ArticleGenome research2016
Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection.
Article in Genome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed, 75 citations in OpenAlex.
- Natural Selection of the CommonbioRxiv : the preprint server for biology · 2026Article
- Assessing Hardy-Weinberg equilibrium in T2T-aligned 1000 genomes project.PLoS genetics · 2026Article
- Natural selection and adaptive traits in the Maniq, a nomadic hunter-gatherer society from Mainland Southeast Asia.Scientific reports · 2025Article
- Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations.eLife · 2023Article
- Evolutionary Genetics and Admixture in African Populations.Genome biology and evolution · 2023Review
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- The distinct morphological phenotypes of Southeast Asian aborigines are shaped by novel mechanisms for adaptation to tropical rainforests.National science review · 2022Article
- Advances in integrative African genomics.Trends in genetics : TIG · 2022Review
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- Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture.Genome biology and evolution · 2021Review
- The evolution of human skin pigmentation involved the interactions of genetic, environmental, and cultural variables.Pigment cell & melanoma research · 2021Review
- Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression.Genome biology · 2021Article
- The deep population history in Africa.Human molecular genetics · 2021Review
- Identification of novel genetic variants associated with short stature in a Baka Pygmies population.Human genetics · 2020Article
- High Levels of Genetic Diversity within Nilo-Saharan Populations: Implications for Human Adaptation.American journal of human genetics · 2020Article
- From Summary Statistics to Gene Trees: Methods for Inferring Positive Selection.Trends in genetics : TIG · 2020Review
- Recovering signals of ghost archaic introgression in African populations.Science advances · 2020Article
- Complex Phenotypes: Mechanisms Underlying Variation in Human Stature.Current osteoporosis reports · 2019Review
- Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations.Genome biology · 2019Article
- Polygenic adaptation and convergent evolution on growth and cardiac genetic pathways in African and Asian rainforest hunter-gatherers.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
Abstract
African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due to their unique lifestyle in the Central African rainforest. To identify genomic targets of adaptation, we sequenced the genomes of four Biaka Pygmies from the Central African Republic and jointly analyzed these data with the genome sequences of three Baka Pygmies from Cameroon and nine Yoruba famers. To account for the complex demographic history of these populations that includes both isolation and gene flow, we fit models using the joint allele frequency spectrum and validated them using independent approaches. Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 yr ago. We also find that bidirectional asymmetric gene flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. We then applied complementary statistics to scan the genome for evidence of selective sweeps and polygenic selection. We found that conventional statistical outlier approaches were biased toward identifying candidates in regions of high mutation or low recombination rate. To avoid this bias, we assigned P-values for candidates using whole-genome simulations incorporating demography and variation in both recombination and mutation rates. We found that genes and gene sets involved in muscle development, bone synthesis, immunity, reproduction, cell signaling and development, and energy metabolism are likely to be targets of positive natural selection in Western African Pygmies or their recent ancestors.
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