Linked selection shapes the landscape of genomic variation in three oak species
| Autor: | Qing-Qing An, Biao-Feng Zhou, Xue-Yan Chen, Baosheng Wang, Christophe Plomion, Shuai Yuan, Yong Shi, Yi-Ye Liang, Pär K. Ingvarsson |
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| Přispěvatelé: | Key Laboratory of Plant Resources Conservation and Sustainable Utilization (Chinese Academy of Sciences), University of the Chinese Academy of Sciences, Research Center on Fictitious Economy & Data Science (FEDS), Chinese Academy of Sciences [Beijing] (CAS), Swedish University of Agricultural Sciences (SLU), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) |
| Rok vydání: | 2021 |
| Předmět: |
0106 biological sciences
ancestral recombination graph Physiology Population Plant Science Biology 010603 evolutionary biology 01 natural sciences Genome linked selection 03 medical and health sciences Negative selection Quercus selective sweeps Selection Genetic education Selection (genetic algorithm) 030304 developmental biology recombination rate 0303 health sciences education.field_of_study Genetic diversity Natural selection Genetic Variation Genomics 15. Life on land Background selection background selection Fixation (population genetics) Genetics Population Evolutionary biology [SDE]Environmental Sciences genomic variation human activities |
| Zdroj: | New Phytologist New Phytologist, Wiley, In press, ⟨10.1111/nph.17793⟩ |
| ISSN: | 1469-8137 0028-646X |
| Popis: | International audience; Natural selection shapes genome-wide patterns of diversity within species and divergence between species. However, quantifying the efficacy of selection and elucidating the relative importance of different types of selection in shaping genomic variation remain challenging. We sequenced whole genomes of 101 individuals of three closely related oak species to track the divergence history, and to dissect the impacts of selective sweeps and background selection on patterns of genomic variation. We estimated that the three species diverged around the late Neogene and experienced a bottleneck during the Pleistocene. We detected genomic regions with elevated relative differentiation ('F-ST-islands'). Population genetic inferences from the site frequency spectrum and ancestral recombination graph indicated that F-ST-islands were formed by selective sweeps. We also found extensive positive selection; the fixation of adaptive mutations and reduction neutral diversity around substitutions generated a signature of selective sweeps. Prevalent negative selection and background selection have reduced genetic diversity in both genic and intergenic regions, and contributed substantially to the baseline variation in genetic diversity. Our results demonstrate the importance of linked selection in shaping genomic variation, and illustrate how the extent and strength of different selection models vary across the genome. |
| Databáze: | OpenAIRE |
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