Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers
Open accessAbstract
The evolutionary history of the human pygmy phenotype (small body size), a characteristic of African and Southeast Asian rainforest hunter-gatherers, is largely unknown. Here we use a genome-wide admixture mapping analysis to identify 16 genomic regions that are significantly associated with the pygmy phenotype in the Batwa, a rainforest hunter-gatherer population from Uganda (east central Africa). The identified genomic regions have multiple attributes that provide supporting evidence of genuine association with the pygmy phenotype, including enrichments for SNPs previously associated with stature variation in Europeans and for genes with growth hormone receptor and regulation functions. To test adaptive evolutionary hypotheses, we computed the haplotype-based integrated haplotype score (iHS) statistic and the level of population differentiation (FST) between the Batwa and their agricultural neighbors, the Bakiga, for each genomic SNP. Both |iHS| and FST values were significantly higher for SNPs within the Batwa pygmy phenotype-associated regions than the remainder of the genome, a signature of polygenic adaptation. In contrast, when we expanded our analysis to include Baka rainforest hunter-gatherers from Cameroon and Gabon (west central Africa) and Nzebi and Nzime neighboring agriculturalists, we did not observe elevated |iHS| or FST values in these genomic regions. Together, these results suggest adaptive and at least partially convergent origins of the pygmy phenotype even within Africa, supporting the hypothesis that small body size confers a selective advantage for tropical rainforest hunter-gatherers but raising questions about the antiquity of this behavior.
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Height seems to be under positive selection within European and African populations separately.
“While height seems to be under positive selection within European and African populations separately [19,34], it does not appear to be driven by divergent selection pressures across the populations considered here.”
From Investigating the case of human nose shape and climate adaptation (2017) · cites this paper as [34]
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- Authors
- Perry, G. H., Foll, M., Grenier, J.-C., Patin, E., Nédélec, Y., Pacis, A., Barakatt, M., Gravel, S., Zhou, X., Nsobya, S. L., Excoffier, L., Quintana-Murci, L., Dominy, N. J., & Barreiro, L. B.
- Affiliations
- Pennsylvania State University (US)
- SIB Swiss Institute of Bioinformatics (CH)
- Centre Hospitalier Universitaire Sainte-Justine (CA)
- Institut Pasteur, Unit of Human Evolutionary Genetics, 75015 Paris, France;
- School of Computer Science, and
- McGill University (CA)
- University of Chicago (US)
- Department of Pathology, Makerere University, Kampala, Uganda;
- University of Bern (CH)
- Dartmouth College (US)
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2014-08-18
- Volume
- 111
- Issue
- 35
- Pages
- E3596-603
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC4156716
- OpenAlex
- W2141155485
- Cited by
- 105
- References
- 67
- Citations by year
- 2026: 6 · 2025: 3 · 2024: 4 · 2023: 11 · 2022: 6 · 2021: 13 · 2020: 7 · 2019: 10 · 2018: 16 · 2017: 3 · 2016: 14 · 2015: 11 · 2014: 1
- FWCI
- 6.33
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- BORIS (University Library Bern) (submittedVersion)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- small body size, Batwa, polygenic adaptation, convergent evolution, integrated haplotype score, genetic differentiation, growth hormone receptor, admixture mapping, Baka, farmers, tropical rainforest
- MeSH terms
- Adaptation, Physiological, Biological Evolution, Growth Disorders, Humans, Models, Genetic, Phenotype, Selection, Genetic, Uganda, Genome, Human, Polymorphism, Single Nucleotide, Black People, Body Size, Genome-Wide Association Study
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