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PedScope is a software tool for advanced pedigree analysis, with applications in captive breeding programmes for endangered species conservation and safe breeding practices within closed or small populations such as pedigreed livestock, cats, dogs, etc. PedScope is available for both Windows and Mac.
Main Table - Listing various metrics computed for each individual, including generation number (GN), inbreeding coefficient (F)
PedScope can compute many pedigree-related metrics for every animal in a population:
All these individual metrics can be calculated and displayed in the main PedScope window as a table. You can sort the table on any column by clicking the headings.
PedScope also calculate partial inbreeding coefficients and kinship coefficients: see Relations Reports.
Founder Metrics - Contribution Detail 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
Founder Metrics Contribution Detail Report - Matrix with founders in columns and group members in rows, giving the %contribution of each founder to each descendant
Metrics of genetic diversity can be computed for any group of individuals. Typically such a group defines the 'current population', or a subset of current population that is available for breeding. In addition, you choose the depth of ancestry of the group members to be analysed.
PedScope provides various ways to analyse the relationship between any group of individuals and their founders (where a founder is defined as an ancestor that has neither sire nor dam within the ancestry under study), and can compute the following important values:
You can tabulate all the founding ancestors of a group, including columns for:
You can then drill down to display a founder contribution matrix that gives the %contribution of each founder to each descendant within the group, or to view the genome uniqueness for each founder with respect to each descendant (i.e., the probability that the given descendant is the only member of the current population that has inherited the respective founder's genes). To compute these metrics PedScope performs a gene drop analysis for the individuals under study and their ancestors .
Prospective Offspring Inbreeding Matrix - Showing the inbreeding for every sire/dam combination within a chosen group of males and females
Prospective Offspring Inbreeding List - Ranking list of prospective pairings, ordered by offspring inbreeding
Mate Recommendations Report - Pairings ranked by composite breeding value
PedScope can make breeding (mating) recommendations by analyzing 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.
Breeders of fancy animals such as dogs and cats are often particularly interested in limiting the inbreeding of the potential offspring. To help with this one of the available measures is simply the coefficient of inbreeding of the offspring. 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. You can immediately see which matings give rise to low or high inbreeding.
In addition to the ranking values it is also possible to list the kinship between each of the prospective parents with a specific known ancestor. For example, breeders of fancy animals are sometimes interested in seeking matings that maximize the influence of particular prized individuals from the past whose influences they are trying to promote in their own breeding lines. I.e. it lets you easily answer the question: against which sire from a group of potential sires should I mate my female against in order to get offspring with the greatest influence from a particular significant ancestor? You simply sort the mate recommendations according to the sire's KC with the significant ancestor and read off the top result.
As with the measures of genetic diversity (above), you use the breeding prediction feature by first defining a group of individuals that represents the available sires and dams, and then you choose the depth of ancestry to be considered in the calculations (including the option of all known ancestry).
The following methods of ranking potential breedings are provided:
Summary Stats - Summarizing individuals falling into date ranges; in this example showing the numbers of animals in years 2008 + 2009, and statistics about the generation number and inbreeding coefficients (F)
Detailed Stats - Summary for all individuals falling within a given date period
PedScope can compute statistics on groups of individuals.
For each value associated with an individual - such as the coefficient of inbreeding, or the #offspring, or its longevity - PedScope can report the min, max, mean, median, mode, standard deviation, variance and coefficient of variability.
If the source data includes dates/years of birth then the software will automatically compute summary stats for all individuals born in each date period. Periods can be decade, year, quarter, month etc. You can also 'drill down' to see detailed stats for each date period.
In addition it will produce stats for any user-chosen group of individuals. You just tag the individuals of interest then view the summary record details of the tagged set.
PedScope can generate various types of graphs/charts.
Line graphs plot any of the individual statistics against date periods. E.g. to plot how average inbreeding varies over time.
The example shown here charts the average inbreeding coefficient (F) per year, in this case for the UK Golden Retriever pedigree (note: during the years of World War 1 very little data is available and this causes significant variation in that period.)
Frequency charts show a bar chart giving the frequency of ranges of metric value for a given set of individuals. This lets you visualize the frequency distribution of, say, inbreeding, within any group of individuals.
The example shown here plots the distribution of inbreeding coefficients within the UK Golden Retriever pedigree. The mean inbreeding is near 22% and the plot visualizes nicely how the frequency distribution clusters around the mean. The apparently spuriously high frequency for COI 0% is caused by unknown ancestry in the pedigree - dogs where close ancestors are unknown.
Scattergram charts can be used to visualize the correlation between any two metrics for a group of individuals. E.g. you could chart the relation between the inbreeding and longevity. It also computes correlation coefficients, both the Product Moment Correlation Coefficient (r) and Spearman Rank Correlation Coefficient (rs).
In the example shown here, inbreeding (F) has been plotted against the pedigree completeness, showing a weak correlation. In a closed population with considerable inbreeding, such as a pedigreed dog population from which this example is taken, you would expect the computed inbreeding coefficient to trend higher as more ancestry is available. The main intended use however for correlation plots is when your source data includes 'real' per-individual measurements such as weight, or height; these can then be correlated against other metrics computed by PedScope, such as the inbreeding coefficient.
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
PedScope will compute and display relationship matrices.
You can display the additive relationship matrix (the 'A' or NRM matrix), the dominance relationship matrix, or the genomic relationship matrix. Coefficients can be displayed as numbers, percentages, and as fractions. Matrix cells can be color coded to make it easy to see high values.
Relationship matrices can be printed and exported (e.g. to a spreadsheet) - as with all other tables, reports and charts.
Ancestors Report - Showing columns for kinship and partial inbreeding coefficients with respect to founders
All Relatives Report - Showing genealogical relation descriptions
PedScope will create detailed reports of relatives such as ancestors, descendants and other relations.
These reports can be produced both for a single individual - e.g. to list all ancestors to a given depth of ancestry for a specific animal. Or, they can be created for a whole group of individuals at a time, in which case the report is first run separately for all individuals in the group, and the results merged and displayed - e.g. to show all the ancestors of a chosen set of individuals. The group report will show the number of times each relative has been seen and associated statistics. E.g. if you run a group ancestors report you can see, for each ancestor, the number of animals in the group of which it is an ancestor, the closest appearance of that ancestor to any group member, the maximum % of blood it has to any animal in the group, and so on.
Ancestor reports include: the number of occurrences (of the ancestor in the individual's pedigree), the min/max generation at which the ancestor occurred, overall path lengths if it is a common ancestor, the kinship coefficient between the ancestor and the individual under study, and, if the ancestor is a founder, the partial inbreeding coefficient for that ancestor (the inbreeding due to that founder ancestor). You can order the results using any of the values reported. E.g. to find the founder ancestor with the greatest contribution to inbreeding within a given group of animals you just produce a group ancestors report, then order the table by the partial inbreeding coefficients. Ancestor reports can be limited so they only display the founders, or the common ancestors, of the individual(s) under study.
Descendant reports operate similarly to ancestor reports except they are the 'other way round', and (obviously) do not include details specific to common ancestors and founders.
You can also list all the relatives of an individual (or group) within a given generation span. For this report, PedScope first explores back through the ancestry to find the ancestors to the given depth, and then forward from all ancestors found by the given depth, resulting in a report that includes siblings, uncles/aunts, nephews/nieces, and cousins. You can filter this report to only include particular relations. The genealogical description of the relation (e.g. 'Cousin Twice Removed', 'Half Brother' etc) is given, and you can order the individuals by closeness of relation.
PedScope will list the litters and families of which an individual is a parent. For this purpose we define a litter as being all animals with the same parents and date of birth, and a family as being all animals with the same parents.
PedScope can display simple individual pedigree charts showing the ancestors of an individual up to 6 generations, with optional highlighting of common or repeat ancestors.
PedScope works with data stored externally in text/CSV files. It will work with almost any compatible text file format so long as: (a) the data comprises one line per individual, with columns for different fields; and (b) the columns include, as a minimum, the individual name/ID, sire name/ID and dam name/ID. It can work with data sets comprising many millions of records. Please see System Requirements for more information.
For examples of actual data showing some of the supported input layouts see: Import Examples.
The data can optionally include:
NOTE: PedScope does not provide any means to interactively enter data, e.g. to update a pedigree database. At present, the data must be supplied externally in a file.
1. Using Windows 7, 64 bit, AMD Phenom II X6 1035T processor 2.6Gz, 8Gb memory.
2. Ballou, JD. Ancestral Inbreeding Only Minimally Affects Inbreeding Depression in Mammalian Populations, Journal of Heredity 1997, 8:169-178.
3. Thompson, E. Pedigree Analysis in Human Genetics. Johns Hopkins University Press, Baltimore., 1986.
4. Brinks, J., R. Clark, and F. Rice. Estimation of genetic trends in beef cattle, J. Anim.Sci 20: 903, 1962.
5. Lacy, RC. Analysis of founder representation in pedigrees: Founder equivalents and founder genome equivalents. Zoo Biology 8:111-124, 1989.
6. 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.
7. MacCluer, JW, VandeBerg JL, Read B and Ryder OA. Pedigree analysis by computer simulation. Zoo Biology 5, 147/160, 1986.
PedScope is a product of Tenset Technologies Ltd, © 2011-14 All Rights Reserved. v2.4.01, June 2014