Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America

Abstract

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 present-day Inuit and Yup’ik1–3. The genetic relationship between Paleo-Eskimos and Native American, Inuit, Yup’ik and Aleut populations remains uncertain4–7. Here we present new genomic data for 48 ancient individuals from Chukotka, East Siberia, the Aleutian Islands, Alaska, and the Canadian Arctic. We co-analyze these data with new data from present-day Alaskan Iñupiat and West Siberian populations and published genomes. Employing new methods based on rare allele and haplotype sharing as well as established methods4,8–10, we show that Paleo-Eskimo-related ancestry is ubiquitous among populations speaking Na-Dene and Eskimo-Aleut languages. We develop a comprehensive model for the Holocene peopling events of Chukotka and North America, and show that several key migrations connected to the origin of the Na-Dene peoples, the peopling of the Aleutian Islands, and the spread of Yup’ik and Inuit across the Arctic region are genetically linked to a single Siberian source related to Paleo-Eskimos.

The genomic formation of First American ancestors in East and Northeast Asia

“…S42). This finding received attention in previous studies (4,10,11,15,17,33), but here the signal was detected in an unsupervised way. These targets served as positive controls, as well as Native Americans having well-known colonial European admixture (Figs.…”

“…We added one or two additional ancestry sources to each target, testing all possible source combinations within the clade of anatomically modern humans. In the case of USR1 (Data S4a, S4b), only one model in each class was significantly different from others according to the likelihood cut-off of 3 ln-units (11), and each additional gene flow resulted in a log-likelihood (LL) difference and/or difference in the worst model residuals (WR) that was associated with a false positive (FP) rate below 5% on data simulated according to the 14population skeleton graph ( Fig. 3d, Table S18, Supplementary Text 2).…”

“…The peopling of America remains an area of active debate in archaeogenetics (1,2): the time and place of the "Beringian standstill" (3)(4)(5)(6), dates and routes of the first colonization (5,(7)(8)(9), and the Asian source for the later migration about 5000 cal yr BP (4,10,11) are all contentious. Two recent discoveries are critical for constraining models of American settlement (2).…”

“…20000 years ago in Beringia (4). We tested all possible topologies for USR1, an ancient Athabaskan individual (I5321) admixed with Paleo-Inuit (11) and representing the NNA clade, a Clovis individual (Anzick) (16), and an ancient Peruvian individual (IL7) demonstrating no signal of extra Asian admixture (Data S6). The latter two individuals represented the SNA clade.…”

Investigating the likely association between genetic ancestry and COVID-19 manifestations

“…We hypothesized that this variation in COVID-19 severity may be attributed to the genetic ancestry of Central and South American populations. It has been reported that all present-day Native Americans have descended from at least four distinct ancient migration waves from Asia [20]. Two of them being ancient migrations (~15,000 years ago) from south-central Siberia (Mal'ta Upper Palaeolithic site: MA1 related) and the more recent (~5000 years ago) when Palaeo-Eskimos spread throughout the American Arctic [21].…”