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Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species
Umea Univ, Umea Plant Sci Ctr, Dept Ecol & Environm Sci, SE-90187 Umea, Sweden..
Umea Univ, Umea Plant Sci Ctr, Dept Plant Physiol, SE-90187 Umea, Sweden..
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Umea Univ, Umea Plant Sci Ctr, Dept Ecol & Environm Sci, SE-90187 Umea, Sweden.;Uppsala Univ, Uppsala Multidisciplinary Ctr Adv Computat Sci, SE-75105 Uppsala, Sweden..
Umea Univ, Umea Plant Sci Ctr, Dept Ecol & Environm Sci, SE-90187 Umea, Sweden..
2016 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 202, no 3, 1185-1200 p.Article in journal (Refereed) PublishedText
Abstract [en]

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.

Place, publisher, year, edition, pages
2016. Vol. 202, no 3, 1185-1200 p.
Keyword [en]
Populus, whole-genome resequencing, nucleotide polymorphism, recombination, natural selection
National Category
Evolutionary Biology
URN: urn:nbn:se:uu:diva-282826DOI: 10.1534/genetics.115.183152ISI: 000371596400026PubMedID: 26721855OAI: diva2:917571
Swedish Research Council
Available from: 2016-04-07 Created: 2016-04-07 Last updated: 2016-04-07Bibliographically approved

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