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Comparing parentage inference software: Reanalysis of a red deer pedigree

Walling, Craig A.; Pemberton, Josephine M; Hadfield, Jarrod D.; Kruuk, Loeske

Description

Knowledge of the parentage of individuals is required to address a variety of questions concerning the evolutionary dynamics of wild populations. A major advance in parentage inference in natural populations has been the use of molecular markers and the development of statistical methods to analyse these data. Cervus, one of the most widely used parentage inference programs, uses molecular data to determine parent-offspring relationships. However, Cervus does not make use of all available...[Show more]

dc.contributor.authorWalling, Craig A.
dc.contributor.authorPemberton, Josephine M
dc.contributor.authorHadfield, Jarrod D.
dc.contributor.authorKruuk, Loeske
dc.date.accessioned2015-12-13T22:50:37Z
dc.identifier.issn0962-1083
dc.identifier.urihttp://hdl.handle.net/1885/80870
dc.description.abstractKnowledge of the parentage of individuals is required to address a variety of questions concerning the evolutionary dynamics of wild populations. A major advance in parentage inference in natural populations has been the use of molecular markers and the development of statistical methods to analyse these data. Cervus, one of the most widely used parentage inference programs, uses molecular data to determine parent-offspring relationships. However, Cervus does not make use of all available information: additional phenotypic information may exist predicting parent-offspring relationships, and additional genetic information may be exploited by simultaneously considering multiple types of relationships rather than just pairwise or just parent-offspring relationships. Here we reanalyse data from a wild red deer population using two programs capable of using this additional information, MasterBayes and COLONY2, and quantify the impact of these alternative approaches by comparison with a 'known pedigree' estimated using a larger suite of microsatellite makers for a subset of the population. The use of phenotypic information and multiple relationships increased the number of correct assignments. We highlight the differences between programs, particularly the use of population- rather than individual-level statistical confidence in Cervus. We conclude that the use of additional information allows MasterBayes and COLONY2 to assign more correct paternities, whereas their use of individual- rather than population-level confidence generates fewer erroneous assignments. We suggest that maximal information may be gained by combining outputs from different programs. Higher accuracy and completeness of pedigree information will improve parameters estimated from pedigree information in studies of natural populations.
dc.publisherBlackwell Publishing Ltd
dc.sourceMolecular Ecology
dc.subjectKeywords: microsatellite DNA; animal; article; Bayes theorem; biological model; comparative study; computer program; deer; female; genetics; male; pedigree; phenotype; population genetics; Animals; Bayes Theorem; Deer; Female; Genetics, Population; Male; Microsatel Cervus; COLONY2; MasterBayes; Maternity; Microsatellite; Parentage analysis; Paternity
dc.titleComparing parentage inference software: Reanalysis of a red deer pedigree
dc.typeJournal article
local.description.notesImported from ARIES
local.identifier.citationvolume19
dc.date.issued2010
local.identifier.absfor060411 - Population, Ecological and Evolutionary Genetics
local.identifier.ariespublicationf5625xPUB9170
local.type.statusPublished Version
local.contributor.affiliationWalling, Craig A., University of Edinburgh
local.contributor.affiliationPemberton, Josephine M, University of Edinburgh
local.contributor.affiliationHadfield, Jarrod D., University of Edinburgh
local.contributor.affiliationKruuk, Loeske, College of Medicine, Biology and Environment, ANU
local.description.embargo2037-12-31
local.bibliographicCitation.issue9
local.bibliographicCitation.startpage1914
local.bibliographicCitation.lastpage1928
local.identifier.doi10.1111/j.1365-294X.2010.04604.x
local.identifier.absseo970106 - Expanding Knowledge in the Biological Sciences
dc.date.updated2016-02-24T09:45:14Z
local.identifier.scopusID2-s2.0-77951154678
local.identifier.thomsonID000276794300013
CollectionsANU Research Publications

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