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

Abstract

Recent genomic 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 because of its association with coastal migration models and genetic ancestral patterns that are difficult to reconcile with modern DNA alone. Here, we report the low-coverage genome 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 ∼10,300 calendar (cal) y B.P. We also analyze low-coverage genomes of three more recent individuals from the nearby coast of British Columbia dating from ∼6,075 to 1,750 cal y B.P. 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 y B.P. We also infer that population structure existed in the late Pleistocene of North America with Shuká Káa on a different ancestral line compared with other North American individuals from the late Pleistocene or early Holocene (i.e., Anzick-1 and Kennewick Man). Despite regional shifts in mtDNA 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.

Exceeding Hrdlička's aims: 100 Years of genetics in anthropology

“…That meant that entry into the heart of the Americas could not have occurred via the interglacial corridor east of the Rocky Mountains, since that route had been closed for some 6,000 years during the height of the Wisconsin glaciation (see Szathmáry, ). An alternate route along the Pacific coast of the Americas is now receiving the most attention both among archaeologists and anthropological geneticists (Lindo et al, ). However, some archaeologists have posited that it is premature to close the door to an interior route, as a tight window of opportunity remains for interior entry, no occupation sites are known from eastern Beringia of an appropriate antiquity, and some think northeast Asia rather than Beringia is a more likely place for origin (Potter et al, ).…”

“…Many of the same questions that interested me are now being tackled with more powerful tools than previous generations had at their disposal. Given Hrdlička's regional interests, he would have especially welcomed the fine studies on the peoples of the Aleutian Islands (e.g., Crawford et al, ), evidence on the genetic divergence of ancient Eskimos and ancestors of Athapaskan‐speaking Alaskans (e.g., Dulik, Owings, Gaieski, & Schurr, ), origins of Neo‐Eskimos (Raff & Bolnick, ) and the demonstration of regional continuity in population structure along the northwest coast (Lindo et al, ). These studies, along with analyses of prehistoric samples, for example, from the southwest (Smith et al, 2011), Great Basin (Kaestle & Smith, ), southeast (Bolnick & Smith, ), and eastern United States (e.g., Bolnick, Bolnick, & Smith, ; Halverson & Bolnick, ; Stone & Stoneking, ), would statisfy him that his dictum had been observed.…”

Genetic Diversity and Relationships of Tlingit Moieties

“…This genetic pattern seems to have been already well established around the time the Northwest Coast tradition emerged (e.g. before 3000 YBP), and haplotypes observed in the region have shown continuity throughout time (Raff et al 2011;Cui et al 2013;Lindo et al 2017).…”

“…With regards to temporal continuity, it was not possible to detect a direct matrilineal link between Shuká Kaa, the male individual found in On Your Knees Cave (Kemp et al 2007), and modern Northwest Coast populations, since no individuals in this study exhibited haplotypes belonging to subhaplogroup D4h3a. One possibility for the absence of this lineage in contemporary Tlingit populations is that D4h3a decreased in frequency over time due to genetic drift, despite continuity of nuclear DNA in the region (Lindo et al 2017). This would make the lineage rare in certain areas, where certain founding lineages might have been replaced others (Schurr et al 2012:430).…”

How Subjectivity Strengthens Research: Developing an Integrative Approach to Investigating Human Diet in the Pacific Northwest Coast

“…; Lindo et al. ), we developed a project focused on reconstructing the diet of the ancestral Coast Tsimshian community. We are investigating how changes in diet, both in the distant past and those experienced more recently by many Indigenous communities as part of ongoing colonization in North America, may be reflected in the composition or function of the human oral microbiome.…”