title: Genomics of divergence along a continuum of parapatric population differentiation.
abstract: 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.
authors: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany; Institute for Evolution and Biodiversity, Evolutionary Bioinformatics, Westfälische Wilhelms University, Münster, Germany.
authors: Philine G D
authors: PG
authors: Feulner
authors: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
authors: Frédéric J J
authors: FJ
authors: Chain
authors: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
authors: Mahesh
authors: M
authors: Panchal
authors: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
authors: Yun
authors: Y
authors: Huang
authors: School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.
authors: Christophe
authors: C
authors: Eizaguirre
authors: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
authors: Martin
authors: M
authors: Kalbe
authors: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
authors: Tobias L
authors: TL
authors: Lenz
authors: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
authors: Irene E
authors: IE
authors: Samonte
authors: Genetic Epidemiology, Westfälische Wilhelms University, Münster, Germany.
authors: Monika
authors: M
authors: Stoll
authors: Institute for Evolution and Biodiversity, Evolutionary Bioinformatics, Westfälische Wilhelms University, Münster, Germany.
authors: Erich
authors: E
authors: Bornberg-Bauer
authors: Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.
authors: Thorsten B H
authors: TB
authors: Reusch
authors: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
authors: Manfred
authors: M
authors: Milinski
mesh_terms: D000818:Animals; D004463:Ecology; D019143:Evolution, Molecular; D051456:Gene Flow; D005787:Gene Frequency; D049810:Genetic Speciation; D014644:Genetic Variation; D005828:Genetics, Population; D023281:Genomics; D060106:Lakes; D060047:Reproductive Isolation; D012641:Selection, Genetic; D023701:Smegmamorpha / Q000235:genetics*