Evidence that the rate of strong selective sweeps increases with population size in the great apes

Kiwoong Nam; Kasper Munch; Thomas Mailund; Alexander Nater; Maja Patricia Greminger; Michael Krützen; Tomàs Marquès-Bonet; Mikkel Heide Schierup

doi:10.1073/pnas.1605660114

Evidence that the rate of strong selective sweeps increases with population size in the great apes

Kiwoong Nam, Kasper Munch, Thomas Mailund, Alexander Nater, Maja Patricia Greminger, Michael Krützen, Tomàs Marquès-Bonet, Mikkel Heide Schierup

Institut for Molekylærbiologi og Genetik - Center for Bioinformatik (BiRC)

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer review

Abstract

Quantifying the number of selective sweeps and their combined effects on genomic diversity in humans and other great apes is notoriously difficult. Here we address the question using a comparative approach to contrast diversity patterns according to the distance from genes in all great ape taxa. The extent of diversity reduction near genes compared with the rest of intergenic sequences is greater in a species with larger effective population size. Also, the maximum distance from genes at which the diversity reduction is observed is larger in species with large effective population size. In Sumatran orangutans, the overall genomic diversity is ∼30% smaller than diversity levels far from genes, whereas this reduction is only 9% in humans. We show by simulation that selection against deleterious mutations in the form of background selection is not expected to cause these differences in diversity among species. Instead, selective sweeps caused by positive selection can reduce diversity level more severely in a large population if there is a higher number of selective sweeps per unit time. We discuss what can cause such a correlation, including the possibility that more frequent sweeps in larger populations are due to a shorter waiting time for the right mutations to arise.

Originalsprog	Engelsk
Tidsskrift	Proceedings of the National Academy of Sciences
Vol/bind	114
Nummer	7
Sider (fra-til)	1613-1618
Antal sider	6
ISSN	0027-8424
DOI	https://doi.org/10.1073/pnas.1605660114
Status	Udgivet - feb. 2017

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title = "Evidence that the rate of strong selective sweeps increases with population size in the great apes",

abstract = "Quantifying the number of selective sweeps and their combined effects on genomic diversity in humans and other great apes is notoriously difficult. Here we address the question using a comparative approach to contrast diversity patterns according to the distance from genes in all great ape taxa. The extent of diversity reduction near genes compared with the rest of intergenic sequences is greater in a species with larger effective population size. Also, the maximum distance from genes at which the diversity reduction is observed is larger in species with large effective population size. In Sumatran orangutans, the overall genomic diversity is ∼30% smaller than diversity levels far from genes, whereas this reduction is only 9% in humans. We show by simulation that selection against deleterious mutations in the form of background selection is not expected to cause these differences in diversity among species. Instead, selective sweeps caused by positive selection can reduce diversity level more severely in a large population if there is a higher number of selective sweeps per unit time. We discuss what can cause such a correlation, including the possibility that more frequent sweeps in larger populations are due to a shorter waiting time for the right mutations to arise.",

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Evidence that the rate of strong selective sweeps increases with population size in the great apes. / Nam, Kiwoong; Munch, Kasper; Mailund, Thomas et al.
I: Proceedings of the National Academy of Sciences, Bind 114, Nr. 7, 02.2017, s. 1613-1618.

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer review

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AU - Munch, Kasper

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AU - Krützen, Michael

AU - Marquès-Bonet, Tomàs

AU - Schierup, Mikkel Heide

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N2 - Quantifying the number of selective sweeps and their combined effects on genomic diversity in humans and other great apes is notoriously difficult. Here we address the question using a comparative approach to contrast diversity patterns according to the distance from genes in all great ape taxa. The extent of diversity reduction near genes compared with the rest of intergenic sequences is greater in a species with larger effective population size. Also, the maximum distance from genes at which the diversity reduction is observed is larger in species with large effective population size. In Sumatran orangutans, the overall genomic diversity is ∼30% smaller than diversity levels far from genes, whereas this reduction is only 9% in humans. We show by simulation that selection against deleterious mutations in the form of background selection is not expected to cause these differences in diversity among species. Instead, selective sweeps caused by positive selection can reduce diversity level more severely in a large population if there is a higher number of selective sweeps per unit time. We discuss what can cause such a correlation, including the possibility that more frequent sweeps in larger populations are due to a shorter waiting time for the right mutations to arise.

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Evidence that the rate of strong selective sweeps increases with population size in the great apes

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