Inference of Purifying and Positive Selection in Three Subspecies of Chimpanzees (Pan troglodytes) from Exome Sequencing

• DOI: 10.1093/gbe/evv058
• Publication Date: 2015-04-02T16:49:05Z
• Authors: Thomas Bataillon; Jinjie Duan; Christina Hvilsom; Xin Jin; Yingrui Li; Laurits Skov; Sylvain Glemin; Kasper Munch; Tao Jiang; Yu Qian; Asger Hobolth; Jun Wang; Thomas Mailund; Hans R. Siegismund; Mikkel H. Schierup
• Keywords: Nonsynonymous substitution; Subspecies; Negative selection; Troglodytes; Nucleotide diversity; Indel; Synonymous substitution

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