Open AccessGenomics of Divergence along a Continuum of Parapatric Population Differentiation
Author(s) -
Philine G. D. Feulner,
Frédéric J. J. Chain,
Mahesh Panchal,
Yun Huang,
Christophe Eizaguirre,
Martin Kalbe,
Tobias L. Lenz,
Irene E. Samonte,
Monika Stoll,
Erich BornbergBauer,
Thorsten B. H. Reusch,
Manfred Milinski
Publication year - 2015
Publication title -
plos genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.587
H-Index - 233
eISSN - 1553-7404
pISSN - 1553-7390
DOI - 10.1371/journal.pgen.1004966
Subject(s) - biology , parapatric speciation , gene flow , evolutionary biology , population genomics , population , genetics , genetic drift , genome , reproductive isolation , genetic algorithm , effective population size , genomics , genome evolution , genetic variation , gene , demography , sociology
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.