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.