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PedScope User Guide

1. But if not you can change this click the margins button dH Understanding Printer Margins This section contains a more detailed explanation of how PedScope sets paper margins and how margin settings work with your printer and chosen paper size Most printer devices have physical limitations on their printing capabilities Obviously the supported paper sizes vary But in addition most printers are not physically capable of printing on the entire sheet of paper there are usually parts of the sheet that the printer simply cannot physically print on You can instruct PedScope to attempt to print onto that maximum part of the paper by selecting the Full page option within the Print Margins window Your computer will also have a default margin setting for the chosen printer This should be a sensible default its actual size is system specific You can instruct PedScope to use the default margins by selecting the Use printer default margins option within the Print Margins window This is the normal setting and an in ideal world will produce a good result without you having to change anything But you can opt to override the default margin selection by disabling both the Full page and Use printer default margins options in the Print Margins window and then entering the actual margins you would like Measurements can be entered in a variety of units including centimeters e g you could enter 1 2cm and inches e g 0 25in Note that setting margi
2. Partial Inbreeding Coefficients A partial inbreeding coefficient of an animal with respect to a specific founder is the probability that the animal is IBD for an allele descended from the specific founder It is that part of the animals inbreeding that is due to that founder PedScope can tabulate partial inbreeding coefficients when you list ancestors For further information see Reports Relations Ancestral Inbreeding Coefficients The ancestral inbreeding coefficient of an animal is the cumulative proportion of an animal s genome that has been previously exposed to inbreeding in its ancestors 3 Ancestral inbreeding coefficients can be tabulated in the main record table Relationship Matrix 29 A relationship matrix is used in population genetics to express the genetic relations within a set of animals and their ancestors Such matrices are always square they have one row and one column for each animal It is accepted practice that the rows columns are ordered such that offspring are always preceded by their parents Thus the first row column will always hold a founder of the group under study The most commonly used matrix is the matrix of additive genetic relationships This is sometimes referred to in population genetics literature as the A matrix Each cell in this matrix say the intersection of row I and column J gives the additive genetic relationship between animals I and J When I is not equal to J i e for off diagonal
3. Age Of Dam At Birth The time period between this animal s date of birth and that of its dam Living and Age If Living These columns primarily exist to provide a way for large data sets to be sorted so as to bring all animals with a given current age or all animals known to be living together in the main record table This makes it easier to tag the current population i e those that are alive using a range tagging operation You may well want to do this if you are using PedScope to make mating recommendations Columns Computed By Pedigree Analysis These are columns whose values can be computed by analyzing the pedigree of each animal at the same time as the inbreeding coefficient is computed The depth of ancestry i e the number of generations used in this analysis is a configurable parameter the Inbreeding generations setting on the General tab of the Document Settings window File Document Settings You can either set a specific depth limit such as 8 generations or you can instruct PedScope to include all available ancestry by setting it to zero It may seem surprising but if you have a very large data set with many generations of ancestors present PedScope will normally calculate these metrics much more quickly if you direct it to include all known ancestry This is because of algorithmic optimizations that are used when analyzing the entire pedigree in a single step rather than having to identify a separate sub pedigree f
4. Open Control Panel and select Uninstall a Program or Add Remove Software Mac Just drag PedScope to the trash can What extra do I get with the full paid version It is not limited to 30 days use u It works with data files of up to 20 000 000 records whereas the free trial is limited to 500 Export and print facilities are enabled in the paid version they are disabled in the trial except when used with the bundled examples or simulated pedigrees B Access to support and updates You can test any of the features of the full version even if you only have the free trial by opening one of several inbuilt pedigree data files use File Examples or by creating a simulated pedigree use File Simulate Pedigree These are not subject to the trial version record limit How do I place an order See our web site My question isn t answered here where else can I look Please see the Frequently Asked Questions page on our web site which we update regularly This addresses many additional topics and questions to those listed here My question isn t answered in the FAQs neither here nor on the PedScope web site How can I contact product support Please see Product Support on our web site 35 Product Support To contact customer service please see the Product Support page on our web site Before contacting customer service be sure to check the FAQs on our web site first This covers many commonly asked
5. Revision History 36 37 37 38 Getting Started Begin by selecting PedScope from the Windows Start menu or from an icon on your desktop To load data choose File Open i e select the Open option on the File menu This accepts text CSV files in a variety of formats For further information see Importing Data You might like to know that PedScope has various examples built in for demonstration purposes To choose one of these select File Examples You can also create a simulated pedigree useful if you want to create a large data set just to explore the BE program s handling of large pedigrees choose File Simulate Pedigree en Once the file is loaded the Main Window is displayed lee Inbuilt Examples Importing Data To load data choose File Open then select your import file The file needs to be a text CSV file the kind of file that you might export from a spreadsheet but which can also be produced by many database and pedigree programs You are then taken through a series of windows that let you set options to control the way PedScope processes the import file Note that in many cases there will be few if any of these settings that you need to change because PedScope inspects the data file and chooses sensible defaults for the file format and its contents NOTE To see some examples of acceptable import data see Import Examples Character Encoding The Character Encoding window selects the
6. Vx Data Kinship values and the associated mating ranking metric Offspring GV Delta see Reports Mate Recommendations require reproductive values of the animals concerned This data is age specific and defined as the expected future lifetime reproduction reproductive value Vx see Fisher R The Genetical Theory of Natural Selection 1930 There are 2 ways you can supply this data to the program u Ina file that is automatically loaded when you import your data When PedScope loads data from a text CSV file it always checks for the existence of a file with the same name as the import file but with kvweights inserted in front of the import file extension E g if you import a file called mystudbook txt then PedScope will also look for a file mystudbook kvweights txt OR entered separately through the document settings Choose File Document Settings click on the KV Weights tab and key in the Vx data or click Load to read froma file In both cases the data should be formatted as separate lines giving SEX AGE VXVALUE E g m 3 0 8 would mean that males of age 3 years have a Vx value of 0 8 A longer example ind oie Mp OS Mm ar04 m 6 01 35 MUS Mores ja 0 Or lids Ht 10 4 0 nee mg Ep Oa 4 0 8 to Oke TERORS aip Oai 2 00 32 Saving Data PedScope provides several options for saving and exporting data and reports Saving As A PedScope Data File You can save the entire state of a di
7. and deeper The rows shown are as follows Row Purpose Field The meaning of the data in this column Type The type of the data such as Text Integer Date etc For some fields e g date of birth the type is implicit and you cannot change it Label The label that is to be used for the field once the data has been imported into PedScope This is only meaningful for fields that will become user fields in the main table Input Header This will be shown in blue and shows the text from any header line that was found in the input data file This is displayed purely for your convenience when checking that the Field and Type have been set correctly Input Data Up to 4 lines of data again shown in blue taken from the input data file for reference You should review the Field Type and Label settings for each input column to be sure they are correct for the particular input data Ensure that the date format and male female sex values are consistent for the input data file then click Finish to proceed with the import Fields The full list of fields is given in the table below NOTE Several of these fields are related to each other and need to be consistent within the input file in order to successfully import data These are the Name and ID fields Each input record i e each animal must have an ID field a Sire ID field and a Dam ID field These are used by PedScope to construct the ancestral linkages i e they are how it works out w
8. animal records for all animals falling within the selected date period This operates in a very similar way to the correlation charts available for animal records u Frequency Chart plots a frequency bar chart for any single column from the animal records for all animals falling within the selected date period This operates in a very similar way to the frequency charts available for animal records 12 Customization PedScope provides various configuration customization options These are divided into two groups accessed through separate windows The Preferences window is used for settings that are independent of any particular data file It is accessed through the File menu Changes to the preferences do not cause data to be re calculated They have global effect preferences are not specific to any particular data file They tend to be related to the appearance and presentation of data not the data themselves The Document Settings window is used for all settings that can alter the current data set in some way It is accessed through the File menu These settings affect what data is stored or how it is stored how it is calculated or the accuracy with which it is calculated These settings can be saved along with the imported pedigree information and computed data see Saving Data Saving As A PedScope Data File Setting Inbreeding depth generations Coefficient Display Coefficient Precision Computation of Pedigree Me
9. have PedScope treat the presence of the gene in at most 3 animals as meaning unique The probability of alleles retained and genome uniqueness are computed using a gene drop analysis You can customize the number of simulations used to compute these values 22 Reports Influential Ancestors To view this report choose Influential Ancestors from the report selector at the top of the report pane in the main window This report displays the most influential ancestors of a group of animals To use this report you must first tag the animals whose influential ancestors you want to locate This report does not operate with a single ancestor The influential ancestors are those ancestors with the greatest contributions to the Influential Ancestors Report computation of the number of effective ancestors fa The table displayed includes a column that gives the marginal contribution of each ancestor to the current population The algorithm for determining influential ancestors 1 starts with the ancestor with the highest genetic contribution to the current population and then proceeds to list other ancestors in decreasing order of their genetic contribution whilst attempting to ensure that contributions already explained by influential ancestors previously found do not get considered twice The number of effective ancestors fa is also computed and displayed above the report along with the numbers of founder equivalents and foun
10. increased through mutation and migration i e the introduction of truly ee Be J unrelated new founders But within smaller populations such as closed populations Founder Metrics Contribution Detail Report of fancy animals or with endangered species where there are very limited numbers of Matrix with founders in columns and group animals remaining the extent of retained genetic diversity can be limited and the members in rows giving the contribution extent to which different founder s are represented within the current population can of each founder to each descendant vary sometimes greatly The number of founder equivalents Lacy 4 is a measure of the genetic diversity of a current population It is the number of equally contributing founders that would be expected to produce the same level of genetic diversity as the current population It has a standard symbol in population genetics literature fe In a large population with no selection and in the absence of genetic drift fe remains relatively constant because founder contributions do not vary much from one generation to another When there is extensive selection fe can lose value such as with fancy animals when popular sires can give rise to huge numbers of offspring and hence magnify the representation of their founders within the current population at the expense of those of unpopular sires The number of founder genome equivalents Lacy 4 is a related measure which unl
11. lists the founders and for each founder it En en ara el J gives its Founder Metrics Contribution Detail Report listing the founders of a group of Contribution The proportion of the genes in the current population due to that animals showing the contribution to the founder group the founder alleles retained and Alleles Retained The proportion of the genes of that founder that have probably the likelihood that each founders genes been retained in the current population have only been passed down to at most Founder Genome Uniqueness The probability that genes from that founder are ONE member or the group only present in normally 1 member of the current population We say normally because you can adjust the genome uniqueness threshold on the General tab of the Document Settings window As with all other tables in PedScope you can sort the founders by clicking on the columns It is therefore very easy indeed to work out which founders have had the main influence on any group of animals and which have the least The other two founder metrics reports Contribution Detail and Genome Uniqueness Detail display matrices that give the contribution and genome uniqueness values between every member of the current population and every founder The matrix columns hold the founders and the rows the members of the current population The top two matrix rows always contain the summary value i e forras the contribution
12. of the calculation see below Below the displayed matrix are some further controls Order caus Order rons by V Transpose V Color coded Export Matrix Order columns by and Order rows by these let you select the ordering of the rows and columns The default order is the ordering used internally when computing the matrix which is an ordering chosen to guarantee that all parents come before i e left above their offspring However you might find it easier to work with the displayed result if the rows columns are sorted by e g name Note that changing the ordering will destroy any natural matrix structure e g with the additive matrix the diagonal always contains values that are 1 the inbreeding coefficient Changing the sort order will obviously mean that no longer holds Changing the sort order does not recompute the matrix 3 Transpose this will swap the rows and columns Color coded when this option is turned on cells will be shaded according to their value The higher the degree of relationship the darker the shading This provides a very quick way to see at a glance where the closest relationships are Export Matrix click this button to export the matrix e g to a PDF text or XML file The XML files generated by PedScope can be directly loaded into Excel and provide a very easy way to transfer a computed matrix When showing a relationship matrix the property pane to the right w
13. or genome uniqueness with respect to the whole group and the alleles of each founder retained by the whole group the same values as given in the summary table The properties pane comprises two columns and contains the record al ed details for the currently selected matrix cell Founder Metrics Contribution Detail Report All founder reports let you choose the depth of ancestry to be considered when Matrix with founders in columns and group building the report PedScope searches the pedigrees of all animals in the current members in rows giving the Y contribution population to that depth to provide a list of ancestors and then locates animals of each founder to each descendant within that group that are founders with respect to the group This is an important distinction see Population Genetics Founders All founder reports also include the following measures of genetic diversity which are single values computed for the whole of the current population fe the number of founder equivalents u fg the number of founder genome equivalents u fa the number of effective ancestors N the total number of animals analysed for the report current population ancestors You can customize the definition of genome uniqueness By default a gene froma given founder is considered to be inherited uniquely when it is present in only one member of the current population You can increase this threshold e g you could choose to
14. supported date formats after the import window has been displayed ID Sex DOB Sire Dam Abbots Wisdom M 30 03 1930 Diver Of Woolley Sewardstone Tess Abbotsford Rosa of Tasvane F 30 04 1986 Tasvane Taraius Rachenco Sunshine Alexander of Elsiville M 15 05 1944 Torrdale Tinker Zena Of Elsiville Alexia of Tillwood Rachenco F 30 04 1973 Spartan of Rachenco Wayfarer of Tillwood Alresford Advertiser M 15 04 1951 Alexander of Elsiville Alresford Mall Main Window Record Type Main Record Report Pane Report Selector _ Filter Table Pulldown Pane I z r i f i H s a am com psw ama A ann nw Summer Carmen aE EO BE om sauye u E v r CEC mt nn nn i Catan Ooty Omen 12 2 ame ose ame au E permo o PELPTESEEELORELEOLGEL ITRGESEHTRETRERRERERTG Find Report Pane Property Controls Controls Pane The main window is divided into 1 or more sections When you first open the a data file you will have from left to right The Main Record Table This lists the input data with one animal per row You should see columns for name ID sex sire dam and so on The exact columns present depend not only on what is present in the input data but also the current document settings It is possible to customize PedScope so that specific input columns are hidden and to control which calculations are performed For details of all the possible columns see Main Table Columns The Report Pane This displays one o
15. 16 generations Whenever such an artificial cutoff is applied the definition of founder takes on a slightly different meaning it means an animal within the subset of the population that comprises the animal s under study and however many generations of their ancestors that has been selected that either has no known sire and or dam or whose sire and or dam even though known in the entire population do not fall a ame m ome mr mse mn E within the subset under study It is as if the program pretends that the deeper Founder Metrics Contribution Detail ancestry is simply unknown Report listing the founders of a group of animals showing the contribution to the group the founder alleles retained and the likelihood that each founders genes have only been passed down to at most one member of the group Alleles Genes amp Identity by State Descent Most animals have two sets of chromosomes They have one copy of each gene on each chromosome Such genes are said to be autosomal The particular location on a chromosome where a gene is found is called its focus An animal therefore has 2 copies of a gene for any particular locus An allele is one of two or more forms of a gene The presence of different combinations of alleles can affect physical traits in the animal such as coat color in some animals This description is a deliberate simplification but sufficient for our purposes E g we ignore sex chromosomes etc If both all
16. PedScope User Guide Version 2 3 01 March 2014 Table of Contents Table of Contents Getting Started Importing Data Character Encoding Column Formatting Columns Fields Data Types Examples Import Examples Main Window Main Record Table Report Pane Tagging Records Other Record Types Main Table Columns Columns That Do Not Require Pedigree Analysis Columns Computed By Pedigree Analysis Statistics Customization Reports Reports Relations Reports Families Litters Reports Record Details Reports Correlation Chart Reports Frequency Chart Reports Relationship Matrices Reports Founder Metrics Reports Influential Ancestors Reports Unknown Founders Reports Gene Diversity Metrics Reports Mate Recommendations Reports Pedigree Population Genetics Founders Alleles Genes amp Identity by State Descent Kinship Inbreeding Coefficients amp Common Ancestors Partial Inbreeding Coefficients Ancestral Inbreeding Coefficients Relationship Matrix Founder Equivalents amp Founder Genome Equivalents Effective Ancestors Mean Kinship Mk Kinship Value KV Gene Diversity GD Gene Value GV Genome Uniqueness Gene Drop Analysis Vx Data Saving Data Saving As A PedScope Data File Exporting Printing Saving As PDF Image Files Pedigree Margins Understanding Printer Margins FAQs a es es ee ee ek OON DOWN 0000 OO SO OT TH I NNN NNN DN On WN O Product Support Release Notes System Requirements
17. ailable Relations Founder Metrics Influential Ancestors Unknown Founders Gene Diversity Metrics Mate Recommendations Pedigree Correlation Chart Frequency Chart Relationship Matrices Families Litters Record Details 15 Mate Recommendations x of Tagged Records tisted F Lock Ancestry to 106 Rankby Inbreeding View as Matrix gt 2 E amp F 2 5 g ele 2 a a z Ej 3 s S amp 2 3 a a 4 g S g 8 S y k E amp F Ei Taoa 3 g lt a S 8 z n a o Achnagairl Kimono 1 3 a 1 14 89 14 89 14 89 14 03 14 03 Dawn Gloria 2 2 62 7 71 7 71 7 71 7 04 7 04 Dawn Gold of Auberjean 3 3 61 11 30 11 30 11 30 10 28 10 28 Dawn Lassie of Kimmbess 4 3 71 14 55 14 55 14 55 13 10 13 10 Ginger Gem 45 5 2 77 9 54 9 54 9 54 8 85 8 85 Glady s Golden Girl 6 3 19 10 57 10 57 10 57 9 65 9 65 Prospective Offspring Inbreeding Matrix Showing the inbreeding for every sire dam combination within a chosen group of males and females Reports Relations To view this report choose Relations from the report selector at the top of the report pane in the main window Beneath the report selector are other options to choose the type of relations you want listed and to restrict the results in various ways e g to limit ancestors to the maternal paternal side or to limit the depth of ancestry searched etc The matching relations are then lis
18. ank by pulldown The following table describes the different rankings in detail and gives some of advantages and disadvantages of each Ranking Method Description Inbreeding Breeders of fancy animals such as dogs and cats Ss oF faced Records tinted El tock are often particularly interested in limiting the Ancestry to 3063 Rarkby inbreeding 7 View as Matiz inbreeding of the offspring of a prospective mating To help with this one of the available ranking methods is simply the coefficient of inbreeding of the potential offspring snasnBiny yseypueys UosMeg SEJPUeIS 9 dof Ae Jo ony jag yseypueys Te deus soBug Z snBuy yseypuers E ojody yseypueys The results can be listed either in a table ordered by ranking or as a color coded matrix of inbreeding coefficients with the sires in columns and the dams in rows Ss Achnagairl Kimono 1 3 61 14 89 14 89 14 89 14 03 14 03 Dawn Gloria 2 2 62 7 71 7 71 7 71 7 04 7 04 a A P Dawn Gold of Auberjean 3 3 61 11 30 11 30 11 30 10 28 10 28 If your aim in using the mate recommendations report is to maximize genetic diversity over the longer term simply minimizing the inbreeding in immediate breeding decisions is not necessarily the best way to go Prospective Offspring Inbreeding Matrix Better results will be obtained by using a ranking Showing the inbreeding for every sire dam method that uses Kinship Value KV such as the comb
19. ch animal is needed Which means in practice that the input data to PedScope must include the date year of birth Secondly the program needs the weights to be assigned to each animal PedScope provides 2 ways in which the weights can be entered for KV calculation For further information see Vx Data 30 Gene Diversity GD The gene diversity symbol GD of a population is defined as 1 minus the mean MK i e the mean of the MK s of every animal in the current population including with itself The lower the mean MK of all animals in a population the less related on average they are to each other GD is simply a different way to view the same number Maximizing GD can be a good basis for a breeding programme e g for an endangered species with a small population but with known ancestry though it is inferior to GV Gene Diversity Metrics Report Gene Value GV The gene value symbol GV of a population is defined as 1 minus the mean KV i e the mean of the kinship values of every animal in the current population including with itself GV is to KV what GD is to MK Since KV s are in effect an improved form of MK so GV is an improvement upon GD If you have age structure data for the current population along with reproductive values GV should normally be preferred over GD as the method of ranking breeding decisions Genome Uniqueness The genome uniqueness GU of an animal with respect to a current population of whic
20. ch as the NRM or A matrix of additive genetic relations between any group of related animals The matrix is calculated for all of the source animal records plus a given depth of their ancestors and optionally their descendants The matrix can be saved i e exported including to spreadsheets When the report pane is set to display relationship matrices several extra pulldown menus are available below the report selector a sa R un ip Matrix This shows the A matrix for the stud Roan Gauntlet from Wrights original 1922 paper on inbreeding with the A matrix values are shown as fractions Ancestry to Matrix type Indude descendants to V Show ancestors Ancestry to here you select the generations of ancestors of the source animals to be included when calculating the relations Matrix type select between Additive Dominance and Genomic Include descendants to here you select the generations of descendants of the source animals to be included Show ancestors this checkbox controls whether the ancestors used in the calculations are to be displayed in the visible matrix This can be useful when you are interested in the relations between a small number of ancestors but you don t want the screen cluttered up with a huge matrix showing hundreds or even thousands of their ancestors that have been used in calculating the relationships Note that turning this option off has no effect on the memory requirements
21. character set encoding and line ending format If the options presented here don t mean anything to you don t worry because in practice you are very unlikely to need to change these settings If in doubt simply click Next to proceed The character set defines how the bytes in the file are encoded such as UTF or ISO 8859 1 The line ending format says whether input lines are terminated by carriage return line feed or both Column Formatting The Column Formatting window controls the way that the columns are formatted in the file This is where you choose whether the file is comma or TAB separated whether there is a header line and whether column values are quoted Again it is unlikely you will need to change anything here Typically you just need to click Next to proceed Columns The Columns window is where you define the meaning of each import column i e where the name sex sire etc are to be found in the input data It is more likely that you will need to alter the settings here than in the previous windows However in many cases again PedScope is still able to deduce the correct meaning of columns in your data file Before it displays the Columns window it will inspect the first few lines of the input file and attempt to make a reasonable guess as to which columns contain the main pedigree data name id sire dam sex and date of birth To make changes click the Customize checkbox It can help at this stage to make the window wider
22. cient with every other member of the group including itself If an animal s MK is low this means it is less related on the whole to the rest of the population than an animal with a higher MK MK plays an important part in breeding decisions in programmes designed to maintain genetic diversity in small populations Leaving aside other factors if you had to choose between one sire and another for a mating decision it would be better to choose the one with lower MK But it is inferior to a related measure kinship value Kinship Value KV The kinship value symbol KV is a weighted variant of mean kinship The weighting used is the reproductive value of the animal concerned it is age specific and defined as the expected future lifetime reproduction Fisher s reproductive value Vx 6 Clearly an animal in the current population that is no longer reproductive e g a female nearing the end of her life is of no value in maintaining future genetic diversity because she can no longer produce offspring to add to the population and yet calculations based on MK do not take this into account Likewise it follows that if you have two animals with the same MK but one is older than the other then and ignoring any other factors a greater priority ought to be given to breeding from the older animal first to lessen the risk that its genes are lost for good In order to compute KV additional information is required Firstly the current age of ea
23. der genome equivalents For further information about the number of effective ancestors and related metrics see Population Genetics 1 Boichard D Maignel L and Verrier E The value of using probabilities of gene origin to measure genetic variability in a population Genetics Selection Evolution 1997 29 1 5 23 23 Reports Unknown Founders To view this report choose Unknown Founders from the report selector at the top a enna ns ae of the report pane in the main window DT E ET Founder An unknown founder in PedScope refers to the situation when one parent of an g ton animal is not known but the other is The unknown parent is considered to be an er unknown founder This report will list the unknown founders of the current population within a given h Fer z depth of ancestry Unknown Founders Report 24 Reports Gene Diversity Metrics To view this report choose Gene Diversity Metrics from the report selector at the top of the report pane in the main window PedScope can tabulate various gene diversity metrics of a group of animals as used in the separate mate recommendations report Typically this would be used to study a group of animals that make up a current population or otherwise a group from which future breeding is to occur In the description that follows current population means the group of tagged animals from the main record
24. der to compute the kinship values For further information see Vx Data This is where a weighted combination of any of the other breeding metrics above alongside the offspring inbreeding coefficient is used This is probably the most ranking powerful method It lets you combine the various measures in whichever way you like weighted according to the values you wish to prioritize You can also set a limit threshold for the offspring inbreeding so as to remove from the rankings any pairings that would result in excessively highly inbred animals irrespective of the other merits of the pairing To customize the weightings used by the composite ranking use the KV Weights tab of Mate Recommendations Report Pairings the Document Settings window ranked by composite breeding value For further information see Population Genetics 27 Reports Pedigree To view this report choose Pedigree from the report selector at the top of the Bm report pane in the main window i Ea You can display a simple pedigree chart for the currently selected animal in the main oravan cei en record table and include between 2 and 6 generations of ancestors Mans em Use the Highlight pulldown to select options for highlighting ancestors ARNEE No highlight as it says Highlight repeat ancestors ancestors that occur more than once within the displayed generations are highlighted with a unique color Ve
25. e then click in the Find box enter the name then click Next Near the Find controls are buttons labelled Export and Print These are used to export the displayed table e g to a spreadsheet or PDF file and to print it Report Pane The report pane to the right of the main animal table displays reports that are generated from one or more of the animals from the main table At the top of the report pane is a pulldown selector menu that you use to choose the type of report you want The way to choose the animals to which the report pane applies to is by using the pulldown menu that appears to the right of the report selector This can be set to 1 of 3 options u Selected Record the report is specific to a single animal the one you most recently highlighted in the main record table e g by clicking a row u Tagged Records Listed the report is specific to a group of one or more animals the currently tagged animals see below All Records Listed the report is not specific to any of the animals listed it will be run for all animals listed Some reports are implicitly specific to a single record E g the pedigree chart is specific to showing the pedigree for the selected animal only Other reports are only meaningful to multiple records and for these you typically use tagging see below to select those records For further information on the various reports available please see Relations Founder Metrics Influent
26. ect which two columns from the main record table are to be plotted One is F plotted against the X axis the other the Y axis A dot is placed at the appropriate bE position on the chart for every source animal record that has values present in both columns In addition the program will compute the Product Moment Correlation Coefficient r and Spearman Rank Correlation Coefficient rs for the charted data These are displayed above the chart A typical use of this feature would be to plot a correlation of say the inbreeding Correlation Chart coefficient against a sample metric such as weight or height 19 Reports Frequency Chart To view this report choose Frequency Chart from the report selector at the top of 7 m the report pane in the main window A frequency chart is a bar chart where each bar gives the number frequency of animals where a given metric column falls within a given range of values This lets you visualize the frequency distribution of say inbreeding coefficients within any group of animals You select which column from the main record table is to be charted and the maximum number of bars to be plotted Frequency Chart 20 Reports Relationship Matrices To view this report choose Relationship Matrices from the report selector at the AE A m top of the report pane in the main window reget H je PedScope will compute and display various relationship matrices su
27. eles for a given locus are the same the animal is said to be homozygous for that gene The phrase identical by state IBS means the same thing the alleles are functionally the same If the alleles are different they are said to be heterozygous A related term is identical by descent IBD Two alleles are said to be IBD if one of them is a physical copy of the other or if they are both physical copies of the same allele in a particular ancestor IBD implies IBS but not vice versa Kinship The kinship coefficient KC also known as coancestry between any two animals is the probability for any particular locus that an allele selected randomly from one animal is IBD to an allele selected randomly from the other An animal gets half its genes from its father half from its mother So that means the that kinship coefficient between an animal and either of its parents must be one half i e 50 or 0 5 right Wrong The KC between an offspring and either parent is one quarter i e 25 Why is this First there is a 50 chance that any allele chosen at random in an animal is from a particular parent the sire say And secondly there is then a 50 chance that that is the same as any particular allele chosen randomly in the sire So there is a 0 5 0 5 chance i e 0 25 or 25 that they are IBD Inbreeding Coefficients amp Common Ancestors Inbreeding occurs when an animal has one or more common ancestors The term common ancestor has a ve
28. en listing descendants this is the blood contributed by the subject animal to the descendant When listing ancestors this is the blood contributed by that ancestor to the subject animal but only when considering the paternal side of the pedigree When listing ancestors this is the blood contributed by that ancestor to the subject animal but only when considering the maternal side of the pedigree When listing ancestors this is the kinship coefficient between the ancestor and the subject animal When listing ancestors if the ancestor is a founder this is the partial inbreeding coefficient for that ancestor i e that part of the inbreeding coefficient of the subject animal that is due to that founder ancestor When listing siblings this is the other parent of a sibling if not a full sibling When listing All Relatives or Uncles Aunts or Nephews Nieces or Cousins this is the genealogical description of the relation e g Cousin Twice Removed Half Brother etc You can sort the relatives by closeness of relation by clicking this column s heading You can adjust these descriptions using the Precise relation descriptions setting on the General tab of the Preferences window 16 Reports Families Litters To view these reports choose Families or Litters from the report selector at the men top of the report pane in the main window Matching families litters are listed in the report pane Statistics on the number
29. ental KV Composite It can be detrimental to pair animals with widely differing mean kinships because this has the effect of combining rare gene lines with over represented lines A lower MK delta is better and ranks higher This is the average of the genome uniqueness of the sire and the dam It is the total probability for all founders that the animal is the only one normally in the current population containing genes from any one founder Therefore the higher an animal s genome uniqueness the greater the chance that if that animal is not bred from then under represented gene lines will disappear forever from the current population This is the mean of the parental kinship values The kinship value of an animal is related to the MK but is weighted according to the age structure of the current population This can be a better metric upon which to base breeding decisions than the mean kinship but requires that you also have reproductive values for the different age classes of the current population Vx data and obviously you have the age data of the current population E g the current population may include animals that are past reproductive age Clearly such animals can never be bred from so it is better if the genetic diversity contributed by those animals to the current population be discounted when making breeding decisions Use of KV values enables this This method requires that you have Vx data set up in or
30. etc When listing ancestors if an ancestor is a common ancestor only this will give the minimum length of path to the common ancestor on one side of the pedigree and back down the other When listing ancestors or descendants this gives the closest generation at which the ancestor descendant was seen When listing ancestors this gives the closest generation on the paternal side of the pedigree at which the ancestor was seen When listing ancestors this gives the closest generation on the maternal side of the pedigree at which the ancestor was seen When listing ancestors or descendants this gives the furthest generation at which the ancestor descendant was seen When listing ancestors this gives the furthest generation on the paternal side of the pedigree at which the ancestor was seen When listing ancestors this gives the furthest generation on the maternal side of the pedigree at which the ancestor was seen When listing ancestors or descendants this is the number of times the ancestor descendant was seen This is gt 1 when there are multiple paths between the subject animal and the particular ancestor descendant When listing ancestors the number of times this ancestor was seen on the paternal side of the pedigree When listing ancestors the number of times this ancestor was seen on the maternal side of the pedigree When listing ancestors this is the blood contributed by that ancestor to the subject animal Wh
31. f several different reports tables Above the report pane is a pulldown menu which is used to change the displayed report type We call this the report selector Initially the report selector is set to display the Relations report u The Property Pane This is used to show drill down detail of whatever is currently selected in the report pane The property pane is not always visible Typically its used to show the record details for a highlighted result E g with the Relations report once you have relations listed such as ancestors you can select an ancestor click it and have all details for that ancestor shown in the properties pane You can resize the main window panes by dragging the divider between the panes Main Record Table You can sort the main table by clicking any of the column headings Clicking a heading again will reverse the sort order You will see some columns in blue These represent values that PedScope has computed you can change this color and various other highlighting effects by selecting Preferences from the File menu and clicking on the Highlighting tab Above the main record table are some pulldown menus to filter the displayed records E g you can choose to only display animals that have offspring or animals that are founders or females only etc Below the main record table is a box labelled Find To locate a record quickly e g find an animal given its name first ensure the animals are sorted by nam
32. h it is part is the probability that it contains founder alleles not present in any other single normally animal in that current population GU can also be computed with respect to a specific founder in which case it is the probability that the genes from that founder are inherited uniquely GU can be used as a factor when making breeding mate recommendations Informally if an animal is the only one carrying a particular founder s genes then you d likely want to breed from that animal so as not to lose those genes from the population forever We say normally here because PedScope lets you configure what is meant by genome uniqueness in that you can define that number of animals in the current population for which if any given founder s alleles are only present in that number or fewer of the current population then it is considered unique For further information see Customization A better term might be genome rarity or founder rarity but the term genome uniqueness is already established in the literature Genome uniqueness is determined using gene drop analysis Gene Drop Analysis A gene drop analysis MacCluer et al 7 is a computer simulation technique for analyzing a group of animals comprising a current population and their ancestors The founders of the group are first identified The computer then simulates Mendelian inheritance by dropping a gene comprising pair of unique alleles for each founder through the
33. has one distinct from its ID The input ID of this animal if it has one that is distinct from its name The input sequence number This is always equal to the order in which the records were read in from the input file with the first record given sequence number 1 This may or may not be the same as the ID or Rec depending on the order in which records are presented in the input data and how your input IDs are assigned The internal PedScope assigned record number of this animal This is not the same thing as the record name or ID as given in the input data nor is it the same as the input sequence number During the importing of data PedScope has to renumber reorder the input records to ensure that they are in an order that guarantees that parents always precede their offspring This ordering is required to implement certain algorithms quickly and also enables PedScope to discover any self parenting errors during input a self parenting error being when an animal appears to be descended from itself which can happen when there are errors in the input data See also the Age If Living column below Name or ID of the sire of this animal Name or ID of the dam of this animal The gender of this animal Normally displayed as M or F though you can change this see Customization It will be shown in a faded color if the sex has been deduced on input this happens when the sex is not stated in the input data but has been deduced from
34. hich parents any given animal is descended from The ID fields can be numeric or text Numeric IDs are generally record numbers keys as generated by whatever software created the import file Optionally the import data may also contain a Name field If you are importing data that contains just the name of each animal its sire and dam without any kind of record number key you should import these columns as the Animal ID Sire ID and Dam ID and not as Name fields Obviously the Sire Dam ID Name fields need to contain consistent data so that PedScope can work out the ancestral links correctly Field Description Animal ID A unique number or key for this animal The Animal ID is mandatory if the Name is not given otherwise optional Sire ID Sire key number If present the Animal ID field must also be included Dam ID Dam key number If present the Animal ID field must also be included Name Animal name Sex Gender The allowed values for male female are given in boxes beneath the import definition table Date of Birth The date format is set using a dropdown menu beneath the import definition table Date of Death The date of death uses the same date format as date of birth Sire Name Name of the sire If present the Animal Name field must also be included 5 Dam Name Name of the dam If present the Animal Name field must also be included User Field A user defined column Such columns will be loaded and tabulated within the main rec
35. hted color Different highlight colors can be set for males and females by default these are a light blue and light pink You can change these color and various other highlighting effects by selecting Preferences from the File menu and clicking on the Highlighting tab Other Record Types Along the top of the main window there is a series of tabs normally labelled Animals Families Litters and Stats You can use these to switch to display record types other than the animal records These other record types are automatically generated from the input animal data by PedScope you cannot import these directly u Families PedScope groups animals together into what it calls families where a family is defined as all animals that share the same parents You can browse the families to see values and statistics computed at the family level and easily browse all offspring of the family Litters PedScope further groups animals within individual families into litters where a litter is defined as all animals that share the same parents and date of birth The Litters tab is disabled if your input data does not contain data for the date year of birth Otherwise it operates similarly to the family records tab u Stats last but by no means least we have the statistics tab This is one of the most powerful features of PedScope If your data includes date year of birth then PedScope will compute statistics for all animals falling in each period You ca
36. ial Ancestors Unknown Founders Gene Diversity Metrics Mate Recommendations Pedigree Correlation Chart Frequency Chart Relationship Matrices Families Litters Record Details Tagging Records Record tagging is the way to select multiple records for a report To tag a single row in the main record table select it click it or use Find to locate it then press CTRL T or choose Record Tag Selected Record When tagged the record is highlighted in the main table To tag a range of rows select the starting row to be tagged and press CTRL M or choose Record Set Marker Then move to the end of the range to be tagged select that record by clicking it and press CTRL SHIFT T or choose Record Tag From Selection To Marker When you use tagging to select the records for a report make sure that you ve set the report to be run for the Tagged Records Listed you will find this option to the right of the report selector at the top of the report pane There are other options to control tagged records on the Record menu e g for untagging There is also a Tag All Matches button below the main record table this can be used to tag all records matching the Find pattern There is a Tagged Only option above the main record table to limit it so it only shows tagged records and possibly limited also to other record selection conditions you may have chosen such as Males Only Tagged records are listed in the main table using a highlig
37. ike the number of founder equivalents takes genetic drift into account It is the number of equally contributing founders with no random loss of alleles in the offspring that would be expected to produce the same level of genetic diversity as the current population It has standard symbol fg The calculation of fg is more involved than fe because it requires knowledge of the extent to which each founders alleles are present in the current population i e the degree of genetic drift This can be calculated using a gene drop analysis fg will always be less than or equal to fe Effective Ancestors Another useful metric is the number of effective ancestors Boichard et al 5 It is similar to the number of founder equivalents except that it also takes into account bottlenecks in the pedigree It does this by working out the marginal contribution of each ancestor not each founder to the current population to find the ancestor with the most influence and repeats the process taking care not to consider the contribution of any previously identified influential ancestor more than once Influential Ancestors Report The result is a list of the most influential ancestors and a metric the number of effective ancestors It has standard symbol in population genetics fa This number will always be less than or equal to fe Mean Kinship MK The mean kinship symbol MK of an animal within a group of animals is the mean of its kinship coeffi
38. ill display the details of the selected cell Just click a matrix cell to have the details of the row column animals displayed There are various other ways you can customize the display of matrices On the General tab of the Preferences window you can specify whether coefficients are displayed as numbers percentages or even fractions For numbers and percentages you can set the number of decimal places shown On the General tab of the Document Settings window you can specify the data storage type used internally for the matrix This can affect both the memory required internally to store the matrix which can be very large and the speed of calculation Memory Usage It is important to be aware that computing relationship matrices can require a very large potentially huge amount of memory A relationship matrix contains as many rows and columns as the number of animals and their ancestors and descendants that you have chosen to display E g lets say you choose to display the additive matrix for 10 particular animals plus 16 generations of their ancestors And that once those ancestors have been found this results in a total of 10 000 animals A matrix with 10 000 rows and columns contains 100 000 000 cells If each cell takes say 8 bytes of storage typical for a floating point number on many systems this would be 800 Mb memory Which is a lot Whilst the program can and does use optimizations where it can to reduce the memory footprin
39. imals that have either the same sire or the same dam as this animal but not both If either sire or dam is not known this is always 0 No of other animals with the same sire as this animal If the sire is not known this is always 0 No of other animals with the same dam as this animal If the dam is not known this is always 0 No of other animals with either the same sire or the same dam as this animal or both 10 Generation Number GN The generation number of this animal defined as 1 plus the maximum of the sire and dam 1 Parental Max generation numbers Founders always have GN 0 Generation Number GN The generation number of this animal defined as 1 plus the average of the sire and dam 1 Parental Avg generation numbers Founders always have GN 0 Age at Death The time period between the date of birth and date of death of this animal Age If Living The current age of this animal but only if it is considered as being alive see Living column Age At First Offspring The time period between this animal s date of birth and that of its first known offspring Age At Last Offspring The time period between this animal s date of birth and that of its last known offspring Generational Age The average of the time period between this animal s date of birth and the dates of birth of its parents Requires that 3 dates of birth to be known Age Of Sire At Birth The time period between this animal s date of birth and that of its sire
40. ination within a chosen group of Parental KV or Composite rankings see below males and females Dawn Lassie of Kimmbess 4 3 71 14 55 14 55 14 55 13 10 13 10 Ginger Gem 45 5 2 77 9 54 9 54 9 54 8 85 8 85 Gladys Golden Girl 6 3 19 10 57 10 57 10 57 9 65 9 65 Mate Recommendations of Tagged Records tisted y F Lock Ancestry to 106 gt Rankby Inbreeding gt View as Uist Rank F Sire Dam 36 14 89 Standfast Augustus Achnagairl Kimono 35 14 89 Standfast Apollo Achnagairl Kimono I 14 89 Standfast Angus Achnagairl Kimono 33 14 55 Standfast Augustus Dawn Lassie of Kimmbess 32 14 55 Standfast Angus Dawn Lassie of Kimmbess 31 14 55 Standfast Apollo Dawn Lassie of Kimmbess 30 14 03 Standfast Dawson Achnagairl Kimono lz 14 03 Standfast Del Rio of Hayjoy Achnagairl Kimono Prospective Offspring Inbreeding List Ranking list of prospective pairings ordered by offspring inbreeding Gene Diversity Delta GD Gene diversity GD is a measure applied to a whole population that expresses the diversity of genes present Gene diversity Delta is the change in gene diversity of the population as a result of the addition of a single offspring from the prospective mating If every animal in a population is unrelated then by definition you would have the maximum genetic diversity possible for a population of that size A common goal of population management programmes for threatened species i
41. ing coefficient on a year by year basis of the number of animals born per decade Use of this feature requires that your source data includes the date year of birth of each animal It should also be noted that this feature can use a large amount of memory particularly if your source data contains a very large number of records If you do not need this feature you can disable it use the Compute tab of the Document Settings window File Document Settings Main Window With stats pane with details Above the main record table there is a pulldown menu where you specify the date of individuals falling within specific period reporting period you can choose years decades months etc The Period column shows the date range in which animals were born the Count column holds the number falling in each period Above the main record table you will also find an option to restrict the statistics so that only tagged animals are included The Report Pane contains several different reports when displaying date period stats Animals Within Period lists all the animals born within the selected date period Detailed Stats shows detailed summary stats for all animals falling within the selected date period u Date Plot lets you plot any one or two numeric columns derived from the animal records against time E g to plot the average inbreeding coefficient over time Correlation Chart plots a scattergram for any two columns from the
42. ire dam siblings and blood can be tabulated separately for each parental side of the animal s pedigree To enable this check the Separated maternal paternal metrics setting in the Compute tab of the Document Settings window Use either of the settings in the Compute tab of the Document Settings window to enable the GN column There are two settings offering different ways to compute the generation number Use the Relation Columns tab of the Document Settings window Note that the available columns for the relations report are also affected by settings on the Compute tab Use the Precise relation descriptions setting on the General tab of the Preferences window to adjust how genealogical relation descriptions are formatted in the relations report Use the General tab of the Preferences window to adjust the no of decimal places used for numeric values other than inbreeding kinship coefficients they are configured separately PedScope uses a number of terms words such as Sex Male etc To customize these terms select Preferences from the File menu then click on the Terminology tab A number of preset choices are available for English speaking breeders of cats dogs etc Alternatively select Custom from the dropdown menu then can change each term individually 14 Reports PedScope can display a wide variety of reports Reports are displayed on the right hand side of the Main Window The following reports are av
43. n control whether the periods are year decade month etc and you can limit the stats to just the tagged records only The program will then report summary stats on those animals born within the given date periods The report pane will then let you drill down to give details on stats for individual periods and plot graphs e g to plot average inbreeding over time For further information see Statistics Main Table Columns This section describes the columns that can be displayed in the main record table Not all these columns are necessarily displayed you can configure what is actually shown see Customization For details on how to use the main table including sorting filtering and tagging see Main Window The main table columns can be classified into 2 groups those that are computed by analyzing the pedigree of each animal and those that are not Columns That Do Not Require Pedigree Analysis This includes all the main columns containing basic facts about each animal such as name ID sex parents and so on Column Record Name ID Seq Rec Sire Dam Sex Living Date of Birth DOB Date of Death DOD Offspring Males Females Unknown sex Families Litters Full Siblings Litter Siblings Half Siblings Paternal Siblings Maternal Siblings Siblings Symbol if any Main Window Showing main record table with report pane hidden Description Name of this animal if it
44. ns smaller than the physical minimum margins that your printer is capable of generally will not produce acceptable results you will end up with parts of the printout chopped off You may find you need to experiment with different sized margins until you get a pleasing result 34 FAQs Listed here is a selection of some of the more commonly asked questions about PedScope Additional questions and answers can be found on our web site Q A dO DO DO dO dO DO How can interactively enter data You can t sorry This software is purely intended as a standalone program for analyzing a pedigree data set which you import from a text or CSV file It cannot be used to enter data e g onto a database Typical usage of this software is for analyzing a data set stored using a separate database or software from which you export the data into CSV text format for import into this software If you would like to use this software in conjunction with other sources of data please contact us How do I customize PedScope Customizations that are not specific to the current pedigree data file display preferences etc are controlled using the Preferences window select Preferences from the File menu Customization specific to the pedigree data such as the user defined fields are controlled using the Document Settings window select File Document Settings See Customization How do I uninstall PedScope Windows
45. or each animal Columns Symbol Description if any Inbreeding Coefficient F Wright s inbreeding coefficient for this animal computed to the chosen depth of ancestry see above Ancestral Inbreeding Coefficient The ancestral inbreeding coefficient computed using the direct method of Ballou This column is optional To disable it choose File Document Settings click onto the Compute tab then uncheck the Compute ancestral inbreeding coefficients option Generations Seen G Seen These are various metrics about the ancestors found when analyzing the pedigree of Generations Full G Full this animal These are optional to disable them choose File Document Settings Ancestors A click onto the Compute tab then uncheck the Compute individual pedigree Ancestors Unique A metrics option Completeness Unique Generations Seen is the maximum depth of ancestry generations seen Generations Full is the number of generations of ancestors that were full no holes Ancestors is the total number of occurrences of ancestors seen Ancestors occurring multiple times will add 1 to this value for every occurrence Ancestors Unique is the number of distinct ancestors seen Completeness is the proportion of the pedigree that was full no holes 11 Statistics The Stats tab of the main window calculates statistics after grouping the animals by date of birth E g this allows you to compute statistics such as the average inbreed
46. ord display If you also specify a numeric type for such columns then PedScope will sort them appropriately and can report statistics for such columns E g if your data has a column that is some kind of sample measurement for each animal say weight then if you set the column to be a user field with a numeric data type see below then PedScope will compute statistics such as the average weight both for any tagged set of animals but also for date period stats You can also have it plotted in graphs e g to correlate it against other input columns or computed values such as inbreeding etc Alive Living status whether or not the animal is known to be living If used column values TRUE T YES Y or 1 are interpreted as meaning this animal is alive Dead Dead status whether or not the animal is known to be not living If used column values TRUE T YES Y or 1 are interpreted as meaning this animal is not alive Ignore A column to be completely ignored in the input file Data Types The full list of data types is as follows Type Description Text Simple text column Date Date value The date format is set using a dropdown menu beneath the import definition table Integer An integer value i e no decimal point Number A number that may include a decimal point Examples See Import Examples Import Examples PedScope accepts input in various formats For details on how to import data and how to specify
47. pedigree The actual alleles that the current descendants have received are then counted up The whole process is then repeated usually many thousands of times By counting the frequencies of the alleles that the descendants end up with it is possible to work out good approximations for various metrics that otherwise would be difficult to work out exactly PedScope uses gene drop analysis for the computation of genome uniqueness and the proportion of alleles retained in the current population from any given founder which in turn is required for the calculation of the number of founder genome equivalents Wright S Coefficients of inbreeding and relationship American Naturalist 56 330 338 1922 Using Windows 7 64 bit AMD Phenom II X6 1035T processor 2 6Gz 8Gb memory Ballou JD Ancestral Inbreeding Only Minimally Affects Inbreeding Depression in Mammalian Populations Journal of Heredity 1997 8 169 178 Lacy RC Analysis of founder representation in pedigrees Founder equivalents and founder genome equivalents Zoo Biology 8 111 124 1989 Boichard D Maignel L and Verrier E The value of using probabilities of gene origin to measure genetic variability in a population Genetics Selection Evolution 1997 29 1 5 23 6 Fisher R The Genetical Theory of Natural Selection 1930 7 MacCluer JW VandeBerg JL Read B and Ryder OA Pedigree analysis by computer simulation Zoo Biology 5 147 160 1986 uUVPUwWNH 31
48. questions and may well address the problem or query that you have 36 Release Notes System Requirements PedScope requires Windows 8 Windows 7 or Windows Vista either 32 or 64 bit 37 Revision History VERSION RELEASE DETAILS DATE 2 3 01 March 2014 Combined previous Pro and Gold Editions into one PRO September 2012 Discontinued lower record limit version Fixed issue with trial which prevented mate recommendations from being show in some circumstances Stats tab can now be restricted to tagged only records stats period is now selected by a selector within the stats tab and not through the menu 2 1 01 July 2011 Initial public release 2011 14 Tenset Technologies Ltd 38
49. r then a greater priority might be given to breeding from the older animal first to lessen the risk that its genes are lost for good Using KV in such mating decisions allows these factors to be incorporated into the mate ranking algorithm whereas ranking by MK makes no distinction KV can be used in the mate recommendations report You can enter Vx data using the Document Settings window see Vx Data An animal s genome uniqueness is the likelihood that it contains founder alleles that are not present in any other animal normally in the current population Informally if an animal is the only one carrying a particular founder s genes then you d likely want to breed from that animal so as not to lose those genes from the population forever We say normally here because you can actually configure what is meant by genome uniqueness in that you can define that number of animals in the current population for which if any given founder s alleles are only present in that number or fewer of the current population then it is considered unique A better term might be genome rarity or founder rarity but the term genome uniqueness is already established in the literature Genome uniqueness is determined using a gene drop analysis The pedigree unknown value for an animal is that proportion of its founders that are unknown This relates only to situations where an ancestor has one parent missing in the ancestry such mi
50. ry precise meaning in population genetics It means an ancestor that is present at least once on both sides of an animal s pedigree It does not mean an ancestor that just occurs a lot When an animal has common ancestors this raises the possibility that for any particular gene locus both alleles present are in fact physical copies of the exact same allele from one of its common ancestors The inbreeding coefficient is the value of this probability Or put another way it is the probability that both alleles are IBD The inbreeding coefficient as in common use today was first defined in 1922 in a paper by Dr Sewall Wright 1 For this reason it is often known as Wrights Inbreeding Coefficient When an animal has no common ancestors its inbreeding coeffficient is zero The symbol F is commonly used in scientific literature to mean an animal s inbreeding coefficient The inbreeding coefficient can be computed by hand only for relatively simple pedigrees For deep pedigrees it can only realistically be done by computer Calculating inbreeding for very large pedigrees is a computationally intensive process and if not implemented very carefully can take a long time if it is correct at all The computation of inbreeding coefficients in PedScope is amazingly fast E g to compute all inbreeding coefficients to the maximum depth possible for the UK Golden Retriever pedigree some 500 000 dogs going back up to 65 generations took just 7 seconds 2
51. s of offspring etc are shown along with other columns from the main table common to all offspring of each family litter e g the inbreeding coefficient Families Report 17 Reports Record Details To view this report choose Record Details from the report selector at the top of the report pane in the main window Record details can be shown for both single and multiple animal records For single records the record details is simply a list of all data stored for that record For multiple records shown the record details becomes a table of statistics for each field in the records e g giving the min max inbreeding coefficient etc within the chosen records 18 Recardbeisis of Guess Bl od Fed w mn ax ean hho tFuvng cen 1 Par tan 2 50 20 cor 230 27 zur seen 6 16 16 00 Ful 2 14 1260 a seen 125 808 130899 12971360 avne 1357 1 05 1576 81 Comp 96 0 99 9 99 0 lage At First Off y 3y 2 Record Details Report Reports Correlation Chart To view this report choose Correlation Chart from the report selector at the top of m the report pane in the main window A correlation chart scattergram is used to plot the correlation between any two column values over a set of animal records Typically you would use this to chart the relationship between two metrics over a large number of tagged records or perhaps over all records listed in the main record table You sel
52. s to maximize the genetic diversity of the available population When ranking by GD Delta what PedScope does is this for each possible pairing it computes the GD that would result by addition of a single animal with given parents to the current population and then compares this to the GD of the old i e current population An increase in GD as a result of the pairing is a good thing a decrease is a bad thing Gene Value Delta GV This is the change in gene value of the population as a result of the addition of a single offspring from the prospective mating GV is a function of the average kinship value of the population GV is to KV what GD is to MK It should be preferred over GD when kinship values are available because it takes into account the age structure of the current population This method requires that you have Vx data set up in order to compute the kinship values For further information see Vx Data Parental MK This is the mean of the parental mean kinships I e PedScope computes the mean kinship of both sire and dam with respect to the current population and then ranks the prospective matings according to the mean of these two values for each pairing A lower value is better because lower values prioritize mating of animals that share fewer of their genes with the rest of the population Parental MK Delta This is the difference in the mean kinships of the sire and the dam 26 Parental Genome Uniqueness Par
53. se of using additional memory The Worker threads setting on the System tab of the Preferences window controls the number of CPU threads of execution that PedScope will attempt to use Where possible the program uses multi threading parallel computations to speed things up The number of threads used is normally set so as to retain a responsive user interface Increasing the Results cache size setting can speed up PedScope when switching between different reports Use the General tab of the Document Settings window to set the rounds to use when performing gene drop analysis Use the General tab of the Document Settings window to set the genome uniqueness threshold For further information see Reports Founder Metrics Adjust the Assume dead at age setting on the General tab of the Document Settings window Use the checkboxes on the General tab of the Document Settings window For further 13 Family Litter Records Sex specific Offspring Counts Separated Maternal Paternal Metrics Generation Numbers Relations Report Columns Relation Descriptions Number Precision Terminology information see Main Window Other Record Types Use the Compute tab of the Document Settings window to control whether or not to have separate columns for the numbers of male female offspring in the main table use the Compute offspring gender specific metrics setting Some columns in the main table and relations report such as the s
54. select which columns to show in the main table Note that the available columns are also affected by settings on the Compute tab Use the Mating Values and KV Weights tabs of the Document Settings window to adjust parameters that affect the mate recommendations report There is an overall enable disable setting for the tooltips that can appear over the main table and relations report the Show tooltips setting on the General tab of the Preferences window You can also adjust the information shown using the options on the ToolTips tab of the Document Settings window Adjust the screen and printer font using the General tab of the Preferences window Use the General tab of the Preferences window to adjust the colors used in graph and chart reports Use the Highlighting tab of the Preferences window The General tab of the Preferences window has options to control the usage of standard genetics symbols e g F for the inbreeding coefficient in column labels and whether to use concise or longer labels The Large buffer size and Matrix representation settings on the General tab of the Document Settings window affect the memory limits used in individual reports The Results cache size setting on the System tab of the Preferences window controls the amount of memory that PedScope will use to store previously computed results Increasing this value can speed up the program when switching to and fro between different reports at the expen
55. sey Ramona 3 Highlight common ancestors ancestors that occur on both sides of the en pedigree within the displayed generations are highlighted with a unique color eineda Consoidator or sansue 28 Population Genetics This section describes some of the concepts of population genetics that are used by this program If you are knowledgable in this field you probably don t need to read this section But if terms such as mean kinship and founder equivalents are unfamiliar to you then you do need to this section as understanding of these concepts is necessary in order to get the most out of a product such as PedScope Founders A founder within a set of pedigree data is defined as an animal where neither the sire nor dam is known Such an animal may truly be a founding ancestor of a breed or population in the sense that it is not related to any other founder or it may be related possibly closely to other members of the group but the details of its lineage are not known Within PedScope founders are treated as unrelated and non inbred Many features of PedScope involve determining the ancestors of an animal or group and then computing various metrics or reports based on them In most situations PedScope gives you a way to artificially restrict the depth of ancestry that is considered E g you may choose to limit inbreeding calculations to
56. splayed pedigree data set along with all the current Document Settings and computed data inbreeding coefficients etc in a single file that can be easily reopened later Opening such a saved data file is usually much quicker than reloading the original import file To save the data in this format choose File Save or File Save As To subsequently reload such a data file choose File Open change the file type to PedScope data files then locate the saved file Exporting You can export individual reports data tables etc in a variety of file formats To do this you just click the Export or Save button which can be found near the bottom of most the main window panes u Data tables and matrices PDF PostScript text CSV XML for direct import into spreadsheets such as Excel HTML and Open Document Format odt u Graphs and Pedigree charts PDF PostScript JPEG PNG Scaled Vector Graphics svg for websites and other bitmap image formats 33 Printing You can print the main record table and most reports by clicking the Print button beneath the table report Saving As PDF Image Files Instead of printing to a physical printer you can also print to a PDF or image file by exporting to a PDF file Pedigree Margins When printing the pedigree report PedScope sets default paper margins depending on your printer and its setup In most cases this should produce a sensible and consistent margin on all sides of the paper
57. ssing ancestors are considered to be unknown founders missing from the pedigree Sometimes it can be desirable to avoid breeding from animals with a large degree of unknown pedigree for this reason the PU value can be used in the composite mate ranking algorithm 25 Reports Mate Recommendations To view this report choose Mate Recommendations from the report selector at the top of the report pane in the main window PedScope makes breeding recommendations by studying potential pairings and ordering them according to a single value reflecting the respective merit of the pairing In this way it can be used as a tool to guide population management decisions It provides various ways of calculating the merit for each pairing As with the Gene Diversity Metrics report to use this feature you first need to define a group of animals that represents the available sires and dams You do this by tagging the sires and dams in the main record table If you want to include all the living members of the population it can help if you first sort the main record table by the Age if Living or Living columns if available This will bring all the living animals together so you can tag them with a range tagging operation Next you choose the depth of ancestry to be considered in the calculation using the Ancestry to pulldown This includes the option of using all known ancestry Finally you choose the method by which the pairings are to be ordered using R
58. t e g relationship matrices are symmetric which at a stroke halves the memory requirement it is still very easy to run out of memory You can see the amount of memory used in the stats line displayed above the property pane when you have a relationship matrix visible E g N 1 696 memory 6 1Mb says that the relationship matrix contains 1 696 rows columns and occupied 6 1Mb main memory The program will not crash if you try to use more memory than is available but it might become very slow or you might see an error message Note also that if you compute the genomic relationship matrix this will occupy 4 times as much memory for the same number of animals because it has 2 rows and 2 columns for each animal 21 Reports Founder Metrics PedScope can analyse the founders of a single animal or a group of animals and list various measures of genetic diversity associated with them Typically this would be used to analyse the founders of a group of animals that make up a current population or a group from which future breeding is to occur In the description that follows current population means either the currently selected animal or the group of tagged animals whichever has been chosen for the report There are 3 separate founder metrics reports available to choose from the report selector at the top of the report pane E Summary Contribution Detail and Genome Uniqueness Detail The Founder Metrics Summary report
59. table Column Mean Kinship Kinship Value Symbol MK Genome Uniqueness GU Pedigree Unknown PU Gene Diversity Metrics Report Description The mean kinship of an animal is the mean of its kinship coefficients with every animal in the current population including itself The lower the MK value the less an animal is related to other members of the current population on average Informally it makes sense to breed from such animals in order to preserve genetic diversity Note that two animals with low MK may nevertheless be closely related themselves so selecting matings on this basis alone can still give rise to highly inbred offspring Kinship value is simply a weighted variant of the mean kinship weighted according to the age structure of the population For this to work the program needs additional information a the date of birth of each animal from which its age is determined and b the reproductive values of different aged animals as relevant to the particular species so called Vx values see Fisher R The Genetical Theory of Natural Selection 1930 Clearly an animal in the current population that is no longer reproductive e g a female nearing the end of her life is of no value in maintaining future genetic diversity and yet calculations based on MK do not take this into account Likewise it follows that if you have two animals with the same low mean kinship but one is older than the othe
60. ted Some of the columns shown will be the same as those in the main record table Other columns specific to the relations results are given below When you tabulate the relations for more than one animal at a time e g list all the ancestors for a group of tagged records the results will contain additional columns containing the min max values of various of the above statistics whilst other columns are no longer displayed as they are not applicable E g the Kinship Coefficient for Ancestors Report Showing columns for ancestors is not displayed because it will often differ from one source record to kinship and partial inbreeding coefficients another But the min max will still be shown with respect to founders Column Description Where For Ancestors this gives the generation numbers and the side of the pedigree where the ancestor Path Generations Nearest Generation Nearest Generation Paternal Nearest Generation Maternal Furthest Generation Furthest Generation Paternal Furthest Generation Maternal Occurrences Paternal Occurrences Maternal Occurrences Blood Blood Paternal Blood Maternal Kinship Coefficient KC Partial Inbreeding Coefficient Partial F Other Parent Relation was seen E g S5x2 D7 means twice on the sire side in generation 5 and once on the dam side in generation Ts When listing descendants this just gives the generation number 1 children 2 grandchildren
61. the animal s appearance as the sire dam of other animals Whether or not this animal is considered to be alive This is determined from a combination of other information Firstly if the imported data has a Dead or Alive column value see Importing Data then this defines whether or not the Living column is true Failing that if the date of death is known the Living column is set to false Otherwise if the date of birth is known and the current age of the animal exceeds a user chosen threshold then again the Living column is set to false Finally in the absence of any other way to determine the living status it is set to a user chosen default See Customization Date of birth of this animal or litter Date of death of this animal No of immediate descendants of this animal i e the number of other animals for which this animal is either the sire or dam No of immediate descendants of this animal that are male No of immediate descendants of this animal that are female No of immediate descendants of this animal whose sex is not known No of family records in which this animal is a parent No of litter records in which this animal is a parent No of other animals with the same sire and dam as this animal If either sire or dam is not known this is always 0 No of other animals with the same sire and dam and date of birth as this animal If either sire or dam is not known this is always 0 No of other an
62. the input format see Importing Data Shown below are various examples of different input data formats all of which are acceptable This is by no means exhaustive the import window can cope with many different formats For ease of display the examples shown here use comma separated text CSV but you could just as easily use TAB separated or other separator character Example 1 Very simple structure with a column for the gender and columns for the name sire name and dam name SEX NAME SIRE DAM M Comet Favorite Young Phoenix M Favorite Bolingbroke Phoenix M Bolingbroke Foljambe Young Strawberry M Foljambe R Barkers Bull Haughton F Young Strawberry Dalton Duke Favorite cow F Phoenix Foljambe Favorite cow F Favorite cow Alcocks Bull F Young Phoenix Favorite Phoenix Example 2 In this case the animal is given by both a name and an id number and the sire dam linkage is through the id number name sire id dam id id Arripay Arripay Arripay Arripay Arripay Arripay Arripay Arripay Arripay Arripay Blue Surprise 2 29 1 Breaks Everything 26 22 2 Brown Beauty 19 5 3 Brown Boy 4 Candy terel rr o Champagne Charlie 16 22 6 ehoeaholkte 6 297 17 choeeyBchipsyrndr Desh Crystal i Sh Dark Magician 4 25 10 Example 3 Similar to the above but this time with a column for date of birth To control the format of dates e g DD MM YYYY or MM DD YYYY etc you can select from many
63. trics Computation of Ancestral Inbreeding Coefficients Date Display Statistics Main Table Columns Mate Recommendations Report ToolTips Fonts Graph Colors Row amp Cell Highlighting Labels Memory Usage Speed Gene Drop Analysis Genome Uniqueness Defaults for Living Status column Use of How Set Use the General tab of the Document Settings window Inbreeding and kinship coefficients can be displayed in three ways as percentages e g 12 5 or as numbers e g 0 125 or as fractions e g 1 8 To adjust this use the General tab of the Preferences window Use the General tab of the Preferences window to adjust the precision no of decimal places used for inbreeding and kinship coefficients Use the Compute tab of the Document Settings window to adjust the Compute individual pedigree metrics setting This enables main table columns such as G Seen and Ancestors Unique The Compute tab of the Document Settings window has an option to enable the computation of ancestral inbreeding coefficients The display date format is set on the System tab of the Preferences window You can enable disable the date specific statistics tab using a setting on the Stats Columns tab of the Document Settings window There are also options on the Compute tab to control which of the various statistics mean mode median etc are reported Use the Main Columns tab of the Document Settings window to
64. values this is equal to twice the kinship coefficient When I is equal to J i e for the diagonal this is equal to the inbreeding coefficient of animal I plus one Relationship Matrix This shows the A matrix for the stud Roan Gauntlet from Wrights original 1922 paper on inbreeding with the A matrix values are shown as fractions Founder Equivalents amp Founder Genome Equivalents The founders of a population under study contain all the genetic diversity available to be inherited by their descendants However not necessarily all of the genetic variation present in the founders may have made it to the current population due to genetic drift selection and inbreeding Genetic drift refers to the loss by chance of genetic diversity present in the founders E g when a founder has only one offspring but that offspring is then the ancestor of one or more members of the current population then by definition at least half of the genetic diversity that was present in that founder must have been lost That is because its sole offspring only inherited half of it Even when a founder has many offspring and from which there may be large numbers of descendants in the current population it is not likely that all its genes will still be present Larger populations with larger numbers of founders large families and little or no Er selection i e truly random mating usually maintain genetic diversity Genetic diversity can be

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