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Post by Admin on Jun 2, 2021 21:29:13 GMT
In 2015, scientists discovered something surprising: that some Indigenous peoples in the Brazilian Amazon were distantly—but distinctly—related to native Australians and Melanesians. The genetic signal of Australasian ancestry in so far-flung a population sent researchers scrambling for answers. A new study reveals this genetic signal is more prevalent throughout South America than thought and suggests the people who first carried these genes into the New World got it from an ancestral Siberian population. The finding also sheds light on those people’s migration routes to South America. “It’s a really nice piece of work,” says Jennifer Raff, an anthropological geneticist at the University of Kansas, Lawrence, who wasn’t involved in the study. It shows that the 2015 finding “wasn’t just an artifact. It really is a widespread genetic signal.” Anthropologists think bands of hardy hunter-gatherers left Siberia and entered the now-submerged land of Beringia, which then connected Eurasia and Alaska, when sea levels were much lower than today—perhaps about 20,000 years ago. Then, about 15,000 years or so ago, some departed Beringia and fanned out into North and South America. These early migrants made good time: By 14,800 years ago at the latest, radiocarbon dates suggest they were setting up camp in Monte Verde in southern Chile. The 2015 DNA studies revealed Australasian ancestry in two Indigenous Amazonian groups, the Karitiana and Suruí, based on the DNA of more than 200 living and ancient people. Many bore a signature set of genetic mutations, named the “Y signal” after the Brazilian Tupi word for “ancestor,” ypikuéra. Some scientists speculated the Y signal was already present in some of the earliest South American migrants. Others suggested a later migration of people related to present-day Australasians could have introduced the Y signal into people already living in the Amazon. The new study, led by geneticist Tábita Hünemeier at the University of São Paulo, São Paulo, examined genetic data from 383 modern people from across South America, including dozens of newly genotyped individuals living in the Brazilian Amazon and central plateau. The researchers worked closely with Indigenous people, and Hünemeier says they are collaborating with historians, anthropologists, and geneticists “to assure the results would be transferred in the best way to the Indigenous communities.” For the first time, scientists identified the Y signal in groups living outside the Amazon—in the Xavánte, who live on the Brazilian plateau in the country’s center, and in Peru’s Chotuna people, who descend from the Mochica civilization that occupied that country’s coast from about 100 C.E. to 800 C.E. Next, the researchers used software to test different scenarios that might have led to the current DNA dispersal. The best fit scenario involves some of the very earliest—possibly even the earliest—South American migrants carrying the Y signal with them, the researchers report today in the Proceedings of the National Academy of Sciences. Those migrants likely followed a coastal route, Hünemeier says, then split off into the central plateau and Amazon sometime between 15,000 and 8000 years ago. “[The data] match exactly what you’d predict if that were the case,” Raff agrees. David Meltzer, an archaeologist at Southern Methodist University who co-authored the 2015 study identifying the Y signal, says that explanation makes sense. Still, he adds, finding Australasian ancestry in ancient coastal remains would boost his confidence in the authors’ conclusions. Pontus Skoglund, a population geneticist at the Francis Crick Institute who was a co-author on one of the 2015 studies with Hünemeier, says he’s glad to see South American scientists building on the previous work. “I’m excited that local research groups in Brazil are picking this up. They’re doing exactly what needed to be done.” One unanswered question is why the Y signal hasn’t turned up in any North or Central American Indigenous groups. One possibility, Hünemeier suggests, is that the Y signal–bearing migrants simply stuck to the coast and made it to South America without leaving any genetic legacy up north. It’s also possible that groups with Y ancestry did live in North and Central America, but died out in the deadly aftermath of European colonization. “The population Y signal is a puzzle,” Meltzer says, “but this is an interesting piece to add to it.”
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Post by Admin on Jun 2, 2021 22:08:58 GMT
A mysterious group of humans crossed the Bering land bridge from Siberia into the Americas thousands of years ago, genetic analyses reveal. Modern-day signatures of this ‘ghost population’ survive in people who live deep in the Brazilian Amazon, but the two research teams who have made the discovery have different ideas about when and how these migrants reached the Americas1,2. "This is an unexpected finding," says Jennifer Raff, an anthropological geneticist at the University of Texas at Austin who was not involved in either study. "It’s honestly one of the most exciting results we’ve seen in a while." North and South America were the last continents that humans settled. Previous studies of DNA from modern and ancient Native Americans suggest that the trek was made at least 15,000 years ago (although the timing is not clear-cut) by a single group dubbed the ‘First Americans’, who crossed the Bering land bridge linking Asia and North America. “The simplest hypothesis would be that a single population penetrated the ice sheets and gave rise to most of the Americans,” says David Reich, a population geneticist at Harvard Medical School in Boston, Massachusetts. In 2012, his team found evidence for a single founding migration in the genomes from members of 52 Native American groups3. So Reich was flabbergasted when a colleague called Pontus Skoglund mentioned during a conference last year that he had found signs of a second ancient migration to the Americas lurking in the DNA of contemporary Native Amazonians. Reich wasted no time in verifying the discovery. “During the session afterward, he passed his laptop over the crowd, and he had corroborated the results,” says Skoglund, who is now a researcher in Reich’s lab. Skoglund’s discovery — which is published online on 21 July in Nature2 — was that members of two Amazonian groups, the Suruí and the Karitiana, are more closely related to Papua New Guineans and Aboriginal Australians than other Native Americans are to these Australasian groups. The team confirmed the finding with several statistical methods used to untangle genetic ancestry, as well as additional genomes from Amazonians and Papuans. “We spent a lot of time being sceptical and incredulous about the finding and trying to make it go away, but it just got stronger,” says Reich. Their explanation is that distant ancestors of Australasians also crossed the Bering land bridge, only to be replaced by the First Americans in most of North and South America. Other genetic evidence suggests that modern-day Australasians descend from humans who once lived more widely across Asia. “We think this is an ancestry that no longer exists in Asia, which crossed Beringia at some point, but has been overwritten by later events,” Reich says. The team calls this ghost population “Population Y”, after the word for ancestor, Ypykuéra, in the languages spoken by the Suruí and Karitiana. They contend that Population Y reached the Americas either before or around the same time as the First Americans, more than 15,000 years ago. Timing dispute Skoglund was not the only scientist to uncover an unexpected connection between Americans and Australasians. As part of a study tracing the timing of humans’ migration across the Bering land bridge, Eske Willerslev, an evolutionary geneticist at the Natural History Museum of Denmark in Copenhagen, and his colleagues also noticed the link. But they contend that Australasian DNA reached the Americas less than 9,000 years ago. They discovered traces of Australasian ancestry in contemporary Aleutian islanders living off the coast of Alaska and propose that ancient Aleutians introduced the DNA into other Native American groups after the islands were first settled. Their study is published in Science1. “Our interpretation might differ as to how this gets in, but the signal is obvious in both papers,” says Maanasa Raghavan, an evolutionary geneticist who is part of the Copenhagen team. Both teams dismiss the possibility that the ancestry was carried more recently by trans-Pacific mariners, she notes. Lars Fehren-Schmitz, a biological anthropologist at the University of California, Cruz, who is collaborating with Reich on a separate project to sequence DNA from ancient South Americans, questions whether the hypothesis of a more recent migration can explain the presence of Australasian DNA in the Amazon. “This scenario makes no sense to me. Why should they travel all the way from the far north to the Amazon without leaving any trace in the Americas?” he says. Raghavan says that interbreeding between neighbouring populations could have carried the Australasian DNA from the Aleutians to the Amazon, even if no individuals made the trek. Raff, too, favours Reich and Skoglund’s interpretation. She thinks that the humans who colonized America from Siberia were more diverse than was once thought, with ‘Population Y’ isolated enough from the ‘First Americans’ to leave distinct genetic signatures. DNA gleaned from ancient skeletons in the Americas may settle the debate. “They’re going to need to sample more ancient genomes from the Amazon. Good luck with that,” says Raff. “The Amazon is quite possibly the worst place imaginable for DNA preservation,” with its humid climate, says Skoglund. But further sampling should be possible in other parts of the Americas and in Siberia, where Population Y presumably once lived. “We’ve got very different models. The rubber will meet the road when we get more ancient genomes,” says David Meltzer, an archaeologist at Southern Methodist University in Dallas, Texas, who is part of the Copenhagen team.“I think this is actually pretty awesome.” References 1 Raghavan, M. et al. Science dx.doi.org/10.1126/science.aab3884 (2015) 2 Skoglund, P. et al. Nature dx.doi.org/10.1038/nature14895 (2015). 3 Reich, D. et al. Nature 488, 370–374 (2012).
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Post by Admin on Jun 3, 2021 19:57:01 GMT
Researchers first noted the astonishing link back in 2015, but a new study from the University of São Paulo has confirmed that Australian DNA is even more widespread in Indigenous South Americans than originally thought. “Our results showed that the Australasian genetic signal, previously described as exclusive to Amazonian groups, was also identified in the Pacific coastal population,” noted the study’s senior researcher, professor Tábita Hünemeier. Along with co-lead researcher and doctoral student Marcos Araújo Castro e Silva, Hünemeier and their team set out to build upon the original 2015 study that found a link between the people of Australasia ⏤ which includes Indigenous Australians and Melanesians, or people from islands in the Oceania region ⏤ and two tribes in Brazil, the Karitiana and the Suruí people. The researchers had a feeling that the link was just the tip of the iceberg. They were right. “This Australasian−Native American connection persists as one of the most intriguing and poorly understood events in human history,” the researchers wrote. The shared genetic marker between Australasian and South American tribes was dubbed the “Y signal” for “Ypikuéra,” which is an Indigenous word from Brazil’s Tupi people that means “ancestor.” This year, the University of São Paulo began to search for the Y signal within a larger set of genetic data from 383 Indigenous people in South America. They consequently found the Y signal in the Karitiana and the Suruí people and also in several other tribes, including the Chotuna people of Peru and the Guaraní Kaiowá and Xavánte people of Brazil. The Guaraní Kaiowá people live in the center-west of Brazil; the Xavánte live near the center of the country. These results proved that the Y signal was indeed more widespread within South America than originally thought. “Genetics is an ally to unravel unrecorded histories and populations,” said Hünemeier and Castro e Silva, noting that waves of European colonization has obscured Indigenous history. So, how did people from Australasia get to South America in the first place? The researchers theorize that, some 20,000 years ago, the ancient people who crossed the Bering Land Bridge between Asia and North America carried Australian DNA with them. Ancient people moved across the Bering Land bridge thousands of years ago. They likely started from southeastern Asia, moved north, and then mixed with ancient Siberian and Beringian people. “It is as if these genes had hitched a ride on the First American genomes,” Hünemeier and Castro e Silva said. From there, these ancient people would have made the long trek across the Bering Land Bridge. These “first settlers” then began to populate the Pacific coast, stretching down from Alaska to southern Chile. Hünemeier and Castro e Silva suspect that they settled along the coast “due to their subsistence strategies and other cultural aspects adapted to life by the sea.” Then, a second wave of people moved further inland. “In this context, the expansion to the Amazon, passing through the northern Andes, would have been a secondary movement,” the researchers explained. But there’s one mystery that the study didn’t solve. Although researchers found the Y signal in South American tribes, it’s yet to be found in North American Indigenous people. If ancient Australasians crossed the Bering Land Bridge and then moved South, wouldn’t they have left genetic evidence along the Pacific coast of North America as well? The researchers have a few theories as to why not. First, it’s possible that the ancient people stuck to the coast and moved quickly, leaving no genetic markers behind.
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Post by Admin on Jun 4, 2021 5:54:24 GMT
Deep genetic affinity between coastal Pacific and Amazonian natives evidenced by Australasian ancestry PNAS April 6, 2021 118 (14) e2025739118; doi.org/10.1073/pnas.2025739118Abstract Different models have been proposed to elucidate the origins of the founding populations of America, along with the number of migratory waves and routes used by these first explorers. Settlements, both along the Pacific coast and on land, have been evidenced in genetic and archeological studies. However, the number of migratory waves and the origin of immigrants are still controversial topics. Here, we show the Australasian genetic signal is present in the Pacific coast region, indicating a more widespread signal distribution within South America and implicating an ancient contact between Pacific and Amazonian dwellers. We demonstrate that the Australasian population contribution was introduced in South America through the Pacific coastal route before the formation of the Amazonian branch, likely in the ancient coastal Pacific/Amazonian population. In addition, we detected a significant amount of interpopulation and intrapopulation variation in this genetic signal in South America. This study elucidates the genetic relationships of different ancestral components in the initial settlement of South America and proposes that the migratory route used by migrants who carried the Australasian ancestry led to the absence of this signal in the populations of Central and North America. A signal of genetic affinity between present-day and ancient natives from South America and present-day indigenous groups of South Asia, Australia, and Melanesia has been previously reported (1⇓⇓–4). This Australasian−Native American connection persists as one of the most intriguing and poorly understood events in human history. The controversial Australasian population genetic component (i.e., “Ypikuéra population” or “Y population” component) was identified exclusively in the present-day Amazonian populations (2), suggesting at least two different founding waves leading to the formation of the people of this region. The first wave was inferred to be composed of direct descendants of the Beringian standstill population, and a second wave was formed by an admixed population of Beringian and southeast Asian ancestors that reached Beringia more recently. Both these populations would have settled and admixed in the Amazon region. The contribution of an unsampled population to the autochthonous gene pool is thought to have led to the origin of the Australasian shared ancestry (2). In this sense, the Y population would be part of the first colonizing groups of the American continent. However, data from ancient South American samples indicated a weak Y signal around 10,000 yBP (3). This evidence indicates that, rather than a second wave entering South America from southeast Asia, the Y ancestry might be traced back to common ancestors of Native Americans, who lived in northeast Asia. Furthermore, a new line of evidence indicates that the first American clades split in East Asia, not in Beringia, which makes the gene flow of the Y ancestry from the ancestral East Asian groups even more likely (5). However, the paucity of the signal among present-day and ancient groups, along with the endemic and apparently random pattern of detection, has raised the possibility that it could be a false-positive detection, likely due to the strong genetic drift effects experienced by the Amazonian populations (and other indigenous South Americans). However, it might be the other way around, a scenario in which the signal went below the significance level in some populations, due to the high drift effects they experienced (i.e., false negatives). We explored our dataset (SI Appendix, Extended Methods), which is currently the most comprehensive set of genomic data from South American populations (383 individuals; 438,443 markers), to shed light on this question. Ethical approval for sample collection was provided by the Brazilian National Ethics Commission (CONEP Resolutions 123 and 4599). CONEP also approved oral consent for the use of these samples in population history and human evolution studies. Individual and/or tribal informed oral consent was obtained from participants who were not able to read or write. Our results showed that the Australasian genetic signal, previously described as exclusive to Amazonian groups, was also identified in the Pacific coastal population, pointing to a more widespread signal distribution within South America, and possibly implicating an ancient contact between Pacific and Amazonian dwellers. In addition, a significant amount of interpopulation and intrapopulation variation of this genetic signal was detected.
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Post by Admin on Jun 4, 2021 21:10:30 GMT
To test the existence of this excess allele sharing, we calculated the D(Mbuti, Australasian; Y, Z) statistic for every pair of Y and Z indigenous groups or individuals in our dataset (Dataset S1A), where “Australasian” is also iterated over the Australasian groups, namely Australian (and Australian.DG), Melanesian, Onge (i.e., ONG.SG), and Papuan (6⇓⇓–9). In the tests between groups, signal detection was reproduced in Karitiana and Suruí (Amazonia), but it was also observed in Chotuna (Mochica descendants from the Pacific coast), Guaraní Kaiowá (central west Brazil), and Xavánte (Central Brazilian Plateau) (Dataset S3). When we used the maximum unrelated set of individuals (Dataset S1A), the signal lost significance level in Karitiana, Suruí, and Guaraní Kaiowá (Dataset S3). However, the signal was still evident in the Pacific coast population and in the central Brazilian natives (Fig. 1 and Dataset S3). Fig. 1. Relative patterns of genetic affinity of Australasians among Native American groups. (A) Maximum Z values per population interpolated with the inverse distance weighting method. (B) Distribution of all estimated Z values (y axis) for each “Z” population (x axis) as violin and box plots. In B, the black dots represent outliers, and the red dashed lines indicate the Z-value thresholds of Z = −3 and Z = 3. We also aimed to detect whether some individuals would present a higher number of significant tests than others from the same population, which could indicate a heterogeneous genetic ancestry within the positive populations. Our analysis showed that, indeed, some individuals presented a higher number of tests pointing to excess allele sharing, but also that some are more likely to present a significant deficit of this ancestry in comparison to the others (Fig. 2 and Dataset S4 C and D). From these results, it is evident that the loss of signal significance upon the shift from the complete set to the maximum unrelated set of samples (Dataset S3) was caused by the exclusion of specific individuals with higher levels of allele sharing with Australasians rather than by the removal of a bias caused by the relatedness among the tested samples in the first place. Fig. 2. Excess affinity of Native Americans with Australasians. The y axis indicates the group affiliation of the individual used at the Z position of the statistic (excess in allele sharing). The x axis represents the group affiliation of the individual at the Y position of the statistic (deficit in allele sharing). Estimates were clustered by groups, and the number of significant tests was weighted by the number of individuals in the comparison. This provides strong evidence that a significant variability of this signal exists not only at an interpopulation level but also between individuals from the same populations. These results suggest that the intrapopulation variability of this signal is not rare (Fig. 2) and is observed in several groups (Apalai, Guaraní Nãndeva, Karitiana, Munduruku, Parakanã, and Xavánte). Most significant tests detected this excess signal in Tupí-speaking individuals, but the signal was also detected in individuals from every major linguistic group (Fig. 2 and Dataset S4) and, at the same time, presented a widespread geographic distribution within South America (Fig. 1). Conversely, a considerable number of samples were inferred to have a deficit of allele sharing with Australasians (Fig. 2 and Dataset S4D). Strikingly, the individual PAR137 (Parakanã) presented an extremely high proportion of significant tests (31.64%), indicating a relative deficit. This individual is not an outlier neither in the principal component analysis of the Native American samples (Dataset S1 B and C), nor regarding its missingness rate (Dataset S1A), nor in a multidimensional scaling (MDS) of pairwise genetic distances between samples in the unrelated and unadmixed subset (Dataset S1D). Besides, the distribution of Y-population ancestry among present-day indigenous groups of South America showed no relationship with ethnolinguistic diversity or geographic location. To further characterize the ancestry of Central and South American indigenous groups, we replicated a series of tests performed with qpWave by Skoglund et al. (2) to investigate the minimum number of ancestry streams necessary for the formation of these populations. Essentially, we selected four populations from each of the six global regions (sub-Saharan Africa, western Europe, East Asia, South Asia, Siberia/central Asia, and Oceania) as outgroups, and 14 indigenous groups with more than three unadmixed and unrelated individuals as test groups (SI Appendix, Extended Methods). These groups were tested in a few combinations, and the results are summarized in Dataset S5 (qpWave weights for the full dataset in Dataset S5B). These results reproduce the estimates obtained by Skoglund et al. (2) also indicating that at least two streams of migration are necessary to explain the present-day genetic diversity of Central and South American populations.
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