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

John Lindo, Alessandro Achilli, Ugo Perego, David Archer, Cristina Valdiosera, Barbara Petzelt, Joycelynn Mitchell, Rosita Worl, E. James Dixon, Terence E. Fifield, Morten Rasmussen, Eske Willerslev, Jerome S. Cybulski, Brian M. Kemp, Michael DeGiorgio, Ripan S. Malhi
doi: https://doi.org/10.1101/093468
John Lindo
1Department of Human Genetics, University of Chicago, 920 E 58th St, Chicago, IL 60637, USA
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Alessandro Achilli
2Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Via Ferrata 9, Pavia, Italy
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Ugo Perego
2Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Via Ferrata 9, Pavia, Italy
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David Archer
3589 Fifth Avenue East, Prince Rupert, B.C. V8J 3Y3 Canada
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Cristina Valdiosera
4Department of Archaeology and History, La Trobe University, Melbourne, VIC 3086, Australia
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Barbara Petzelt
5Metlakatla Treaty Office, PO Box 224, Prince Rupert, BC, Canada V8J 3P6
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Joycelynn Mitchell
5Metlakatla Treaty Office, PO Box 224, Prince Rupert, BC, Canada V8J 3P6
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Rosita Worl
6Sealaska Heritage Institute, One Sealaska Plaza, Suite 400, Juneau, AK 99801
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E. James Dixon
7Maxwell Museum and Department of Anthropology, MSC01 1050-1 University of New Mexico, Albuquerque, NM 87131-0001, USA
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Terence E. Fifield
8University of Alaska Southeast, Ketchikan and USDA Forest Service, Tongass National Forest (retired), USA
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Morten Rasmussen
9Department of Genetics, School of Medicine, Stanford University, 291 Campus Drive, Stanford, CA 94305, USA
10Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark
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Eske Willerslev
10Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark
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Jerome S. Cybulski
11Canadian Museum of History, 100 Rue Laurier, Gatineau, Quebec K1A 0M8, Canada; University of Western Ontario, London, Ontario N6A 3K7, Canada; Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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Brian M. Kemp
12Department of Anthropology, University of Oklahoma, Norman, OK 73019, USA
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  • For correspondence: malhi@illinois.edu mxd60@psu.edu bmkemp@ou.edu
Michael DeGiorgio
13Department of Biology, Pennsylvania State University, 502B Wartik Laboratory, University Park, PA 16802, USA
14Institute for CyberScience, Pennsylvania State University, 502B Wartik Laboratory, University Park, PA 16802, USA
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  • For correspondence: malhi@illinois.edu mxd60@psu.edu bmkemp@ou.edu
Ripan S. Malhi
15Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 W Gregory Dr., Urbana, IL 61820, USA
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  • For correspondence: malhi@illinois.edu mxd60@psu.edu bmkemp@ou.edu
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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 “Shuká Káa” (“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 Shuká Káa 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.

Significance Statement The 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.

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Posted December 15, 2016.
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Ancient individuals from the North American Northwest Coast reveal 10,000 years of regional genetic continuity
John Lindo, Alessandro Achilli, Ugo Perego, David Archer, Cristina Valdiosera, Barbara Petzelt, Joycelynn Mitchell, Rosita Worl, E. James Dixon, Terence E. Fifield, Morten Rasmussen, Eske Willerslev, Jerome S. Cybulski, Brian M. Kemp, Michael DeGiorgio, Ripan S. Malhi
bioRxiv 093468; doi: https://doi.org/10.1101/093468
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Ancient individuals from the North American Northwest Coast reveal 10,000 years of regional genetic continuity
John Lindo, Alessandro Achilli, Ugo Perego, David Archer, Cristina Valdiosera, Barbara Petzelt, Joycelynn Mitchell, Rosita Worl, E. James Dixon, Terence E. Fifield, Morten Rasmussen, Eske Willerslev, Jerome S. Cybulski, Brian M. Kemp, Michael DeGiorgio, Ripan S. Malhi
bioRxiv 093468; doi: https://doi.org/10.1101/093468

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