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

Bataillon, Thomas, Duan, Jinjie, Hvilsom, Christina, Jin, Xin, Li, Yingrui, Skov, Laurits, Glemin, Sylvain, Munch, Kasper, Jiang, Tao, Qian, Yu, Hobolth, Asger, Wang, Jun, Mailund, Thomas, Siegismund, Hans R. and Schierup, Mikkel H. (2015) Inference of purifying and positive selection in three subspecies of chimpanzees (Pan troglodytes) from exome sequencing. Genome Biology and Evolution, 7 4: 1122-1132. doi:10.1093/gbe/evv058


Author Bataillon, Thomas
Duan, Jinjie
Hvilsom, Christina
Jin, Xin
Li, Yingrui
Skov, Laurits
Glemin, Sylvain
Munch, Kasper
Jiang, Tao
Qian, Yu
Hobolth, Asger
Wang, Jun
Mailund, Thomas
Siegismund, Hans R.
Schierup, Mikkel H.
Title Inference of purifying and positive selection in three subspecies of chimpanzees (Pan troglodytes) from exome sequencing
Formatted title
Inference of purifying and positive selection in three subspecies of chimpanzees (Pan troglodytes) from exome sequencing
Journal name Genome Biology and Evolution   Check publisher's open access policy
ISSN 1759-6653
Publication date 2015-04
Sub-type Article (original research)
DOI 10.1093/gbe/evv058
Open Access Status DOI
Volume 7
Issue 4
Start page 1122
End page 1132
Total pages 11
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Collection year 2016
Language eng
Formatted 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.
Keyword Fitness effect
Mutation
Selection
Effective size
Deleterious mutations
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Non HERDC
Institute for Molecular Bioscience - Publications
 
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