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Post by Admin on Jun 5, 2021 5:31:53 GMT
As the Chotuna group in the Pacific coast also exhibited excess allele sharing (Fig. 1 and Dataset S3) with the Australasians as estimated by D statistic (Mbuti; Australasians: Y, Z), we created admixture graph models based on the scaffold of Skoglund et al. (2) (Fig. 3A) with the addition of the Pacific coastal groups Sechura, Chotuna, and Narihuala. The best-fitted model showed that the Pacific coast is a mixed group of South American ancestry and a small non-American contribution associated with a sister branch of Onge (Fig. 3C), as also observed for Karitiana and Suruí. When the Xavánte were included in the analysis, the best-fitted model showed a direct contribution of the Australasian component in the Pacific coast, followed by a strong drift of this signal, giving rise to Amazonian groups (Fig. 3D). Although Fig. 3D could indicate two independent events, the small genetic distances between the nodes in this model reinforced the single admixture event evidence. The Treemix (10) analysis also showed a pattern of diversification in which Pacific coastal and Andean groups diverged first (Dataset S6), followed by the eastern Andean slopes populations and then, finally, the Amazonians and other eastern South Americans. These findings suggest that the Y-population contribution was introduced before the formation of the Amazonian branch, likely in the ancestors of Pacific coastal/Amazonian populations. Fig. 3. Admixture graph modeling of the Y-population contribution to Amazonia and Pacific coast. (A) Previously published model proposed by Skoglund et al. (2). To investigate these genetic affinities, we first create (B and C) admixture graphs adding the Pacific coastal groups Sechura, Chotuna, and Narihuala (Pac_Cos) to the previous models, and (D) add Xavánte and the Pacific coast, followed by Suruí and Karitiana. Different migration routes to the South American region have been previously proposed and evidenced. Archeological and genetic data demonstrated that both routes, Pacific coastal and inland, were likely used by the first migrants (11). Our models point to an ancient genetic affinity between the Pacific coast and Amazonian populations that could be explained by the presence of Y ancestry in both geographic regions. In addition, this shared ancestry seems to precede the separation of the Pacific and Amazon branches, showing an entry through the west coast, followed by successive events of genetic drift in the Brazilian populations. This genetic evidence for the presence of Y ancestry on the South American Pacific coast indicates that this ancestry likely reached this region through the Pacific coastal route, and therefore could explain absence of this genetic component in the populations of North and Central America studied so far. Data Availability The newly genotyped datasets reported in this paper have been deposited in the European Genome-phenome Archive and are available for download under accession no. EGAS00001005022. www.pnas.org/doi/full/10.1073/pnas.2025739118
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Post by Admin on Jun 5, 2021 22:58:46 GMT
A genomic view of the peopling of the americas Pontus Skoglund, David Reich doi: doi.org/10.1101/058966Abstract Whole-genome studies have documented that most Native American ancestry stems from a single population that diversified within the continent more than twelve thousand years ago. However, this shared ancestry hides a more complex history whereby at least four distinct streams of Eurasian migration have contributed to present-day and prehistoric Native American populations. Whole genome studies enhanced by technological breakthroughs in ancient DNA now provide evidence of a sequence of events involving initial migration from a structured Northeast Asian source population, followed by a divergence into northern and southern Native American lineages. During the Holocene, new migrations from Asia introduced the Saqqaq/Dorset Paleoeskimo population to the North American Arctic ~4,500 years ago, ancestry that is potentially connected with ancestry found in Athabaskan-speakers today. This was then followed by a major new population turnover in the high Arctic involving Thule-related peoples who are the ancestors of present-day Inuit. We highlight several open questions that could be addressed through future genomic research. Introduction The peopling of the Americas represented the culmination of a Late Pleistocene expansion of anatomically modern humans out of Africa. Archaeological evidence indicates that groups subsisting on hunting lived in extreme northeast Siberia (71°N) by at least 28,000 years ago [1]. Human groups adapted to the mammoth steppe habitat were thus poised to enter Beringia—the landmass between Alaska and Eurasia that is now submerged—by this time [2,3]. The path from Beringia to the more temperate parts of the American continents, however, was blocked by the merged Laurentide and Cordilleran ice sheets that covered northern North America until the end of the Last Glacial Maximum. The ice retreated from parts of the Pacific coast ~16,000 years ago, raising the possibility of a coastal migration after this time, and within a few thousand years a habitable corridor through the center of the continent opened between the two ice sheets [4]. The first unambiguous evidence of modern humans in the Americas dates to between 14,000 and 15,0 years ago [5–8], and was likely the consequence of migration from Beringia. Major debates about the peopling of the Americas have focused on the question of whether the first early human populations in the Americas are directly ancestral to present-day Native Americans, as well as on the number, mode, and timing of secondary migrations to the Americas. Advances in genomics have, within the last five years, enabled the collection of far more data from present-day Native Americans than was available previously, and have also made it possible for the first time to access DNA from ancient Native American remains. Analysis of these data has highlighted a minimum of four distinct streams of Asian ancestry some of which were not clear from the archaeological evidence. We review the contributions of genomic data to understanding the prehistory of the Americas, and highlight outline outstanding questions where it may be able to provide additional insight.
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Post by Admin on Jun 6, 2021 2:30:42 GMT
The power of the whole genome The first meaningful genetic insights about Native American population history came from mitochondrial DNA, a segment of about 16,500 base pairs (approximately 1/200,000th of the genome) that is passed exclusively along the maternal line. Mitochondrial DNA was one of the first parts of the genome to be heavily investigated to learn about human population history for several reasons. First, it is highly variable on a per-nucleotide level and thus sequencing only a short stretch can detect non-trivial amounts of human variation. Mitochondrial DNA’s high variability and short length meant that it was practical to sequence in large numbers of samples at a time when it was prohibitively expensive to generate genome scale data. For ancient DNA studies, mitochondrial DNA had the further advantage that it exists in about a thousand-fold higher copy number than any other single place in the genome. Since one of the main challenges of ancient DNA is obtaining sufficient amount of material from any position in the genome to be able to analyze, beginning with more starting material can be an advantage [9].
The greatest contribution of mitochondrial DNA studies to the understanding of Native American prehistory has been in the area of reconstruction of population size history. Mitochondrial DNA analyses were the first to document that the ancestry of most Native Americans derives from a population that experienced a profound founder event [10], with a relatively small number of individuals giving rise to a large number of descendants today. The evidence for this is that all Native American mitochondrial DNA lineages today descend from just five founding maternal lines [11–13] that each had a common ancestor around 18,000 to 15,0 years ago, implying a population size bottleneck around this time [14–18]. The evidence for a profound population bottleneck has since been confirmed and its intensity measured more accurately with genome scale data [19–23], but it is important to note that there are still challenges with disentangling the number of founder individuals from the duration of the population size reduction using all the reported methods.
A second finding about Native American population history based on mitochondrial DNA data is the evidence that the founder event may have been proceeded by an extended period (many thousands of years) of little or no shared ancestry with non-Native American mitochondrial DNA lineages. This suggested to some researchers the hypothesis of a ‘Beringian standstill’, whereby the first founding population of the Americas was isolated from Eurasian populations prior to its radiation into a multitude of sub-populations in America [15].
At the same time, some observations from mitochondrial DNA studies of the Americas have been more confusing than helpful. For example, the mitochondrial DNA subtype called D4h3a is today almost entirely restricted to Pacific coastal populations, both in North and South America. This observation led to the hypothesis that D4h3a was carried by the members of a population that carried Native Americans south of the ice sheets along a coastal route, in a migratory movement that was distinctive from what led to many other Native American populations [24]. However, ancient DNA studies have since found the same mitochondrial DNA type in a ~12,600 year old individual from present-day Montana, which based on its genome-wide data is unambiguously from the main ancestral lineage leading to most Native Americans [25].
It is now clear that so many founder events and fluctuations in population size have occurred before, during, and after the peopling of the Americas that the evidence from one position in the genome—mitochondrial DNA, the Y chromosome, or any other location—is too subject to random changes in frequency (genetic drift) to be meaningful by itself. Only by taking the independent testimony of many locations in the genome simultaneously can we obtain a high-resolution picture of the deep past. The remainder of this article focuses on insights from whole genome studies about Native American history. While these studies are still in their early days, they have already upended our understanding of key events in Native American population history. Application of ancient DNA technology promises further insights in years to come.
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Post by Admin on Jun 6, 2021 22:11:03 GMT
Sources of Native American ancestry Under the hypothesis where Native American ancestry stems from a single founder population that separated earlier from Eurasian populations, differences in allele frequencies between Native American groups should have developed independently from Eurasian allele frequencies. This simply null hypothesis makes it possible to explicitly test hypotheses about the number of American founder populations. Reich et al. [23] applied this idea to the first comprehensive genome-wide data from Native American populations (52 populations, but none from the continental United States), and concluded that at least three ancestral populations—or streams of gene flow—were required to explain the similarities between Native Americans and East Asians. According to the initial study [23], all Native American groups from Central and South America fit a model of a single founder population. An additional source of ancestry was necessary to explain genetic variation in Eskimo-Aleut speakers. In addition, analysis of the Athabaskan-speaking Chipewyan revealed that they could not solely have their ancestry from the same founding population as other Northern-, Meso-and South American populations. The main ancestral stream giving rise to Native American ancestry One of the most important pieces of genetic evidence relevant to the peopling of the Americas was the sequencing of a genome from the remains of a child (‘Anzick-1’) buried with Clovis artifacts in western Montana and directly dated to 12,600 before present (BP) [25]. This child was consistent with deriving all of his ancestry from the same founding population as Central and South Americans (Figure 1), contradicting the ‘Solutrean hypothesis’ [26] that posits genetic discontinuity between the makers of the Clovis industry and present-day Native Americans [27]. Figure 1. Eurasian source populations of the earliest Native Americans. A) Diverse population lineages that genetic evidence suggest were present in Northeast Asia and contributed to the ancestry of present-day Native Americans. These comprise people with ancestry related to present-day Andamanese and Australo-Melanesians (red), people related to present-day East Asians such as Han Chinese (pink), and people related to the 24,000 year old Mal’ta child buried near Lake Baikal (dark blue). By 12,600 years ago, at least the Mal’ta-related and east Asian-related ancestries were already present in the proportions found in Native Americans today in the Anzick child from Western Montana (B). Today, the Andamanese-related ancestry can be detected as an excess affinity to present-day Amazonians (B). The most surprising finding was that the Anzick individual is from a population more closely related to Central-and South Americans than to some northern North Americans (including all speakers of Algonquian languages studied to date), despite the apparent common ancestral origin of Native Americans across the continents. This suggests that the present-day population structure of the main ancestry in Native Americans [23] dates back to more than 12,600 years ago [25], and that this diversification divided the ancestry of present-day Native Americans into two main streams, one of which includes the ancestors of present-day Northern Native Americans analyzed (‘NNA’: Cree, Ojibwa, and Algonquin), and the other of which includes the Anzick individual and present-day Central-and South American groups (‘SA’:e.g. Mixe, Quechua, and Yaghan). While we thus have evidence for SA ancestry in the Late Pleistocene in the form of the Anzick genome, an outstanding question is where the ancestors of NNA were localized. One possibility is that they were confined to ice-free regions north of the corridor between the Cordilleran and Laurentide ice sheets, and only expanded south after 12,600 BP, where this ancestry would eventually displace the SA populations represented by Anzick (Figure 2). Another possibility might be an expansion of the Clovis industry from a southern origin that also represented a population expansion by SA populations into regions where NNA populations were located (Figure 2). Thus SA populations might have brought Clovis technology to some regions in northern North America only to later be displaced by an NNA resurgence. Figure 2. Two scenarios explaining that the 12,600 year old Anzick individual is more closely related to South and Central-Americans than Northern Native Americans. A) Clovis technology appears first in the southern parts of North America. It is thus possible that Anzick, being associated with Clovis artifacts and dating to the end of the Clovis period, represents a northwards expansion into a region where the ancestors of present-day northern Native Americans were already established. B) An alternative is that the southern lineage associated with the Anzick individual represents the first migration south of the ice sheets, whereas the ancestors of present-day Northern Native Americans resided north of the ice sheets at 12,600 years ago and only later migrated southwards, replacing the Anzick-like population. C) Both these scenarios could explain the observation that Anzick is more closely related to Southern Native American populations. More recent genome sequencing [28] of the ~9,000 year-old Kennewick individual (‘the Ancient One’) did not provide resolution about this issue. While the genome analysis showed that the Kennewick individual had the great majority of its ancestry from the same deep source as other present-day Native Americans, his affinity to the SA and NNA lineages remains ambiguous.
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Post by Admin on Jun 7, 2021 5:43:12 GMT
Major admixture during the formation of the ancestral population of Native Americans Until 2014, efforts to infer demographic parameters for the peopling of the New World based on genetic data focused on modeling Native Americans as an offshoot of East Asian ancestry [17,20,23,29–34]. However, the analysis of the genome of a 24,000 year-old individual from the Mal’ta site near Lake Baikal in Central Siberia revealed that this model is untenable. The Mal’ta individual shared genetic affinities to both European (West Eurasian) and Native American populations [35]. Analyses showed that a scenario in which Mal’ta descended from an admixture between a West Eurasian population and an ancient population that was also ancestral to Native Americans could not explain all features of the data [35]. However, a scenario in which Native Americans are admixed between lineages related to Mal’ta (between 1/4 and 1/2 of Native American ancestry) and East Asians can explain the data (Figure 1). Thus, Native Americans and East Asians do not in fact descend from a common ancestral population that separated earlier from a lineage leading to Mal’ta and to West Eurasians [35].
The finding of ancient mixture in the ancestry of Native American—prior to diversification within the Americas—also has consequences for modeling other features of Native American population history. Genetic debate about the date of the first migrants into the Americas has had, as one of its important themes, estimation of the date of genetic divergence of the lineages giving rise to Native American and East Asian populations [31]. The major admixture related to the Mal’ta lineage in the ancestry of all Native Americans is inconsistent with the assumption of a simple population split between Native Americans and East Asians that has been the basis for the most attempts to date to infer the population split times, and which have suggested dates of around 23,000 years ago [33,34]. The substantial contribution of the Mal’ta lineage to Native Americans may have the effect of upwardly biasing estimates of the time of divergence of Native Americans and East Asians. Future models estimating parameters for the founding populations of the Americas will need to consider this admixture explicitly.
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