Dataset Information

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

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.

SUBMITTER: Bataillon T

PROVIDER: S-EPMC4419804 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature

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Publications

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

Bataillon Thomas T Duan Jinjie J Hvilsom Christina C Jin Xin X Li Yingrui Y Skov Laurits L Glemin Sylvain S Munch Kasper K Jiang Tao T Qian Yu Y Hobolth Asger A Wang Jun J Wang Jun J Mailund Thomas T Siegismund Hans R HR Schierup Mikkel H MH

Genome biology and evolution 20150330 4

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 ...[more]

PMID: 25829516

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Project description:Planning is a type of problem solving in which a course of future action is devised via mental computation. Potential advantages of planning for tool use include reduced effort to gather tools, closer alignment to an efficient tool design, and increased foraging efficiency. Chimpanzees (Pan troglodytes troglodytes) in the Goualougo Triangle use a variety of different types of tools. We hypothesized that procurement strategy (brought to the termite nest, manufactured or acquired at the termite nest, or borrowed from others) reflects planning for current needs, with tool transport behavior varying by tool type and by age and sex class. It is also possible that chimpanzees anticipate the need for tools at future times, which would be evidenced by transporting multiple tool types for a sequential task. One year of video recordings at termite nests were systematically screened for tool procurement; data comprised 299 tool procurement events across 66 chimpanzees. In addition, we screened video recordings of leaf sponging and honey gathering, which resulted in another 38 procurement events. Fishing probes, which are typically used during a single visit, were typically transported to termite nests, while puncturing tools, which are durable and remain on site, were more often acquired at termite nests. Most tools transported in multiples were fishing probes, perhaps in anticipation that a single probe might not last through an entire foraging bout or might be transferred to another chimpanzee. We further documented that chimpanzees transported tool sets, comprising multiple different tool types used in sequence. Mature chimpanzees transported tools more often than did immatures. These observations suggest that chimpanzees plan tool use flexibly, reflecting the availability of raw materials and the likelihood that specific tool types will be needed for particular tasks. Developmental studies and further integration of behavioral, spatial, and archaeological data will help to illuminate the decision making and time depth of planning associated with tool technologies in living primates and hominin ancestors.

Dataset Information

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

Publications

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

Similar Datasets

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