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Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.ORCID iD: 0000-0002-3793-3264
Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.ORCID iD: 0000-0001-6031-005X
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Department of Ecology and Genetics: Evolutionary Biology, Uppsala University, Uppsala; Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Uppsala .ORCID iD: 0000-0001-5235-6461
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.ORCID iD: 0000-0001-9225-7521
2016 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 202, no 3, 1185-1200 p.Article in journal (Refereed) Published
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 PopulusPopulus tremulaP. 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
Genetics Society of America , 2016. Vol. 202, no 3, 1185-1200 p.
Keyword [en]
Populus, whole-genome resequencing, nucleotide polymorphism, recombination, natural selection
National Category
Natural Sciences Evolutionary Biology Genetics
Research subject
Genetics
Identifiers
URN: urn:nbn:se:umu:diva-117941DOI: 10.1534/genetics.115.183152ISI: 000371596400026OAI: oai:DiVA.org:umu-117941DiVA: diva2:909576
Available from: 2016-03-07 Created: 2016-03-07 Last updated: 2016-05-16Bibliographically approved
In thesis
1. The genomic signatures of adaptive evolution in Populus
Open this publication in new window or tab >>The genomic signatures of adaptive evolution in Populus
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Understanding the genetic basis of adaptive evolution, and how natural selection has shaped patterns of polymorphism and divergence within and between species are enduring goals of evolutionary genetics. In this thesis, I used whole genome re-sequencing data to characterize the genomic signatures of natural selection along different evolutionary timescales in three Populus species: Populus tremula, P. tremuloides and P. trichocarpa. First, our study shows multiple lines of evidence suggesting that natural selection, due to both positive and purifying 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. Second, we characterize the evolution of genomic divergence patterns between two recently diverged aspen species: P. tremula and P. tremuloides. Our findings indicate 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. We further explore different mechanisms that may explain the heterogeneity of genomic divergence, and find that variation in linked selection and recombination likely plays a key role in generating the heterogeneous genomic landscape of differentiation between the two aspen species. Third, we link whole-genome polymorphic data with local environmental variables and phenotypic variation in an adaptive trait to investigate the genomic basis of local adaptation in P. tremula along a latitudinal gradient across Sweden. We find that a majority of single nucleotide polymorphisms (SNPs) (>90%) identified as being involved in local adaptation are tightly clustered in a single genomic region on chromosome 10. The signatures of selection at this region are more consistent with soft rather than hard selective sweeps, where multiple adaptive haplotypes derived from standing genetic variation sweep through the populations simultaneously, and where different haplotypes rise to high frequency in different latitudinal regions. In summary, this thesis uses phylogenetic comparative approaches to elucidate how various evolutionary forces have shaped genome-wide patterns of sequence evolution in Populus.

Place, publisher, year, edition, pages
Umeå: Umeå University, 2016. 52 p.
Keyword
Populus, adaptive evolution, natural selection, genomic diversity and divergence, recombination, Next-generation sequencing, local adaptation
National Category
Ecology
Identifiers
urn:nbn:se:umu:diva-120286 (URN)978-91-7601-463-9 (ISBN)
Public defence
2016-06-08, KB3B1, KBC-huset, Umeå, 13:00 (English)
Opponent
Supervisors
Note

The research in this thesis was supported by the Swedish research council (to Pär K. Ingvarsson) and the JC Kempe Memorial Scholarship Foundation (to Jing Wang). The PhD study of Jing Wang in Sweden was funded by the State Scholarship from China Scholarship council.

Available from: 2016-05-18 Created: 2016-05-13 Last updated: 2016-05-26Bibliographically approved

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Wang, JingStreet, NathanielScofield, DouglasIngvarsson, Pär
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Department of Ecology and Environmental SciencesUmeå Plant Science Centre (UPSC)Department of Plant Physiology
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