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Frantz, Laurent/0000-0001-8030-3885; Ersmark, Erik/0000-0003-4186-7498; Sjogren, Karl-Goran/0000-0003-1791-3175; Bergstrom, Anders/0000-0002-4096-9268 WOS:000583031800042 PubMed ID: 33122379 Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry. SciLifeLab National Projects; Erik Philip Sorensen Foundation; Francis Crick Institute from Cancer Research UK [FC001595]; UK Medical Research CouncilMedical Research Council UK (MRC); Wellcome TrustWellcome Trust [210119/Z/18/Z]; European Research CouncilEuropean Research Council (ERC) [852558]; Wellcome Trust Investigator awardWellcome Trust [217223/Z/19/Z]; Vallee Foundation; Social Sciences and Humanities Research Council of CanadaSocial Sciences and Humanities Research Council of Canada (SSHRC) [SSHRC IG 435-2014-0075]; State Assignment of the Sobolev Institute of Geology and Mineralogy; ZIN RAS [AAA-A19119032590102-7]; Smithsonian's Peter Buck Postdoctoral Fellowship; AHRC [AH/J001406/1]; SNIC-UPPMAX [b2016004]; UOXF ARC facilityAustralian Research Council; Wolfson College (University of Oxford); ERCEuropean Research Council (ERC) [ERC-2013-StG-337574-UNDEAD]; Natural Environmental Research CouncilNERC Natural Environment Research Council [NE/K005243/1, NE/K003259/1]; NERC Radiocarbon Facility [NF/2016/2/4] Ancient genome sequencing was supported by SciLifeLab National Projects and the Erik Philip Sorensen Foundation (to P.S.). A.B., T.D., and P.S. were supported by the Francis Crick Institute core funding (FC001595) from Cancer Research UK, the UK Medical Research Council, and the Wellcome Trust. P.S. was also supported by the European Research Council (grant no. 852558), a Wellcome Trust Investigator award (217223/Z/19/Z) and the Vallee Foundation. R.J.L. was supported by the Social Sciences and Humanities Research Council of Canada (#SSHRC IG 435-2014-0075). Y.K. was supported by State Assignment of the Sobolev Institute of Geology and Mineralogy. M.S. was supported by ZIN RAS (state assignment no. AAA-A19119032590102-7). A.T.L. was supported by the Smithsonian's Peter Buck Postdoctoral Fellowship. Archaeological work in Serbia was supported by AHRC grant AH/J001406/1. Computations were supported by SNIC-UPPMAX (b2016004) and the UOXF ARC facility. L.F. was supported by the Wellcome Trust (grant 210119/Z/18/Z) and by Wolfson College (University of Oxford). G.L. was supported by the ERC (grant ERC-2013-StG-337574-UNDEAD). G.L. and K.D. were supported by the Natural Environmental Research Council (grants NE/K005243/1 and NE/K003259/1). Dating was supported by the NERC Radiocarbon Facility (NF/2016/2/4).