Paleo-Eskimo genetic legacy across North America

Paleo-Eskimos were the first people to settle vast regions of the American Arctic around 5,000 years ago, and were subsequently joined and largely displaced around 1,000 years ago by ancestors of the present-day Inuit and Yupik. The genetic relationship between Paleo-Eskimos and Native American populations remains uncertain. We analyze ancient and present-day genome-wide data from the Americas and Siberia, including new data from Alaskan Iñupiat and West Siberian populations, and the first genome-wide DNA from ancient Aleutian Islanders, ancient northern Athabaskans, and a 4,250-year-old individual of the Chukotkan Ust’-Belaya culture. Employing new methods based on rare allele and haplotype sharing as well as established methods based on allele frequency correlations, we show that Paleo-Eskimo ancestry is widespread among populations who speak Na-Dene and Eskimo-Aleut languages. Using phylogenetic modelling with allele frequency correlations and rare variation, we present a comprehensive model for the complex peopling of North America.- Results -- Dataset -- Gradient of Paleo-Eskimo-related ancestry -- Source of distinct ancestry in Na-Dene -- No evidence for population turnover in the Aleutian Islands around 1,000 calBP -- A Paleo-Eskimo with West Siberian ancestry -- Demographic modelling - Discussion - Methods -- Ancient DNA sampling, extraction and sequencing -- Sampling present-day populations -- Dataset preparation -- ADMIXTURE analysis -- Principal component analysis (PCA) -- Admixture modelling with qpWave and qpAdm -- fineSTRUCTURE clustering -- Haplotype sharing statistics -- Dating admixture events using haplotype sharing statistics -- Rare allele sharing statistics -- Demographic modellin