Genomics of Divergence along a Continuum of Parapatric Population Differentiation

Feulner, Philine; Chain, Frédéric J. J.; Panchal, Mahesh; Huang, Yun; Eizaguirre, Christophe; Kalbe, Martin; Lenz, Tobias L.; Samonte, Irene E.; Stoll, Monika; Bornberg-Bauer, Erich; Reusch, Thorsten B. H.; Milinski, Manfred; Zhang, Jianzhi (2015). Genomics of Divergence along a Continuum of Parapatric Population Differentiation. PLoS genetics, 11(2), e1004966. Public Library of Science 10.1371/journal.pgen.1004966

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The patterns of genomic divergence during ecological speciation are shaped by a combination of evolutionary forces. Processes such as genetic drift, local reduction of gene flow around genes causing reproductive isolation, hitchhiking around selected variants, variation in recombination and mutation rates are all factors that can contribute to the heterogeneity of genomic divergence. On the basis of 60 fully sequenced three-spined stickleback genomes, we explore these different mechanisms explaining the heterogeneity of genomic divergence across five parapatric lake and river population pairs varying in their degree of genetic differentiation. We find that divergent regions of the genome are mostly specific for each population pair, while their size and abundance are not correlated with the extent of genome-wide population differentiation. In each pair-wise comparison, an analysis of allele frequency spectra reveals that 25–55% of the divergent regions are consistent with a local restriction of gene flow. Another large proportion of divergent regions (38–75%) appears to be mainly shaped by hitchhiking effects around positively selected variants. We provide empirical evidence that alternative mechanisms determining the evolution of genomic patterns of divergence are not mutually exclusive, but rather act in concert to shape the genome during population differentiation, a first necessary step towards ecological speciation.

Item Type:

Journal Article (Original Article)


08 Faculty of Science > Department of Biology > Institute of Ecology and Evolution (IEE)
08 Faculty of Science > Department of Biology > Institute of Ecology and Evolution (IEE) > Aquatic Ecology

UniBE Contributor:

Feulner, Philine


500 Science > 570 Life sciences; biology




Public Library of Science




Marcel Häsler

Date Deposited:

21 Jul 2015 08:36

Last Modified:

23 Feb 2016 08:29

Publisher DOI:


PubMed ID:





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