOWN If only the month or year of birth is known that should be entered with a Date Estimate of Month or Year this indicates that only the month or year of birth is known see page 32 on estimating dates Every effort should be made to identify the parents unknown parentage has profound effects on genetic analyses If parentage cannot be established either one or both parent studbook numbers should be entered as UNK Rearing method should be entered if known see page 41 on how to enter rearing type Version 2 3 February 10 2012 43 PopLink
212. notes are transferred to the Specimen Notes table for the specimen you re entering with a description of Event Table Notes and the date of entry 6 In Depth Lost to Follow Up Events In PopLink Lost to follow up is entered as an actual event and an individual can go LTF and return from LTF e g if a specimen went to an institution where it was not tracked and then returned to an institution that you get records from Note that in SPARKS LTF is indicated with an unknown removal date at the last reported location e a U in the Removal Date Estimate field or as a Ywhen SPARKS asks if the specimen is lost to follow up Entering LTF as an actual event clarifies this sometimes confusing data entry convention Lost to follow up indicates that a specimen s whereabouts are unknown from the date of the Go LTF event Thus in PopLink you might have a LTF specimen that looks like this Studbook Transaction Transaction Transaction Location Local ID ID Code Date Date Est 66 Hatch CHICAGOLP B8138 3 26 1981 Mone 66 Transfer CHICAGOBR s300 17 1 20 1989 Mone 66 Transfer CHICAGGLP B8138 1 25 1991 Mone 66 igo LF CHICAGOLP 138 1 25 1991 e None This type of entry indicates that this soecimen was transferred to an institution that does not report to the studbook keeper it goes LTF on the same day as transfer Alternately a specimen might be known to be at a location for a period of time but then disappears from that institu
213. nt Fields These fields e g Current Sex Current Location display the current for living individuals or last for dead lost to follow up or released individuals information for any given field Note that if you set an As Of date filter see Chapter 5 for more details these fields do not reflect the current status as of that date but the current status as of today s date If a specimen has a completely unknown birthdate age cannot be calculated and the Current Age field will display The Current Enclosure field is based on data in the Enclosures table if relevant records exist for an individual these data are optional and may not be tracked in all studbooks If there are no relevant enclosure records this field will display Not Reported if an animal has some Enclosure records but none are current last this field will display None Current Owner In general studbook keepers are not expected or encouraged to track ownership as doing so can often cause problems e g confusing ownership with physical location or unintended consideration of the studbook as a legal document However for some species ownership information may be useful to the operation of cooperative management plans In such a case it is possible to track ownership in PopLink see page 41 for more details If ownership was tracked in the imported SPARKS studbook the OWNER field in the Master Data Table will display
214. nternational studbook or in a regional studbook for a different region It can also happen if a birth or hatch is reported for parents whose names or studbook numbers have never been recorded in any studbook before If the parents are in another studbook international or another region then those parents should be assigned regional numbers and added to the studbook All ancestors of those newly identified parents should be given studbook numbers and entered in the studbook It is essential that the studbook trace the ancestors of each specimen back to wild i e to specimens with dam and sire listed as WILD or to specimens of unknown origin All those ancestors must be in the regional studbook so that any possible relationships among present or future specimens in the population will be documented If the dam and or sire is not yet in any studbook but some information is available on them then they should be assigned studbook numbers and added to the studbook Most likely it will be uncertain if those parents are living or dead all that will be known are their names or maybe where they had been when the offspring was born In this case the parents in the new studbook entries just made for them should be recorded as lost to follow up see page 49 on lost to follow up Those new parents should be given dams and sires i e the grand parents of the original specimen that started all this mess of 1 WILD if the parents are from a game ranch a br
215. number of individuals at risk for Qx e Age Specific Fecundity Rate Mx the number of same sex offspring an individual is expected to produce produced on average during an age class e Number At Risk for Qx Sample size that Qx rate was based on for a given age class e Number At Risk for Mx Sample size that Mx rate was based on for a given age class Mortality Rate Calculation No individuals with unknown birthdates are used in mortality rate calculations All birth date estimates are ignored the entered birth date is used in all calculations 1 Tally the number of deaths in each age class that occurred in the demographic window Version 2 3 February 10 2012 92 PopLink User s Manual a Male deaths are attributed to male age classes female deaths are attributed to female age classes b Deaths of unknown sex individuals are tallied as 0 5 to the male age class and 0 5 to the female age class 2 Tally the number of individuals at risk for death in each age class a An individual that has lived through an entire age class gets tallied as 1 0 for that age class b An individual that has lived through a portion of an age class e g was born midway through a year or was transferred out midway through a year or the date window started or ended midway through an age class is tallied as whatever portion of that age class except in case c below For example if an individual was transferred out of the demographic window when 6 years
216. ny evaluation of reproductive rate PopLink offers eight categories of hand rearing Hand Parent Foster Peer Unknown Not Reared Colony Group or Supplemental Although PopLink does not have default rearing types usually wild caught specimens are parent reared captive born or unknown origin specimens may be any of the rearing types Rearing type for stillbirths and premature births should be listed as not reared The Rearing field can be used to set Filters see Chapter 5 so it is potentially very useful If additional rearing categories are needed creating a rearing UDF is the best tactic see page 54 on how to create and use UDFs A UDF will also allow the species manager to set a Filter to select a specific rearing type for analysis and reports Many studbook keepers will want to develop species specific conventions for rearing types There are no established standards for categories for parent reared hand reared foster reared partial parent rearing etc Categories will vary from species to species and may be based on length of time type of individual doing the rearing etc Rearing categories can be a combination or a continuum of options For example rearing may cover several years with a combination of parent and hand rearing or hand reared infants can be reintroduced to parents at a later date The Western Lowland Gorilla SSP has created a UDF category Partial to describe this situation Conventions should be based on the b
217. o date if their status changes It is easy to forget this step in updating the studbook because the specimen is already entered The UDF is only as good as the studbook keeper s updating service SOCIAL DATA TABLE File Edit View Overlay Validate Reports Export Help D o A al ve Totals 52 55 6 113 at 50 Institutions No Sort Order Applied Currentness Date 1 1 2007 Master Sex Reproductive Events Specimen Notes UDFs Social Enclosures Medical Studbook Overview Related _ Specimen Event Date Date Est Outcome Comment Edit Event Introduction 8 1 1990 None Altercation 8 8 2011 None Breeding Inte 8 8 2011 None The Social Data Table is new in PopLink 2 2 2 3 and allows you to track the social interactions for individuals within your studbook if desired This module enables tracking over time of major social events which individuals are involved and the events general outcomes These types of data can be useful when trying to answer questions like have these two individuals been introduced before or are they behaviorally compatible This module can also be helpful when tracking breeding compatibility and competency if it is consistently used to record breeding behavior and outcomes This can help answer questions such as who has this individual shown breeding behaviors towards how closely is this pair bonded or at what age did an individual first start exhibit
218. odes when entering a death event for aspecimen PopLink does not automatically prompt you to enter these codes However if you would like to continue tracking these data in your studbook you can do this in one of three ways 1 by entering them by hand in the Specimen Notes table 2 by entering codes into the local ID field of the death event where SPARKS stores the current death codes or 3 by tracking relevant data through a UDF see page 54 for more on UDFs Note that you cannot filter data for any of these except a UDF but you can see subsets of relevant specimens by sorting if these data are stored in the Specimen Notes table or the local ID field To track more specific information about a death in the Specimen Notes you can add the following types of notes see page 52 for more details on how to enter edit Specimen Notes Death Notes Carcass Note Carcass Recipient Death Number Disposition Note and Necropsy Results Death Codes imported from your SPARKS dataset are stored in the translated PopLink data in the Local ID associated with the death event If you wish to continue entering death notes in this manner you can manually enter the letter codes pertaining to specific death information into the Local ID field for any new death event Codes should consist of 3 letters one letter from each of the three tables below in the following order 1 Circumstance of death 2 Carcass Disposition 3 Necropsy Code Topographic e g a specimen
219. ood bad neutral or prosocial antisocial no response Because of this it is important to develop standard definitions for your species or studbook The level and type of interaction required to determine 0 will vary by species Some examples might be e chimpanzees spending time exhibiting grooming or breeding behavior could be considered positive e tigers displaying aggressive behavior which is ultimately a part of their normal breeding behavior could be considered positive or negative depending on your data conventions and the ultimate outcome of the attempted pairing e wolves presenting play bows as a prosocial invitation to play could be considered a positive social interaction Species specific conventions should be recorded in the Species Notes Section of the Studbook Overview Version 2 3 February 10 2012 57 PopLink User s Manual 4 Related Specimen Related Specimen refers to the individuals involved with the focal individual in the Social Event This term does not have any reference to genetic or familial relations Adding a record to one individual s record adds an identical record to the Social Events Table of any other Related Specimens in the event You can type studbook IDs into the Related Specimen field separated by commas but the easier way to enter the associated individuals is to click on the FIND button to pop up the Specimen Selector Fems 6 727 Female Male aa a ra Male
220. opLink will then generate results for the report you selected to run this can take a few minutes depending on the size and complexity of your dataset The next sections give details on the general methodological approaches and on each report specific calculations are included in the Detailed Methodology section at the end GENERAL METHODOLOGY USED IN THE SURVIVAL TOOL Survival probabilities are calculated using the non parametric Kaplan Meier approach also called the Product Limit estimator Klein and Moeschberger 1997 Skalski et al 2005 This approach is useful because it is applicable regardless of right censoring e g individuals that are alive at the end of the analysis window or left truncation also called staggered entry e g individuals that enter the dataset after their birthdate As many captive datasets have both right censored and left truncated data Kaplan Meier estimates were deemed to be generally more appropriate than other analytical methods that can be affected by these types of data Further details on equations used to calculate survival probabilities can be found in the section later in this appendix entitled Calculations of Kaplan Meier Survival Probabilities page 151 Data quality has an important effect on whether estimates are reliable and can be used for communication and management The PopLink Survival Tool uses five data quality tests to determine whether sufficient high quality data exist to make reliable
221. ow as a key to help you think through important evidence that may influence your decisions when trying to create assumptions for animals with unknown ancesiry See Table 3 below to determine possible changes to make in the analytical studbook and the consequences of such changes Evidence to consider when making assumptions about birth origin or parentage A Birth date 1 The animal was born before the first recorded captive birth for the species Assume wild born 2 The animal was born when captive births were frequent and widespread Assume captive born unless other evidence suggests otherwise 3 Birth date unknown or born when imports and captive births were equally common Make no assumptions and move on to review other evidence B Birth location or first source of entry into the population 1 The animal was obtained from a known dealer a The dealer was known to be an importer of wild caught animals Assume wild born b The dealer was known to buy and sell captive born animals Assume captive born c The dealer handled both imports of wild born animals and transfers of captive born animals This section is almost entirely taken from S Long s monograph for Population Management II and is based on the approaches used by the AZA Population Management Center to create analytical assumptions Version 2 3 February 10 2012 135 PopLink User s Manual Make no assumptions and move on to review other evidence 2 The animal
222. ows filtering of studbook data to a selected age range To select an age filter highlight Between Ages and use the start age stop age entry boxes to set the desired range When calculating age PopLink filters everything down to and including the start age and up to and including the stop age For example if the age range was 3 0 to 5 0 individuals that were exactly 3 0 between 3 and 5 and exactly 5 0 would be included in the filter PopLink calculates an individual s age based on that individual s entered birth date ignoring any birth date estimate if an individual has an unknown birthdate estimate i e birthdate is unknown that individual s age cannot be calculated and that individual is excluded from the filtered data Sex The Sex filter allows filtering of studbook data by five different sex types Female Male Abnormal Hermaphrodite and Unknown Sex To select Sex filters check the box next to one or more of the options PopLink will return all specimens that fit at least one of the criteria In PopLink a specimen s sex can change throughout its lifetime e g it can go from Unknown sex to Male In the Sex filter Pop Link filters for specimens that had ever had that sex regardless of whether a date filter has been set or not Filtering by SEX Example Record Filter By Studbook ID 441 Sex Female Birth Date 1 13 2004 Date As Of 1 13 2004 Sex Unknown on 1 13 2004 Living is automatically turned on an
223. p in this table with population sizes of 0 MEDICAL NOTES REPORT lei superbbirdofparadise Medical Note Report _ sx Medical Notes Report For 55 co Enter a specific studbook ID or ALL to generate this report for all individuals in the studbook The displayed animal s sex age and enclosure are as of the Medical Notes Start Date Enclosure Mame Category Type Indoor HOU Medical Proce Visual Assess Clinical Sign Cardiopulmon Diagnostics Culture To generate a Medical Notes Report enter the Studbook ID for the desired specimen and press Go The Medical Notes Report includes all the medical notes recorded for the focal individual as well as the individual s Sex Age and Enclosure Name as of the medical note date if enclosure data is recorded in the Enclosure data table As not every medical note type has data in all the fields some fields in this report will display to reflect unnecessary fields Version 2 3 February 10 2012 124 PopLink User s Manual Chapter 9 ANALYTICAL DATA AND OVERLAYS IN POPLINK2 BACKGROUND CONCEPTS Although a studbook is intended to be a true and accurate record of a population s history in captivity we often need to use assumptions half truths and necessary fictions for the purpose of population management PopLink has the ability to hold both TRUE studbook data and ANALYTICAL or hypothetical data on each individual As in SPARKS your mai
224. pane 4 Inthe editor pane write a query and then click the Execute button if the query does not contain any error it will display the result set in a window below the query If it does contain any errors then it will display the errors in a new window below the query F Microsoft SQL Server Management Studio Express File Edit View Query Tools Window Community Help Dinew Query D Gf id at BB aG up ANTEATER z jaf Exeaste v Ea lag AG LET ma Cp aokeozz ee Object Explorer e ix see sql Table dbo Master Summary v x KE 3 27 E al e EES SQL Server 2 SELECT FROM DBO MASTER EN a System Databases WHERE sire WILD u Acondor05 J Acondor05_2 J ANTEATER Database Diagrams 9 Tables System Tables a dbo DeletedEvent dbo DeletedHistory a dbo DeletedMaster a CC dbo DeletedReproductive 3 E dbo DeletedSex 4 dbo DeletedSpecimenNote CC dbo DeletedUserDefinedFieldv dbo Event a dbo History ay a dbo Master i Ki a E dbo OverlayEvent F Results EN Messages a E dbo OverlayHistory MM o E dbo Overlayinformation UniguelD Studbook Sire Dam BirthDate BDateEst LastAge LastStatus LastHouseName BirthType Rearing ConceptionDate Owner Genera a E dbo OverlayMaster 1 D A WILD WILD 1879 01 01 00 00 00 000 Unknown NULL NULL NULL Wild Bom Parent NULL Not Reported 3CE74 a 3 dbo OverlayReproductive 2 2 2 WILD WILD 1881 01 01 00
225. pecies Type Egg Laying Incubation Period 28 Days Maximum Hatch Date Range For Clutch Mates 3 Days 45 reported dams with 132 123 174 429 offspring not including 33 offspring of UNK MULT dams 45 reported sires with 130 123 172 425 offspring All ages are at darn conception Select Filters ies applied to parents No Filters Applied Sire Age At First Estimated Conception Sire Age At All Estimated Conceptions Number Of Offspring Per Sire Studbook Age At Dam s Hatch Date 7 1 1967 7 1 1970 Unknown 7 1 1970 Unknown 20 553 10 5 1982 None JS 9 L se 19 65 10 5 1982 None 508 28 20 Lee 104 163 1 9 529 508 19 491 10 5 1982 None gt 09 501 502 EI S Offspring s ID Estimate Unknown 18 984 10 5 1982 None 18 697 10 5 1982 None 18 459 10 5 1982 None 17 711 5 25 1988 None 6 Number of Offspring Per Dam Version 2 3 February 10 2012 111 PopLink User s Manual The Number of Offspring Per Dam tab lists the number of offspring born to each dam throughout the dam s life This list is ordered in descending number of offspring Sunbittern Reproductive Report REPRODUCTIVE REPORT Export Species Type Egg Laying Incubation Period 28 Days Maximum Hatch Date Range For Clutch Mates 3 Days 45 reported dams with 132 123 174 429 offspring not including 33 offspring of UNK MULT dams 45 reported sires with 130 123 172 425 offspring All ages are at
226. pedigree of each specimen in the studbook After all documentation of pedigrees is the primary reason for keeping a studbook When it is necessary to make assumptions about some tricky or unusual parentage determinations those assumptions should be documented clearly in a Specimen Notes field A PMC or SPMAG advisor can help you determine if a parentage assumption should be recorded in the true studbook or the analytical studbook see Chapter 9 for more details Remember the computer files are the only permanent records of the studbook knowledge A studbook keeper s scribbled notes and recollections of what was done and why will soon be lost Any information worth knowing should be in the studbook Version 2 3 February 10 2012 38 PopLink User s Manual 3 Birth Type Use the pull down menu to select captive born wild born or unknown You should not enter free text into this field Note that Birth Type is equivalent to Origin of a specimen IS Guidelines Note 7 How to Enter Birth Type IG This data field is important because along with the Dam and Sire fields it can be used to help decide which specimens are likely to carry unique genetic information The options for this data field are straightforward If the specimen was collected from the wild its birth type should be entered as W LD BORN The birth event should be interpreted as physical separateness from a parent or parents Therefore an immature specimen collect
227. pooled from multiple males it might be possible to specify that the sire or dam is one of several known individuals In these cases enter MULT or MULT1 MULT2 etc if earlier MULT_ were already used is used to indicate that any one of several males or females could have been the sire or dam The possible sires or dams for MULT must be recorded in a Special Data field In genetic analyses a single sire and dam must be assigned to each specimen Therefore analytical software programs PM2000 PMx or ZooRisk treat MULT in the same way as UNK and MULT7 like UNK1 With MULT or UNK for a parent during analysis these programs create a hypothetical founder that stands in for the parent that is totally unknown UNK or one of a handful of possibilities MULT lf MULT is treated like UNK then why use MULT at all The advantage to using MULT instead of UNK when the parent is Known to be one of several specimens is that the documentation of that information might allow and encourage future determination perhaps by molecular genetic techniques of which specimen actually was the parent It would also be possible though not easy for someone to analyze the genetic and demographic characteristics of the population under alternative assumptions about the parentage Finally future genetic analysis programs might be able to deal with assignment of more than one sire and one dam for offspring In summary the key is to enter everything known about the
228. pop up window will be displayed Use the form to specify the Studbook ID Number can be a numerical or alohanumerical sex and local ID for your duplicated individuals simultaneously and when done hit Apply If Studbook ID is left unchanged PopLink will then generate sequential studbook IDs for each duplicated specimen In addition by clicking on the Edit you have the option of opening the specimen editor window where you can add additional information for each individual After selecting OK the individuals created using the Batch Editor Form will be displayed in your viewer If Cancel is selected any time before Apply Changes is pressed the additional specimens will be lost and only the original soecimen will be created and added to the studbook Ten TE eg Enter sex and local ID and PopLink will automatically duplicate the information from the specimen you just created to the newly generated specimens below Studbook ID Local ID Auto Generated Sex Auto Generated Sex Auto Generated Sex Auto Generated Sex Auto Generated Sex Apply OK Cancel Version 2 3 February 10 2012 71 PopLink User s Manual Chapter 5 FILTERING DATA IN POPLINK INTRODUCTION OVERVIEW PopLink provides the option of filtering studbook data by many demographic genetic and life history variables This filtering process is analogous to setting views within SPARKS
229. port where you can see the in depth data this report is based on in the Social data table Version 2 3 February 10 2012 120 PopLink User s Manual ei Social Compatibility Parameters Select setup options for this report below Status Required Institution PopLink allows the user to filter this report using an initial pop up the Social Compatibility Parameters box You can select a Status of Living Dead or All and an Institution If Institution is left blank the Social Compatibility Report will default to display all institutions or you can specify a specific institution by entering that institution s mnemonic see above Once the report is generated the filters are indicated directly above the table NOTE The Social Compatibility Report is only as complete as the data in the Social data table You should recognize that there are many social interactions between individuals that are either not observed or have not been recorded in that table In addition the table may include multiple interactions over a lifetime for two individuals while this table boils all of those interactions down to the single most recent event Version 2 3 February 10 2012 121 PopLink User s Manual FOCAL INDIVIDUAL ENCLOSURE REPORT vi superbbirdofparadise Focal Individual Enclosure Report ZE PS Focal Individual Enclosure Report For 73 el This table represents all of the enclosure events recorded for a
230. ps the dam in a multi male multi female social group or perhaps the sire in a herd with one breeding male In this case enter the studbook number of the known parent and enter UNK for the unknown parent Just as with WILD genetic analyses will assume that each UNK parent is unique i e unrelated to all others in the studbook Entering UNK for a parent should be the last recourse of a frustrated studbook keeper Unknowns cause real problems for genetic analyses demographic analyses and even documentation of the legal status of a specimen When a dam or sire is UNK it means there is no clue as to whether the specimen is captive born or wild caught if it is inbred who its relatives are in the population or if it is a valuable breeder The historical record of the population and all management decisions based on that record are compromised when specimens are recorded with either one or both parents as UNK However if the parents truly Version 2 3 February 10 2012 37 PopLink User s Manual are unknown there is no other option but to enter UNK Analytical assumptions can be made later so that these specimens can be utilized in genetic and demographic analyses see Chapter 9 for more details Dam and Sire Are Almost Known sometimes there is some information about the likely parentage but the identity of the dam or sire is uncertain It would be a shame to throw away some of this information One such case arises when litter mate
231. r Q time Follow up on all tests and results in the comment section even if the results are inconclusive 3 Disease Status Note Category Type Disease Status Minor Start Date 10 4 2011 Observer Comment Gall Bladder problems see diet sheets for restrictions Instructions Apply Changes The Disease Status category is intended to keep record of significant changes in the condition of an individual Type Healthy Minor Moderate Severe Grave or Other When a Disease Status note is entered you should include a Comment explaining the specifics of the status In this category the Type and Start Date are the only required fields You could enter a single Disease Status note for an individual and edit that note over time to always reflect their current status or enter multiple Disease Status notes to track changes in status over time Version 2 3 February 10 2012 65 PopLink User s Manual 4 General Medical Note Note Category General Medical Note v Start Date 10 4 2011 Observer tg quarantine for 90 days beginning 10 4 2011 Instructions Apply Changes The General Medical Note category is intended to allow flexibility in the tyoe of medical information kept Here the only required field is the Start Date The Observer and Comment fields are optional Use the Comment field to describe more details about what you are noting If you have common Medical Note types
232. racter code for each institution of up to 9 characters Although this institution list is easily viewed in PopLink the current version does not include a search function to easily look up mnemonics or other institutional data Until this functionality is added into the program we ve included an nstitution List xls file in your PopLink folder unless otherwise specified found as a default in My Documents PopLink which you can open in Excel and easily search using the Find function Ctrl F 2 User Defined Institutions Table In the View pull down Menu you can select the option to view a table of User Defined Institutions For more information on this table see page 87 3 Deleted Translated Data Table In the View pull down Menu you can select the option to view tables of any information that you deleted during past editing For more information on this table see page 70 4 User Defined Enclosures Data Table In the Edit pull down Menu you can select the option to view a table of User Defined Enclosures For more information on this table see page 60 Version 2 3 February 10 2012 31 PopLink User s Manual Chapter 4 ENTERING and EDITING DATA IN POPLINK OVERVIEW Captive animal populations are constantly fluctuating as individuals are born die and are transferred Studbook databases evolve along with such changes as well as with a studbook keeper s understanding of the population s history In order to effec
233. rectly to Excel by right clicking within the table and selecting Export to Excel Note that if you would like to save multiple versions of the same report within your studbook folder you will need to re name each report Version 2 3 February 10 2012 Open With Choose the program you want to use to open this file File AgePyramidChart htm Programs e Recommended Programs A Ei Internet Explorer D Microsoft Office Excel w Microsoft Office Word T Notepad A WordPad EH Other Programs 7 Zip Console BB Adobe Reader 8 1 RD EasyGPS WE r wi C Always use the selected program to open this kind of file Browse If the program you want is not in the list or on your computer you can look for the appropriate program on the Web 97 PopLink User s Manual SPECIMEN REPORT w Sunbittern1 473 Sen Descendents poemon Eara Studbook ID Location Local ID Current Last Origin Status Living Sire 165 Age 10 831 Dam 99 Age Est None Hatch Type Captive Hatch Sex Female Hatch Date 12 20 2000 Reproductive Not Contracepted Hatch Date Est None Location CHICAGOLP Est Conception Date 11 22 2000 Local ID 21309 Rearing Parent House Name Owner Not Reported First Location CHICAGOBR n Secondary Reproductive Reproductive Event Date Event Not Contracepted 12 20 2000 None mW p Transaction Date Transaction Date Est CHICAGOBR 397 12 20 2000 None LOWRY 204765 1
234. results can be easily extracted right click to export to Excel and used in further analyses There are several categories of results included 1 2 Analysis Window Background gives details on the setup parameters for the specific analysis Dataset Information gives counts of the number and types of individuals included in your analysis These counts can give you a sense of your sample size and further structure within your Included Individuals e g the number of wild caught vs captive born individuals Note that the of left truncated specimens includes individuals that entered the geographic window after their birth or were alive at the start of the window and the of right censored specimens includes those that were still alive at the end of the date window and that exited the geographic window Note that the of individuals with birth date death date is presented for reference as these individuals are handled differently depending on the report In the Descriptive report they are excluded from the analysis and are not included in any of the rest of the counts in Dataset Information in the Analytical report they are included in the analysis and thus and are included in the counts in this section Maximum Longevity gives ages and studbook numbers for the oldest censored dead and overall oldest of censored or dead individuals Note that the user entered maximum longevity may be slightly higher than entered e g 70 is entered bu
235. rioritizing data clean up e Assist with analytical assumption making for the purposes of population management replacement of SPARK plug e Import and compare data from multiple sources SPARKS SPARK plug other PopLink studbooks e Export data to software used in population management PM2000 ZooRisk PMx e Export data back to SPARKS format Version 2 3 February 10 2012 13 PopLink User s Manual Chapter 2 GETTING STARTED IN POPLINK For users accustomed to SPARKS software PopLink will have some familiar features and some very different features Highlights of some of the new features in PopLink include e The ability to view all of your data much like an Excel or Access spreadsheet e Multiple systems for tracking and documenting your database including tracking the user entering or editing data sophisticated note keeping systems and storage of data histories e g old data for records that have been edited e A tool that allows you to compare different versions of a studbook and find differences e Enhanced data validation routines to facilitate error clean up e New reports to assist you in cleaning up data researching unknown data and making analytical assumptions e Storage of true studbook data and analytical assumptions in the same database to facilitate population management e The ability to right click on any table displaying data and quickly export that table to Excel e Capabilities to track data related to soc
236. risk values are the value of the last Kaplan Meier entry before the age of interest for example if a survival time of 1 8 years had an at risk of 210 individuals and the next survival time was 2 3 years with an at risk of 200 the at risk value for the 2 year old age class in the life table would be 210 individuals Mortality rates are then back calculated from survival rates Ly x 1 1 T Qx 1 Calculations of Confidence Intervals around Median Life Expectancy Confidence intervals are calculated based on a log transformed confidence interval Klein and Moeschberger 1997 where the interval is defined by calculating Z for each survival time t z inl In L Inf 1n 0 5 LE nt W where L is the Kaplan Meier survival estimate and the standard error of L is K amp M equation 4 5 5 modified for clarity p112 mK d WV Ly _ K amp M equation 4 2 2 modified for clarity p84 LS NON d where d deaths and N number at risk at a given time The reported confidence intervals are the 95 Confidence intervals Z is 1 96 these Cls are the values of L where Z lt 1 96 and Z gt 1 96 Statistical Comparisons of Male and Female Survival Statistics Comparisons of median life expectancies using confidence intervals In the Descriptive Report the statistical test used to determine whether male and female data subsets are reported separately or pooled together is a comparison of the median life expectancies of each sex
237. rom an existing SPARKS studbook 2 importing the dataset from a ZIMS download note that although this option exists in the program until ZIMS is completed the option is not fully functional or 3 creating anew empty database within PopLink Under Step 2 you designate specific information depending on the method used to create your database for SPARKS you can navigate to the folder containing the studbook you wish to import from SPARKS usually in your SPARKS folder on your C drive and highlight the desired studbook for ZIMS download navigate to the ZIMS file for an empty PopLink database you can specify whether the species is live bearing or egg laying Under Step 3 you can enter a name for your PopLink database and a description If you re importing from SPARKS or ZIMS the default name will be the existing file s name you may leave this default or change the studbook name PopLink has no character length limitations on file name but does not allow your studbook name to start with a number or include dashes spaces slashes or other restricted characters The program may prompt you to choose a new name if your studbook name has invalid characters 2 a text description of your new database this is a good place to record details about the purpose of the database e g this is a database created for use in the June 2011 planning meeting at Lincoln Park Zoo When these steps are completed click
238. roperly entered first events i e the first event record is not a birth or capture PopLink will display a warning These specimens affect the Census Details report and errors in the records should be fixed more details on individuals with this error can be found in the Validation Report Sunbittern Census Details SE Census Details Census taken from January 01 to December 31 Restricted to Associaton AZA fed AND No restrictions on UDFs Hatch Death Enter Exit eS EU Eer eI a eer 2008 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2007 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2006 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2005 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2004 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2003 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2002 5 3 0 0 8 2 2 0 0 4 0 0 0 0 0 0 0 0 0 The Census Details report tallies annual numbers of various events based on data in the Event Data Table births deaths entrances into the geographic window you selected exits from the geographic window transfers captures from the wild releases recaptures go LTFs and return from LTF the last six tallies are not pictured in the screen capture above The Enter Exit columns are only tallied if you select a geographic window for example in this case Enter can be interpreted as the number of individuals transferred into an AZA institution from a non AZA facility in a given year SURVIVAL TOOL REPORT For full details on this report ple
239. rs may also be i expected to change as a population s age structure changes For example if the population has not been maintained in zoos and aquariums long enough to have many adults living into old age median life expectancy will likely be an underestimate until more data accrue in older age classes Thus users of these reports should recognize that the results produced will likely vary over time or depending on the subset of data selected Although for many species including humans survival statistics often differ for males and females for these analyses male and female statistics were not statistically differenti these results therefore include pooled data from males females and unknown sex individuals e el 1 The Summary tab displays the Descriptive Survival Statistics Report designed to produce a concise description of survival information for communication public relations and general audience purposes To produce the results included in the report PopLink a Calculates Kaplan Meier survival probabilities median life expectancies confidence intervals around the median life expectancy the age to which 25 of individuals survive and 1 year survival rates for the Pooled Male and Female data subsets as described in the Detailed Methodology section Version 2 3 February 10 2012 144 PopLink User s Manual b Determines whether Pooled Male and Female subsets pass the five data quality tests Data subsets that fail d
240. rship is a cumulative measure i e the survivorship of age class 10 is influenced by all of the survival rates in all the age classes from birth until 10 Survivorship is represented as L in life tables and can also be called the Kaplan Meier estimate or the Product Limit Estimator Mortality rate Q the probability that an animal alive at age x will die during that age class Version 2 3 February 10 2012 141 PopLink User s Manual Survival rate P the probability that an animal alive at age x will Survive to age x 1 Note that survival rate is not cumulative but is over a single age class and that Qx Px 1 HOW TO RUN AN ANALYSIS IN THE SURVIVAL TOOL Before you run your analyses in the Survival Tool it s a good idea to get a sense of your data quality You can do this by running The Data Validation routine certain data validation errors will affect your survival statistics either by excluding an individual specimen with errors from the analysis or including only part of its data Errors to especially look out for and correct if possible are 1 a EH 01 Currentness date is more than one year old if your database is not reasonably current a year or more out of date you probably want to use the currentness date for your end date for the analysis window see below Using the currentness date ensures that you are only including individuals in the analysis for as long as you have tracked them EM 17 Invalid Ev
241. rth date estimates can be entered by using the edit button next to the Birth Date Estimate data entry field For more information on entering dates and date estimates see page 48 Version 2 3 February 10 2012 39 PopLink User s Manual D Guidelines Note 8 Estimated birth dates If the exact date of birth is known it should be entered into the Birth Date field with the Date Estimate field as None If the exact date of birth is not known every effort should be made to develop a reasonable estimate The best date estimate is one based on information specific to the specimen and or species For example in a herd situation where the female was observed to be pregnant and then seen again with the offspring three days later the exact date is not known however it was born within the last three days The condition or behavior of the offspring may give additional clues to the exact date of the birth A similar situation may occur when a nest is only checked every three days to avoid disturbance If hatching occurs between nest checks then the hatch date can easily be estimated to day see pages 48 on date estimates Marsupials bears and cavity nesting birds among other taxa are examples of species whose biology can be used to estimate the birth hatch date In these cases the studbook keeper should work with the holding institution e g keepers and curatorial staff to back calculate from the date the specimen was first observ
242. rtionally included in the analysis as described in the Detailed Methodology section DESCRIPTIVE SURVIVAL STATISTICS REPORT The majority of the statistics calculated in the Descriptive Survival Statistics Report are based on a starting age of 365 days the median life expectancy confidence intervals and the age to which 25 of individuals survive exclude any individuals who did not survive to their first birthday These individuals are excluded because this Report is focused on providing median survival estimates for the typical individual that survives the vulnerable infant stage In other words this report answers the question how long is this species expected to live once it has reached its first birthday After selecting the Descriptive Survival Statistics Report option and setting your demographic window PopLink produces a report with three tabs Summary Included Individuals Table and Data Quality Table 13 PM2_SavTam09 Descriptive Survival Statistics Report EI E DESCRIPTIVE SURVIVAL STATISTICS REPORT d Summary Included Individuals Table Data Quality Table li DESCRIPTIVE SURVIVAL STATISTICS REPORT SAVAGE TAMARIN Studbook AZA SAVAGE Hypothetical North American Studbook Studbook data current as of 11 2 2009 II I Compiled by Charles Darwin PopLink Studbook filename PM2_SavTam09 PopLink User Who Exported Report Lisa Faust Date of Export 1 31 2012 i Data Filtered by StartDate 1 31 198
243. s Export to ZooRisk 3 8 PopLink creates the files master dbf and moves dbf that ZooRisk can import to create its projects Once you ve exported your data from PopLink go to the Create a Single Species Project in ZooRisk and follow the instructions for importing the master dbf and moves dbf files which will be stored in C Users tgazlay Documents PopLink PopLink Databases Sunbittern ZooRisk Export For more details on how to use these files to create a ZooRisk project please see README ZOORISK EXPORT in C Documents and Setting LFaust ZooRiskExport Version 2 3 February 10 2012 94 PopLink User s Manual Upon export to ZooRisk an excel file is displayed listing PopLink fields that are incompatible with ZooRisk The ZooRisk Export Errors file is saved in C Documents and Settings User Name My Documents PopLink PopLink Databases Studbook Name ZooRisk Export Default values are chosen that are compatible with ZooRisk and should be corrected within PopLink Please read the ReadMe file located in your PopLink ZooRisk export folder for further details When your ZooRisk export files are created they are placed in your ZooRisk export folder eg C Documents and Settings User Name My Documents PopLink PopLink Databases Studbook Name ZooRisk Export When you open ZooRisk go to the Create a Single Species Project and follow the instructions for opening the master dbf and moves dbf files SPARKS EXPORT PopL
244. s Manual Chapter 7 EXPORTING DATA FROM POPLINK PM2000 EXPORT PopLink will create standard PM2000 export files for your studbook database You can export from your true studbook e g Sunbittern or from your studbook with an analytical overlay applied e g Sunbittern Faust1 The database displayed at the top of the screen will indicate which database is being exported When you select the PM2000 export from the Export drop down menu this screen will be displayed EE Sunbittern File Edit View Validate Reports Export Help D o A a al se 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 ifSunbittern prn Sunbittern ped Male Demographics File Name Genetics Filters File Name mSunbittern prn Sunbittern txt 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 filters The following are default filters Locations N AMERICA AND During Locations N AMERICA AND As of 1 1 1900 11 14 2006 AND Status 11 14 2006 AND Status Living Living Ok The file names on the left hand side are defaults that are chosen based on your database name you can change the file names if you desire but
245. s Manual STUDBOOK OVERVIEW File Edit View Overlay Validate Reports Export Help D o e al ve Select Filters As of 10 25 2011 AND Status Living Totals 61 47 11 119 at 52 Institutions No Sort Order Applied No Edits Currentness Date 3 22 2010 Cd e Tr Master Sex Reproductive Events Specimen Notes UDFs Social Enclosures Medical Studbook Overview Name PopLink Version Studbook Description Studbook Keeper Studbook Keeper Institution Studbook Keeper Email Studbook Scope Class Order Family Scientific Name Common Name Species Notes Species Type Incubation Period In Days Maximum Hatch Date Range For Clutch Mates In Days Currentness Date Date Created User Created Date Last Edited User Last Edited Edit Value pe Talia Gazlay ES Lincoln Park Zoo E Ka Regional AVES a GRUIFORMES Esl EURYPYGA HELIAS SUNBITTERN Sexing ZooGen can sex Did so for Audubon Ez Egg Laying 28 Ej 3 22 2010 11 16 2007 joanne 10 25 2011 SEHR Total Specimens In Studbook 182 171 256 609 The Studbook Overview contains data imported from your SPARKS dataset or entered directly for new PopLink databases as well as additional fields for documenting your database s history and status Any fields that are editable are denoted with an Edit button The Species Notes field is an important place to document essential information about your studbook s convent
246. s Manual sunbittern File Edit View Validate Reports Export Help D o A a als User Defined Institutions General Location JARANOL Joseph Aranol Rochester NY dealer who went out of business in 1980 N AMERICA Mnemonic Edit Address State Country Phone Add User Defined Synonyms Real Institution Mnemonic Synonym Edit Add You can add new user defined institutions or edit existing ones using this screen In PopLink these user defined institutions travel with the studbook database so once you have defined them for your database other PopLink users will always be able to recognize them UDF CASING CLEAN UP TOOL After initial importation of your studbook there may be some UDFs with mixed casing i e some of the specimens may have YES and some may have yes Although not critical to data quality you can use the Clean Up UDF Casing option in the Validate pull down menu to assign a consistent casing scheme DELETE EMPTY UDF ROW TOOL After initial importation of your studbook there may be some specimens with extra blank rows in the UDF table eg a specimen may have a row with filled data fields and a second row with blank data fields Although not critical to data quality you can use the Delete Empty UDF Rows option in the Validate pull down menu to delete out all of these blank rows which cleans up the UDF data table Version 2 3 February 10 2012 88 PopLink User
247. s birth location or source is not known a The animal is most likely not related to other animals in the population based on its probable source or other evidence Give the animal wild parents b The animal is most likely related to other animals in the population Make no assumptions unless other evidence allows you to connect the animal to an existing family line 3 The animal first appeared at a known institution First investigate potential parentage by determining if there were potential parents of reproductive age at the individual s institution during the time frame of interest and excluding any that might have already been pregnant a There were no potential parents recorded at the institution Give the animal and all similar animals originating from the institution hypothetical wild caught parents unless other evidence suggests a relationship to another family line or institution b There were potential parents males and females of reproductive age at the institution at the time of the unknown e conception and birth i There was only one set of potential parents at the institution Assume these animals were the parents unless evidence suggests otherwise li There was more than one possible sire or dam at the institution 1 The potential sires dams are closely related Arbitrarily choose one of the relatives as the sire dam or else choose the most likely one based on information such as breeding age number of living
248. s features and uses language specific to the species type selected upon dataset creation e g egg laying or live bearing this manual refers to all births and hatches as births and to all litters and clutches as litters regardless of species type Program Information If you have any comments questions bugs or compliments to report about PopLink please contact us directly at software Ilpzoo org We will attempt to identify and fix run time errors within the software especially in the initial release period more substantive changes may be made as time and resources allow The latest version of the PopLink program and the manual will be accessible via the website http www lozoo org poplink You should check the website occasionally to ensure that you re running the most up to date and bug free version You can also email software I pzoo org to be added to the mailing list to receive updates about new PopLink releases Version 2 3 February 10 2012 PopLink User s Manual System Requirements Hardware Minimum system requirements 2 0 GHz CPU 2 GB RAM Operating System PopLink 2 3 is compatible with Windows XP Windows Vista and Windows 7 including 32 bit and 64 bit machines Although primarily developed for PCs it has been successfully run on Macs using Boot Camp or Parallels which require a version of the Windows operating system before PopLink can be installed following normal installation instructions Getting Help
249. s not recorded a black hole in the pedigree of the population If the number of animals starting the black hole can be estimated and the number of animals produced is known one can calculate the likely relatedness of the unpedigreed offspring coming out of the group using Equation 9 and Table 2 from Willis 2001 Equation 9 estimates the effective number of alleles in the group Version 2 3 February 10 2012 137 PopLink User s Manual A gt Max Min In Max In Min where Max is the maximum number of effective alleles contributed by the founders of the black hole and Min is the minimum number of effective alleles that could have possibly been contributed usually four two alleles from a single male and two alleles from a single female Max founding males founding females x 2 alleles each Min 1 male 1 female x 2 alleles each 4 For example if a black hole group were started from 2 males and 4 females the maximum number of effective alleles contributed if all reproduced would be twelve 2 males 4 females 6 founders x 2 alleles for each founder 12 The minimum number of effective alleles would be four 1 male 1 female 2 X 2 alleles for each 4 Completing the equation gives a value of 7 28 Ao Using the number of effective alleles Az and knowing the number of unpedigreed individuals coming out of the black hole group one can use Table 2 of Willis 2001 to estimate the likely relatedness
250. s or nest mates or egg mass mates are brought into captivity Often it is either known or suspected that they are siblings but the parents are WILD In this case enter W LD1 and WILD2 for the parents of each sibling or WILD3 and WILD4 etc if the earlier WILD_ numbers have already been used Genetic analyses will then correctly use the knowledge that these specimens are siblings that came from a single pair in the wild If a pregnant or gravid female is brought into captivity then the studbook number of the dam would be recorded while the sire would be listed as WILD A similar situation can arise when a litter or clutch or brood is conceived and born or hatched in captivity but the dam and or sire is unknown In this case the unknown parent s should be entered as UNK7 and or UNk2 etc This will show that the siblings have the same parents but also indicate that it is not known who those parents are When multiple offspring have UNK7 as a parent genetic analyses will assume that UNK7 is a specimen who was a parent to each of those offspring but a parent to no one else in the studbook Thus while specimens with UNK for parents are assumed to be unrelated each UNK is unique specimens with UNK7 and UNK2 for parents are assumed to be siblings Occasionally such as when specimens are housed in large social groups when multiple males are rotated through an enclosure with a female or when artificial insemination is done with semen
251. s report you need to enter the age in days at which you d like your analyses to start see the Expert report description below on how to choose this age The bottom check box can be selected to generate a separate pop up window with advanced results for any of the analyses you ve run see below for further details Version 2 3 February 10 2012 142 PopLink User s Manual After making this selection you ll be prompted to make decisions about the analysis window of Survival Tool Parameters Select your wind for e analyses below Start Date 1 31 2012 si MM DD YYYY End Date 1 31 2012 zk MM DD YYYY Institution All Institutions Additional No Filters Applied s i Filters i Ok Cancel The Survival Tool analyses are based on survival records which trace an individual s life from its entry into the population to its exit out of the population The population in question is defined by the analysis window entered when you begin running the Survival Tool and can be based on a time window using a start date and end date and if desired a geographic or institutional window such as North America AZA institutions or Germany these are entered using mnemonics page 47 You can also further filter the data by UDF origin etc with the Additional Filters option Individuals are excluded and included in this window as described in the Detailed Methodology section on page 150 P
252. s report generates fecundity Mx and mortality Qx values at each age class for males and females in the studbook Note for each offspring each parent gets 0 5 of the birth attributed to him her If a birth is attributed to unknown parents or parents of unknown ages you have the option of proportionally factoring these births into the fecundity See page 92 for more details on how these values are calculated Version 2 3 February 10 2012 116 PopLink User s Manual SPECIMENS WITH UNK MULT PARENTAGE AND DESCENDENTS REPORT File Edit View D o A el al ve Validate Reports Export Help SPECIMENS WITH UNK MULT PARENTAGE AND DESCENDANTS Export Select Filters No Filters Applied SPECIMENS WITH UNKNOWN PARENTAGE Studbook Current Sire Dam Birth Birth Date First Second Current AZA Total 4S ID Status Date Est Location Location Location Living Des Living Desc E 15 LTF UNK UNK 1 1 1949 Year SURABAYA ROTTERDA UNKNOWN 42 169 1835 1960 18 Dead UNK 14 6 11 1950 None ROTTERDA ROTTERDA ROTTERDA 42 175 1031 1448 mm 136 Dead 72 UNK 3 18 1965 None CATSKILL CHICAGOBR CHICAGOB 35 91 1031 1448 a 121 Dead 72 UNK 12 17 196 None CATSKILL CHICAGOBR AUDUBON 35 9i 1448 iq 426 Dead UNK UNK 8 4 1975 None SURABAYA ROTTERDA ROTTERDA 29 125 1988 157 Dead UNK UNK 12 20 1965 None CATSKILL FRANKLINP LEE 22 74 1447 19 LTF UNK UNK 6 1 1935 Month CHERIBON JAKARTA JAKARTA 22 127 1523 1954 i 462 Dead 157 UNK 5 31 1
253. s such as this an approximate birth date in the middle of the breeding season should be used see page 32 on how to estimate dates Sometimes birth dates cannot be reliably estimated to the nearest calendar year In such cases the date of birth should be entered as unknown Estimated birth dates must precede all known event dates Eggs collected in the wild that hatch in captivity should be entered with the hatch type CAPTIVE HATCH see Guidelines Note 11 on captive born specimens Rearing method for wild born specimens should be recorded as PARENT HAND or UNKNOWN The first event for a wild caught specimen should be WILD CAPTURE For species that originate from a single country the event location should be listed as the origin country or a region within that country If capture location can be identified to a continent or region e g all wild caught gorillas must have been captured in Africa then the location should be entered as region e g AFRICA When specimens could have originated from one of several continents and their location of capture is not known the origin should be entered as UNKNOWN The date of capture will rarely be known and will usually be estimated to month or year see page 32 on estimating dates Capture dates should always occur after the estimated date of birth Because specimens captured from the wild are not usually maintained for long periods prior to arrival at the first owner s location or the last de
254. sion 1 0 20111013 Chicago Zoological Society Brookfield Illinois USA ISIS 2002 SPARKS 1 52 Single Population Analysis and Record Keeping System Apple Valley MN International Species Information System Lacy R C and J D Ballou 2002 PM2000 version 1 163 Chicago Zoological Society Brookfield IL Pollak J P R C Lacy and J D Ballou 2002 Population Management 2000 version 1 163 Chicago Zoological Society Brookfield IL Thompson S D Earnhardt J M and Turner Erfort G 1997 Guidelines for Data Entry and Maintenance of North American Regional Studbooks Lincoln Park Zoo Chicago Illinois Willis K 1993 Use of animals with unknown ancestries in scientifically managed breeding programs Zoo Biology 12 121 172 Willis K 2001 Unpedigreed populations and worst case scenarios Zoo Biology 20 305 314 Version 2 3 February 10 2012 140 PopLink User s Manual APPENDIX 1 POPLINK SURVIVAL TOOL INTRODUCTION Correct and accurate interpretation of mortality data of captive populations is essential to the continued success of the cooperative management programs such as Species Survival Plans and any other AZA managed species day to day management of specimens at zoos and aquariums and the reputation of Zoos and aquariums in the eyes of the public the media and animal advocacy groups The PopLink Survival Tool was created through the support of an Association of Zoo and Aquariums Conservation Endo
255. social group change end date Group Size The number of individuals in the enclosure this includes the focal individual Focal Age at Start End The focal individual s age at the start and end date of an enclosure event Group Male Female Age Range at Start End The sex specific age ranges of other animals in the social group at the start and end dates excluding the focal individual Born Hatched Died In Out These fields list the Studbook IDs of animals that enter exit an enclosure or social group via being born hatched into the enclosure being transferred in or out of the enclosure or dying Even if an individual is entered into exited out of an enclosure on their birth death date there must be a comment added by PopLink to count as a born died in an enclosure Group Members The Studbook IDs of all the individuals in the enclosure including the focal individual You can use this report to look at which enclosures an individual has been in over its lifetime which other animals it has been with and which life history stages the animal has been with e g has the focal individual ever been housed with adult males Version 2 3 February 10 2012 122 PopLink User s Manual ENCLOSURE REPORT id superbbirdofparadise Enclosure Report ZE me Enclosure Report With a During date span this report shows the group composition in an enclosure at each change in composition each time one or more animals enter
256. st offspring s birth their birth date and estimate and the ID of their first offspring by ascending order of dam s age at first birth You can view the Specimen Report of any dam by double clicking on the Studbook ID or of any offspring by clicking on the Offspring s ID Sunbittern Reproductive Report REPRODUCTIVE REPORT Export Species Type Egg Laying Incubation Period 28 Days Maximum Hatch Date Range For Clutch Mates 3 Days 45 reported dams with 132 123 174 429 offspring not including 33 offspring of UNK MULT dams 45 reported sires with 130 123 172 425 offspring All ages are at dam conception Select Filters ies applied to parents No Filters Applied LI L EN gt Kai M gt gt 3 1 1983 None 1 55 10 24 1988 None 158 9 1 1982 None 247 1 667 4 19 1995 None 424 1 678 10 15 1995 None 446 1 719 8 1 1987 None 162 2 152 6 1 1973 None 47 2 229 7 12 1986 None 156 2 404 6 28 1996 None 461 2 661 1 23 1991 None 295 5 Dam Age at All Births This tab lists all dams with offspring their age at the time of each offspring s birth their birth date and estimate and the ID of each of their offspring A dam with more than one offspring will be listed more than once You can view the Specimen Report of any dam by double clicking on the Studbook ID or any offspring by clicking on the Offspring s ID Sunbittern Reproductive Report REPRODUCTIVE REPORT S
257. sures table see left Notes about the name change can be recorded in the Description field in the User Defined Enclosures table Name Location Description t OUTI ICHICAGOLP South Outdoor Yard 9 28 2011 OUT2 CHICAGOLP North Outdoor Yard 9 28 2011 OUT3 CHICAGOLP East Outdoor Yard 9 28 2011 MED CHICAGOLP Medical Holding 9 28 2011 QUAR CHICAGOLP Quarantine Holding 9 28 2011 INDOOR1 CHICAGOLP West Indoor Housing 9 28 2011 Old Value Change Date NightHouse 10 19 2011 User tgazlay NOTE Merging And Splitting Enclosures Enclosures may be combined or split to accommodate changing collection and institutional needs over time Since PopLink only allows a specimen to be in one enclosure at a time it is easiest to create a new User Defined Enclosure to represent each different combination or parts of a split enclosure For example if enclosure A B amp C are combined it is best to create a new User Defined Enclosure representing all three of those enclosures i e a User Defined Enclosure of ABC with a description explaining the combination Following this same logic when a single enclosure is split it is easiest to create a new User Defined Enclosure for each sub enclosure created The Enclosures data table only allows entry into one enclosure at a time which may be complicated when an individual is given access to more than one enclosure at once If an individual is given access to more than one e
258. t 70 00014 is displayed this is rounding error in translating between years and days and the impact is minimal Survival Statistics Summary gives median life expectancy 84 and 95 Cl 95 Cl are displayed in all reports 84 are used for statistical analysis of comparison of medians as well as results observed and expected deaths x test statistic of log rank test comparing male and female curves General Dataset Quality gives counts of the number of records with estimated birth or death dates and information on when sample size becomes small below 30 individuals at risk Version 2 3 February 10 2012 149 PopLink User s Manual 6 Data Quality Tests gives results for the 5 data quality tests DETAILED METHODOLOGY USED IN THE SURVIVAL ANALYSES Inclusion Exclusion of Individuals Individuals included in a specific analysis can be viewed in the Included Individuals Table The Survival Tool determines which portions of an individual s lifespan is included excluded by extracting the subset of individuals from your studbook that lived for any period of time during your extraction window the date and institutional filters you set at the beginning of the report Individual specimens enter the analysis by 1 being born into the population defined by the analysis window 2 being transferred into the geographic window after the start date or 3 being alive in the geographic window on the start date the last two types
259. t between sire and dam 0 5 to each and tallied as an unknown sire birth or an unknown dam birth e g a generic bin for all specimens with unknown parents i If one parent is Known and one is unknown 0 5 is assigned to the age class of the known parent and 0 5 is added to the unknown parent tally ii After initial M calculations are made PopLink gives users the option of proportionally distributing data from unknown parents see 3a below for more details 2 Tally the number of individuals at risk for reproduction in each age class a An individual that has lived through an entire age class gets tallied as 1 0 for that age class b An individual that has lived through a portion of an age class e g was born midway through a year or was transferred out midway through a year or the date window started or ended midway through an age class is tallied as whatever portion of that age class For example if an individual was transferred out of the demographic window when 6 years and 3 months old then for the 6 7 age class that individual would be tallied as 3 12 0 25 c Males are attributed to male risk tallies females to female risk tallies Unknown sex individuals are tallied 0 5 to male age class tallies and 0 5 to females 3 Calculate each age specific fecundity rate as number of births attributed to a particular age class number of individuals at risk for that age class Version 2 3 February 10 2012 93 PopLink User s M
260. te are the only required fields Unless a medication is permanent there will usually be an End Date as well NOTE To make the Medication Note category effective use the Comment field to record d dr the dosage frequency of a medication e g 2x daily for 1 week special dosage instructions j mix powder with 2 oz of apple juice and administer as the first item for a feed or any other SE important information e g do not mix with any citrus fruit reaction potential Also use this space to provide a complete medication prescription description Version 2 3 February 10 2012 67 PopLink User s Manual 8 Weight Note Category Weight Value Unit of Measurement Start Date 50 Pound s 10 4 2011 Observer Comment tg annual weight Instructions Apply Changes The Weight category allows easy tracking of body weight over time In this category the Value Unit of Measurement and Start Date are the only required fields In the Value enter the numerical weight free text and in the Unit of Measurement field use the dropdown menu to choose from the selection Microgram s Milligram s Gram s Kilogram s Pound s or Ounce s The Comment section can be useful for tracing possible causes of weight gain loss etc Version 2 3 February 10 2012 68 PopLink User s Manual ENTERING EDITING DATA IN THE STUDBOOK OVERVIEW TABLE ww Edit Studbook Overview Studbook Keeper Species Notes
261. the date an old value was changed and the user who changed it This system should give more information on how and when data are changed which will be helpful as consecutive studbook keepers maintain a studbook database Gi E AU AU AU FIAL EEN I ce cee oor ETT Sec H Captive Hate 5 17 1 m D Value ha Date User bptive Hate 3 26 41 _ 10 12 2006 Lat Je e Hate 10 5 1 e Kee gen E Capive EIE eis 6 ff ENTERING A NEW SPECIMEN The same Specimen Editor screens used to edit data for an individual specimen are also used to enter an entirely new specimen To add a new specimen to your dataset select the New Specimen option from the Edit pull down menu This will produce a specimen editor pop up window with tabs for editing relevant information from each data table For new specimens the data fields will be blank To appropriately enter data for a new individual you will have to fill in data in the Master Sex Reproductive and Events Tables Specimen Notes and UDFs are optional As the specimen editor for editing existing data and entering data for a new specimen is the same we will describe both processes together for each data table Note that there are mandatory fields that must be completed to have a valid specimen record if you have skipped one of those fields PopLink will pop up a reminder before you exit the specimen editor Version 2 3 February 10 2012 34 PopLink User s Manual ENTER
262. the most recent owner based on the ownership transactions in the SPARKS MOVES dbf file If no ownership events were detected on import this field will display not recorded IO Guidelines Note 1 Ownership Specimen ownership can be a very involved issue particularly with the advent of multi party breeding loans Although owners often report information that indicates specimens were transferred via loans tracking the actual ownership of studbook specimens is not the responsibility of the studbook keeper The terms of individual transfers should be tracked by the institutions themselves In most cases there is no reason for ownership to be included in the database Ownership does not usually impact development of population management plans There are good reasons to omit ownership from studbooks For example there have been several instances of ownership records in studbooks being consulted for legal issues Some state and governmental agencies may consider studbooks to be the official legal record of a specimen s history Under some interpretations therefore a transfer could be construed as a sale loan donation trade or exchange unless different types of transfers are clearly noted Version 2 3 February 10 2012 22 PopLink User s Manual for every specimen in the studbook Under extreme circumstances this could also place the studbook keeper in litigation Ownership has in the past been confused with location t
263. this report if she has had multiple reproduction events at ages older than those of other females e Sire Age at First Birth is simplified into two tables that list 1 the 10 youngest sires at first reproduction by ascending age and 2 the 10 oldest sires at first reproduction by descending age Sires with UNK birthdate estimates are excluded from these tables e Sire Age for All Births is simplified into one table that lists the 10 reproductive events single births or litters of offspring of the oldest males listed in descending order of age at reproduction Note that a male may be listed more than once in this report if he has had multiple reproduction events at ages older than those of other males e The Number of Offspring Per Dam and The Number of Offspring Per Sire are each simplified to list only the 10 dams and 10 sires with the greatest number of offspring e The Interbirth Interval is modified to include only the 10 shortest intervals between single births or litters Interbirth intervals of births within the same litter are ignored in this list CURRENT INSTITUTIONAL HOLDINGS REPORT Sunbittern Current Institutional Holdings CURRENT INSTITUTIONAL HOLDINGS Select Fiters As of 9 21 2009 AND Status Living AZA INSTITUTIONS 53 44 10107 at 45 Institutions Institution Male Female Unknown Other Ja LI L m D C Es C INN Ss d IT kel JS d I kk ww m ken S ke 0 T gt Sk Ko LU w
264. tion in the Edit drop down menu Within the specimen editor you can also delete portions of an individual s record such as specific rows of data in the Sex Reproductive Event UDF and Species Notes tables Be careful as there is no undo option when you are deleting data To view data that you have deleted use the View Deleted Translated Data option in the View drop down menu It will display a table with data from specific tables that have been deleted CB sunbittern File Edit View Validate Reports Export Help D o A el alk Master Sex Reproductive Events Specimen Notes Studbook Hatch Date i Date User ID Sire Dam Hatch Type Hatch Date Est Rearing Owner Deleted Deleted 521 UNK UNK Wild Hatch 10 11 2006 None 10 12 2006 LFaust T1052 WILD WILD 10 12 2006 None 10 12 2006 LFaust You cannot click on a button to undelete these data but you can reenter them by hand if the deletion was a mistake RENUMBERING SPECIMENS Generally you should not change a permanent studbook number once you have assigned it see Guidelines Note 5 on page 35 for more details If you have assigned a temporary number to a specimen there is a function within PopLink to reassign that individual a permanent studbook number If you select Re number Specimen from the Edit pull down menu a tool will pop up which lists all non numerical IDs in the studbook CR Re number Specimen Sele This utility allows you to re number any Stu
265. tion s records this specimen becomes lost to follow up at some point after the arrival date at the known institution and would be entered like this Studbook Transaction Transaction Transaction Location Local ID ID Code Date Date Est 66 Hatch CHICAGOLP B8138 3 26 1981 None 66 Transfer CHICAGOBR 890017 1 20 1989 None 66 Transfer CHICAGOLP B8138 1 25 1991 None 66 Go LTF CHICAGOLP 8138 1 25 2001 e None Note that PopLink also includes the event option of Return from LTF You can use this option if a specimen comes back into an institution from a place that did not track it or you get a report of an event e g a death after a period of non reporting In such cases you can enter the same date for your specimen for Return from LTF and Transfer Death Version 2 3 February 10 2012 49 PopLink User s Manual IO Guidelines Note 17 Lost to Follow Up A specimen is considered lost to follow up LTF when its disposition is unknown Lost to follow up should be used to designate specimens whose status is uncertain This includes specimens transferred to institutions that don t report to the studbook keeper specimens that may have or probably have died and specimens that have just disappeared While Go LTF can be an specimen s final event PopLink does allow specimens to Return from LTF page 49 this may occur if soecimens are transferred to institutions that don t report to a studbook keeper Go LTF and lat
266. tion will code individuals as 1 2 Has Bred black Has Not Bred white iv Parent and Breeder this option combines the two above options showing Founder Has Bred Founder has not bred etc Note that individuals in the Detailed Age Pyramid are only known age individuals if you would like to see the unknown age specimens in your population you can do that via the Unknown Age Report File Edit View Validate Reports Export Help Dill a ve Age Pyramid Report Known Age 55 43 12 110 Unknown Age 0 1 0 1 Select Filters As of 11 14 2006 AND Status Living Total Sreccccccccvccsscscosoveveccecvseqeoceccsocossscecsevecoseseovooescssseccsooocvovooocccosessecooeoeed Wild Hatch Captive Hatch Unknown Age Clees M F ul al M Flulal mMi rlulal mMi elfula We Mm hm Ni ti Ww amp Wore GO NM OO NM FA Alin h W NR oO We We Wi Mm NM oO r O 0 0 0 0 0 0 O 0 0 0 0 0 0 oO OO OO OO CH O 0 0 0 0 0 0 O 0 0 0 0 08 0 We We W Mm hme Oe O 0 0 0 0 0 0 oi Oi Oi Oi OO O oO OO OO OO CH O 0 0 0 0 0 0 OO Oro Gi amp This tab displays counts of the number of individuals in each age class in your population the table is organized by birth type total wild born captive born and unknown birth type and separated by sex Male Version 2 3 February 10 2012 Female Unknown Abnormal Other 105 PopLink User s Manual UNKNOWN AGE REPORT Sunbittern Unknown
267. tively manage populations it is necessary that all such changes be recorded accurately and promptly in the studbook database BASIC CONCEPTS HOW TO ENTER DATES AND DATE ESTIMATES In the course of editing or entering a specimen s record dates need to be entered in several fields and these general guidelines should be used in all of those cases All dates in PopLink are in the format MM DD YYYY Note that this is the North American date format e g Jan 1 2006 rather than the European date format e g 1 Jan 2006 that SPARKS uses When uncertainty exists around the exact date for an event date estimates can be used to express that uncertainty Date estimates can be entered by using the edit button next to any Date Estimate data entry field Possible date estimates include the Standard estimates of None Day Month Year and Unknown or by a Date Range estimate of a number of months or years BJ Guidelines Note 4 How to Enter Transaction Dates The function of the transaction date goes far beyond the determination of when a specimen arrives at or leaves an institution Transaction dates for births captures transfers and deaths are essential data for demographic analysis Demographic analyses are performed by including individual specimens in specific age classes individual units of age usually measured in years For example if a specimen is in the captive population from its third to its fourth birthday it is counted as
268. tracepted 7 1 1961 Unknown Reproductive Event Date Add Delete PopLink assumes that specimens are not contracepted at birth Specimens that were contracepted or neutered sterile in SPARKS will have an additional event on the date that the studbook was imported in PopLink You can change the event date if you have more information on when the contraception started or neutering occurred To edit the existing reproductive events highlight the desire event and alter any of the fields below When completed click Apply Changes Reproductive Status Not Contracepted Event Date Event Date Estmate 7 1 1961 Unknown Bel MM DDAYYYY Click here to add change notes Notes Batch Input ji Ok Cancel Version 2 3 February 10 2012 45 PopLink User s Manual The screen for entering editing reproductive data for a specimen is similar to that for sex data Remember that reproductive data are tracked as a data stream and an individual will start out its life as not contracepted and can then be switched to contracepted or neutered sterile sometimes multiple times Not contracepted should be used when an individual s reproductive status is not known and neutered sterile should be used when an individual is neutered or reproductively sterile for some other reason To edit existing reproductive status event s highlight the desired event and edit the data in the fields to enter a new reproductive st
269. ttern Life Table Report Seles Life Table Report Export Select Filters No Filters Applied Please note that the following numbers are calculated slightly differently than SPARKS For each offspring each parent gets 0 5 of the birth attributed to him her There are 405 total births in the demographic window 295 births are attributed to known parents with a known age 92 births are attributed to known parents with an unknown age 18 births are attributed to unknown parents This means that 27 of the total births are attributed to unknown parents or parents with unknown ages For this report the births were proportionally factored into the fecundity Fecundity Mix Mortality Ox 0 1 0 000 110 2 0 000 107 8 0 490 203 4 0 480 197 3 0 030 0 2 0 070 oF 0 090 94 5 0 090 33 6 2 3 0 190 skl 0 180 SE 0 050 24 0 0 040 oo 0 260 fed 0 270 76 6 0 040 E 0 100 20 6 4 5 0 280 FOD 0 230 fl 0 010 ek 0 010 fe 0 390 foe 0 310 ZA 0 030 Gef 0 040 7125 6 7 0 280 ES 0 360 67 6 0 070 FAS 0 040 BS 0 200 GE 0 300 61 4 0 000 68 6 0 050 S 0 140 of 0 300 or 0 0 030 62 3 0 0 0 SR 9 10 0 260 Doe 0 2 0 49 6 0 000 SR 0 000 49 6 10 11 0 200 See 0 180 46 2 0 000 Sech 0 000 46 2 11 12 0 200 SR 0 330 42 2 0 020 21 0 0 020 42 9 12 13 0 160 45 38 0 250 33 1 0 020 46 1 0 030 Ee 13 14 0 100 43 0 0 200 3D 0 020 EES 0 000 Sof 14 15 0 210 33 5 0 040 St 0 000 38 5 0 030 32 0 15 16 0 090 S12 0 000 29 0 0 030 215 0 0 0 23 7 T MM 23 as wh D T o Thi
270. tudbook and how that information is used during analyses As noted above PopLink treats estimated dates as exact values A knowledgeable studbook keeper can improve the precision and often the accuracy of the date data by knowing the biology and history of the species For example if a species gives birth only during a particular season and the studbook keeper knows that a specimen is born during a particular year the level of precision can often be narrowed to a period of a few months If a species usually gives birth either during January or February the studbook keeper could enter 1 February 19 the mean date in the Transaction Date field and 1 MONTH in the Date Estimate field This would be far more precise in the demographic calculations than entering 1 July 19 and estimating the birth to the year Date estimates should be interpreted as on any date within the estimated period Thus an estimate to calendar year means that the event could have occurred on any of the 365 days of that year with equal probability Great care must be given to avoid overlap between events with estimated dates and events with known dates These overlaps indicate that dates can be estimated with greater precision For example if information is provided that an event e g a birth can be estimated to a calendar year but a known event e g a transfer on 12 August occurred within that same calendar year then the birth even cannot be estimated to calendar
271. two individuals in question Note that this reflects the most recent interaction only the individuals in question may have had multiple interactions over their histories with other outcomes For more details on the type of interaction involved double click on the ID to see the individual s Specimen Report and go to the Social Events table Status All Living Dead AND Institution All 18 af 30 37 38 45 80 HONOLULU HONOLULU SD WAP SANDIEGO SANDIEGO SANDIEGO SANDIEGO Male Male Female Male Female Male Male 18 HONOLULU Male 27 HONOLULU SANDIEGOZ Male The Social Compatibility Report is a pairwise matrix of all individuals which have a social interaction recorded in the Social data table At each matrix intersection compatibility based on the outcome of the most recent social event between the two individuals recorded in the Social data table The outcome of a social event can be positive negative neutral or none meaning there hasn t ever been a social event between those two individuals represented as green with a red with a blue with a 0 or a blank box respectively The column and row headers automatically display the Studbook ID Number current Location and Sex The column headers display the current location of a specimen but not necessarily the same location that individual was in when a Social Event took place Double clicking on the column or row header will pop up a specimen re
272. u can easily do that by sorting the Master Table by studbook number See the Guidelines Note below for further details on assigning studbook numbers S A Guidelines Note 5 Studbook Numbers B i The primary purpose of the studbook identification number studbook ID is to provide a unique identifier for every specimen for which information is available Once a specimen is published with a permanent studbook number that number should never be changed The studbook numbering system used by the studbook keeper should be as Version 2 3 February 10 2012 35 PopLink User s Manual simple as possible The studbook is meant to continue beyond the studbook keeper and simplicity will help ensure that it can be interpreted now and will remain useful into the future Embedded coding or complicated numbering systems such as those indicating year of birth collection date or initial location should not be incorporated into studbook numbers there are other fields within the studbook that record this information Few individuals besides the initial studbook keeper will understand the system correctly and confusion will increase with time If a regional studbook is started and no international studbook exists regional studbook numbers should begin with 1 and increase without a break in the sequence Numbers need not be sequential according to birth or capture date Letters and leading zeros should not be used in the permanent studbook numbers
273. uctive Events Specimen Notes UDFs Social Enclosures Medical Free Flight LOWRY 9 16 2011 None Det _ Enclosure Name Enter Date Enter Date Estimate Free Flight LOWRY 9 16 2011 None Ei MM DD YYYY Exit Date Current Enclosure Exit Date Estimate None Ei MM DD YYYY Comment tranferred into geriatric group in Free Flight Instructions M Batch Input e To enter historic enclosure events e g track where an individual has been over its lifetime use the Exit Date and Exit Date Estimate fields to reflect the timeframe the individual was in an enclosure To activate these fields so that data can be entered select the checkbox next to the Exit Date Exit Date 7 10 0 2011 sl MM DD YYYY PopLink enters today s date as a default when you select the checkbox but you can edit the Date and the Date Estimate as appropriate When a new Enclosure event is added that would occur after another event based on the Enter Date PopLink attempts to fill in an appropriate Exit Date based on the new record s Enter Date You should check the Enter and auto filled Exit dates carefully to assure accuracy and edit the Exit dates if PopLink s auto entered assumption is incorrect Note that individuals are not required to have a continuous Enclosures history there are no data checks for gaps in time during data entry Version 2 3 February 10 2012 62 PopLink User s Manual hy wy NOTE Pop
274. unknown other sex Q mortality rate at a given age Version 2 3 February 10 2012 151 PopLink User s Manual If Dy De gt 0 at age x distribute proportionally by sex ratio and infant mortality Dy D Dyu Dy Det Dy E eh MaleQx N FemaleQx N Ny N N N F Na E E N N If Dy De 0 at age x distribute proportionally according to sex ratio N N Py N N Py N N MaleQx M a FemaleQx M Ny N a N N d Nap ENa NEEN These adjusted mortality rates are used in the Kaplan Meier Statistics Table to calculate adjusted Kaplan Meier survival probabilities Calculations of Age based Life Table Using the Kaplan Meier survival probabilities PopLink also generates an age based life table with 1 year age cohorts for use in population management software such as PM2000 and ZooRisk this life table is only created for the Analytical report PopLink generates a table with values for Pooled Male and Female subsets with unknowns incorporated into males and females as described above This table displays the age class number of individuals at risk survival rate Lx and mortality rate Qx The survival rates from the Kaplan Meier Statistics table which in that table are given for every age at death in the sample are collapsed into annual estimates If a Kaplan Meier estimate does not fall exactly on the start of an age class the estimate of the last Kaplan Meier entry before that age is used At
275. ur studbook database the true and known data and your overlay any analytical data such as assumptions half truths etc still applies We ll walk through the mechanics of creating overlays in PopLink and then go into more details on how to make appropriate analytical data edits Version 2 3 February 10 2012 127 PopLink User s Manual How to Create and Document Analytical Assumptions in PopLink POPLINK OVERLAYS General Features To create analytical assumptions for specimens in your studbook you first need to create the overlay in which they will be stored In the View drop down menu selecting the Overlays option will display this screen Sunbittern Faust File Edit View Overlay Validate Reports Export Help D o A al all Overlays Overlays are used to store analytical data about your studbook specimens Any data that is known and verified should be stored in your main true studbook Use the overlay to store your hypotheses or best guesses about unknown data You can then use your overlay in your genetic and demographic analyses Name Edit Description Date Edited User Edited Notes Created Created analytical assumptions created for June 2006 meeting 11 17 2006 cschloss 11 21 2006 cschloss Faust 1 New Open Copy Delete Selecting New will display a dialogue box that will allow you to name and describe a new overlay Your studbook database can have multiple overlays which
276. utton to document any necessary facts about the fields you have just edited or entered such as sources discrepancies with institutional records type of test used for sexing or lab at which sexing took place etc When you enter notes closing the box saves the notes the notes are transferred to the Specimen Notes table for the specimen you re entering with a description of Sex Table Notes and the date of entry Guidelines Note 13 Sex The sex of each specimen should be recorded in the studbook The studbook keeper should make every attempt to resolve unknown sexes by contacting the holding institution If sex is not recorded for a specimen its history is useless in determining accurate sex specific demographic parameters Knowledge of a specimen s sex is essential if that specimen is to be paired for breeding For demographic analyses specimens whose sex is entered as UNKNOWN ABNORMAL or HERMAPHRODITE are considered 50 male and 50 female Thus for life table analyses e g exports to PM2000 and ZooRisk an abnormal or unknown sex specimen is assigned as one half male and one half female When trying to make recommendations for the current living population if unknown sex specimens exist they will usually need to be kept out of genetic and demographic analyses this can be done with the assistance of a SPMAG or PMC advisor ENTERING EDITING REPRODUCTIVE DATA Edit True Data 8 Studbook Event Date ID Est 8 Not Con
277. verlay Validate Reports Export Help 0 o A a x DIFFERENCES BETWEEN PRIMARY LSNGUENON FAUST1 AND SECONDARY XXLSP Master Sex Reproductive Events Specimen Notes UDFs Studbook Overview The following records are in the primary database only Studbook Birth Date ID Sire Dam Birth Type Birth Date Est Rearing Owner The following records are in the secondary database only Studbook i Birth Date 8 ID Birth Type Birth Date Est Rearing HYPOO1 WILD WILD Wild Born 11 27 2006 Unknown Unknown HYPOO2 WILD WILD Wild Born 11 27 2006 Unknown Unknown Not Reported The folowing records differ in the two databases Studbook ID Birth Date Est Birth Type Birth Date Rearing UNK Unknown 9 7 1985 Unknown Not Reported 1153 WILD WILD Unknown 9 7 1985 Month Unknown Not Reported 1164 UNK UNK Captive Born 1 1 1987 None Unknown Not Reported 1164 WILD WILD Captive Born 1 1 1987 None Unknown Not Reported v Resolve Differences In ay Your primary database should include all of your true data and the xxstudbook should include that true data plus analytical assumptions In terms of comparing records between the two datasets this should mean that a There should be no individuals in the primary database only displayed in the top table b Any individuals in the secondary database only displayed in the middle table should be hypothetical individuals e g HYP001
278. what the studbook keeper doesn t know and can t find out Assumptions in an analytical studbook must be clearly documented to avoid any confusion between fact and fiction The assumptions in analytical studbooks should be updated as often as necessary to incorporate new information or new hypotheses about unknown data Before an analytical studbook with assumptions is created the true studbook on which an analytical studbook is based must be as complete consistent and correct as possible First the true studbook should be updated to contain all available information Unknown information should be indicated as unknown rather than left blank to avoid ambiguity Data Validation routines should be run and errors or inconsistencies should be resolved or documented Once a studbook dataset reflects the truth as it is currently known analytical assumptions can be created Guidelines Note 18 Assumptions and Conventions Although a studbook should be the best representation of the true history of the population most studbooks will contain a few minor assumptions and or conventions Conventions are rules developed by the studbook keeper for consistent application of assumptions Conventions are usually based on the biology or husbandry of the studbook Parts of this chapter are adapted from Sarah Long s Creating an Analytical Database teaching monograph which is used in the AZA s profession school course Population Management II
279. who died from injury from exhibit mate has an unknown carcass disposition and no necropsy planned would have a death event Local ID code CHN Table 1 Sparks Death Codes Code Death Self Inflicted Injuries A integumentary C Given to an C Musculoskeletal Institution Respiratory ES Sold to an Institution Hemic and Lymph H Mate Destruction SPARKS Carcass SPARKS Necropsy Code Old Age Infection Associated a Mounted or Digestive Preserved G Injury from Predator E H _ Rendered Reproductive Reproductive No Necropsy Later Unknown after Necropsy Conditions Stillbirth Assoc Died in Transit Stranded Beached Other Unknown Version 2 3 February 10 2012 51 PopLink User s Manual ENTERING EDITING SPECIMEN NOTES Edit True Data 122 Studbook ID Description Comment Note Date User Edited Breeder Number DENVER 10 3 9 1988 SPARKS Egg Lay Date infertile eggs 12 5 1992 SPARKS Egg Lay Date infertile eggs 9 1 1993 SPARKS Egg Lay Date infertile eggs 12 10 1993 SPARKS v nmn lata Tmin imde el bie ERE bra lana CMAN O Add Delete To edit the existing notes for this specimen highlight the desired note and alter any of the fields below To add a new note click Add and alter the fields When completed click Apply Changes Note Type Comment Breeder Number DENYER 10 Note Date 3 9 1988 M Batch Input ES Ok Cancel The Spe
280. wment Fund grant The goal of the project was to develop a new scientifically rigorous Standardized approach to the analysis interpretation and presentation of mortality data from zoos and aquariums Through this software tool we apply new advances and alternative approaches to the analysis of mortality data The tool gives users the ability to generate a clear well documented report describing mortality data that should assist in communication both internally within a zoo and externally to members of the press and public It also uses new methods to evaluate data quality and to calculate estimates of mortality for use in population management The Survival Tool allows the user to conduct three types of analyses 1 Descriptive Survival Statistics this produces a concise description of survival information for communication public relations and general audience purposes 2 Analytical Survival Statistics this produces detailed survival analysis results data tables and figures for use in population management 3 Expert Survival Statistics this allows expert users to adjust the analysis starting age Note that the decisions made in the design methodology statistical testing of the Survival Tool were focused on making a useful tool for population management and communication Those interested in using the Survival Tool for research should make sure they understand the implications of those decisions and assess alternate methodologies using more
281. would be displayed in this table once created Multiple overlays may be useful if 1 you have different levels of confidence in your analytical data that you want to differentiate between e g having an overlay for data you are reasonably certain about and another with assumptions that you are less confident about or 2 you or your SPMAG PMC advisor wants to test different hypotheses e g what would be the impact of making all UNK parents WILD vs related to the population The Copy option allows you to take an already created overlay copy and rename it and add additional changes to it Highlighting an overlay e g Faust and selecting Open will apply that overlay to your studbook data when you do this the blue display bar at the screen top reflects that the overlay is applied sunbittern Fausti Without your overlay applied e g sunbittern your studbook viewer displays all the TRUE data for your studbook With the overlay applied e g sunbittern Faust1 the studbook viewer displays analytical data in any fields that have analytical changes and true data for all other fields This is clearly displayed in the viewer with analytical data displayed in red and true data is displayed in black e g see specimen 485 below panes ine Se Gms ba e a ESCH Saas eae eee Sy Studbook a Edit Current Sex EE Current Sire Dam Hatch Date Hatch Date Current Age D Location Local ID Est ORLANDO
282. your analytical overlay Individuals with unknown age estimates will not be displayed in this report CENSUS REPORT When you select the Census Report a pop up will ask you to enter a month and day that each annual census will be taken on The default is to run the report as of December 31 but for some species e g seasonal breeders populations where individuals are reintroduced at a certain time of year etc it may be more informative to select an alternate date on which to census the population Generally you should leave the year at the default last year but you can enter an earlier year if you don t want certain years data displayed You will then be given the option of limiting your data geographically either to a region or set of institutional mnemonics or by using a FED file You may also filter for specimens that have a specific User Defined Field Sunbittern Census Report Census Report Census taken on December 31 of every year Restricted to Association AZA fed AND No restrictions on UDFs Year Male Female Unknown Other Total SE marvels Wild Hatch Unknown preety Annual Lambda Captive car lee 2 2008 53 44 10 0 107 1 000 3 0 104 1 000 2007 53 44 10 0 107 1 000 1 000 last 2 years 3 0 104 1 000 1 000 2006 53 44 10 0 107 1 000 1 000 last 3 years 3 0 104 1 000 1 000 2005 53 44 10 0 107 1 000 1 000 last 4 years 3 0 104 1 000 1 000 2004 53 44 10 0 107 1
283. ype is intended to capture information pertaining to an individual s reproductive development and behavior As with the Altercation or Prosocial category this event can be one sided i e one individual showing interest or attempting with an uninterested participant or can involve two or more individuals These events can be very helpful to reference when planning breeding recommendations Other Intended to capture any species specific social events missed by the other five categories Although each species may have slightly different social dynamics and introduction protocols ideally you should use these Social Events consistently over time and across institutions in ways relevant to your species If you encounter an event atypical to your set conventions give more details in the event Comments field You should document any standard definitions in the Species Notes section of the Studbook Overview table 2 Event Date amp Event Date Estimate Enter the date that the social interaction took place if it was a multi day event you can use the start date for the interaction and note in the comments the length of the interaction 3 Outcome The outcome of each social interaction can be scored as positive negative or neutral 0 The outcome of a social interaction can be very subjective and species dependent The 0 symbols could be used to represent different words or ideas such as successful unsuccessful outcome unclear or g
284. yses If the curves are significantly different results are reported for males and females separately d Determines which results to display based on whether data quality filters have been passed and whether male and female curves are statistically different 2 The Included Individuals table shows the partial or full lifesoans of each individual included in the survival analyses see the Detailed Methodology section page 152 for more on how this table is constructed Unlike in the Descriptive report the Analytical Survival Statistics Report does not exclude individuals whose birth date and death date are identical However since Kaplan Meier probabilities must start at 1 0 at the starting age day 0 one day is added to the death date for any individuals with identical birth and death dates This does not substantially change results 3 The Data Quality table which reports data quality test results for the Pooled Male and Female datasets 4 The Kaplan Meier Survival Statistics Table and the Kaplan Meier Graph reports and displays the survival rates by age at death in days If this table is blank it means that data quality tests were failed 5 The 30 Day Mortality Graph shows the distribution of male female and unknown sex deaths in the first 30 days this graph can be useful when looking for patterns in early mortality 6 The Age Based Life Table which is created as described in the Detailed Methodology section page 152 If this t

Chapter 1 - Lincoln Park Zoo

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