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Post by Admin on Jun 19, 2015 3:06:30 GMT
The relatives of a much-debated 8,500-year-old skeleton found in Kennewick, Washington, have been pinned down: The middle-age man was most closely related to modern-day Native Americans, DNA from his hand reveals. The new analysis lays to rest wilder theories about the ancestry of the ancient American, dubbed Kennewick Man, said study co-author Eske Willerslev, an evolutionary biologist at the Natural History Museum of Denmark at the University of Copenhagen.  "There have been different theories, different mythology, everything from him being related to Polynesians, to Europeans, to [indigenous people] from Japan," Willerslev told Live Science. "He is most closely related to contemporary Native Americans." At a news conference then, researchers studying the skeleton said the ancient man was "Caucasoid," an archaic, 19th-century term that includes a wide swath of people with origins in Africa, Western Asia and Europe. Reporters heard the word "Caucasian," and all of a sudden people were wondering how a European showed up in North America and was shot thousands of years before Europeans set foot on the continent, Meltzer said. In the new study, which was published today (June 18) in the journal Nature, Meltzer, Willerslev and their colleagues took a second look at DNA from a sliver of Kennewick Man's hand bone. They then compared that DNA with that of several modern-day Native American populations, as well as Ainu and Polynesian populations. The team also reanalyzed the skull and concluded that, because it was just one sample, it was well within the range of variation that could have been found among ancestral Native American populations. "There's no getting around it, Kennewick Man is Native American," Meltzer said. The team also found the closest genetic match came from people living along the Northwest coast, particularly the Colville people, who were some of the first to claim Kennewick Man as one of their own. But because not all the tribes that claim the Kennewick Man as an ancestor submitted DNA, and few other Native Americans have submitted DNA samples, other tribes could be even more closely related to him, Meltzer added.  Scientists who examined the remains had concluded that the skull looked different from those of contemporary Native Americans — more like Polynesians or members of the Japanese aboriginal group known as the Ainu. But past efforts to glean ancient DNA from Kennewick Man failed, notes Eske Willerslev, a palaeogenomicist at the Natural History Museum of Denmark in Copenhagen, who led the current study. Willerslev’s team used cutting-edge methods to extract snippets of DNA from a 0.2-gram flake of finger bone. “We got a very, very tiny sample,” he says. “We sampled it to complete exhaustion — there’s nothing left." It was so small that the team were only able to obtain a low-quality genome sequence. Kennewick Man’s genome reveals that he is more closely related to contemporary Native Americans than to any other humans on the planet — dashing the remote possibility that he represents a mysterious migration from the east. To trace Kennewick Man’s genetic legacy, the team compared his genome to that of members of dozens of groups from across North and South America, including several members of the Confederated Tribes of the Colville Reservation, one of the five groups seeking Kennewick Man’s reburial. Members of the other four groups — the Nez Perce, the Umatilla, the Yakama and the Wanapum — opted not to contribute DNA to the study.  The fate of Kennewick Man's remains is still uncertain. In concluding that NAGPRA did not apply, federal courts effectively decided that the remains were not Native American. “I’m quite certain we’ve made the case that Kennewick was Native American,” says David Meltzer, an archaeologist at Southern Methodist University in Dallas, Texas, who was part of Willerslev’s team. “I think this would have been useful evidence in the original NAGPRA decision and might have led to a different result,” says Hank Greely, a legal scholar at Stanford University in California. Gail Celmer, an archaeologist at the US Army Corps of Engineers in Portland, Oregon, met with tribal representatives this week and says they are still eager to pursue repatriation. Her agency now plans to reconsider whether Kennewick Man falls under NAGPRA and therefore must be returned, in light of the genome study and other new evidence. "We expect challenges, so we’re going to have to be very careful about how we do our reviews," she says. “We have a long road ahead of us." |
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Post by Admin on Jun 20, 2015 2:49:32 GMT
 Figure 1: Genetic affinities between Kennewick Man and a panel of World-wide populations. We obtained ~1 × coverage of the genome, from 200 mg of metacarpal bone specimen (Supplementary Information 1) using previously published methods12, 13. The endogenous DNA content was between 0.4% and 1.4% for double-stranded and single-stranded libraries, respectively (Supplementary Information 2). Average fragment length was 53.6 base pairs (bp) and exhibited damage patterns typical of ancient DNA, with excessive deamination of cytosine towards the ends of the fragments (Supplementary Information 2). Similarly, patterns of DNA decay agree with published expectations14, and display an estimated molecular half-life corresponding to 3,670 years for 100-bp molecules (Supplementary Information 3). The mitochondrial genome was sequenced to ~71× coverage and is placed at the root of haplogroup X2a (Extended Data Fig. 1, Supplementary Information 2), and the Y-chromosome haplogroup is Q-M3 (Extended Data Fig. 2, Supplementary Information 5); both uniparental lineages are found almost exclusively among contemporary Native Americans15, 16. We used the X chromosome to conservatively estimate contamination to be 2.5%, which is within the normal range obtained observed in genomic data from ancient human remains17, and we further show this contamination to be of European origin (Supplementary Information 4). We compiled an autosomal reference data set consisting of published SNP array data18, 19, 20, 21, 22, 23 as well as new data generated from one of the claimant tribes, the Colville (Supplementary Information 10). Due to high levels of recent admixture in many Native American populations, we masked European ancestry from the Native Americans (Supplementary Information 6). No masking was done on the Kennewick Man. When we compare Kennewick Man with the worldwide panel of populations, a clear genetic similarity to Native Americans is observed both in principal components analysis (PCA) and using f3-outgroup statistics (Fig. 1a, b). In particular, we can reject the hypothesis that Kennewick Man is more closely related to Ainu or Polynesians than he is to Native Americans, as seen in a D-statistic-based test where no trees of the type ((CHB,Ainu/Polynesian),(X,Karitiana)) with X being Kennewick Man, the Clovis age Anzick-1 child (ref. 12) or a modern Native American genome are rejected (Extended Data Fig. 3). Model-based clustering using ADMIXTURE24 shows that Kennewick Man has ancestry proportions most similar to those of other Northern Native Americans (Fig. 1c, Supplementary Information 7), especially the Colville, Ojibwa, and Algonquin. Considering the Americas only, f3-outgroup and D-statistic based analyses show that Kennewick Man, like the Anzick-1 child, shares a high degree of ancestry with Native Americans from Central and South America, and that Kennewick Man also groups with geographically close tribes including the Colville (Fig. 2a, b; Extended Data Fig. 4). Despite this similarity, Anzick-1 and Kennewick Man have dissimilar genetic affinities to contemporary Native Americans. In particular, we find that Anzick-1 is more closely related to Central/Southern Native Americans than is Kennewick Man (Extended Data Fig. 5). The pattern observed in Kennewick Man is mirrored in the Colville, who also shows a high affinity with Southern populations (Fig. 2c), but are most closely related to a neighbouring population in the data set (Stswecem’c; Extended Data Fig. 4c). This stands in contrast to other populations such as the Chipewyan, who are closer related to Northern Native Americans rather than to Central/Southern Native Americans in all comparisons (Fig. 2d; Extended Data Fig. 4d).  Figure 2: Shared ancestry among samples within the Americas. Our results are in agreement with a basal divergence of Northern and Central/Southern Native American lineages as suggested from the analysis of the Anzick-1 genome12. However, the genetic affinities of Kennewick Man reveal additional complexity in the population history of the Northern lineage. The finding that Kennewick is more closely related to Southern than many Northern Native Americans (Extended Data Fig. 4) suggests the presence of an additional Northern lineage that diverged from the common ancestral population of Anzick-1 and Southern Native Americans (Fig. 3). This branch would include both Colville and other tribes of the Pacific Northwest such as the Stswecem’c, who also appear symmetric to Kennewick with Southern Native Americans (Extended Data Fig. 4). We also find evidence for additional gene flow into the Pacific Northwest related to Asian populations (Extended Data Fig. 5), which is likely to post-date Kennewick Man. We note that this gene flow could originate from within the Americas, for example in association with the migration of paleo-Eskimos or Inuit ancestors within the past 5 thousand years25, or the gene flow could be post colonial19.  Figure 3: Illustration of Native American population history. We used a likelihood ratio test to test for direct ancestry of Kennewick Man for two members of the Colville tribe who show no evidence of recent European admixture. This test allows us to determine if the patterns of allele frequencies in the Colville and Kennewick Man are compatible with direct ancestry of the Colville from the population to which Kennewick Man belonged, without any additional gene flow. As a comparison we also included analyses of four other Native Americans with high quality genomes: two Northern Athabascan individuals from Canada25 and two Karitiana individuals from Brazil12, 13. While the test rejects the null hypothesis of direct ancestry with no subsequent gene flow in all cases, it only does so very weakly for the Colville tribe members (Table 1, Supplementary Information 8). These findings can be explained as: (1) the Colville individuals are direct descendants of the population to which Kennewick Man belonged, but subsequently received some relatively minor gene flow from other American populations within the last ~8.5 thousand years, in agreement with our findings above; (2) the Colville individuals descend from a population that ~8.5 thousand years was slightly diverged from the population which Kennewick Man belonged or (3) a combination of both. It has been asserted that “…cranial morphology provides as much insight into population structure and affinity as genetic data”2. However, although recent and previous craniometric analyses have consistently concluded that Kennewick Man is unlike modern Native Americans, they disagree regarding his closest population affinities, the cause of the apparent differences between Kennewick Man and modern Native Americans, and whether the differences are historically important (for example, represent an earlier, separate migration to the Americas), or simply represent intra-population variation2, 3, 7, 10, 26, 27, 28. These inconsistencies are probably owing to the difficulties in assigning a single individual when comparing to population-mean data, without explicitly taking into account within-population variation. Reanalysis of W. W. Howells’ worldwide modern human craniometric data set29 (Supplementary Information 9) shows that biological population affinities of individual specimens cannot be resolved with any statistical certainty. While our individual-based craniometric analyses confirm that Kennewick Man tends to be more similar to Polynesian and Ainu peoples than to Native Americans, Kennewick Man’s pattern of craniometric affinity falls well within the range of affinity patterns evaluated for individual Native Americans (Supplementary Information 9). For example, the Arikara from North Dakota (the Native American tribe representing the geographically closest population in Howells’ data set to Kennewick), exhibit with high frequency closest affinities with Polynesians (Supplementary Information 9). Yet, the Arikara have typical Native-American mitochondrial DNA haplogroups30, as does Kennewick Man. We conclude that the currently available number of independent phenetic markers is too small, and within-population craniometric variation too large, to permit reliable reconstruction of the biological population affinities of Kennewick Man. In contrast, block bootstrap results from the autosomal DNA data are highly statistically significant (Extended Data Fig. 3), showing stronger association of the Kennewick man with Native Americans than with any other continental group. We also observe that the autosomal DNA, mitochondrial DNA and Y chromosome data all consistently show that Kennewick Man is directly related to contemporary Native Americans, and thus show genetic continuity within the Americas over at least the past 8 thousand years. Identifying which modern Native American groups are most closely related to Kennewick Man is not possible at this time, since our comparative DNA database of modern peoples is limited, particularly for Native-American groups in the United States. However, among the groups for which we have sufficient genomic data we find that the Colville, one of the Native American groups claiming Kennewick Man as ancestral, show close affinities to that individual or at least to the population to which he belonged. Additional modern descendants could be identified as more Native American groups are sequenced. Finally, it is clear that Kennewick Man differs significantly from the Anzick-1 child who is more closely related to the modern tribes of Mesoamerica and South America12, possibly suggesting an early population structure within the Americas. Nature (2015) doi:10.1038/nature14625 |
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Post by Admin on Jul 7, 2015 2:50:22 GMT
It seemed like a victory of science over myth when, in 2004, the United States Court of Appeals for the 9th Circuit ruled that a group of Native American tribes would not be allowed to re-bury the 8,500-year-old skeleton known as Kennewick Man. The remains had been found eight years earlier on the banks of the Columbia River in Washington state, and, based on their oral traditions, the tribes argued that Kennewick Man was one of their ancestors. Under the 1990 U.S. Native American Graves Protection and Repatriation Act, they were entitled to take possession of any ancient human remains that relate to "a tribe, people, or culture that is indigenous to the United States." But according to a group of scientists who sued to gain access to one of the most important anthropological finds in North America, Kennewick Man's unusual Caucasian features meant that he belonged to an unknown but different ancient population unrelated to contemporary Native Americans. The Court agreed with the scientists, finding that "scant or no evidence of cultural similarities between Kennewick Man and modern Indians exists." The remains would stay in the museum where they were being kept, and scientific research could go forward.  That scientific research has now proved that the Native Americans were basically right. A study of Kennewick Man's genome published a few weeks ago shows that he belonged to an ancient population closely related to present-day members of the tribes who sought to re-bury the bones. This development in the Kennewick Man story is just the latest in a series of sometimes dramatic revisions to earlier ideas about how the Americas were first settled, thanks in large part to new evidence from genetics. In fact, what the scientists found in Kennewick Man’s DNA was not especially surprising, because the findings are consistent with several other important genetic studies published over the past decade. The evidence from these studies is cracking open one of the biggest mysteries in anthropology: Who were the ancestors of today's Native Americans? Prior to these genetic studies, scientists had developed several conflicting theories about how the Western Hemisphere was first settled. Most of these theories rooted from several widely accepted ideas: First, the Americas were the last region of the world to be populated by modern humans, almost certainly less than 20,000 years ago. Those first settlers were the first humans of any kind to arrive—unlike Africa, Asia, and Europe, the Americas contain no fossils of archaic humans like Neanderthals or Homo erectus. Also, the first settlers gradually migrated from Siberia to Alaska across the Bering land bridge, which is now under water but was then a wide, fertile plain with plenty of game. Consistent with this theory, Native Americans possess unmistakable anatomical similarities to Siberians and East Asians.  Beyond these points of consensus, there has been little agreement. Thirteen-thousand-year-old stone tools, made in a consistent style called Clovis (named for the New Mexico site where they were first discovered), have been found from northern Canada to the tip of South America, leading some scientists to propose that a single wave of original settlers colonized the entire hemisphere. But later discoveries of distinct pre-Clovis artifacts and remains led to the idea that the Clovis settlers were preceded by an earlier migration. According to this idea, these so-called "Paleoamericans" were unrelated to later Native Americans and were eventually replaced by the Clovis people, from whom today's Native Americans descend. Another major theory, based on an analysis of Native American languages, is that there were three waves of migration: a first wave of Amerindians, who populated most of North and South America; a second wave of Na-Dene, who settled northern Canada and Alaska; and a third, relatively recent Eskimo-Aleut wave. Given this heated mix of competing hypotheses, it's easy to see why scientists were so eager to study Kennewick Man when his remains turned up.  Recent genetic studies based on technologies developed after the court’s Kennewick Man ruling offer a powerful new source of evidence to help resolve these disagreements. Researchers can now survey the DNA of large numbers of different Native American populations and compare them to other populations from around the world, especially Siberia and East Asia. More and more often, the DNA of living populations can be directly and extensively compared with DNA from ancient bones. One of the major casualties of these new studies is the Paleoamerican replacement idea on which the Kennewick Man ruling was based—just four years after the Court issued its ruling, one review of the field bluntly concluded that "genetic data do not support this model." Paleoamericans were not a distinct group, unrelated to the later Clovis people.  Since then, additional genetic analyses have shown that, as one key study published in 2012 put it, "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 ago." That study, led by Harvard geneticist David Reich and one of the most exhaustive to date, included DNA surveys of 60 different living Native American and Siberian populations. The genetic data also showed that two other groups arriving from Asia after these “First Americans” contributed some DNA to members of the Eskimo-Aleut-speaking tribes in the Arctic and to the Na-Dene-speaking Native Americans in Canada. These results are somewhat consistent with the earlier three-wave theory based on linguistic analysis, but they show that coupling between original settlers and later arrivals played an important role. Last year, a team led by the University of Copenhagen scientist Eske Willerslev published an analysis of the genome of a ~13,000 year-old infant discovered in a grave in western Montana that supports these findings. A comparison of the child’s DNA to that of living Native Americans and Siberians, as well as to ancient DNA from remains found in Siberia, led the researchers to conclude that the evidence "demonstrates that contemporary Native Americans are descendants of the first people to settle successfully in the Americas." Given this evidence, it is really no surprise that the recent DNA analysis of Kennewick Man, also performed by Willerslev and his team, shows a close relationship with modern Native Americans. In fact, the researchers found that one of the tribes, the Washington state-based Confederated Tribes of the Colville Reservation, that claimed Kennewick Man as its own is part of a group that is especially closely related to Kennewick Man. And what about Kennewick Man’s unusual Caucasian features? Willerslev’s team reviewed the evidence and concluded that there aren’t enough distinct anatomical features “to permit a reliable reconstruction” of Kennewick Man’s relationship to present-day populations. The genetic data is much better. |
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Post by Admin on Jul 9, 2015 2:43:09 GMT
The incongruity between anatomy and genome-enabled heredity seen in the Kennewick Man calls into question what scientists know about how the American continents were peopled. Deep in an underwater cave in the Yucatan lie the 12,000 year old remains of a teenage girl that could help solve this conundrum.  Paleontologists have nicknamed this skeleton Naia. Like the Kennewick Man, Naia's bone structure is inconsistent with patterns seen in Native Americans. Even though Naia had been in a submerged cave for millennia, scientists were still able to recover a DNA sample. Using part of her genome, they have formulated a hypothesis for why the bones of Paleoamericans seem out of place. These results were published in Science last May.  Previous genetic research supported the theory that ancient humans trekked across the Bering land bridge to populate what would become present day America. Morphometric analyses of the oldest Paleoamerican remains like Naia and the Kennewick Man cast doubt on this theory, as they do not fit with modern Native Americans or Siberians.  The genome showed that though Naia looks different, key genetic signatures indicate she is related to the group who once crossed the land over the Bering Strait. Naia's DNA goes a long way towards bolstering confidence in the origins of Native Americans. "It helps support the consensus view, from archaeological, genetic and linguistic evidence, that the Americas were initially peopled 15,000–20,000 years ago from Siberia," said the Wellcome Trust Sanger Institute's Chris Tyler-Smith.  HN is a 62-m-diameter, subterranean, bellshaped, collapsed dissolution chamber (pit) containing the skeletons of one human and at least 26 large mammals (Fig. 1 and table S2). The three passages joining HN are 10 m below sea level (mbsl); the pit drops to a maximal depth of 55 mbsl. The bottom is strewn with roof-collapse boulders and marked by guano, accumulations of calcite raft sediment, and a few stalagmites. HN contains layered fresh and saltwater, with a halocline at 15 to 22 mbsl. This permeable aquifer tracks sea level to within 1 to 2 m. The skeletal material lies at the base of the pit, 600 m from the nearest entrance when it was a dry cave. HN is now accessible only by technical dive teams. Information collected to date has been derived primarily through videography, photography, minimal sampling, and three-dimensional modeling from remote images.  HN5/48 is among the small group of Paleoamerican skeletons, a group that is morphologically distinct from Native Americans. We extracted DNA from the skeleton’s upper right third molar and analyzed the mtDNA using methods developed for poorly preserved skeletal elements, with independent replication. The mtDNA haplogroup for the HN skeletal remains was determined through restriction fragment analysis, direct Sanger sequencing, and second-generation sequencing after target enrichment. The AluI 5176 site loss, in combination with Sanger and Illumina sequence data, confirm its placement in haplogroup D, subhaplogroup D1 (Fig. 3). Subhaplogroup D1 is derived from an Asian lineage but occurs only in the Americas, having probably developed in Beringia after divergence from other Asian populations (1).  D1 is one of the founding lineages in the Americas (1). Subhaplogroup D1 occurs in 10.5% of extant Native Americans (23), with a high frequency of 29% in indigenous people from Chile and Argentina (24). This suggests that HN5/48 descended from the population that carried the D1 lineage to South America. The discovery of a member of subhaplogroup D1 in Central America, ~4000 km southeast of any other pre–10-ka DNA in the Americas, greatly extends the geographic distribution of Pleistocene-age Beringian mtDNA in the Western Hemisphere. Science 16 May 2014: Vol. 344 no. 6185 pp. 750-754. DOI: 10.1126/science.1252619 |
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Post by Admin on Jul 30, 2015 1:46:00 GMT
Researchers found that the Suruí, Karitiana and Xavante peoples in the Amazon are more closely related to indigenous populations in Australasia than any other modern group and they hypothesised that these ancient tribes travelled into the Americas via the Bering Land Bridge just like other native Siberians (Skoglund et al. 2015). It's estimated that Australasian DNA reached the Americas less than 9,000 years ago, much later than the first wave of humans’ migration across the Bering Land Bridge. It's unlikely that primitive tribes from Australasia were capable of travelling all the way to Siberia before crossing the Bering Land Bridge as there is no trace of their (Denisovan) DNA in North America and Russia at all. The most likely scenario is that the ancestors of the Suruí, Karitiana and Xavante peoples crossed the Pacific Ocean to Latin America without taking circuitous routes via Siberia. There could have been numerous small islands between Australasia and Latin America 9,000 years ago, which enabled Australasians to cross an ocean by a series of shorter journeys through island hopping. “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.  How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we find that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (KYA), and after no more than 8,000-year isolation period in Beringia. Following their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 KYA, one that is now dispersed across North and South America and the other is restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative ‘Paleoamerican’ relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model. Skoglund, P. et al. Nature dx.doi.org/10.1038/nature14895 (2015). |
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