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

Department of Molecular Biology and Genetics - Bioinformatics Research Centre (BiRC)

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › 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.

Original language	English
Journal	Proceedings of the National Academy of Sciences
Volume	114
Issue	7
Pages (from-to)	1613-1618
Number of pages	6
ISSN	0027-8424
DOIs	https://doi.org/10.1073/pnas.1605660114
Publication status	Published - Feb 2017

Keywords

Adaptive evolutionary rate
Great ape
Mutation limitation
Population size
Selective sweep

Access to Document

10.1073/pnas.1605660114

Cite this

@article{71acc5d1fa204340b1c38e6703544e93,

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.",

keywords = "Adaptive evolutionary rate, Great ape, Mutation limitation, Population size, Selective sweep",

author = "Kiwoong Nam and Kasper Munch and Thomas Mailund and Alexander Nater and Greminger, {Maja Patricia} and Michael Kr{\"u}tzen and Tom{\`a}s Marqu{\`e}s-Bonet and Schierup, {Mikkel Heide}",

year = "2017",

month = feb,

doi = "10.1073/pnas.1605660114",

language = "English",

volume = "114",

pages = "1613--1618",

journal = "Proceedings of the National Academy of Sciences",

issn = "0027-8424",

publisher = "The National Academy of Sciences of the United States of America",

number = "7",

}

Evidence that the rate of strong selective sweeps increases with population size in the great apes. / Nam, Kiwoong; Munch, Kasper; Mailund, Thomas et al.
In: Proceedings of the National Academy of Sciences, Vol. 114, No. 7, 02.2017, p. 1613-1618.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

TY - JOUR

T1 - Evidence that the rate of strong selective sweeps increases with population size in the great apes

AU - Nam, Kiwoong

AU - Munch, Kasper

AU - Mailund, Thomas

AU - Nater, Alexander

AU - Greminger, Maja Patricia

AU - Krützen, Michael

AU - Marquès-Bonet, Tomàs

AU - Schierup, Mikkel Heide

PY - 2017/2

Y1 - 2017/2

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.

AB - 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.

KW - Adaptive evolutionary rate

KW - Great ape

KW - Mutation limitation

KW - Population size

KW - Selective sweep

UR - http://www.scopus.com/inward/record.url?scp=85012978019&partnerID=8YFLogxK

U2 - 10.1073/pnas.1605660114

DO - 10.1073/pnas.1605660114

M3 - Journal article

C2 - 28137852

SN - 0027-8424

VL - 114

SP - 1613

EP - 1618

JO - Proceedings of the National Academy of Sciences

JF - Proceedings of the National Academy of Sciences

IS - 7

ER -

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

Abstract

Keywords

Access to Document

Other files and links

Fingerprint

Cite this