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Post by Admin on Aug 2, 2022 20:07:17 GMT
Fig. 3 Testing migrations into the Americas by using a climate-informed model. Estimates of difference in genetic divergence between Amerindians (from southern North America and Central and South America) or Koryak versus Athabascan and Greenlandic Inuit and the ancient Saqqaq and Anzick-1 genomes (black vertical lines), compared with posterior probability distribution predicted from a climate-informed spatial genetic model reconstructing a single wave into the Americas (curves, the colored part represents the 95% credibility interval). ΔT for population X is defined as T(X, Koryak) – T(X, Central and South Amerindians) (28). Both Anzick-1 and the Athabascans were part of the same wave into the Americas to which other Amerindian populations from southern North America and Central and South America belonged, whereas the Inuit and Saqqaq are the descendants of different waves (observed values outside the 95% credibility interval). In all cases, the best fit of the demographic models to the IBS tract distribution and relative CCR by MSMC required gene flow between Siberian and Native American populations after their initial split (Fig. 2, B to D). We also found strong evidence for gene flow between Athabascans and the Inuit (table S11B), supported by results from ADMIXTURE (fig. S4), TreeMix (fig. S5), D-statistics using both whole-genome and SNP chip genotype data (figs. S6 and S8A) (28, 46, 47), and outgroup f3-statistics using whole-genome data (fig. S12) (28, 47). We attempted to estimate the divergence times between Inuit and Siberians as well as Inuit and Native Americans (table S11 and figs. S19 and S25 to S27), but our analyses were complicated by gene flow between Inuit and Athabascans as well as complex admixture patterns among Arctic groups (fig. S5). We tested the duration and magnitude of post-split gene flow between Native Americans and Siberians using diCal2.0 by introducing stopping time of gene flow as a free parameter (28). We still obtained the highest likelihood for a divergence time of 22 ka between Amerindians and Siberians as well as Athabascans and Siberians, although estimates for gene-flow rate and end of the gene flow differ (table S11C and fig. S22). Gene flow between Athabascans and Siberians seems to have stopped ~12 ka (table S11C), suggesting a link to the breaching of the Beringian Land Bridge by rising sea levels (48). Overall, our results support a common Siberian origin for all Native Americans, contradicting claims for an early migration to the Americas from Europe (49), with their initial isolation and entrance into the Americas occurring no earlier than 23 ka, but with subsequent admixture with East Asian populations. This additionally suggests that the Mal’ta-related admixture into the early Americans (4), representing ancestors of both Amerindians and Athabascans (Fig. 1 and fig. S5), occurred sometime after 23 ka, after the Native American split from East Asians.
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Post by Admin on Aug 3, 2022 1:21:07 GMT
Subsequent in situ diversification of Native American groups That Amerindian and Athabascan groups were part of the same migration implies that present-day genetic differences observed between them must have arisen later, after ~23 ka. Using the clean-split model in diCal2.0 on the modern genomes data set, we estimated that Athabascans and Karitiana diverged ~13 ka (95% confidence interval of ~11.5 to 14.5 ka, estimated from parametric bootstrap results) (table S11A and fig. S16), which is consistent with results from MSMC (fig. S27) (28). Where the divergence between Karitiana and Athabascans occurred is not known. However, several independent lines of evidence suggest that it is more likely to have occurred in lower-latitude North America instead of eastern Beringia (Alaska). These include the equidistant split times of Amerindians and Athabascans to Asian populations, the relatively brief interval between their estimated divergence date range and the age of Anzick-1 (12.6 ka) (5), and last, the geographic location of Anzick-1 to the south of the North American ice sheets and its clear affiliation with the “southern branch” of Native Americans (taken broadly to include Amerindians from southern North America and Central and South America) (5), as determined with outgroup f3-statistics by using SNP chip genotype data from present-day worldwide populations (Fig. 4 and figs. S13 and S14) (47). Divergence in North America would also be consistent with the known pre-Clovis age sites in the Americas, such as Monte Verde (14.6 ka) (50). The most parsimonious model would be that both Amerindians and Athabascans are descendants of the same ancestral Native American population that entered the Americas then subsequently diversified. However, we cannot discount alternative and more complex scenarios, which could be tested with additional ancient samples. Fig. 4 Diversification within the Americas. SNP chip genotype data–based outgroup f3-statistics (47) of the form f3(X, Ancient; Yoruba) were used to estimate the shared ancestry between ancient samples from the Americas and a large panel of worldwide present-day populations (X), including Athabascan and Amerindian groups from North America (table S3), some of which were masked for non-native ancestry before the analysis (28). The outgroup f3-statistics are depicted as heat maps, with the sampling location of the ancient sample marked by the dotted lines, and corresponding ranked plots with error bars are shown in fig. S14. “BP” refers to time before present. We find the Anzick-1 sample to share most ancestry with the southern branch of Native Americans when using multiple northern Native Americans sequenced in this study, which is consistent with (5). The seven Holocene age samples share most ancestry with Native Americans, with a general tendency to be genetically closer to present-day Native American populations from the same geographical region. By the Clovis period (~12.6 ka), the ancestral Native American population had already diversified into “northern” and “southern” branches, with the former including ancestors of present-day Athabascans and northern Amerindian groups such as Chipewyan, Cree, and Ojibwa and the latter including Amerindians from southern North America and Central and South America (Fig. 4 and fig. S14). We tested whether later gene flow from East Asian sources, such as the Inuit, might explain the genetic differences between these two branches. Using D-statistics on SNP chip genotype data (47) masked for non-native ancestry, we observed a signal of gene flow between the Inuit and northwest Pacific Coast Amerindians such as Coastal Tsimshian and Nisga’a, residing in the same region as the northern Athabascans (fig. S8B) (28). However, this signal of admixture with the Inuit, also detected in Athabascans (figs. S6 and S8A), was not evident among northern Amerindian populations located further east, such as Cree, Ojibwa, and Chipewyan (fig. S8C) (28). This suggests that the observed difference between the northern and southern branches is not a consequence of post-split East Asian gene flow into the northern branch and also provides a possible explanation as to why the southern branch Amerindians such as Karitiana are genetically closer to the northern Amerindians located further east than to northwest coast Amerindians and Athabascans (fig. S9). In contrast to Anzick-1, several of the Holocene individuals from the Americas—including those sequenced in this study, as well as the 8500-year-old Kennewick Man (51)—are closely related to present-day Native American populations from the same geographical regions (Fig. 4 and figs. S13 and S14). This implies genetic continuity of ancient and modern populations in some parts of the Americas over at least the past 8500 years, which is in agreement with recent results from Kennewick Man (51).
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Post by Admin on Aug 3, 2022 20:32:14 GMT
Evidence of more distant Old World gene flow into some Native Americans When testing for gene flow between Athabascans and Inuit with masked SNP chip genotype data–based D-statistics (47) (fig. S8), we observed a weak tendency for the Inuit to be much closer to the Athabascans than to certain Amerindians such as the North American Algonquin and Cree, and the Yaqui and Arhuaco of Central and South America (respectively), as compared with other Amerindians such as the Palikur and Surui of Brazil (fig. S8).
To further investigate this trend, we tested for additional gene flow from Eurasian populations into the Americas with D-statistics using the masked SNP chip genotype data set (47). We found that some American populations—including the Aleutian Islanders, Surui, and Athabascans—are closer to Australo-Melanesians as compared with other Native Americans, such as North American Ojibwa, Cree, and Algonquin and the South American Purepecha, Arhuaco, and Wayuu (fig. S10). The Surui are, in fact, one of closest Native American populations to East Asians and Australo-Melanesians, the latter including Papuans, non-Papuan Melanesians, Solomon Islanders, and South East Asian hunter-gatherers such as Aeta (fig. S10). We acknowledge that this observation is based on the analysis of a small fraction of the whole-genome and SNP chip genotype data sets—especially for the Aleutian Islander data, which is heavily masked owing to recent admixture with Europeans (28)—and that the trends in the data are weak.
Nonetheless, if it proves correct, these results suggest that there may be a distant Old World signal related to Australo-Melanesians and East Asians in some Native Americans. The widely scattered and differential affinity of Native Americans to the Australo-Melanesians, ranging from a strong signal in the Surui to a much weaker signal in northern Amerindians such as Ojibwa, points to this gene flow occurring after the initial peopling by Native American ancestors. However, how this signal may have ultimately reached South America remains unclear. One possible means is along a northern route via the Aleutian Islanders, previously found to be closely related to the Inuit (39), who have a relatively greater affinity to East Asians, Oceanians, and Denisovan than Native Americans in both whole-genome and SNP chip genotype data–based D tests (table S10 and figs. S10 and S11). On the basis of archaeological evidence and mtDNA data from ancient and modern samples, the Aleutian Islands are hypothesized to have been peopled as early as ~9 ka by “Paleo-Aleuts” who were succeeded by the “Neo-Aleuts,” with present-day Aleutian Islanders potentially resulting from admixture between these two populations (52, 53). Perhaps their complex genetic history included input from a population related to Australo-Melanesians through an East Asian continental route, and this genomic signal might have been subsequently transferred to parts of the Americas, including South America, through past gene flow events (Fig. 1). Evidence for this gene flow is supported with diCal2.0 and MSMC analyses showing a weak but recent gene flow into South Americans from populations related to present-day Northeast Asians (Koryak) (Fig. 2C and table S11C), who might be considered a proxy for the related Aleutian Islanders.
Testing the Paleoamerican model The detection of an Australo-Melanesian genetic signal in the Americas, however subtle, returns the discussion to the Paleoamerican model, which hypothesizes, on the basis of cranial morphology, that two temporally and source-distinct populations colonized the Americas. The earlier population reportedly originated in Asia in the Late Pleistocene and gave rise to both Paleoamericans and present-day Australo-Melanesians, whose shared cranial morphological attributes are presumed to indicate their common ancestry (23). The Paleoamericans were, in turn, thought to have been largely replaced by ancestors of present-day Amerindians, whose crania resemble modern East Asians and who are argued to be descendants of later arriving Mongoloid populations (14, 23, 26, 54). The presence of Paleoamericans is inferred primarily from ancient archaeological specimens in North and South America and a few relict populations of more recent age, which include the extinct Pericúes and Fuego-Patagonians (24, 25, 55).
The Paleoamerican hypothesis predicts that these groups should be genetically closer to Australo-Melanesians than other Amerindians. Previous studies of mtDNA and Y chromosome data obtained from Fuego-Patagonian and Paleoamerican skeletons have identified haplogroups similar to those of modern Native Americans (55–57). Although these results indicate some shared maternal and paternal ancestry with contemporary Native Americans, uniparental markers can be misleading when drawing conclusions about the demographic history of populations. To conclusively identify the broader population of ancestors who may have contributed to the Paleoamerican gene pool, autosomal genomic data are required.
We therefore sequenced 17 ancient individuals affiliated to the now-extinct Pericúes from Mexico and Fuego-Patagonians from Chile and Argentina (28), who, on the basis of their distinctive skull morphologies, are claimed to be relicts of Paleoamericans (23, 27, 58, 59). Additionally, we sequenced two pre-Columbian mummies from northern Mexico (Sierra Tarahumara) to serve as morphological controls because they are expected to fall within the range of Native American morphological cranial variation (28). We found that the ancient samples cluster with other Native American groups and are outside the range of Oceanian genetic variation (Fig. 5 and figs. S32, S33, and S34) (28). Similarly, outgroup f3-statistics (47) reveal low shared genetic ancestry between the ancient samples and Oceanians (figs. S36 and S37) (28), and genome-based and masked SNP chip genotype data–based D-statistics (46, 47) show no evidence for gene flow from Oceanians into the Pericúes or Fuego-Patagonians (fig. S39) (28).
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Post by Admin on Aug 4, 2022 1:47:18 GMT
Fig. 5 The Paleoamerican model. (A) Principal component analysis plot of 19 ancient samples combined with a worldwide reference panel, including 1823 individuals from (6). Our samples plot exclusively with American samples. Plots with other reference panels consisting of Native American populations are provided in fig. S32. (B) Population structure in the ancient Pericú, Mexican , and Fuego-Patagonian individuals from this study. Ancestry proportions are shown when assuming six ancestral populations (K = 6). The top bar shows the ancestry proportions of the 19 ancient individuals, Anzick-1 (5), and two present-day Native American genomes from this study (Huichol and Aymara). The plot at the bottom illustrates the ancestry proportions for 1823 individuals from (6). Our samples show primarily Native American (ivory, >92%) and Siberian (red, ~5%) ancestry. The plot with K = 13 is provided in fig. S33. Because the Paleoamerican model is based on cranial morphology (23, 27, 58, 59), we also measured craniometric data for the ancient samples and assessed their phenotypic affinities to supposed Paleoamericans, Amerindians, and worldwide populations (28). The results revealed that the analyzed Fuego-Patagonians showed closest craniometric affinity to Arctic populations and the Paleoamericans, whereas the analyzed female Pericúes showed closest craniometric affinities to populations from North America, the Arctic region, and Northern Japan (table S15). Our analyses demonstrated that the presumed ancestral ancient Paleoamerican reference sample from Lagoa , Brazil (24) had closest affinities to Arctic and East Asian populations (table S15). Consequently, for the Fuego-Patagonians, the female Pericúes, and the Lagoa Paleoamerican sample, we were not able to replicate previous results (24) that report close similarity of Paleoamerican and Australo-Melanesian cranial morphologies. Male Pericúes samples displayed more craniometric affinities with populations from Africa and Australia relative to the female individuals of their population (fig. S41). The results of analyses based on craniometric data thus are highly sensitive to sample structure and the statistical approach and data filtering used (51). Our morphometric analyses suggest that these ancient samples are not true relicts of a distinct migration as claimed and hence do not support the Paleoamerican model. Similarly, our genomic data also provide no support for an early migration of populations directly related to Australo-Melanesians into the Americas. Discussion
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Post by Admin on Aug 4, 2022 21:57:46 GMT
Discussion That Native Americans diverged from their East Asian ancestors during the LGM and no earlier than 23 ka provides an upper bound, and perhaps the climatic and environmental context, for the initial isolation of their ancestral population and a maximum estimate for the entrance and subsequent spread into the Americas. This result is consistent with the model that people entered the Americas before the development of the Clovis complex and had reached as far as southern South America by 14.6 ka. Because archaeological evidence provides only a minimum age for human presence in the Americas, we can anticipate the possible discovery of sites that approach the time of the divergence of East Asians and Native Americans. However, our estimate for the initial divergence and entry of Native American ancestors does not support archaeological claims for an initial peopling substantially earlier than the LGM (8–10).
Although our data cannot provide the precise geographical context for the initial peopling process, it has allowed us to more accurately estimate its temporal dynamics. This, in turn, has enabled us to reassess the Beringian Incubation Model, which, based on mtDNA data and the timing and geographical distribution of archaeological sites, hypothesized a ~15,000-year-long period of isolation of ancestral Native Americans in Beringia during the LGM (19–21). Our results, along with recent findings of mtDNA haplogroup C1 in Iceland and ancient northwest Russia (60), do not fit with the proposed 15,000-year span of the Beringian Incubation Model (19–21). It is possible that a shorter period of isolation occurred (~8000 years), but whether it occurred in Siberia or Beringia will have to be determined from future ancient DNA and archaeological findings. Given the genetic continuity between Native Americans and some East Asian populations (figs. S4 and S5), other demographic factors, such as surfing during population expansions into unoccupied regions (61), may ultimately need to be taken into account to better understand the presence of a large number of high-frequency private variants in the indigenous populations of the Americas.
The data presented here are consistent with a single initial migration of all Native Americans and with later gene flow from sources related to East Asians and, more distantly, Australo-Melanesians. From that single migration, there was a diversification of ancestral Native Americans leading to the formation of northern and southern branches, which appears to have taken place ~13 ka within the Americas. This split is consistent with the patterns of uniparental genomic regions of mtDNA haplogroup X and some Y chromosome C haplotypes being present in northern, but not southern, populations in the Americas (18, 62). This diversification event coincides roughly with the opening of habitable routes along the coastal and the interior corridors into unglaciated North America some 16 and 14 ka, respectively (63, 64), suggesting a possible role of one or both of these routes in the isolation and subsequent dispersal of Native Americans across the continent.
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