Journal
HEREDITY
Volume 109, Issue 6, Pages 361-371Publisher
SPRINGERNATURE
DOI: 10.1038/hdy.2012.51
Keywords
divergent selection; divergence hitchhiking; outlier detection; linkage disequilibrium; score tests; Quercus
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Funding
- Commission of the European Communities, via the 'Quality of life and Management of Living resources' research Program (Project OAKFLOW) [QLK5-2000-00960]
- LINKTREE project from the Eranet Biodiversa programme [ANR-08-BDVA-006]
- EU network of excellence EVOLTREE
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Genome scans are increasingly used to study ecological speciation, providing a useful genome-wide perspective on divergent selection in the presence of gene flow. Here, we compare current approaches to detect footprints of divergent selection in closely related species. We analyzed 192 individuals from two interfertile European temperate oak species using 30 nuclear microsatellites from eight linkage groups. These markers present little intraspecific differentiation and can be used in combination to assign individual genotypes to species. We first show that different outlier detection tests give somewhat different results, possibly due to model constraints. Second, using linkage information for these markers, we further characterize the signature of divergent selection in the presence of gene flow. In particular, we show that recombination estimates for regions with outlier markers are lower than those for a control region, in line with a prediction from ecological speciation theory. Most importantly, we show that analyses at the haplotype level can distinguish between truly divergent (bi-directional) selection and positive selection in one of the two species, offering a new and improved method for characterizing the speciation process. Heredity (2012) 109, 361-371; doi:10.1038/hdy.2012.51; published online 19 September 2012
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