Inference of purifying and positive selection in three subspecies of chimpanzees (Pan troglodytes) from exome sequencing
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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 Redlef; Schierup, Mikkel H.
In: Genome Biology and Evolution, Vol. 7, No. 4, 2015, p. 1122-1132.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Inference of purifying and positive selection in three subspecies of chimpanzees (Pan troglodytes) from exome sequencing
AU - Bataillon, Thomas
AU - Duan, Jinjie
AU - Hvilsom, Christina
AU - Jin, Xin
AU - Li, Yingrui
AU - Skov, Laurits
AU - Glemin, Sylvain
AU - Munch, Kasper
AU - Jiang, Tao
AU - Qian, Yu
AU - Hobolth, Asger
AU - Wang, Jun
AU - Mailund, Thomas
AU - Siegismund, Hans Redlef
AU - Schierup, Mikkel H.
N1 - © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
PY - 2015
Y1 - 2015
N2 - 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.
AB - 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.
U2 - 10.1093/gbe/evv058
DO - 10.1093/gbe/evv058
M3 - Journal article
C2 - 25829516
VL - 7
SP - 1122
EP - 1132
JO - Genome Biology and Evolution
JF - Genome Biology and Evolution
SN - 1759-6653
IS - 4
ER -
ID: 135066364