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

We study genome-wide nucleotide diversity in three subspecies of extant chimpanzees using exome capture. After strict filtering, SNVs and indels were called and genotyped for >50% of exons at a mean coverage of 35x per individual. Central chimpanzees (P. t. 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 vs. autosomal polymorphism and divergence previously reported in Central chimpanzees is also found in Eastern and Western chimpanzees. We show that the direction of selection (DoS) statistic exhibits a strong non-monotonic relationship with the strength of purifying selection S, making it inappropriate for estimating S. We instead use counts in synonymous vs. non-synonymous frequency classes to infer the distribution of S coefficients acting on non-synonymous 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.

本研究采用外显子组捕获（exome capture）技术，对现存黑猩猩的三个亚种开展全基因组范围内的核苷酸多样性分析。经过严格过滤后，我们对超过50%的外显子区域完成了单核苷酸变异（Single Nucleotide Variants, SNV）与插入缺失变异（insertions-deletions, indel）的检出及基因分型工作，每个个体的平均测序覆盖度达35倍。中部黑猩猩（P. t. troglodytes）的多态性最高，其核苷酸多样性θw为每位点0.0023，其次为东部黑猩猩（P. t. schweinfurthii，θw=0.0016）与西部黑猩猩（P. t. verus，θw=0.0008）。除观测到西部黑猩猩向东部黑猩猩存在近期基因流的信号外，无基因流的分化种群历史模型可较好地拟合常染色体同义核苷酸多样性的分布模式。此前在中部黑猩猩中报道的X染色体连锁（X-linked）与常染色体多态性及分化间的显著差异，在东部与西部黑猩猩中同样存在。本研究表明，选择方向（Direction of Selection, DoS）统计量与纯化选择强度S之间存在显著的非单调关联，因此该统计量不适用于S的估算。为此，我们转而利用同义与非同义突变的频率类别计数，推断各亚种中作用于非同义突变的S系数分布。我们推断的纯化选择强度与各亚种的有效种群大小差异相一致：中部黑猩猩所经受的纯化选择最强，其次为东部与西部黑猩猩。编码区插入缺失变异对改变读码框的变异的选择压，高于人类群体中的观测水平。