ArticleGenome biology and evolution2015
Inference of purifying and positive selection in three subspecies of chimpanzees (Pan troglodytes) from exome sequencing.
Article in Genome biology and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Inferring Patterns of Purifying, Positive, and Balancing Selection in the Coppery Titi Monkey (Plecturocebus cupreus) Utilizing a Well-Fit Evolutionary Baseline Model.Genome biology and evolution · 2026Article
- Article
- A whole-genome scan for evidence of positive and balancing selection in aye-ayes (Daubentonia madagascariensis) utilizing a well-fit evolutionary baseline model.G3 (Bethesda, Md.) · 2025Article
- Local genetic adaptation to habitat in wild chimpanzees.Science (New York, N.Y.) · 2025Article
- Genome-scale evolution in local populations of wild chimpanzees.Scientific reports · 2025Article
- A whole-genome scan for evidence of recent positive and balancing selection in aye-ayes (bioRxiv : the preprint server for biology · 2024Article
- Local genetic adaptation to habitat in wild chimpanzees.bioRxiv : the preprint server for biology · 2024Article
- Honey Bee Habitat Sharing Enhances Gene Flow of the Parasite Nosema ceranae.Microbial ecology · 2022Article
- Changing Population Size in McDonald-Kreitman Style Analyses: Artifactual Correlations and Adaptive Evolution between Humans and Chimpanzees.Genome biology and evolution · 2022Article
- Current Progress in Evolutionary Comparative Genomics of Great Apes.Frontiers in genetics · 2021Review
- Urine as a high-quality source of host genomic DNA from wild populations.Molecular ecology resources · 2021Article
- Similar patterns of genetic diversity and linkage disequilibrium in Western chimpanzees (Pan troglodytes verus) and humans indicate highly conserved mechanisms of MHC molecular evolution.BMC evolutionary biology · 2020Article
- Somatic genetic drift and multilevel selection in a clonal seagrass.Nature ecology & evolution · 2020Article
- Population Genomics in the Great Apes.Methods in molecular biology (Clifton, N.J.) · 2020Article
- Comparison of the Full Distribution of Fitness Effects of New Amino Acid Mutations Across Great Apes.Genetics · 2019Article
- The impact of genetic adaptation on chimpanzee subspecies differentiation.PLoS genetics · 2019Article
- Humans and Chimpanzees Display Opposite Patterns of Diversity inG3 (Bethesda, Md.) · 2019Article
- Genetic Variation in Pan Species Is Shaped by Demographic History and Harbors Lineage-Specific Functions.Genome biology and evolution · 2019Article
- Pleiotropy Modulates the Efficacy of Selection in Drosophila melanogaster.Molecular biology and evolution · 2019Article
- Inference of Distribution of Fitness Effects and Proportion of Adaptive Substitutions from Polymorphism Data.Genetics · 2017Article
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Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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