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Mol Biol Evol. 2016 Jul;33(7):1754-67. doi: 10.1093/molbev/msw051. Epub 2016 Mar 15.

Variation in Linked Selection and Recombination Drive Genomic Divergence during Allopatric Speciation of European and American Aspens.

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Department of Ecology and Environmental Science, Umeå University, Umeå, SE, Sweden.
Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, SE, Sweden.
Department of Ecology and Environmental Science, Umeå University, Umeå, SE, Sweden Department of Ecology and Genetics: Evolutionary Biology, Uppsala University, Uppsala, Sweden Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Uppsala, Sweden.
Department of Ecology and Environmental Science, Umeå University, Umeå, SE, Sweden


Despite the global economic and ecological importance of forest trees, the genomic basis of differential adaptation and speciation in tree species is still poorly understood. Populus tremula and Populus tremuloides are two of the most widespread tree species in the Northern Hemisphere. Using whole-genome re-sequencing data of 24 P. tremula and 22 P. tremuloides individuals, we find that the two species diverged ∼2.2-3.1 million years ago, coinciding with the severing of the Bering land bridge and the onset of dramatic climatic oscillations during the Pleistocene. Both species have experienced substantial population expansions following long-term declines after species divergence. We detect widespread and heterogeneous genomic differentiation between species, and in accordance with the expectation of allopatric speciation, coalescent simulations suggest that neutral evolutionary processes can account for most of the observed patterns of genetic differentiation. However, there is an excess of regions exhibiting extreme differentiation relative to those expected under demographic simulations, which is indicative of the action of natural selection. Overall genetic differentiation is negatively associated with recombination rate in both species, providing strong support for a role of linked selection in generating the heterogeneous genomic landscape of differentiation between species. Finally, we identify a number of candidate regions and genes that may have been subject to positive and/or balancing selection during the speciation process.


Populus tremula; Populus tremuloides; demographic histories; heterogeneous genomic differentiation; linked selection; recombination; whole-genome re-sequencing

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