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Identifying outlier loci in admixed and in continuous populations using ancestral population differentiation statistics
Author(s) -
Martins Helena,
Caye Kevin,
Luu Keurcien,
Blum Michael G. B.,
François Olivier
Publication year - 2016
Publication title -
molecular ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.619
H-Index - 225
eISSN - 1365-294X
pISSN - 0962-1083
DOI - 10.1111/mec.13822
Subject(s) - biology , fixation index , population , evolutionary biology , outlier , fixation (population genetics) , local adaptation , principal component analysis , quantitative trait locus , selection (genetic algorithm) , genetics , statistics , microsatellite , artificial intelligence , allele , computer science , mathematics , gene , demography , sociology
Finding genetic signatures of local adaptation is of great interest for many population genetic studies. Common approaches to sorting selective loci from their genomic background focus on the extreme values of the fixation index, F ST , across loci. However, the computation of the fixation index becomes challenging when the population is genetically continuous, when predefining subpopulations is a difficult task, and in the presence of admixed individuals in the sample. In this study, we present a new method to identify loci under selection based on an extension of the F ST statistic to samples with admixed individuals. In our approach, F ST values are computed from the ancestry coefficients obtained with ancestry estimation programs. More specifically, we used factor models to estimate F ST , and we compared our neutrality tests with those derived from a principal component analysis approach. The performances of the tests were illustrated using simulated data and by re‐analysing genomic data from European lines of the plant species Arabidopsis thaliana and human genomic data from the population reference sample, POPRES .