Evidence that the rate of strong selective sweeps increases with population size in the great apes
Kiwoong Nam a,1, Kasper Munch a, Thomas Mailund a, Alexander Nater b,c, Maja Patricia Greminger b,c, Michael Krützen c, Tomàs Marquès-Bonet d,e,f, and Mikkel Heide Schierup a,g,1
Author Affiliations
aBioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark;
bDepartment of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland;
cAnthropological Institute and Museum, University of Zurich, 8057 Zurich, Switzerland;
dInstitut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia 08003, Spain;
eInstitució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia 08010, Spain;
fCentre for Genomic Regulation-Centro Nacional de Analisis Genomico, 08023 Barcelona, Spain;
gDepartment of Bioscience, Aarhus University, DK-8000 Aarhus C, Denmark
Edited by Molly Przeworski, Columbia University, New York, NY, and accepted by Editorial Board Member Andrew G. Clark December 29, 2016 (received for review April 29, 2016)
Source/Fonte: Max Planck Gesselschaft
Significance
The rate of genomic adaptation is determined by the rate of environmental change, the availability of beneficial mutations, and the efficiency of positive selection. The relative importance of these factors has been actively discussed. We address the questions using whole genome sequences of great apes, which have very different population sizes whereas their genomic architectures are highly similar. We infer that the impact of selection on the genomic diversity of a species increases with the effective population size, most likely due to the differential influx rate of beneficial mutations. This explanation is, among other possibilities, expected if adaptive evolution is limited by the waiting time for new favorable mutations in 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.
selective sweep population size great ape adaptive evolutionary rate mutation limitation
Footnotes
1To whom correspondence may be addressed. Email: kiwoong.nam@hotmail.com or mheide@birc.au.dk.
Author contributions: K.N. and M.H.S. designed research; K.N., K.M., and T.M. performed research; K.N., K.M., T.M., A.N., M.P.G., M.K., and T.M.-B. analyzed data; and K.N., K.M., and M.H.S. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission. M.P. is a Guest Editor invited by the Editorial Board.
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1605660114/-/DCSupplemental.
Freely available online through the PNAS open access option.
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