Impact of mutation rate and selection at linked sites on DNA variation across the genomes of humans and other homininae
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- dc.contributor.author Castellano Esteve, David
- dc.contributor.author Eyre-Walker, Adam
- dc.contributor.author Munch, Kasper
- dc.date.accessioned 2020-03-27T09:26:57Z
- dc.date.available 2020-03-27T09:26:57Z
- dc.date.issued 2020
- dc.description.abstract DNA diversity varies across the genome of many species. Variation in diversity across a genome might arise from regional variation in the mutation rate, variation in the intensity and mode of natural selection, and regional variation in the recombination rate. We show that both noncoding and nonsynonymous diversity are positively correlated to a measure of the mutation rate and the recombination rate and negatively correlated to the density of conserved sequences in 50 kb windows across the genomes of humans and nonhuman homininae. Interestingly, we find that although noncoding diversity is equally affected by these three genomic variables, nonsynonymous diversity is mostly dominated by the density of conserved sequences. The positive correlation between diversity and our measure of the mutation rate seems to be largely a direct consequence of regions with higher mutation rates having more diversity. However, the positive correlation with recombination rate and the negative correlation with the density of conserved sequences suggest that selection at linked sites also affect levels of diversity. This is supported by the observation that the ratio of the number of nonsynonymous to noncoding polymorphisms is negatively correlated to a measure of the effective population size across the genome. We show these patterns persist even when we restrict our analysis to GC-conservative mutations, demonstrating that the patterns are not driven by GC biased gene conversion. In conclusion, our comparative analyses describe how recombination rate, gene density, and mutation rate interact to produce the patterns of DNA diversity that we observe along the hominine genomes.
- dc.description.sponsorship This study was supported by the Danish Council For Independent Research (grant number 4181-00358
- dc.format.mimetype application/pdf
- dc.identifier.citation Castellano D, Eyre-Walker A, Munch K. Impact of mutation rate and selection at linked sites on DNA variation across the genomes of humans and other homininae. Genome Biol Evol. 2020 Jan 1; 12(1): 3550-3561. DOI: 10.1093/gbe/evz215
- dc.identifier.doi http://dx.doi.org/10.1093/gbe/evz215
- dc.identifier.issn 1759-6653
- dc.identifier.uri http://hdl.handle.net/10230/44065
- dc.language.iso eng
- dc.publisher Oxford University Press
- dc.relation.ispartof Genome Biology and Evolution. 2020 Jan 1;12(1):3550-61
- dc.rights © 2020 David Castellano Esteve, Adam Eyre-Walker, Kasper Munch. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. Published by Oxford University Press. This is an Open Access article distributed under the terms of a Creative Commons Attribution License
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
- dc.subject.other Genètica
- dc.subject.other Genomes
- dc.subject.other Recombinació ADN
- dc.title Impact of mutation rate and selection at linked sites on DNA variation across the genomes of humans and other homininae
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion