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.人类矮小人表型（即身材矮小，为非洲与东南亚雨林狩猎采集人群的典型特征）的演化历史迄今尚未明晰。本研究通过全基因组混血图谱分析（genome-wide admixture mapping analysis），在来自乌干达（中非东部）的雨林狩猎采集人群巴特瓦（Batwa）中，鉴定出16个与矮小人表型显著相关的基因组区域。所鉴定的基因组区域具备多项可为其与矮小人表型真实关联提供佐证的属性：包括富集了此前在欧洲人群中与身高变异相关的单核苷酸多态性（Single Nucleotide Polymorphism, SNP），以及生长激素受体及调控功能相关基因。为验证适应性演化假说，本研究针对每个基因组SNP计算了基于单体型的整合单体型得分（integrated haplotype score, iHS），以及巴特瓦与其农耕邻群巴基加（Bakiga）之间的群体分化水平（FST）。巴特瓦矮小人表型相关区域内的SNP的|iHS|值与FST值均显著高于基因组其余区域，这是多基因适应性演化（polygenic adaptation）的标志性特征。与之相反，当我们将分析范围扩展至来自喀麦隆与加蓬（中非西部）的巴卡（Baka）雨林狩猎采集人群，以及其邻近平民农耕群体恩泽比（Nzebi）和恩齐梅（Nzime）时，并未在上述基因组区域中观测到升高的|iHS|或FST值。综上，上述结果表明，即便在非洲大陆内部，矮小人表型也存在适应性演化且至少部分为趋同起源，这支持了“身材矮小对热带雨林狩猎采集人群具有选择优势”的假说，但同时也引发了关于该适应性行为起源年代的疑问。