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Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):1613-1618. doi: 10.1073/pnas.1605660114. Epub 2017 Jan 30.

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

Author information

1
Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark; kiwoong.nam@hotmail.com mheide@birc.au.dk.
2
Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark.
3
Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland.
4
Anthropological Institute and Museum, University of Zurich, 8057 Zurich, Switzerland.
5
Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia 08003, Spain.
6
Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia 08010, Spain.
7
Centre for Genomic Regulation-Centro Nacional de Analisis Genomico, 08023 Barcelona, Spain.
8
Department of Bioscience, Aarhus University, DK-8000 Aarhus C, Denmark.

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

PMID:
28137852
PMCID:
PMC5320968
DOI:
10.1073/pnas.1605660114
[Indexed for MEDLINE]
Free PMC Article

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