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Evolution of the African pygmy phenotype

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 iHS statistic and the level of population differentiation (FST) between the Batwa and their agricultural neighbors, the Bakiga, for each 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.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00010000616 230
Publications Citations
Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers.
Proc Natl Acad Sci U S A 111: 2014 E3596-603
The epigenomic landscape of African rainforest hunter-gatherers and farmers.
Nat Commun 6: 2015 10047
An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease.
Genome Biol 17: 2016 171
Natural selection contributed to immunological differences between hunter-gatherers and agriculturalists.
Nat Ecol Evol 3: 2019 1253-1264
Population interconnectivity over the past 120,000 years explains distribution and diversity of Central African hunter-gatherers.
Proc Natl Acad Sci U S A 119: 2022 e2113936119
Whole genomes from Angola and Mozambique inform about the origins and dispersals of major African migrations.
Nat Commun 14: 2023 7967