Data from: Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers

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.