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ACKNOWLEDGMENTS. We thank B. Grønnow, F. Racimo, B. Sacks, and E. Ostrander for input and comments in the conceptualization and early drafts of this study. This research used both the University of Oxford’s Advanced Research Computing and Queen Mary’s Apocrita High Performance Computing facility. We would like to acknowledge support from Science for Life Laboratory, the Swedish National Genomics Infrastructure for providing assistance in DNA sequencing. The following institutions are acknowledged for providing additional access to collections and logical support: museum of Institute of Plant and Animal Ecology of the Ural Branch of the Russian Academy of Sciences (Ekaterinburg) and Arctic Research Center (Salekhard). T.R.F. was supported by the European Union’s EU framework programme for research and innovation Horizon 2020 under Grant Agreement 676154. T.R.F. also received funding for analysis through the Qimmeq Project that came from the Velux Foundations and the Aage og Johanne Louis-Hansens Fond. M.-H.S.S. was supported by the Independent Research Fund Denmark (8028-00005B). L.A.F. and G.L. were supported by European Research Council grants (ERC-2013-StG-337574-UNDEAD and ERC-2019-StG-853272-PALAEO-FARM) and Natural Environmental Research Council grants (NE/K005243/1, NE/K003259/1, NE/S007067/1, and NE/S00078X/1). L.A.F. and A.C. were supported by the Wellcome Trust (210119/Z/18/Z). R.J.L. and T.N. were supported by a Social Sciences and Humanities Research Council Grant IG 435-2014-0075. O.S. was supported by the European Union’s Horizon 2020 program (H2020-MSCA-IF-2015, project “EpiCDomestic,” Grant 704254). Collection of specimens was performed under the State Contract of the IPAE UB RAS (No. AAAA-A19-119031890086-0). Dogs have been essential to life in the Siberian Arctic for over 9,500 y, and this tight link between people and dogs continues in Siberian communities. Although Arctic Siberian groups such as the Nenets received limited gene flow from neighboring groups, archaeological evidence suggests that metallurgy and new subsistence strategies emerged in Northwest Siberia around 2,000 y ago. It is unclear if the Siberian Arctic dog population was as continuous as the people of the region or if instead admixture occurred, possibly in relation to the influx of material culture from other parts of Eurasia. To address this question, we sequenced and analyzed the genomes of 20 ancient and historical Siberian and Eurasian Steppe dogs. Our analyses indicate that while Siberian dogs were genetically homogenous between 9,500 to 7,000 y ago, later introduction of dogs from the Eurasian Steppe and Europe led to substantial admixture. This is clearly the case in the Iamal-Nenets region (Northwestern Siberia) where dogs from the Iron Age period (∼2,000 y ago) possess substantially less ancestry related to European and Steppe dogs than dogs from the medieval period (∼1,000 y ago). Combined with findings of nonlocal materials recovered from these archaeological sites, including glass beads and metal items, these results indicate that Northwest Siberian communities were connected to a larger trade network through which they acquired genetically distinctive dogs from other regions. These exchanges were part of a series of major societal changes, including the rise of large-scale reindeer pastoralism ∼800 y ago. © 2021 National Academy of Sciences. All rights reserved.

Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP. Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP.