{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"contact_person":["George Perry"],"full_dataset_link":["https://ega-archive.org/dacs/EGAC00001000216"],"host":["EGA"],"description":["EGA DAC EGAC00001000216"],"repository":["EGA"],"email":["ghp3@psu.edu"],"pubmed_abstract":["The genetic history of African populations is increasingly well documented, yet their patterns of epigenomic variation remain uncharacterized. Moreover, the relative impacts of DNA sequence variation and temporal changes in lifestyle and habitat on the human epigenome remain unknown. Here we generate genome-wide genotype and DNA methylation profiles for 362 rainforest hunter-gatherers and sedentary farmers. We find that the current habitat and historical lifestyle of a population have similarly critical impacts on the methylome, but the biological functions affected strongly differ. Specifically, methylation variation associated with recent changes in habitat mostly concerns immune and cellular functions, whereas that associated with historical lifestyle affects developmental processes. Furthermore, methylation variation--particularly that correlated with historical lifestyle--shows strong associations with nearby genetic variants that, moreover, are enriched in signals of natural selection. Our work provides new insight into the genetic and environmental factors affecting the epigenomic landscape of human populations over time.","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."],"pubmed_title":["The epigenomic landscape of African rainforest hunter-gatherers and farmers.","Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers."],"pubmed_authors":["Perry George H GH, Foll Matthieu M, Grenier Jean-Christophe JC, Patin Etienne E, Nédélec Yohann Y, Pacis Alain A, Barakatt Maxime M, Gravel Simon S, Zhou Xiang X, Nsobya Sam L SL, Excoffier Laurent L, Quintana-Murci Lluis L, Dominy Nathaniel J NJ, Barreiro Luis B LB","Fagny Maud M, Patin Etienne E, MacIsaac Julia L JL, Rotival Maxime M, Flutre Timothée T, Jones Meaghan J MJ, Siddle Katherine J KJ, Quach Hélène H, Harmant Christine C, McEwen Lisa M LM, Froment Alain A, Heyer Evelyne E, Gessain Antoine A, Betsem Edouard E, Mouguiama-Daouda Patrick P, Hombert Jean-Marie JM, Perry George H GH, Barreiro Luis B LB, Kobor Michael S MS, Quintana-Murci Lluis L"],"additional_accession":[]},"is_claimable":false,"name":"Evolution of the African pygmy phenotype","description":"Data Access Committee EGAC00001000216","dates":{"output":"2025-1-9"},"accession":"EGAC00001000216","cross_references":{"TAXONOMY":["9606"],"pubmed":["26616214","25136101"],"EGA":["EGAS00001000908","EGAD00010000616"]}}