Relative accuracy of three common methods of parentage analysis in natural populations

Handle URI:
http://hdl.handle.net/10754/562469
Title:
Relative accuracy of three common methods of parentage analysis in natural populations
Authors:
Harrison, Hugo B.; Saenz Agudelo, Pablo; Planes, Serge; Jones, Geoffrey P.; Berumen, Michael L. ( 0000-0003-2463-2742 )
Abstract:
Parentage studies and family reconstructions have become increasingly popular for investigating a range of evolutionary, ecological and behavioural processes in natural populations. However, a number of different assignment methods have emerged in common use and the accuracy of each may differ in relation to the number of loci examined, allelic diversity, incomplete sampling of all candidate parents and the presence of genotyping errors. Here, we examine how these factors affect the accuracy of three popular parentage inference methods (colony, famoz and an exclusion-Bayes' theorem approach by Christie (Molecular Ecology Resources, 2010a, 10, 115) to resolve true parent-offspring pairs using simulated data. Our findings demonstrate that accuracy increases with the number and diversity of loci. These were clearly the most important factors in obtaining accurate assignments explaining 75-90% of variance in overall accuracy across 60 simulated scenarios. Furthermore, the proportion of candidate parents sampled had a small but significant impact on the susceptibility of each method to either false-positive or false-negative assignments. Within the range of values simulated, colony outperformed FaMoz, which outperformed the exclusion-Bayes' theorem method. However, with 20 or more highly polymorphic loci, all methods could be applied with confidence. Our results show that for parentage inference in natural populations, careful consideration of the number and quality of markers will increase the accuracy of assignments and mitigate the effects of incomplete sampling of parental populations. © 2012 Blackwell Publishing Ltd.
KAUST Department:
Red Sea Research Center (RSRC); Biological and Environmental Sciences and Engineering (BESE) Division; Marine Science Program; Reef Ecology Lab
Publisher:
Wiley-Blackwell
Journal:
Molecular Ecology
Issue Date:
27-Dec-2012
DOI:
10.1111/mec.12138
PubMed ID:
23278953
Type:
Article
ISSN:
09621083
Sponsors:
We would like to thank Jinliang Wang for kindly sharing the Fortran source code of COLONY2, Samar Aseeri and Dodi Heryadi from the KAUST Supercomputing Laboratory for compiling the program to enable parallel computation on Mac OSX and Wayne Mallett for assistance with the high-performance computing facility at James Cook University. We are grateful for comments from Glenn Almany and would also like to thank Peter Buston and two anonymous reviewers for insightful reviews. HBH was supported by a James Cook University Post-Graduate Research Scholarship in cotutelle with the Ecole Pratique des Hautes Etude, Universite de Perpignan. PSA was supported by a Post-Doctoral Research Fellowship from King-Abdullah University of Science and Technology.
Appears in Collections:
Articles; Red Sea Research Center (RSRC); Marine Science Program; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorHarrison, Hugo B.en
dc.contributor.authorSaenz Agudelo, Pabloen
dc.contributor.authorPlanes, Sergeen
dc.contributor.authorJones, Geoffrey P.en
dc.contributor.authorBerumen, Michael L.en
dc.date.accessioned2015-08-03T10:39:21Zen
dc.date.available2015-08-03T10:39:21Zen
dc.date.issued2012-12-27en
dc.identifier.issn09621083en
dc.identifier.pmid23278953en
dc.identifier.doi10.1111/mec.12138en
dc.identifier.urihttp://hdl.handle.net/10754/562469en
dc.description.abstractParentage studies and family reconstructions have become increasingly popular for investigating a range of evolutionary, ecological and behavioural processes in natural populations. However, a number of different assignment methods have emerged in common use and the accuracy of each may differ in relation to the number of loci examined, allelic diversity, incomplete sampling of all candidate parents and the presence of genotyping errors. Here, we examine how these factors affect the accuracy of three popular parentage inference methods (colony, famoz and an exclusion-Bayes' theorem approach by Christie (Molecular Ecology Resources, 2010a, 10, 115) to resolve true parent-offspring pairs using simulated data. Our findings demonstrate that accuracy increases with the number and diversity of loci. These were clearly the most important factors in obtaining accurate assignments explaining 75-90% of variance in overall accuracy across 60 simulated scenarios. Furthermore, the proportion of candidate parents sampled had a small but significant impact on the susceptibility of each method to either false-positive or false-negative assignments. Within the range of values simulated, colony outperformed FaMoz, which outperformed the exclusion-Bayes' theorem method. However, with 20 or more highly polymorphic loci, all methods could be applied with confidence. Our results show that for parentage inference in natural populations, careful consideration of the number and quality of markers will increase the accuracy of assignments and mitigate the effects of incomplete sampling of parental populations. © 2012 Blackwell Publishing Ltd.en
dc.description.sponsorshipWe would like to thank Jinliang Wang for kindly sharing the Fortran source code of COLONY2, Samar Aseeri and Dodi Heryadi from the KAUST Supercomputing Laboratory for compiling the program to enable parallel computation on Mac OSX and Wayne Mallett for assistance with the high-performance computing facility at James Cook University. We are grateful for comments from Glenn Almany and would also like to thank Peter Buston and two anonymous reviewers for insightful reviews. HBH was supported by a James Cook University Post-Graduate Research Scholarship in cotutelle with the Ecole Pratique des Hautes Etude, Universite de Perpignan. PSA was supported by a Post-Doctoral Research Fellowship from King-Abdullah University of Science and Technology.en
dc.publisherWiley-Blackwellen
dc.subjectaccuracyen
dc.subjectcolonyen
dc.subjectFaMozen
dc.subjectmicrosatelliteen
dc.subjectparentage analysisen
dc.titleRelative accuracy of three common methods of parentage analysis in natural populationsen
dc.typeArticleen
dc.contributor.departmentRed Sea Research Center (RSRC)en
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentMarine Science Programen
dc.contributor.departmentReef Ecology Laben
dc.identifier.journalMolecular Ecologyen
dc.relation.referencesHarrison, H. B., Saenz-Agudelo, P., Planes, S., Berumen, M. L., & Jones, G. P. (2012). Data from: Relative accuracy of three common methods of parentage analysis in natural populations (Version 1) [Data set]. Dryad Digital Repository. https://doi.org/10.5061/dryad.2ht96en
dc.relation.referencesDOI:10.5061/DRYAD.2HT96en
dc.relation.referencesHANDLE:http://hdl.handle.net/10754/624168en
dc.contributor.institutionJames Cook Univ, Sch Marine & Trop Biol, Townsville, Qld 4811, Australiaen
dc.contributor.institutionJames Cook Univ, Australian Res Council, Ctr Excellence Coral Reef Studies, Townsville, Qld 4811, Australiaen
dc.contributor.institutionUniv Perpignan, USR CRIOBE CNRS EPHE 3278, CBETM, F-66860 Perpignan, Franceen
dc.contributor.institutionLab Excellence CORAIL, Moorea 98729, Fr Polynesiaen
dc.contributor.institutionWoods Hole Oceanog Inst, Dept Biol, Woods Hole, MA 02543 USAen
kaust.authorSaenz Agudelo, Pabloen
kaust.authorBerumen, Michael L.en
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