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Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.ORCID-id: 0000-0002-3793-3264
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.ORCID-id: 0000-0001-6031-005X
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. 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 universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.ORCID-id: 0000-0001-9225-7521
2016 (engelsk)Inngår i: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 202, nr 3, s. 1185-1200Artikkel i tidsskrift (Fagfellevurdert) 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.

sted, utgiver, år, opplag, sider
Genetics Society of America , 2016. Vol. 202, nr 3, s. 1185-1200
Emneord [en]
Populus, whole-genome resequencing, nucleotide polymorphism, recombination, natural selection
HSV kategori
Forskningsprogram
genetik
Identifikatorer
URN: urn:nbn:se:umu:diva-117941DOI: 10.1534/genetics.115.183152ISI: 000371596400026OAI: oai:DiVA.org:umu-117941DiVA, id: diva2:909576
Tilgjengelig fra: 2016-03-07 Laget: 2016-03-07 Sist oppdatert: 2018-06-07bibliografisk kontrollert
Inngår i avhandling
1. The genomic signatures of adaptive evolution in Populus
Åpne denne publikasjonen i ny fane eller vindu >>The genomic signatures of adaptive evolution in Populus
2016 (engelsk)Doktoravhandling, med artikler (Annet vitenskapelig)
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.

sted, utgiver, år, opplag, sider
Umeå: Umeå University, 2016. s. 52
Emneord
Populus, adaptive evolution, natural selection, genomic diversity and divergence, recombination, Next-generation sequencing, local adaptation
HSV kategori
Identifikatorer
urn:nbn:se:umu:diva-120286 (URN)978-91-7601-463-9 (ISBN)
Disputas
2016-06-08, KB3B1, KBC-huset, Umeå, 13:00 (engelsk)
Opponent
Veileder
Merknad

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.

Tilgjengelig fra: 2016-05-18 Laget: 2016-05-13 Sist oppdatert: 2018-06-07bibliografisk kontrollert

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