Mal'ta Boy (ANE): Origins of Native Americans

new

Admin
Administrator

Posts: 81,662

Mal'ta Boy (ANE): Origins of Native Americans Mar 31, 2019 17:43:32 GMT

Quote

Post by Admin on Mar 31, 2019 17:43:32 GMT

Links to ancient genomes
Genetic affinity between modern Siberians and Ust'-Ishim
To uncover ancient demographic events and reveal genetic links between present-day individuals and ancient ancestral populations, we compared 60 genomes from modern-day humans (Table 1; Supplemental Table S2) to 46 ancient genomes (Supplemental Table S3), including a 45,000-yr-old Siberian Ust’-Ishim individual (Fu et al. 2014), a 24,000-yr-old Siberian Mal'ta boy (MA-1), and a 17,000-yr-old Siberian individual (AG-2) from the Krasnoyarsk region (Raghavan et al. 2014).

Given that the bone from the Ust’-Ishim individual was found in Western Siberia, we reasoned that Ust’-Ishim might be related to modern Siberian populations. Indeed, this hypothesis was well supported by the TreeMix model (Fig. 6). We observed that the common ancestor of Siberians and East Asians traced 38% (95% CI: 28%–48%) of their ancestry to Ust’-Ishim's lineage (Fig. 6; Supplemental Fig. S14). In agreement with this, the D-statistics analysis (Fig. 5C; Supplemental Figs. S13C, S15) showed that Ust’-Ishim had higher genetic affinity with East Asians and Siberians, particularly Eastern Siberians, than with modern Europeans. This was also supported by the Y haplotype analysis. Previously, the ancient Siberian Ust’-Ishim (Fu et al. 2014) was thought to belong to the K2 Y-Chromosome clade, which is ancestral to haplogroup R (a Y-Chromosome clade extremely common in Europe), haplogroup Q (common among Native Americans and certain Siberians populations), haplogroup N (common in Siberia and Northeastern Europe), and haplogroup O (common in East Asia). However, we observed that Ust’-Ishim had a single derived SNP on Y-Chromosome specific to the NO branch (hg19 coordinate Chr Y 7,690,182) (Supplemental Fig. S12). This branch is associated with Siberians and some Northeastern European groups, as well as East Asians. Therefore, unlike previous claims, Ust’-Ishim's haplogroup most likely belongs to a more recent NO clade rather than to the more diverged K2 clade. Based on these lines of evidence, we conclude that Ust’-Ishim contributed more ancestry to the East Asian and Siberian populations than to modern Europeans or Native Americans.

Western Siberians are descendants of ANEs and Eastern Siberians
Our tree model grouped ANEs MA-1 and AG-2 with Western Siberians (Mansi and Nenets), suggesting a genetic link between ANEs and modern Western Siberians (Fig. 7). Furthermore, TreeMix estimated that 41% (95% CI: 36%–45%) of the ancestry of Andean Highlanders, the Native Americans, is attributable to the ANE lineage (Fig. 7; Supplemental Fig. S16). This is consistent with previous reports that Paleo-Americans trace ∼42% of their autosomal genome to an ancient Eurasian lineage related to MA-1 (Raghavan et al. 2014). We further tested these predictions using D-statistics by evaluating whether a modern individual shared significantly more derived alleles with MA-1 or AG-2 than with the East Asian Han individual (Fig. 5D; Supplemental Fig. S17A). Mansi, Khanty, Nenets, and Native Americans all had very strong ANE ancestry, demonstrated by their significant genetic affinities with MA-1 and AG-2. Therefore, Western Siberians share common ANE ancestry with Native Americans. The remaining ancestry of Western Siberians could be attributed to a population related to Eastern Siberians. The TreeMix model (Fig. 7) inferred that 43% of Mansi ancestry was derived from the admixture with a population related to Eastern Siberians Evenks and Evens, while 57% is attributable to the ANE ancestry. Therefore, genomes of Mansi people harbor significant ancestries from Siberian ANE people as well as Eastern Siberian populations in approximately equal proportions.

Figure 7.
Genetic relationships with ancient North Eurasians MA-1 and AG-2. Autosomal TreeMix admixture graph that includes ancient 7000-yr old La Brana (Spain) and low-coverage genomes of ancient Siberians MA-1 and AG-2. Residual plot for this graph is shown in Supplemental Figure S16. TreeMix model indicated multiple admixture events: 41% admixture (95% CI: 36%–45%) from the ANE clade represented by MA-1 and AG-2 individuals into Native Americans represented by Andean Highlanders, 43% admixture (95% CI: 38%–47%) between population related to Evenk and a common ancestor of Western Siberians (Mansi and Nenets), and 26% (95% CI: 16%–37%) admixture between population related to Even and modern-day Nenets. Additionally, Western Siberians and ANE are grouped together, indicating their shared genetic history.

To examine Siberian-related ancestry among ancient Europeans, we analyzed SNP data from the Holocene Eastern European hunter-gatherers (Haak et al. 2015) from the Samara and Karelia regions in modern Russia and the Motala region in Sweden (6.6–8 kya), as well as more recent Bronze Age Yamnaya samples (4.7–5.3 kya). D-Statistics demonstrated strong admixtures between the Mansi and nearly all hunter-gatherers from Eastern Europe (Supplemental Fig. S21), particularly for the Samara and Karelia samples. Slightly weaker, but significant affinities were present between Eastern Siberian Even and Eastern European hunter-gatherers. As previously mentioned, the time of the split of Eastern and Western Siberian populations was estimated to be around 6.8–9.9 kya. The weaker affinity of Eastern Siberians and Eastern European hunter-gatherers could be attributed to the Eastern Siberian ancestry of Mansi, which permeated into ancient European populations through Mansi-related admixture. Yamnaya samples also showed statistically significant admixtures with Mansi and Evens, but slightly weaker compared with Samara HG, which indicates a dilution of Eastern hunter-gatherer ancestry component of Yamnaya culture samples. The ANE-related ancestry among Eastern European hunter-gatherers could thus be attributed to gene flows between population ancestral to Mansi and Eastern European hunter-gatherers that occurred before 8 kya, as demonstrated by the strong genetic affinity between Mansi and Samara and Karelia hunter-gatherers from 6–8 kya.

Apart from Eastern European hunter-gatherers, Siberians also shared part of their ancestry with Pitted Ware Culture (PWC) 5,000-yr-old hunter-gatherers from Sweden Ire8 and Ajv52 (Skoglund et al. 2012). Ajv52 and particularly Ire8 had strong admixture signals with Western Siberians Mansi (Fig. 5E; Supplemental Fig. S17B), suggesting that like the closely related Yamnaya culture, they had strong ANE ancestries likely due to admixtures with Mansi-related population.

Shared ancestry between Eastern Siberians and ancient human of the Saqqaq culture
Our data also showed evidence of Eastern Siberian ancestry within the genome of a 4000-yr-old Saqqaq individual (Rasmussen et al. 2010) from Greenland. The tree model with Saqqaq genome showed that Saqqaq was related to both East Asians and Eastern Siberians, and 12% of its ancestry was attributable to a population related to modern-day Evens (Supplemental Figs. S19, S20). The detected gene flow was strongly supported by the D-statistics (Supplemental Figs. S7F, S8F). In addition, 18% of American Andeans' ancestry came from Evens (Supplemental Fig. S19). This, together with the substantial gene flow from an ancestor of Evens and Evenks to Altayans, suggests that the signal from Evens to Saqqaq can be a result of ancient admixture happened between the ancestor of Siberians (Eastern Siberians) and early migrants to the Americas.

Figure 8.
Geographical dispersion model. The approximate model of gene flows reflecting divergence of primary clades in Europe, East Asia, and Siberia with approximate divergence times based on Chromosome Y, MSMC, TreeMix, and D-statistics analyses. Percentages represent proportions of ancestry contributed to each lineage from other lineages. The common ancestors of Mansi, Khanty, and Nenets had derived 57% of their ancestry from an ANE population, related to MA-1, AG-2, and Native Americans and 43% from the admixture with a population related to Evens and Evenks. Native Americans trace 42% of their ancestry to ANE and 58% to a common ancestor of Eastern Siberians and East Asians. In the figure, 45 kya represents the split between Y-Chromosome clades QR and NO; 33 kya represents the split between Y-Chromosome Q and R clades and mtDNA N2 and W clades; 17 kya represents Mansi-Andean separation time; 44 kya represents the split of Ust’-Ishim's haplogroup from NO clade; 19 kya represents Han-Andean separation time; 10 kya represents Han-Eastern Siberian separation time; and 5.3–9.9 kya represents Evenk-Mansi MSMC separation time (6.8–9.9 kya) and expansion of N1c1 Y-haplogroup (5.3–7.1 kya). In this figure, Europeans represent a collective term for the following populations from this study: Komi, Veps, Karelians, Russians, and Belarussians.

Discussion
Genomes of indigenous Siberians harbor evidence of many important ancient events that shaped population history and peopling of Eurasia and the New World. Siberia is home to more than 30 ethnic groups that were thus far undersurveyed in population genetic studies. In this work, we examined the genetic history of several Siberian and Eastern European populations and analyzed their genetic links to ancient and modern populations. We summarized our findings in the form of a synthetic geographical dispersion model (Fig. 8), which describes how populations and genetic variation likely spread across Northern Eurasia.

Our analyses demonstrated that both East Asian and Siberian populations shared a significant amount of ancestry (38%) attributable to the ancient Siberian Ust’-Ishim individual, thus pointing to very ancient origins of indigenous Siberians. D-Statistics tests also suggested stronger affinity of Ust’-Ishim to both Eastern and Western Siberians (Fig. 5C; Supplemental Figs. S13C, S15) than to modern Europeans. Another line of evidence pointing to affinity of both East Asians and Eastern Siberians with Ust’-Ishim was provided by the Y-Chromosome haplogroup analysis (Fig. 4A; Supplemental Fig. S12). We showed that Ust’-Ishim's Y-Chromosome haplogroup belonged to NO clade, and its divergence from NO lineage predated the split of Y-Chromosome haplogroup N (particularly common in Siberia and Northeastern Europe) and haplogroup O (the most common Y-Chromosome haplogroup among Eastern and Southern Asian populations). These new relationships were uncovered largely due to the inclusion of the Western and Eastern Siberian genomes, including Mansi, Khanty, Nenets, Evens, Buryat, and other Siberian individuals. Therefore, the new findings described here provide a more accurate interpretation of patterns observed in the original Ust’-Ishim study (Fu et al. 2014).

A particularly surprising finding was the genetic link between 24,000-yr-old Siberian Mal'ta boy, Native Americans, and the Western Siberians Mansi, Khanty, and Nenets. This finding demonstrates a strong genetic link between Western Siberians and Native Americans due to their common ANE ancestry. We estimate that 57% of Western Siberian Mansi and Khanty ancestry was related to the ANE lineage represented by MA-1 and AG-2 ancient individuals. The other important finding was that the remaining 43% of Western Siberian ancestry was related to Eastern Siberian populations, suggesting admixtures between Eastern Siberian groups most related to Evens and Evenks and the common ancestors of Western Siberians (Fig. 2). This is particularly interesting in the context of ancestral relationships of modern Northeastern European populations. Lazaridis et al. (2014) modeled the ancestry of Eastern Europeans such as Mordovians, Finns, Russians, Saami, and Chuvashs but could not completely explain their genetic makeup by a mixture of three early European groups: the ancient northern Eurasians (represented by MA-1), the West European hunter-gatherers (represented by Loschbour), and the early European farmers (represented by Stuttgart). This was proposed to be due to a greater relatedness of Eastern Europeans to East Asians, compared with other European groups. However, our analyses of genetic relationships of Northeastern European populations such as Mezen Russians, Komi, Karelians, and Veps suggested that the unexplained ancestral components among modern Europeans likely resulted from their affinity with both Western and Eastern Siberian populations.

Our findings also showed that Western Siberians Mansi and Khanty and ancient Eastern European populations (Yamnaya and the PWC people) shared a significant amount of ANE-related ancestry. The genetic affinity of ancient Eastern Europeans with Eastern Siberians is relatively weaker (Fig. 5E; Supplemental Figs. S21, S24). Therefore, we propose that the Western Siberian admixture into Northeastern Europeans likely began before the Yamnaya culture period (5.3–4.7 kya), since the admixtures with Mansi are also very strong among hunter-gatherers from Northeastern Europe from 6.6–8 kya (Karelia HG, Samara HG, and to lesser degree Neolithic Motala HG and Hungary Gamba HG) (Supplemental Fig. S21F–Q) that predated the Yamnaya people. Mansi did not share the Late Upper Palaeolithic Caucasus HG ancestry with the Yamnaya people (Supplemental Fig. S25), suggesting that it is unlikely that Mansi have descended from the Yamnaya people. Therefore, Siberian admixtures into Northeastern Europe likely began prior to 6.6 kya, coinciding with the expansion of Y-Chromosome haplogroup N1c1 among Siberians and Northeastern Europeans (7.1–4.9 kya). Since haplogroup N likely originated in Asia (Shi et al. 2013) and currently achieves its highest frequency among Siberian populations, its presence among Eastern Europeans likely reflects ancient gene flows from Siberia into Northeastern Europe.

Genome Res. 2017. 27: 1-14

Admin
Administrator

Posts: 81,662

Mal'ta Boy (ANE): Origins of Native Americans May 19, 2019 18:20:19 GMT

Quote

Post by Admin on May 19, 2019 18:20:19 GMT

Glaciologists, geologists, climatologists, and anthropologists have all had a hand in estimating the age, number, and magnitude of so-called glacial epochs and the warmer interludes between them. Current thinking is that dating way back to before life of any kind existed, there have been nine so-called glacial ages. We are still experiencing the present one, often called the Pleistocene Epoch, which began about 2,600,000 BC. In it there have been eleven interglacial or warmer periods, lasting for about ten to thirty thousand years each.

The next-to-last one, sometimes called Eemian Interglacial, lasted roughly from 130,000 to 115,000 years BC. It was a little warmer than the present warmer period, usually called Late Cenozoic Interglacial or Holocene, which is still going on. During the height of the Eemian, palm trees grew as far north as the Alaskan Panhandle. The Late Cenozoic period began around 15,000 years BC and as everyone conversant with political discussions and debates knows, is continually still getting warmer.

When both Eemian and Late Cenozoic dates are applied to human migrations, several speculative observations suggest themselves. In tropical and sub-tropical latitudes only sea levels are relevant because glacial blockage isn’t a major factor, whereas in Beringia, both harsh subarctic climate and glacial blockage present obstacles as well. However, in the Late Cenozoic only, human cultural evolution brought use of boats onto the scene thus partially negating the obstacles created by rising sea levels. This factor largely applied to areas where early man could view land on the horizon thus risking pushing onward.

Denisovan DNA in America
While both scientists and hobbyists who like early human lore were speculating about who, when, and how humans crossed Beringia from Asia into North America, others of like ilk were pursuing hard answers. Geneticists were busy pushing the boundaries of DNA and protein analysis further and further, whereas earlier radio carbon, strontium, and oxygen-18 dating technologies had been useable only in limited situations. Linguistic anthropologists started to compare languages using computer techniques and to take tribal legends more seriously.

Aerial photography and satellite imagery was finding its way into archaeology. Now it was time to ask an almost sacrilegious question for some, “Did the Denisovans make it into North America?” Or if not, would traces of their DNA turn up among New World peoples, just as Neanderthal DNA had been found in genes of some modern Europeans?

Initially, scholars and hobbyists alike assumed human migration through Beringa occurred only during the Late Cenozoic, during which three distinct migration waves had been identified. Then two additional factors emerged suggesting that Eemian times must have seen some activity too. (1) The scrub vegetation growing in Beringia during the colder Late Cenozoic wouldn’t have supported the large grazing animals like mammoths, mastodons, horses, and camels that once thrived in the Americas.

Researchers like David Reich of the Harvard Medical School and his colleagues suggested that a 40,000 year negative selection Neanderthal and Denisovan genes existed among many Southeast Asians and Pacific Islanders . Would there be time for DNA influences to be carried far and wide in the Western Hemisphere from Late Cenozoic arrivers who had crossed Beringa? These same scientists also found Denisovan genes in the Americas and far north-east Asia.

Other scientists, while not as concerned with Denisovans or DNA evidence, found evidence far to the south of Beringia in both North and South America that suggested human presence dated earlier than the Late Cenozoic. While still not fully authenticated, the Calico site in California was alleged to date as early as 200,000 BC. If this proves to be accurate, it would strongly suggest some humans crossed Beringia during a third-last interglacial warming period. While not citing specific dates, eminent archaeologist Louis Leakey was one of the scientists claiming Calico is a bona fide early man site.

Last Edit: May 19, 2019 18:20:55 GMT by Admin

Admin
Administrator

Posts: 81,662

Mal'ta Boy (ANE): Origins of Native Americans Jun 6, 2019 0:03:43 GMT

Quote

Post by Admin on Jun 6, 2019 0:03:43 GMT

The discovery of teeth frozen in Arctic soil have helped scientists make sense of the waves of human settlement in the Americas.

One discovery, making scientists forever grateful to some ancient tooth fairy, was of two milk teeth from distantly related boys buried near the Yana River in north-eastern Siberia. The site has been excavated for almost 20 years, bringing to light thousands of animal bones, ivory, and stone tools. None of that has been as scientifically valuable, however, as the DNA trapped in the teeth for 31,000 years because of the icy conditions.

The boys were from an ethnic group called the Ancient North Siberians who, despite their location, were twice as closely related to Europeans as east Asians.

Professor Eske Willerslev of Cambridge University said in a statement: "These people were a significant part of human history, they diversified almost at the same time as the ancestors of modern day Asians and Europeans and it's likely that at one point they occupied large regions of the northern hemisphere."

To survive a winter in Siberia today is a challenge. To do it in the middle of the last ice age demonstrates these people's remarkable resilience. Native Americans have DNA that is a mix of that seen in these Ancient North Siberians and East Asians, so the latest discovery provides a missing link in explaining Native American genetic heritage, although a sample of DNA found closer to Mongolia is more closely related to modern Native Americans.

The teeth were the highlight, but Willerslev and co-authors also explored in Nature the ancient genomes from 34 people dating back almost 32,000 to 600 years ago. They revealed that the Ancient North Siberians showed no signs of being inbred, despite what must have been very low local population density. Somehow, they found ways to expand their breeding pool, even if it required immense migrations. In contrast, the last Neanderthals were, around the same time, suffering from severe inbreeding, raising the intriguing possibility that modern humans' greater propensity for finding unrelated mates was what allowed us to outcompete our nearest relatives.

Another paper in the same edition reports on a related study of the genetics of those who have inhabited the Arctic over the last 5,000 years. It compares the genomes of 48 ancient people from the far north and 93 modern individuals living in similar areas. The study confirms that modern populations in eastern Siberia, Alaska, northern Canada, and the Aleutian Islands are descended from a group known as the Paleo-Eskimos, who arrived in North America around 5,000 years ago.

Scientists found the Ancient North Siberians generated the mosaic genetic make-up of contemporary people who inhabit a vast area across northern Eurasia and the Americas—providing the 'missing link' of understanding the genetics of Native American ancestry.

It is widely accepted that humans first made their way to the Americas from Siberia into Alaska via a land bridge spanning the Bering Strait which was submerged at the end of the last Ice Age. The researchers were able to pinpoint some of these ancestors as Asian people groups who mixed with the Ancient North Siberians.

Professor Willerslev added: "The remains are genetically very close to the ancestors of Paleo-Siberian speakers and close to the ancestors of Native Americans. It is an important piece in the puzzle of understanding the ancestry of Native Americans as you can see the Kolyma signature in the Native Americans and Paleo-Siberians. This individual is the missing link of Native American ancestry."

Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of ‘Ancient North Siberians’ who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to ‘Ancient Palaeo-Siberians’ who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name ‘Neo-Siberians’, and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.

Nature (2019)

Admin
Administrator

Posts: 81,662

Mal'ta Boy (ANE): Origins of Native Americans Jun 13, 2019 18:04:49 GMT

Quote

Post by Admin on Jun 13, 2019 18:04:49 GMT

Despite broad agreement that the Americas were initially populated via Beringia, the land bridge that connected far northeast Asia with northwestern North America during the Pleistocene epoch, when and how the peopling of the Americas occurred remains unresolved1,2,3,4,5. Analyses of human remains from Late Pleistocene Alaska are important to resolving the timing and dispersal of these populations.

Figure 1: Genetic affinities between USR1, present-day Native Americans and world-wide populations.

The remains of two infants were recovered at Upward Sun River (USR), and have been dated to around 11.5 thousand years ago (ka)6. Here, by sequencing the USR1 genome to an average coverage of approximately 17 times, we show that USR1 is most closely related to Native Americans, but falls basal to all previously sequenced contemporary and ancient Native Americans1,7,8. As such, USR1 represents a distinct Ancient Beringian population. Using demographic modelling, we infer that the Ancient Beringian population and ancestors of other Native Americans descended from a single founding population that initially split from East Asians around 36 ± 1.5 ka, with gene flow persisting until around 25 ± 1.1 ka. Gene flow from ancient north Eurasians into all Native Americans took place 25–20 ka, with Ancient Beringians branching off around 22–18.1 ka. Our findings support a long-term genetic structure in ancestral Native Americans, consistent with the Beringian ‘standstill model’9. We show that the basal northern and southern Native American branches, to which all other Native Americans belong, diverged around 17.5–14.6 ka, and that this probably occurred south of the North American ice sheets. We also show that after 11.5 ka, some of the northern Native American populations received gene flow from a Siberian population most closely related to Koryaks, but not Palaeo-Eskimos1, Inuits or Kets10, and that Native American gene flow into Inuits was through northern and not southern Native American groups1. Our findings further suggest that the far-northern North American presence of northern Native Americans is from a back migration that replaced or absorbed the initial founding population of Ancient Beringians.

Figure 2: Possible geog

raphic locations for the USR1 and NNA–SNA splits.

The founding population of Native Americans (consisting of Ancient Beringians and NNA and SNA) began to diverge from ancestral Asians as early as around 36 ka, probably in northeast Asia, as there is no evidence of people in Beringia or northwest North America at this period. A high level of gene flow was maintained between them and other Asians until as late as around 25 ka2,13.

The subsequent isolation of the Native American founding population about 24 ka roughly corresponds to a decline in archaeological evidence for a human presence in Siberia30. Both changes may result from the same underlying cause: the onset of harsh climatic conditions during the LGM2. These findings, coupled with a divergence date of around 20.9 ka between USR1 and other Native Americans, are in agreement with the Beringian standstill model9 (Supplementary Information section 21). Ancient Beringians and the common ancestor of NNA and SNA began to diverge around 20.9 ka, after which gene flow ensued, although whether this only involved the latter or the already differentiated NNA and SNA branches cannot be determined owing to the shallow divergence times among groups.

Figure 3: A model for the formation of the different Native American populations.

Scenarios 1 and 2 are compatible with our evidence of continuous gene flow among these groups, but differ as to the location of the Ancient Beringians versus NNA and SNA split at 20.9 ka, whether in northeast Asia (scenario 1) or eastern Beringia (scenario 2). Each has strengths and weaknesses relative to genetic and archaeological evidence: scenario 1 best fits the archaeological and palaeoecological evidence, as the earliest securely dated sites in Beringia are no older than around 15–14 ka, and the LGM cold period is unlikely to be associated with northward-expanding populations30. Scenario 2 is genetically most parsimonious, given evidence of continuous gene flow between the Ancient Beringians and NNA and SNA, suggesting their geographical proximity 20.9–11.5 ka, and that all three were isolated from Asian and/ or Siberian groups after about 24 ka and form a clade.

Scenarios 1 and 2 are both consistent with the NNA–SNA split at around 15 ka2 having occurred in a region south of eastern Beringia. The ice sheets were at that time still a substantial barrier to movement that would have helped to maintain separation from the Ancient Beringian population. Although members of the SNA branch have not been documented in regions that were once north of the Pleistocene glaciers1,18, NNA groups (including Athabascan speakers) are present in Alaska today. Therefore, NNA are likely to be descendants of a population that moved north sometime after 11.5 ka25.

Figure 4: USR1 demographic history in the context of East Asians, Siberians and other Native Americans.

The USR1 results provide direct genomic evidence that all Native Americans can be traced back to the same source population from a single Late Pleistocene founding event. Descendants of that population were present in eastern Beringia until at least 11.5 ka. By that time, however, a separate branch of Native Americans had already established itself in unglaciated North America, and diverged into the two basal groups that ultimately became the ancestors of most of the indigenous populations of the Americas.

Nature volume 553, pages 203–207 (11 January 2018)

Last Edit: May 9, 2020 5:56:34 GMT by Admin

Admin
Administrator

Posts: 81,662

Mal'ta Boy (ANE): Origins of Native Americans Dec 25, 2019 20:36:41 GMT

Quote

Post by Admin on Dec 25, 2019 20:36:41 GMT

The settlement of the Americas occurred at least 15,000 years ago through Beringia, a land bridge between Asia and America that existed during the ice ages1,2,3,4,5. Most analyses of Native American genetic diversity have examined single loci, particularly mitochondrial DNA or the Y chromosome, and some interpretations of these data model the settlement of America as a single migratory wave from Asia6,7,8. We assembled native population samples from Canada to the southern tip of South America, genotyped them on single nucleotide polymorphism (SNP) microarrays, and merged our data with six other data sets. The combined data set consists of 364,470 SNPs genotyped in 52 Native American populations (493 samples; Fig. 1a and Supplementary Table 1), 17 Siberian populations (245 samples; Supplementary Fig. 1 and Supplementary Table 2) and 57 other populations (1,613 samples) (Supplementary Notes).

Figure 1: Geographic, linguistic and genetic overview of 52 Native American populations.

A complication in studying Native American genetic history is admixture with European and African immigrants since 1492. Cluster analysis16 shows that many of the samples we examined have some non-native admixture (an average of 8.5%; Fig. 1b and Supplementary Tables 1 and 3). This admixture is a challenge for learning about the historical relationships among the populations, and to address this complication we used three independent approaches. First, we restricted analyses to 163 Native Americans from 34 populations without evidence of admixture (Supplementary Notes). Second, we subtracted the expected contribution of European and African ancestry to the statistics we used to learn about population relationships (Supplementary Notes). Third, we inferred the probability of non-native ancestry at each genomic segment and ‘masked’ segments with more than a negligible probability of this ancestry (Fig. 1b, Supplementary Notes and Supplementary Fig. 2). Our inferences from these three approaches are concordant (Supplementary Figs 3 and 4).

We built a tree (Fig. 1c) using Fst distances between pairs of populations, which broadly agrees with geography and linguistic categories17 (trees based on masked and unmasked data were similar; Supplementary Fig. 3). An early split separates Asians from Native Americans and extreme northeastern Siberians (Chukchi, Naukan, Koryak), which is consistent with studies that have identified pan-American variants shared with some northeastern Siberians6,7,10,18. Eskimo–Aleut speakers and far-northeastern Siberians form a cluster that is separated from other Native American populations by a long internal branch. Within America the tree shows a series of splits in an approximate north–south sequence beginning with the Arctic, followed by northern North America, northern/central and southern Mexico and lower Central America/Colombia, and ending in three South American clusters (the Andes, the Chaco region and eastern South America). This pattern of splits is consistent with a north–south population expansion, an inference that is also supported by the negative correlation between heterozygosity and distance from the Bering Strait (r = −0.48, P = 0.007). This correlation increases if we use ‘least cost distances’ that consider the coasts as facilitators of migration19,20,21, and persists if we exclude four Native North American populations with ancestry from later streams of Asian gene flow (Supplementary Notes and Supplementary Fig. 5).

Trees provide a simplified model of history that does not accommodate the possibility of gene flow after population separation. Circumstantial evidence that some Native American populations may not fit a simple tree comes from cluster analysis, which infers Siberian-related ancestry in some northern North Americans (Fig. 1b), and from single-locus studies that have identified genetic variants shared between Eurasia and North America that are absent from South America11,22,23. The advent of genome-wide data sets has allowed the development of a formal four-population test for whether sets of four populations are consistent with a tree. This test is robust to the ascertainment bias affecting SNP arrays24. For each of the 52 Native American populations in turn, we tested the hypothesis that they conform to the tree: ((test population, southern Native American), (outgroup1, outgroup2)) for 45 pairs of ten Asian outgroups. We used a Hotelling T-test to evaluate whether all four-population test f4 statistics of this form are consistent with the expectation of zero (Supplementary Notes). The test is not significant for 47 populations, which is consistent with their stemming from the same, presumably first, wave of American settlement; we call this ancestry ‘First American’ (Table 1). In contrast, four populations from northern North America show highly significant evidence of ancestry from additional streams of gene flow from Asia, subsequent to the initial peopling of America, which we confirm through the Hotelling T-test and a complementary test (Supplementary Notes).

Examination of the values of the f4 statistics allows us to infer the minimum number of gene flow events from Asia into America consistent with the data. Each stream of gene flow is expected to produce a distinct vector of f4 statistics, constituting a ‘signature’ of how the ancestral migrating population relates to present-day Asian populations. By finding the minimum number of vectors whose linear combinations are necessary to produce the vector observed in each population, we infer that a minimum of three gene flow events from Asia are necessary to explain the data from all Native American populations jointly, including the Saqqaq Palaeo-Eskimo (Supplementary Notes). These three episodes correspond to First American ancestry (distributed throughout the Americas) and to two additional streams of gene flow detected in a subset of northern North Americans (East Greenland Inuit, West Greenland Inuit, Aleutian Islanders, Chipewyan and Saqqaq). Table 1 shows that f4 statistics in the Inuit and Aleutian islanders are consistent with deriving the non-First-American portions of their ancestry from the same later stream of Asian gene flow, providing support for deep shared ancestry between these linguistically linked groups12,26. The Na-Dene-speaking Chipewyan have a different pattern of f4 statistics from Eskimo–Aleut speakers, implying that they descend at least in part from a separate stream of Asian gene flow.

To develop an explicit model for the settlement of the Americas, we used the admixture graph (AG) framework24. AGs are generalizations of trees that accommodate the possibility of a limited number of unidirectional gene flow events. They are powerful tools for learning about history because they make predictions about the values of f-statistics (such as f4) that can be used to test the fit of a proposed model24 (Supplementary Notes). Figure 2 presents an AG relating selected Native American and Old World populations that is a good fit to the data in the sense that none of the f-statistics predicted by the model are more than three standard errors from what is observed. This supports the hypothesis of three deep lineages in Native Americans: the Asian lineage leading to First Americans is the most deeply diverged, whereas the Asian lineages leading to Eskimo–Aleut speakers and the Na-Dene-speaking Chipewyan are more closely related and descend from a putative Siberian ancestral population more closely related to Han (Fig. 2). We also arrive at the finding that Eskimo–Aleut populations and the Chipewyan derive large proportions of their genomes from First American ancestors: an estimated 57% for Eskimo–Aleut speakers, and 90% in the Chipewyan, probably reflecting major admixture events of the two later streams of Asian migration with the First Americans that they encountered after they arrived (Supplementary Notes). The high proportion of First American ancestry explains why Eskimo–Aleut and Chipewyan populations cluster with First Americans in trees like that in Fig. 1c despite having some of their ancestry from later streams of Asian migration, and explains the observation of some genetic variants that are shared by all Native Americans but are absent elsewhere6,7,10,18. We also infer back-migration of populations related to the Eskimo–Aleut from America into far-northeastern Siberia (we obtain an excellent fit to the data when we model the Naukan and coastal Chukchi as mixtures of groups related to the Greenland Inuit and Asians (Fig. 2 and Supplementary Notes)). This explains previous findings of pan-American alleles also in far-northeastern Siberia6,7,10,18.

Figure 2: Distinct streams of gene flow from Asia into America.

We next used AGs to develop a model for the history of populations who derive all their ancestry from the First American migration, with no ancestry from subsequent streams of Asian gene flow. Figure 3 presents an AG we built for 16 selected Native American populations and two outgroups, which is a good fit to the data in that the largest |Z|-score for a difference between the observed and predicted f-statistics is 3.2 from among the 11,781 statistics we tested (Supplementary Notes) (The AG of Fig. 3 used masked data; however, a consistent set of relationships is inferred for unadmixed samples (Supplementary Fig. 4).) This model provides a greatly improved statistical fit to the data compared with the tree of Fig. 1c and leads to several novel inferences. First, a relatively large fraction of South American populations fit the AG without a need for admixture events, which we speculate reflects a history of limited gene flow among these populations since their initial divergence. In contrast, only a small fraction of Meso-American populations fit into the AG, which could reflect either a higher rate of migration among neighbouring groups or our denser sampling in Meso-America allowing us to detect more subtle gene flow events. Second, some Meso-American populations have experienced very little genetic drift since divergence from the common ancestral population with South Americans (adding up the genetic drifts along the relevant edges of Fig. 3, we infer Fst = 0.014 between the Zapotec and a hypothetical population ancestral to all of Central and South America), suggesting that effective population sizes in Meso-America have been relatively large since settlement of the region. Third, the model infers three admixture events consistent with geographic locations and linguistic affiliations (Supplementary Notes). The Inga have both Amazonian and Andean ancestry, which is consistent with their speaking a Quechuan language but living in the eastern Andean slopes of Colombia and thus interacting with groups in the neighbouring Amazonian lowlands. The Guarani stem from two distinct strands of ancestry within eastern South America. The most striking admixture event is in the Costa Rican Cabecar (Fig. 3) and other Chibchan-speaking populations (Supplementary Notes) from the Isthmo-Colombian area. One of the lineages that we detect in these populations occurs definitively within the radiation of South American populations, and so the presence of these populations in lower Central America suggests that there was reverse gene flow across the Panama isthmus after the initial settlement of South America. There has been controversy about whether Chibchan speakers of lower Central America represent direct descendants of the first settlers in the region or more recent migration across the isthmus, and our results support the view that more recent migration has contributed most of these populations’ ancestry27.

Figure 3: A model fitting populations of entirely First American ancestry.

This is the most comprehensive survey of genetic diversity in Native Americans so far. Our analyses show that the great majority of Native American populations—from Canada to the southern tip of Chile—derive their ancestry from a homogeneous ‘First American’ ancestral population, presumably the one that crossed the Bering Strait more than 15,000 years ago6,7,8. We also document at least two additional streams of Asian gene flow into America, allowing us to reject the view that all present-day Native Americans stem from a single migration wave6,7,8, and supporting the more complex scenarios proposed by some other studies9,10,11,12,13,14,15. In particular, the three distinct Asian lineages we detect—‘First American’, ‘Eskimo–Aleut’ and a separate one in the Na-Dene-speaking Chipewyan—are consistent with a three-wave model proposed9 mostly on the basis of dental morphology and a controversial interpretation of the linguistic data. However, our analyses also document extensive admixture between First Americans and the subsequent streams of Asian migrants, which was not predicted by that model, such that Eskimo–Aleut speakers and the Chipewyan derive more than half their ancestry from First Americans. Further insights into Native American history will benefit from the application of analyses similar to those performed here to whole-genome sequences and to data from the many admixed populations in the Americas that do not self-identify as native28,29,30.

Nature volume 488, pages 370–374 (16 August 2012)

Last Edit: May 9, 2020 5:59:20 GMT by Admin