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Shuká Káa in relation to other Native American groups. Schematic showing Shuká Káa placed on the branch leading to North Americans, which is supported by simulation-based D statistics.
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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 re...
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... modern Tsimshian (masked for European ancestry) (Figs. S4A and B, respectively). Individual 939 is an outgroup to both North and South Americans (Fig. S4C), as is Shuká Káa (Fig. 3B). However, adding a migration event introduces an edge connecting Europeans and Shuká Káa which leads to Shuká Káa forming a clade with the Tsimshian and Athabascan (Fig. S5). The signal may represent Native American dual ancestry (22) or be a result of possible contamination (Table S2). Hypothetical scenarios based on the D statistics are depicted in Figure 4. The D statistic does not support a scenario of genetic continuity between Anzick-1 and Shuká Káa with respect to South Americans (Fig. 4A, Table ...
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... find that the placement of Shuká Káa (based on D statistic simulations) is consistent with residing on a branch with modern-day indigenous people from the Northwest Coast, whereas Anzick-1 fits separately on a branch that leads to the southern lineage, including populations from Central and South America (Fig. 5). Our result suggests that Shuká Káa was part of a population closely related to the ancestors that gave rise to the current populations of the northern Northwest Coast. Northwest Coast . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under ...
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Significance
The peopling of the Americas has been examined on the continental level with the aid of SNP arrays, next generation sequencing, and advancements in ancient DNA, all of which have helped elucidate evolutionary histories. Regional paleogenomic studies, however, have received less attention and may reveal a more nuanced demographic histor...
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... The uniparental lineages manifest in the Anzick infant (Q-Z780 and D4h3a) were widespread in the Americas for several millennia after initial colonization, but ultimately became only minor components of recent native populations (e.g., Lindo et al. 2017). Some 80% of recent Native American males belong instead to another descendant branch of Q-M1107, Q-M3, or one of its several sub-clades. ...
The study of the peopling of the Americas has been transformed in the past decade by astonishing progress in paleogenomic research. Ancient genomes now show that Native American ancestors were formed in Siberia or the Amur region by admixture of ca. 15–30% Ancient North Eurasian genes with those of East Asians. The Anzick infant, buried with Clovis bifaces at 12,900 cal BP, belonged to a group that was ancestral to later Native Central and South Americans. Fishtail points, derived from Clovis, mark the arrival and rapid expansion of Clovis-descended Paleoindians across South America, also evident in the sharp increase of radiocarbon dates, continent-wide, at 13,000–12,500 cal BP. In both North and South America, extinction of most genera of megafauna was virtually simultaneous with Paleoindian expansion. Human hunting must have been involved, perhaps in concert with other indirect impacts. Contrary to the alternative bolide impact theory, there is no evidence of a dramatic human population decline after 12,800 cal BP. Ancient genomes show that divergent lithic traditions after 13,000 cal BP need not be attributed to a separate Pacific Rim migration stream. Several recent finds raise the possibility that pre-Clovis people might have reached the Americas before 20,000 cal BP, but these precursors must have either failed to thrive, or were ultimately replaced by proto-Clovis or Clovis people. Consilient paleogenomic and archaeological data indicate that initial colonization by Paleoindian ancestors of living Native Americans occurred after 14,500 cal BP.
... One of the previously published mitogenomes (GenBank FJ68754) belonging to D4h3a, a haplogroup so far considered a marker of the Paleo-Indian spread along the Pacific coast, has been found in the northeastern part of Brazil (Maranhão state) ( Perego et al. 2009). We now know that this mitogenome does not belong to any of the several D4h3a sub-branches that characterize the western part of South America ( Lindo et al. 2017); instead, it departs directly from the haplogroup root. Therefore a post-peopling event of gene flow from the western part of the sub-continent is a rather unlikely explanation for its presence in northeastern Brazil. ...
Recent and compelling archaeological evidence attests to human presence ∼14.5 thousand years ago (Kya) at multiple sites in South America and a very early exploitation of extreme high-altitude Andean environments. Considering that, according to genetic evidence, human entry into North America from Beringia most likely occurred ∼16 Kya, these archeological findings would imply an extremely rapid spread along the double continent. To shed light on this issue from a genetic perspective, we first completely sequenced 217 novel modern mitogenomes of Native American ancestry from the northwestern area of South America (Ecuador and Peru); we then evaluated them phylogenetically together with other available mitogenomes (430 samples, both modern and ancient) from the same geographic area and, finally, with all closely related mitogenomes from the entire double continent. We detected a large number (N = 48) of novel sub-haplogroups, often branching into further sub-clades, belonging to two classes: those that arose in South America early after its peopling and those that instead originated in North or Central America and reached South America with the first settlers. Coalescence age estimates for these sub-haplogroups provide time boundaries indicating that early Paleo-Indians probably moved from North America to the area corresponding to modern Ecuador and Peru over the short time frame of ∼1.5 Ky comprised between 16.0 and 14.6 Kya.
... mtDNA from two infants has been published already, and we await the report of their nuclear genomes. The study of 10,500-year-old Shuka Kaa from the Alaskan Coast is another example of successful cooperation between anthropologists and native people (Lindo et al., 2016). ...
... D4h3a is a relatively rare clade of haplogroup D; prior to its recognition in the Anzick infant, it was reported mainly from coastal peoples, including the Fuegians of southernmost Chile, the Chumash of southern California, and the Cayapa of Ecuador. The 10,300-year-old skeletal remains from On Your Knees Cave in coastal Alaska belonged to a derived clade of D4h3a (Lindo et al., 2016), but so did Hopewell skeletons, dated ca. AD 180, from Klunk Mounds in Illinois. ...
The close relatives who buried the Anzick infant ca. 12,800 cal BP made classic Clovis tools and were unequivocally the lineal genetic ancestors of all the living Native peoples of southern North America, Central America, and South America. Clovis-derived Fell I fishtail points track the rapid southward migration of this ancestral population all the way to Tierra del Fuego. Any hypothesized earlier populations, if they (improbably) ever existed, must have been replaced or genetically swamped by these Clovis descendants.
... For example, autosomal data were recently generated from First Nations individuals and archaeological remains from British Columbia, Canada. The study of immune-related genes showed signals of selection before and after contact with Europeans (Lindo et al., 2016), while the analysis of genome-wide genetic markers supported population continuity over~10,000 years (Lindo et al., 2017). Beyond local population history, ancient DNA can inform about deep ancestry and promote unconventional views. ...
... More recent demographic events can be inferred by adding more samples and phasing the genome sequences, but this comes at significant extra cost and effort (Raghavan et al., 2015;Schiffels and Durbin, 2014). Conversely, methods that study large numbers of samples at a non-recombining locus such as the mitochondrial DNA can provide robust estimates of recent divergence dates (Forster (Raghavan et al., 2015) 2 3 d~1 30e6000 Argentina, Brazil, Canada, Chile, Mexico 10 13 Y e Y f 1~8500 Kennewick, WA 0 1 Y Y (Sans et al., 2015) 1~1600 Uruguay 1 0 Y N (Tackney et al., 2015) 2~11,500 Upward Sun River, AK 2? 0 Y N (Lindo et al., 2017) (2015) and Rasmussen et al. (2014). (Tamm et al., 2007) 13900 (9980e17820) a 16500 (11208e21792) a 13900 (8608e19192) a 10800 (6880e14720) a n/a n/a Maximum parsimony; global substitution rate c (Achilli et al., 2008) 17200 (13870e20530) a 21200 (16500e25900) a 23800 (15370e32230) a 18600 (14090e23110) a n/a n/a Median-joining network; global substitution rate d (Fagundes et al., 2008) 20552 (14953e26151) a 20307 (15246e25369) a 17227 (11461e22994) a 21580 (13263e29896) a n/a 17983 (6056e29910) a Median-joining network; global substitution rate d (Fagundes et al., 2008) 21290 ...
The timing of the entry of the first humans into the Americas has been a source of debate for decades amongst archaeologists and geneticists. Here we briefly review the evidence for current hypotheses on the peopling process of the Americas and discuss how ancient mitochondrial DNA can provide a unique temporal perspective. We propose that, in absence of skeletal remains from a proto-Native American population for which DNA shows direct ancestry to modern indigenous lineages, high-resolution diachronic mitochondrial genetics will help refine our understanding of the human dispersal to and occupation of the Americas since the first entry in the continent. The relatively low cost of this methodology may empower indigenous communities and heritage organizations. Ultimately, it would promote the training and support of future research leaders who have a relevant cultural background to offer a fresh perspective on the peopling of the Americas.
More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world’s published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases at the time of writing and review of this manuscript, and crossed the threshold of >10,000 individuals with published genome-wide ancient DNA data at the end of 2022. This note is intended as a citable descriptor of the AADR.
Did Beringian environments represent an ecological barrier to humans until <15,000 years ago or was access to the Americas controlled by the spatial-temporal distribution of North American ice sheets? Beringian environments varied with respect to climate and biota, especially in the two major areas of exposed continental shelf. The East Siberian Arctic Shelf (“Great Arctic Plain” [GAP]) supported a dry steppe-tundra biome inhabited by a diverse large-mammal community, while the southern Bering-Chukchi Platform (“Bering Land Bridge” [BLB]) supported mesic tundra and probably a lower large-mammal biomass. A human population with west Eurasian roots occupied the GAP before the Last Glacial Maximum (LGM) and may have accessed mid-latitude North America via an interior ice-free corridor. Re-opening of the corridor <14,000 years ago indicates that the primary ancestors of living First Peoples, who already had spread widely in the Americas at this time, probably dispersed from the NW Pacific coast. A genetic “arctic signal” in non-arctic First Peoples suggests that their parent population inhabited the GAP during the LGM, before their split from the former. We infer a shift from GAP terrestrial to a subarctic maritime economy on the southern BLB coast before dispersal in the Americas from the NW Pacific coast.
An increasing body of archaeological and genomic evidence has hinted at a complex settlement process of the Americas by humans. This is especially true for South America, where unexpected ancestral signals have raised perplexing scenarios for the early migrations into different regions of the continent. Here, we present ancient human genomes from the archaeologically rich Northeast Brazil and compare them to ancient and present-day genomic data. We find a distinct relationship between ancient genomes from Northeast Brazil, Lagoa Santa, Uruguay and Panama, representing evidence for ancient migration routes along South America's Atlantic coast. To further add to the existing complexity, we also detect greater Denisovan than Neanderthal ancestry in ancient Uruguay and Panama individuals. Moreover, we find a strong Australasian signal in an ancient genome from Panama. This work sheds light on the deep demographic history of eastern South America and presents a starting point for future fine-scale investigations on the regional level.
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.
The oldest confirmed remains of domestic dogs in North America are from mid-continent archaeological sites dated approximately 9900 calibrated years before present (cal BP). Although this date suggests that dogs may not have arrived alongside the first Native Americans, the timing and routes for the entrance of New World dogs remain uncertain. Here, we present a complete mitochondrial genome of a dog from southeast Alaska, dated to 10 150 ± 260 cal BP. We compared this high-coverage genome with data from modern dog breeds, historical Arctic dogs and American precontact dogs (PCDs) from before European arrival. Our analyses demonstrate that the ancient dog belongs to the PCD lineage, which diverged from Siberian dogs around 16 700 years ago. This timing roughly coincides with the minimum suggested date for the opening of the North Pacific coastal (NPC) route along the Cordilleran Ice Sheet and genetic evidence for the initial peopling of the Americas. This ancient southeast Alaskan dog occupies an early branching position within the PCD clade, indicating it represents a close relative of the earliest PCDs that were brought alongside people migrating from eastern Beringia southward along the NPC to the rest of the Americas. The stable isotope δ ¹³ C value of this early dog indicates a marine diet, different from the younger mid-continent PCDs' terrestrial diet. Although PCDs were largely replaced by modern European dog breeds, our results indicate that their population decline started approximately 2000 years BP, coinciding with the expansion of Inuit peoples, who are associated with traditional sled-dog culture. Our findings suggest that dogs formed part of the initial human habitation of the New World, and provide insights into their replacement by both Arctic and European lineages.
