The Kets, an ethnic group in the Yenisei River basin, Russia, are considered the last nomadic hunter-gatherers of Siberia, and Ket language has no transparent affiliation with any language family. We investigated connections between the Kets and Siberian and North American populations, with emphasis on the Mal'ta and Paleo-Eskimo ancient genomes, using original data from 46 unrelated samples of Kets and 42 samples of their neighboring ethnic groups (Uralic-speaking Nganasans, Enets, and Selkups). We genotyped over 130,000 autosomal SNPs, identified mitochondrial and Y-chromosomal haplogroups, and performed high-coverage genome sequencing of two Ket individuals. We established that Nganasans, Kets, Selkups, and Yukaghirs form a cluster of populations most closely related to Paleo-Eskimos in Siberia (not considering indigenous populations of Chukotka and Kamchatka). Kets are closely related to modern Selkups and to some Bronze and Iron Age populations of the Altai region, with all these groups sharing a high degree of Mal'ta ancestry. Implications of these findings for the linguistic hypothesis uniting Ket and Na-Dene languages into a language macrofamily are discussed.

A A Kharkevich Institute for Information Transmission Problems Russian Academy of Sciences Moscow Russia

Belozersky Institute of Physico Chemical Biology Lomonosov Moscow State University Moscow Russia

Biomedical Cluster Skolkovo Foundation Skolkovo Russia

Children's Hospital Los Angeles Los Angeles CA USA

Department of Biology and Ecology Faculty of Science University of Ostrava Ostrava Czech Republic

Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Moscow Russia

George Mason University Fairfax VA USA

Institute of Parasitology Biology Centre Czech Academy of Sciences České Budĕjovice Czech Republic

Instituto de Ciências Biomédicas da Universidade do Porto Porto Portugal

Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto Portugal

Pirogov Russian National Research Medical University Moscow Russia

Retired Moscow Russia

Russian Presidential Academy Moscow Russia

Russian State University for the Humanities Moscow Russia

Skolkovo Institute of Science and Technology Skolkovo Russia

Spatial Sciences Institute University of Southern California Los Angeles CA USA

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