Journal
MOLECULAR ECOLOGY
Volume 25, Issue 20, Pages 5029-5042Publisher
WILEY
DOI: 10.1111/mec.13822
Keywords
admixed populations; genome scans for selection; inference of population structure; population differentiation tests
Funding
- 'Ciencias sem Fronteiras' scholarship programme from the Brazilian government
- LabEx PERSYVAL-Lab - French programme Investissement d'Avenir [ANR-11-LABX-0025-01]
- ANR AGRHUM project [ANR-14-CE02-0003-01]
- Grenoble INP
- Agence Nationale de la Recherche [AFRICROP ANR-13-BSV7-0017]
- Agence Nationale de la Recherche (ANR) [ANR-14-CE02-0003] Funding Source: Agence Nationale de la Recherche (ANR)
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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, FST, 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 FST statistic to samples with admixed individuals. In our approach, FST values are computed from the ancestry coefficients obtained with ancestry estimation programs. More specifically, we used factor models to estimate FST, 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.
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