title: Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species.
abstract: 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 use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find 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. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.
authors.affiliation: Department of Ecology and Environmental Science, Umeå University, Umeå SE 90187, Sweden.
authors.forename: Jing
authors.identifier: 0000-0002-3793-3264
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå SE 90187, Sweden.
authors.forename: Nathaniel R
authors.identifier: 0000-0001-6031-005X
authors.initials: NR
authors.lastname: Street
authors.affiliation: Department of Ecology and Environmental Science, Umeå University, Umeå SE 90187, Sweden Department of Ecology and Genetics: Evolutionary Biology, Uppsala University, Uppsala SE 75105, Sweden Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Uppsala SE 75105, Sweden.
authors.forename: Douglas G
authors.identifier: 0000-0001-5235-6461
authors.initials: DG
authors.lastname: Scofield
authors.affiliation: Department of Ecology and Environmental Science, Umeå University, Umeå SE 90187, Sweden par.ingvarsson@umu.se.
authors.forename: Pär K
authors.identifier: 0000-0001-9225-7521
authors.initials: PK
authors.lastname: Ingvarsson
mesh_terms: D019943:Amino Acid Substitution; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D005787:Gene Frequency; D056084:Genetic Fitness; D005828:Genetics, Population; D018745:Genome, Plant; D005838:Genotype; D015810:Linkage Disequilibrium; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D032107:Populus / Q000145:classification / Q000235:genetics*; D011995:Recombination, Genetic; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant
keywords: Populus; natural selection; nucleotide polymorphism; recombination; whole-genome resequencing