Inference of structure in subdivided populations at low levels of genetic differentiation--the correlated allele frequencies model revisited

Bioinformatics
Gilles Guillot

Abstract

This article considers the problem of estimating population genetic subdivision from multilocus genotype data. A model is considered to make use of genotypes and possibly of spatial coordinates of sampled individuals. A particular attention is paid to the case of low genetic differentiation with the help of a previously described Bayesian clustering model where allele frequencies are assumed to be a priori correlated. Under this model, various problems of inference are considered, in particular the common and difficult, but still unaddressed, situation where the number of populations is unknown. A Markov chain Monte Carlo algorithm and a new post-processing scheme are proposed. It is shown that they significantly improve the accuracy of previously existing algorithms in terms of estimated number of populations and estimated population membership. This is illustrated numerically with data simulated from the prior-likelihood model used in inference and also with data simulated from a Wright-Fisher model. Improvements are also illustrated on a real dataset of eighty-eight wolverines (Gulo gulo) genotyped at 10 microsatellites loci. The interest of the solutions presented here are not specific to any clustering model and are hence ...Continue Reading

References

Apr 1, 1996·Genetical Research·B Rannala, J A Hartigan
Jun 1, 1997·Heredity·D J Balding, R A Nichols
Jun 3, 2000·Genetics·J K PritchardP Donnelly
Dec 21, 2002·Science·Noah A RosenbergMarcus W Feldman
Feb 15, 2003·Genetics·Jukka CoranderMikko J Sillanpää
Mar 31, 2004·Nature Genetics·Jonathan MarchiniPeter Donnelly
May 8, 2004·Nature Reviews. Genetics·Mark A Beaumont, Bruce Rannala
Nov 3, 2004·Genetics·Gilles GuillotJean François Cosson
Aug 23, 2006·Nature Reviews. Genetics·Laurent Excoffier, Gerald Heckel
Sep 20, 2006·Nature Reviews. Genetics·David J Balding
Nov 17, 2006·Molecular Ecology·Malgorzata PilotStephan M Funk
Jan 24, 2007·Genetics·John P Huelsenbeck, Peter Andolfatto
Mar 1, 1931·Genetics·S Wright

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Citations

Jan 24, 2013·The Journal of Heredity·Javier PorobicCristián E Hernández
May 5, 2011·International Journal of Molecular Sciences·Toni SafnerStéphanie Manel
Sep 17, 2013·Conservation Biology : the Journal of the Society for Conservation Biology·Catherine I Cullingham, Axel Moehrenschlager
Sep 1, 2015·Comptes rendus biologies·Anne RopiquetConrad A Matthee
Sep 30, 2015·Molecular Ecology·Catarina N S Silva, Jonathan P A Gardner
Sep 30, 2010·Molecular Ecology·Matthieu FollLaurent Excoffier
Jun 22, 2010·Molecular Ecology·Marco V G TorrianiSilvia Dorn
Oct 26, 2011·Evolution; International Journal of Organic Evolution·Juanita Olano-MarinBart Kempenaers
Aug 6, 2013·Molecular Ecology·Eve S McCullochRichard D Stevens
May 14, 2011·Molecular Ecology Resources·Gilles Guillot, Filipe Santos
Apr 11, 2012·Journal of Evolutionary Biology·T D Hether, E A Hoffman
Sep 10, 2010·Biometrics·Brian J Reich, Howard D Bondell
Dec 30, 2014·Ecology and Evolution·Alexander I Putman, Ignazio Carbone
Nov 3, 2009·Molecular Ecology·Gilles GuillotAlain C Frantz
Jul 15, 2015·Molecular Phylogenetics and Evolution·MrinaliniAnita Malhotra
Feb 17, 2015·Molecular Ecology Resources·Naama M KopelmanItay Mayrose
Aug 28, 2014·The Journal of Heredity·Daniel A Marschalek, Mark E Berres
Aug 17, 2011·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Gabriele MargosDurland Fish
Mar 9, 2012·Systematic Biology·Gilles GuillotJulien Claude

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