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1. Evaluating population histories in Patagonia and Tierra del Fuego, Chile, using ancient mitochondrial and Y‐chromosomal DNA

   https://doi.org/10.1002/ajpa.24638  

   Balentine, Christina M. ; Alfonso‐Durruty, Marta ; Reynolds, Austin W. ; Vilar, Miguel ; Morello, Flavia ; Román, Manuel San ; Springs, Lauren C. ; Smith, Rick W. A. ; Archer, Samantha M. ; Mata‐Míguez, Jaime ; et al ( November 2022 , American Journal of Biological Anthropology)

   This study aims to characterize the genetic histories of ancient hunter‐gatherer groups in Fuego‐Patagonia (Chile) with distinct Marine, Terrestrial, and Mixed Economy subsistence strategies. Mitochondrial (mtDNA) and Y‐chromosome data were generated to test three hypotheses. H₀: All individuals were drawn from the same panmictic population; H₁: Terrestrial groups first populated the region and gave rise to highly specialized Marine groups by ~7,500 cal BP; or H₂: Marine and Terrestrial groups represent distinct ancestral lineages who migrated independently into the region.

   Ancient DNA was extracted from the teeth of 50 Fuegian‐Patagonian individuals dating from 6,895 cal BP to after European arrival, and analyzed alongside other individuals from previous studies. Individuals were assigned to Marine, Terrestrial, and Mixed Economy groups based on archeological context and stable isotope diet inferences, and mtDNA (HVR1/2) and Y‐chromosome variation was analyzed.

   Endogenous aDNA was obtained from 49/50 (98%) individuals. Haplotype diversities, F_STcomparisons, and exact tests of population differentiation showed that Marine groups were significantly different from Terrestrial groups based on mtDNA (p < 0.05). No statistically significant differences were found between Terrestrial and Mixed Economy groups. Demographic simulations support models in which Marine groups diverged from the others by ~14,000 cal BP. Y‐chromosome results showed similar patterns but were not statistically significant due to small sample sizes and allelic dropout.

   These results support the hypothesis that Marine and Terrestrial economic groups represent distinct ancestral lineages who diverged during the time populations were expanding in the Americas, and may represent independent migrations into Fuego‐Patagonia.

    

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2. Ancient DNA and deep population structure in sub-Saharan African foragers

   https://doi.org/10.1038/s41586-022-04430-9  

   Lipson, Mark ; Sawchuk, Elizabeth A. ; Thompson, Jessica C. ; Oppenheimer, Jonas ; Tryon, Christian A. ; Ranhorn, Kathryn L. ; de Luna, Kathryn M. ; Sirak, Kendra A. ; Olalde, Iñigo ; Ambrose, Stanley H. ; et al ( March 2022 , Nature)

   Abstract Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa 1–4 . Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations 3,5 . Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80–20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch. 

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3. Coastal occupation and foraging during the last glacial maximum and early Holocene at Waterfall Bluff, eastern Pondoland, South Africa

   https://doi.org/10.1017/qua.2020.26  

   Fisher, Erich C. ; Cawthra, Hayley C. ; Esteban, Irene ; Jerardino, Antonieta ; Neumann, Frank H. ; Oertle, Annette ; Pargeter, Justin ; Saktura, Rosaria B. ; Szabó, Katherine ; Winkler, Stephan ; et al ( September 2020 , Quaternary Research)

   null (Ed.)

   Abstract Waterfall Bluff is a rock shelter in eastern Pondoland, South Africa, adjacent to a narrow continental shelf that limited coastline movements across glacial/interglacial cycles. The archaeological deposits are characterized by well-preserved stratigraphy, faunal, and botanical remains alongside abundant stone artifacts and other materials. A comprehensive dating protocol consisting of 5 optically stimulated luminescence ages and 51 accelerator mass spectrometry 14 C ages shows that the record of hunter-gatherer occupations at Waterfall Bluff persisted from the late Pleistocene to the Holocene, spanning the last glacial maximum and the transition from the Pleistocene to the Holocene. Here, we provide detailed descriptions about the sedimentary sequence, chronology, and characteristics of the archaeological deposits at Waterfall Bluff. Remains of marine mollusks and marine fish also show, for the first time, that coastal foraging was a component of some hunter-gatherer groups’ subsistence practices during glacial phases in the late Pleistocene. The presence of marine fish and shellfish further demonstrates that hunter-gatherers selectively targeted coastal resources from intertidal and estuarine habitats. Our results therefore underscore the idea that Pondoland's coastline remained a stable and predictable point on the landscape over the last glacial/interglacial transition being well positioned for hunter-gatherers to access resources from the nearby coastline, narrow continental shelf, and inland areas. 

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4. Molecular analysis of an ancient Thule population at Nuvuk, Point Barrow, Alaska

   https://doi.org/10.1002/ajpa.23746  

   Tackney, Justin ; Jensen, Anne M. ; Kisielinski, Caroline ; O'Rourke, Dennis H. ( January 2019 , American Journal of Physical Anthropology)

   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.

    

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5. The genomic prehistory of the Indigenous peoples of Uruguay

   https://doi.org/10.1093/pnasnexus/pgac047  

   Lindo, John ; De La Rosa, Rosseirys ; Santos, Andre L. C. d. ; Sans, Mónica ; DeGiorgio, Michael ; Figueiro, Gonzalo ; Nelson, ed., Karen E. ( April 2022 , PNAS Nexus)

   The prehistory of the people of Uruguay is greatly complicated by the dramatic and severe effects of European contact, as with most of the Americas. After the series of military campaigns that exterminated the last remnants of nomadic peoples, Uruguayan official history masked and diluted the former Indigenous ethnic diversity into the narrative of a singular people that all but died out. Here, we present the first whole genome sequences of the Indigenous people of the region before the arrival of Europeans, from an archaeological site in eastern Uruguay that dates from 2,000 years before present. We find a surprising connection to ancient individuals from Panama and eastern Brazil, but not to modern Amazonians. This result may be indicative of a migration route into South America that may have occurred along the Atlantic coast. We also find a distinct ancestry previously undetected in South America. Though this work begins to piece together some of the demographic nuance of the region, the sequencing of ancient individuals from across Uruguay is needed to better understand the ancient prehistory and genetic diversity that existed before European contact, thereby helping to rebuild the history of the Indigenous population of what is now Uruguay.

    

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