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Genome Biol Evol. 2015 Mar 30;7(4):1122-32. doi: 10.1093/gbe/evv058.

Inference of purifying and positive selection in three subspecies of chimpanzees (Pan troglodytes) from exome sequencing.

Author information

1
Bioinformatics Research Centre, Aarhus University, Denmark tbata@birc.au.dk hsiegismund@bio.ku.dk mheide@birc.au.dk.
2
Science and Conservation, Copenhagen Zoo, Denmark Bioinformatics, University of Copenhagen, Denmark tbata@birc.au.dk hsiegismund@bio.ku.dk mheide@birc.au.dk.
3
BGI Shenzhen, China tbata@birc.au.dk hsiegismund@bio.ku.dk mheide@birc.au.dk.
4
BGI Shenzhen, China.
5
Bioinformatics Research Centre, Aarhus University, Denmark.
6
Institut des Sciences de l'Evolution, Universite Montpellier 2, France.
7
BGI Shenzhen, China Section of Metabolic Genetics, The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark The Department of Genetic Medicine, Faculty of Medicine and Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia Department of Biology, University of Copenhagen, Denmark Macau University of Science and Technology, China.
8
Bioinformatics, University of Copenhagen, Denmark tbata@birc.au.dk hsiegismund@bio.ku.dk mheide@birc.au.dk.

Abstract

We study genome-wide nucleotide diversity in three subspecies of extant chimpanzees using exome capture. After strict filtering, Single Nucleotide Polymorphisms and indels were called and genotyped for greater than 50% of exons at a mean coverage of 35× per individual. Central chimpanzees (Pan troglodytes troglodytes) are the most polymorphic (nucleotide diversity, θw = 0.0023 per site) followed by Eastern (P. t. schweinfurthii) chimpanzees (θw = 0.0016) and Western (P. t. verus) chimpanzees (θw = 0.0008). A demographic scenario of divergence without gene flow fits the patterns of autosomal synonymous nucleotide diversity well except for a signal of recent gene flow from Western into Eastern chimpanzees. The striking contrast in X-linked versus autosomal polymorphism and divergence previously reported in Central chimpanzees is also found in Eastern and Western chimpanzees. We show that the direction of selection statistic exhibits a strong nonmonotonic relationship with the strength of purifying selection S, making it inappropriate for estimating S. We instead use counts in synonymous versus nonsynonymous frequency classes to infer the distribution of S coefficients acting on nonsynonymous mutations in each subspecies. The strength of purifying selection we infer is congruent with the differences in effective sizes of each subspecies: Central chimpanzees are undergoing the strongest purifying selection followed by Eastern and Western chimpanzees. Coding indels show stronger selection against indels changing the reading frame than observed in human populations.

KEYWORDS:

effective size; fitness effect; mutation; selection

PMID:
25829516
PMCID:
PMC4419804
DOI:
10.1093/gbe/evv058
[Indexed for MEDLINE]
Free PMC Article

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