Ancient individuals from the North American Northwest Coast reveal 10,000 years of regional genetic continuity

Abstract

Recent genome-wide studies of both ancient and modern indigenous people of the Americas have shed light on the demographic processes involved during the first peopling. The Pacific northwest coast proves an intriguing focus for these studies due to its association with coastal migration models and genetic ancestral patterns that are difficult to reconcile with modern DNA alone. Here we report the genome-wide sequence of an ancient individual known as \"Shuka Kaa\" (\"Man Ahead of Us\") recovered from the On Your Knees Cave (OYKC) in southeastern Alaska (archaeological site 49-PET-408). The human remains date to approximately 10,300 cal years before present (BP). We also analyze low coverage genomes of three more recent individuals from the nearby coast of British Columbia dating from approximately 6075 to 1750 cal years BP. From the resulting time series of genetic data, we show that the Pacific Northwest Coast exhibits genetic continuity for at least the past 10,300 cal BP. We also infer that population structure existed in the late Pleistocene of North America with Shuka Kaa on a different ancestral line compared to other North American individuals (i.e., Anzick-1 and Kennewick Man) from the late Pleistocene or early Holocene. Despite regional shifts in mitochondrial DNA haplogroups we conclude from individuals sampled through time that people of the northern Northwest Coast belong to an early genetic lineage that may stem from a late Pleistocene coastal migration into the Americas.\n\nSignificance StatementThe peopling of the Americas has been examined on the continental level with the aid of single-nucleotide polymorphism arrays, next generation sequencing, and advancements in ancient DNA, all of which have helped elucidate major population movements. Regional paleogenomic studies, however, have received less attention and may reveal a more nuanced demographic history. Here we present genomewide sequences of individuals from the northern Northwest Coast covering a time span of ~10,000 years and show that continental patterns of demography do not necessarily apply on the regional level. In comparison with existing paleogenomic data, we demonstrate that geographically linked population samples from the Northwest Coast exhibit an early ancestral lineage and find that population structure existed among Native North American groups as early as the late Pleistocene.