Indigenous peoples have occupied the island of Puerto Rico since at least 3000 BC. Due to the demographic shifts that occurred after European contact, the origin(s) of these ancient populations, and their genetic relationship to present-day islanders, are unclear. We use ancient DNA to characterize the population history and genetic legacies of precontact Indigenous communities from Puerto Rico. Bone, tooth, and dental calculus samples were collected from 124 individuals from three precontact archaeological sites: Tibes, Punta Candelero, and Paso del Indio. Despite poor DNA preservation, we used target enrichment and high-throughput sequencing to obtain complete mitochondrial genomes (mtDNA) from 45 individuals and autosomal genotypes from two individuals. We found a high proportion of Native American mtDNA haplogroups A2 and C1 in the precontact Puerto Rico sample (40% and 44%, respectively). This distribution, as well as the haplotypes represented, supports a primarily Amazonian South American origin for these populations and mirrors the Native American mtDNA diversity patterns found in present-day islanders. Three mtDNA haplotypes from precontact Puerto Rico persist among Puerto Ricans and other Caribbean islanders, indicating that present-day populations are reservoirs of precontact mtDNA diversity. Lastly, we find similarity in autosomal ancestry patterns between precontact individuals from Puerto Rico and the Bahamas, suggesting a shared component of Indigenous Caribbean ancestry with close affinity to South American populations. Our findings contribute to a more complete reconstruction of precontact Caribbean population history and explore the role of Indigenous peoples in shaping the biocultural diversity of present-day Puerto Ricans and other Caribbean islanders.
The North American archaeological record supports a Holocene origin of Arctic Indigenous peoples. Although the Paleo‐Inuit were present for millennia, archaeological and genetic studies suggest that modern peoples descend from a second, more recent tradition known as the Neo‐Inuit. Origins of the Neo‐Inuit and their relations to the earlier and later Indigenous peoples are an area of active study. Here, we genetically analyze the maternal lineages present at Nuvuk, once the northernmost community in Alaska and located in a region identified as a possible origin point of the Neo‐Inuit Thule. The cemetery at Nuvuk contains human remains representing a nearly one thousand year uninterrupted occupation from early Thule to post‐contact Iñupiat.
We selected 44 individuals from Nuvuk with calibrated dates between 981 AD and 1885 AD for molecular analysis. We amplified and sequenced the hypervariable segment I of the mitogenome. We compared the Nuvuk data with previously published sequences from 68 modern and ancient communities from across Asia and North America. Phylogeographic analyses suggest possible scenarios of Holocene Arctic and sub‐Arctic population movements.
We successfully retrieved sequence data from 39 individuals. Haplogroup frequencies in Nuvuk were typed as 66.7% A2b1, 25.6% A2a, and 7.7% D4b1a2a1a. These results suggest that the population at Nuvuk was closest to the ancient Thule and modern Inuit of Canada, and to the Siberian Naukan people. We confirm that haplogroups A2a, A2b1, D2a, and D4b1a2a1a appear at high frequency in Arctic and sub‐Arctic populations of North America and Chukotka. Sister clades D2b and D4b1a2a1b are present in Asian and Eastern European populations.
The ancient mitochondrial sequences from Nuvuk confirm the link between the North Slope and the Thule who later spread east, and the maternal discontinuity between the Neo‐Inuit and Paleo‐Inuit. We suggest haplogroups A2a, A2b, and D4b1a2a1a are linked to the ancestors of the Thule in eastern Beringia, whereas the D2 and D4b1a2a1 clades appear to have Asian Holocene origins. Further Siberian and Alaskan genomes are necessary to clarify these population migrations beyond a simple two‐wave scenario of Neo‐Inuit and Paleo‐Inuit.
- NSF-PAR ID:
- 10461585
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- American Journal of Physical Anthropology
- Volume:
- 168
- Issue:
- 2
- ISSN:
- 0002-9483
- Page Range / eLocation ID:
- p. 303-317
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Objectives We examined autosomal genome‐wide SNPs and Y‐chromosome data from 15 Siberian and 12 reference populations to study the affinities of Siberian populations, and to address hypotheses about the origin of the Samoyed peoples.
Methods Samples were genotyped for 567 096 autosomal SNPs and 147 Y‐chromosome polymorphic sites. For several analyses, we used 281 093 SNPs from the intersection of our data with publicly available ancient Siberian samples. To examine genetic relatedness among populations, we applied PCA,
F ST, TreeMix, and ADMIXTURE analyses. To explore the potential effect of demography and evolutionary processes, the distribution of ROH and IBD sharing within population were studied.Results Analyses of autosomal and Y‐chromosome data reveal high differentiation of the Siberian groups. The Siberian populations have a large proportion of their genome in ROH and IBD segments. Several populations (ie, Nganasans, Evenks, Yukagirs, and Koryaks) do not appear to have experienced admixture with other Siberian populations (ie, producing only positive f3), while for the other tested populations the composition of mixing sources always included Nganasans or Evenks. The Nganasans from the Taymyr Peninsula demonstrate the greatest level of shared shorter ROH and IBD with nearly all other Siberian populations.
Conclusions Autosomal SNP and Y‐chromosome data demonstrate that Samoyedic populations differ significantly in their genetic composition. Genetic relationship is observed only between Forest and Tundra Nentsi. Selkups are affiliated with the Kets from the Yenisey River, while the Nganasans are separated from their linguistic neighbors, showing closer affinities with the Evenks and Yukagirs.
