TY - JOUR T1 - Comparative population genomics of three related <em>Populus</em> species JF - bioRxiv DO - 10.1101/026344 SP - 026344 AU - Jing Wang AU - Nathaniel R. Street AU - Douglas G. Scofield AU - Pär K. Ingvarsson Y1 - 2015/01/01 UR - http://biorxiv.org/content/early/2015/09/08/026344.abstract N2 - A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we used whole-genome re-sequencing data from three related Populus species to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, population-scaled recombination rate and linkage disequilibrium. Our analyses revealed that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Consistent with this, linkage disequilibrium decay was fastest in P. tremuloides and slowest in P. trichocarpa. Pervasive natural selection has been proven to be the primary force creating significant positive correlations between neutral polymorphism and recombination rate in all three species. Disparate effective population sizes and recombination rates among species, on the other hand, drive the distinct magnitudes and signatures of linked selection and consequent heterogeneous patterns of genomic variation among them. We find that purifying selection against slightly deleterious non-synonymous mutations is more effective in regions experiencing high recombination, which may provide one explanation for a partially positive association between recombination rate and gene density in these species. Moreover, distinct signatures of linked selection dependent on gene density are found between genic and intergenic regions within each species. To our knowledge, the present work is the first comparative population genomic study among forest tree species and represents an important step toward dissecting how the interactions of various evolutionary forces have shaped genomic variation within and among these ecologically and economically important tree species.Author Summary A fundamental goal of population genetics is to understand how various evolutionary forces shape the heterogeneity of genomic variation within and among species. Here, we characterize and compare genome-wide patterns of nucleotide diversity, site frequency spectra, population-scaled recombination rates and linkage disequilibrium among three related Populus species: Populus tremula, P. tremuloides and P. trichocarpa. Pervasive natural selection, mediated by the local recombination environments, is supposed to be the primary force shaping heterogeneous patterns of neutral polymorphism throughout the genome. The disparate magnitudes and signatures of linked selection among the three species, however, likely result from either different effective population sizes and/or differences in recombination rates among them. Moreover, we find distinct patterns of selection between genic and intergenic regions in all three species, indicating these two types of sites may have undergone independent evolutionary responses to selection in Populus. To our knowledge, the present work provides the first phylogenetic comparative study of genome-wide patterns of variation between closely related forest tree species. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species. ER -