Evolutionary Genomics of Samoans

Archaeological studies estimate the initial settlement of Samoa at 2,750-2,880 years ago, and identified only limited human modification to the landscape and settlement until about 1,000-1,500 years ago. A complex history of migration follows Samoa’s initial peopling; first with populations sharing ancestry with Papuan-speaking groups and more recently with Europeans, Africans, and East Asians due to European colonialism. Using 1,197 Samoan high coverage whole genomes, we identify population splits between the major Samoan islands, and detect asymmetrical gene flow to the capital city. Approximately, 25% of Samoan genomes come from Papuan related ancestry, which we find as the likely source of the archaic Denisovan haplotypes in Samoans. We also find that Samoans had an extreme bottleneck until about 1,000 years ago, followed by distinct expansions between the islands, and subsequent bottlenecks consistent with European colonization. These results give insights to an ongoing archaeological debate about the peopling of Samoa.