Genome sequencing indicates Kennewick Man is Native American, reopening the bitter battle over whether he should be reburied or studied 
 
 Genetic tests on one of the most important human skeletons ever found in North America have re-ignited a fierce debate over the rightful fate of the remains. 
 
 The ancient skeleton of Kennewick Man became the focus of a bitter $5m court battle between the US government, which planned to return the bones to Native Americans for reburial, and scientists, who wanted to study the remains. 
 
 
 
 In 2004, a US court ruled in favour of the scientists after it judged that Native American tribes had failed to prove their kinship with Kennewick Man. 
 
 But now the story has taken an ironic twist. Genetic tests made possible by the ruling suggest Kennewick Man probably is Native American. Having rescued the bones for science, scientists have nudged them towards the grave. 
 
 
 
 “This is where all hell breaks lose,” said Eske Willerslev, a world expert in ancient DNA who led the analysis at the University of Copenhagen in Denmark. “I am completely confident Kennewick Man is Native American. He is as much Native American as Native Americans living today.” 
 
 DNA study reveals third group of ancient ancestors of modern Europeans Read more 
 
 Jim Boyd, a member of the Confederated Tribes of the Colville Reservation in northern Washington, who fought for repatriation of the remains, said: “This is a happy time for us. We have maintained throughout that the Ancient One is a relative of ours, so these findings are wonderful for us.” 
 
 “We expect to have a fight, but we would like to see him buried very respectfully in a resting place where he should be. My own belief is that we will get the remains back,” he added. But that is not likely, or justified, some scientists maintain. 
 
 The near-complete skeleton of Kennewick Man was discovered by chance in 1996, when students stumbled upon a skull while wading through the Columbia river near Kennewick in Washington state. 
 
 
 
 The skeleton had the police, archaeologists and the local coroner baffled. Kennewick Man did not look Native American. Adding to the mystery, his teeth were free from fillings and profoundly worn down: a clear dental signature of an ancient diet. 
 
 
 
 Closer inspection of the bones revealed a sharp stone spearpoint wedged in the man’s hip, placing him firmly in prehistory. The true age of the skeleton emerged soon after, when carbon dating of a bone fragment put the man at 9,000 years old. 
 
 
 
 On hearing the age of the remains, the US Army Corps of Engineers, who manage the land where the skeleton was found, claimed ownership and blocked scientists from studying the bones. Local Native Americans then appealed to the corps to return the remains under US repatriation laws. The army corps, already in negotiations with the tribes over fishing rights and pollution problems, agreed. 
 
 
 
 But the looming reburial of Kennewick Man distressed some scientists. One group, led by Douglas Owsley at the Smithsonian Institution in Washington DC, decided to sue the government in the hope of saving the remains for science. The US courts ruled in their favour in 2002, and again in 2004 when the government appealed the decision. Ordered to give the scientists access to the bones, the corps permitted 16 days for researchers to study the remains. 
 
 
 
 The Smithsonian’s research was brief but intense. It pointed to an unusual origin for Kennewick Man. His diet suggested he hunted along the coast, and was not from the region where he was found. From the size and shape of his skull, he appeared to be descended from the people who gave rise to modern Polynesians, the scientists said. 
 
 
 
 But Willerslev now contests those conclusions. He commissioned researchers at the University of Zurich to reanalyse the skull measurements. The group concluded that it was impossible to say where Kennewick Man came from. The remains of one individual are simply not enough to go on, they found. 
 
 
 
 Writing today in the journal Nature, Willerslev and his colleagues describe how they extracted and sequenced DNA from 200 grams of Kennewick Man’s hand bone. When they compared the ancient DNA to samples taken from people around the world, they found the closest match with Native Americans, in particular the Colville tribe, which still lives in the region. 
 
 
 
 “Of all the Native American genome sequences we have, the Colville is the closest we have to Kennewick Man,” Willerslev told the Guardian. “Our data show that the Colville come from same population as Kennewick Man.” In other words, they are his direct descendants. 
 
 But Owsley urges caution. Though impressed by the genetics in the study, he believes Willerslev is making claims his data cannot support. 
 
 “The whole Kennewick Man lawsuit was to try and make studies like this possible,” Owsley told the Guardian. “Any time we gain additional genetic information from a very ancient skeleton is a very important advancement.” 
 
 “Where I really think they really overstep is when they focus on the descendants of Kennewick Man. It is extremely important to stress that when they try to link him to one particular tribe; in reality, he’ll be linked to multiple groups in the Americas.” 
 
 Part of the problem is the paucity of DNA from ancient people to compare with that taken from Kennewick Man. A close match means little if many ancient people are not included in the analysis. 
 
 Owsley said the new data do nothing to undermine the court decision of 2004. He said Kennewick Man still fails to meet the definition of a Native American in the Native American Graves Protection and Repatriation Act (NAGPRA). Under the Act, “Native American” means of, or relating to, a tribe, people, or culture that is indigenous to the United States. 
 
 A challenge in court “would never stand up” Owsley said. “We don’t know anything about his culture. We don’t know who his people are. And we don’t know where he’s coming from.” 
 
 “I’ve worked on thousands of humans skeletons, and I’ve never worked on a set of remains that are as important in helping us understand this time period. There are people who, like myself, think this is one of America’s most important findings. I think we need to take our time. We still don’t know the full story,” he added. 
 
 Willerslev refused to share his own view on what should happen to the remains, but has spoken with the Colville tribe about his findings. 
 
 “They lost their legal case based on what I’d call poor scientific evidence,” he told the Guardian. “They have been devastated ever since the ruling and they feel very strongly about reburying. They believe the spirit won’t rest until it is reburied. I expect they will make a claim again.” 
 
 

 
 
 A clay facial reconstruction of the Kennewick man, who, new research says, was Native American. (Photo by Brittney Tatchell/Smithsonian Institute) 
 
 The skull in the eroded riverbank belonged to a man with a narrow, projecting face. The archeologist who excavated the bones along the Columbia River near Kennewick, Wash., thought he was looking at the remains of a white man, probably a pioneer. Then further analysis showed the skeleton to be thousands of years old. Confusion reigned. People asked: What was a white man doing in the Pacific Northwest back in the Stone Age? 
 
 So began the tortuous tale of the Kennewick Man, a hunter who in life had five broken ribs and a spear point lodged in his hip, and in death a knack for generating scientific and cultural controversy. 
 
 Last year, scientists published a comprehensive book, co-edited by Smithsonian Institution forensic anthropologist Douglas Owsley, which concluded that Kennewick Man appeared to be more closely related to the indigenous Ainu people of Japan and today’s Polynesians than to modern Native Americans. Owsley and colleagues said he came from the frozen north; he conceivably was born in Siberia, descended from a population of coastal-dwelling East Asians that not only reached North America but also gave rise to the Ainu and the Polynesians. 
 
 But on Thursday, a report published in the journal Nature rejected that scenario, citing the first analysis of genetic material extracted from Kennewick Man. He was, the report said, a Native American after all. 
 
 The genetic findings could have legal ramifications in the long battle between scientists, who say the 8,500-year-old remains are a national scientific treasure, and Native American tribes that claim the mystery man as an ancestor and seek to rebury him. 
 
 “We have maintained the belief that the Ancient One is, in fact, one of us, so we’ve never strayed from that theory. So it is good news,” said Jim Boyd, chairman of the Confederated Tribes of the Colville Reservation. The report linked the remains to the Colville tribes. 
 
 The genetic evidence directly challenges conclusions based largely on measurements of the skull. From the very beginning, the people studying Kennewick Man noticed that he didn’t look like a Native American, and the new report doesn’t dispute that. He really does look Ainu or Polynesian. 
 
 That fact has led scientists such as Owsley, of the National Museum of Natural History, to view Kennewick Man as most likely a member of a population distinct from the ancestors of Native Americans. Native Americans are descended from people who, during a period of lower sea levels, walked to Alaska from Siberia over the Bering Land Bridge. 
 
 After analyzing the degraded fragments of DNA from a hand bone, the authors of the Nature paper concluded that Kennewick Man shared close ancestry with Native Americans — especially the Colville tribes — rather than with native populations in Canada or South America. 
 
 “Kennewick Man is more closely related to Native Americans than to any other population worldwide,” said Morten Rasmussen, a post-doctoral fellow at Stanford University and the University of Copenhagen, who was the lead author of the report. “We specifically tested Polynesians, Ainu, Europeans . . . and, in all cases, Kennewick Man comes out closest to Native American populations.” 
 
 So why doesn’t his skull look like that of a Native American? Rasmussen said it’s likely just a case of natural variation in appearance. 
 
 His team does not believe that it is possible to take the anatomical features of one individual, such as Kennewick Man, and draw broad conclusions about a relationship to a larger population of people. “Because there’s large variation within populations, a single individual is not representative,” he said. 
 
 But there’s another possible explanation that’s perhaps even more dramatic: Native Americans may have changed in their appearance over the course of the past 8,500 years, said Deborah Bolnick, an associate professor of anthropology at the University of Texas, who was not involved in the study. 
 
 She said the new genetic evidence “is an important contribution in showing that, despite these different skeletal features, this individual still was biologically related to both ancient and contemporary Native Americans.” 
 
 The Smithsonian’s Owsley and archeologist James Chatters, who excavated most of the bones, pointed out that the study relies on sparse genetic sampling of Native Americans. 
 
 “I think it’s extremely important to stress that these results that they’re presenting right now do not tie Kennewick Man exclusively to one tribe,” Owsley said. “There’s really no way yet known to connect this ancient individual with any modern tribe or individual. You’re talking about some 435 generations, and you can’t just link him to any present-day group.” 
 
 Rasmussen concedes that most Native American groups have been reluctant to participate in genetic testing. The Nature report shows a genetic relationship with the Colville group, which agreed to participate in the study, but four other tribes that also have claimed Kennewick Man as an ancestor did not participate. 
 
 The genetic analysis could not conclusively state that Kennewick Man was a direct ancestor of the modern Colvilles; one interpretation of the data suggested they had a common ancestor who lived about 700 years before Kennewick Man roamed the Pacific Northwest. 
 
 
 
 Previous analysis of the skeleton suggested a Polynesian kinship. (Chip Clark/Smithsonian Institution) 
 
 The discovery of the skeleton led to a protracted court fight between scientists and Native American tribes who wanted the bones returned, as usually required under the Native American Graves Protection and Repatriation Act. The scientists said he didn’t look like a Native American, and his remains should be exempt from NAGPRA. 
 
 The scientists won. The remains are now in the Burke Museum of Natural History and Culture in Seattle. The Army Corps of Engineers has legal custody. 
 
 “The Corps will certainly review those findings, and will be using this review and other information to determine if, and if so how, NAGPRA applies. We will do this as quickly as possible,” Army Corps spokeswoman Michael A. Coffey said. 
 
 It is extremely difficult to take genetic samples from bones that are thousands of years old. Earlier efforts to sequence the genome of Kennewick Man failed. But then came a team largely based in Denmark, with new techniques for sampling and analyzing degraded DNA. 
 
 In a teleconference with reporters, Eske Willerslev, a ­co-author of the paper, acknowledged an obvious irony: Had the tribes prevailed early on, scientists would have been unable to do the DNA analysis that has now found a genetic connection to the modern tribes. 
 
 But Boyd, the Colville tribal chairman, said his people didn’t need the affirmation of the scientific community, because they had their oral tradition. He saw no need for further scientific study of the skeleton. 
 
 “Our oral traditions have basically told us, through that process, that this is a relative of ours. This is our relation. This is our ancestor,” Boyd said. “This person deserves to be buried respectfully and rest in peace. You know how science is — it can keep on going on and on forever. We can always wait for a new technology, but we’re still not sure they’re ever going to find out anything new, and I’m not sure we can wait for that.” 
 
 Read More: 
 
 Kennewick Man had a projectile point in his hip, five broken ribs and a bum shoulder from throwing spears. 
 
 Girl's 12,000-year-old skeleton offers evidence of evolutionary changes in appearance of Native Americans. 

 The skeleton of Kennewick Man was inadvertently discovered in July of 1996 in shallow water along the Columbia River shoreline outside Kennewick, Washington state, USA. On several visits to the locality over the following month, some 300 bone elements and fragments were collected, ultimately comprising ~90% of an adult male human skeleton3. The initial assessment of this individual was that he was a historic-period Euro-American, based largely on his apparently “Caucasoid-like”3 cranium, along with a few artefacts found nearby (later proved not to be associated with the skeletal remains). However, radiocarbon dating subsequently put the age of the skeleton in the Early Holocene1. The claim that Kennewick Man was anatomically distinct from modern Native Americans in general, and in particular from those tribes inhabiting northwest North America4, sparked a legal battle over the disposition of the skeletal remains. Five tribes who inhabit that region requested the remains be returned to them for reburial under the Native American Graves Protection and Repatriation Act (NAGPRA). The US Army Corps of Engineers, which manages the land where Kennewick Man was found, announced their intent to do so. That in turn prompted a lawsuit to block the repatriation2, 5, and generated considerable scientific controversy as to Kennewick Man’s ancestry and affinities (for example refs 3, 6, 7, 8, 9). The lawsuit ultimately (in 2004) resulted in a judicial ruling in favour of a detailed study of the skeletal remains, the results of which were recently published2. 
 
 These studies provide important details on, for example, Kennewick Man’s life history, refine his antiquity to 8,358 ± 21 14C years bp or to within a two sigma range of 8,400–8,690 calibrated years bp, and demonstrate that the body had been intentionally buried and had eroded out shortly before discovery2. They also include anatomical and morphometric analyses, which confirm earlier studies that Kennewick Man resembles circumpacific populations, particularly the Ainu and Polynesians2, 10; that he has certain “European-like morphological” traits2; and that he is anatomically distinct from modern Native Americans2. These results are interpreted as indicating that Kennewick Man was a descendant of a population that migrated earlier than, and independently of, the population(s) that gave rise to modern Native Americans2. 
 
 However, those recent studies did not include DNA analysis. Herein we present the genome sequence of Kennewick Man in order to resolve his ancestry and affinities with modern Native Americans. There were several prior efforts to recover genetic material from Kennewick Man11, but none were successful. 
 
 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 f 3 -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, f 3 -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 1: Genetic affinities between Kennewick Man and a panel of World-wide populations. a, Principal components analysis (PCA) projecting Kennewick Man and Anzick-1 onto a set of out-of-Africa populations. b, Heat map of f 3 -outgroup statistics between Kennewick Man, Native Americans, Siberians and additional populations with suggested relationship to Kennewick Man (in squares). Warmer colours indicate higher allele sharing. For list of population labels, see methods section. c, Admixture proportions for worldwide set of population, including masked Native American, Anzick-1 and Kennewick, shown at K = 14. Full size image (212 KB) 
 
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 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. Depicted is a population tree consistent with the broad affinities between modern and ancient Native Americans. Kennewick Man and the Anzick-1 child are indicated with blue and green stars respectively. Red dashed arrows indicate gene flow (1) of Asian-related ancestry with tribes of the Pacific Northwest and (2) between Colville and neighbouring tribes. Full size image (60 KB) 
 
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 Figures/tables index 
 
 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. 
 
 Table 1: Direct ancestry test Full table Figures/tables index 
 
 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.
– Kennewick Man is not only "one of the most important human skeletons ever found in North America," in the words of the Guardian, it's also one of the most controversial. Now a new DNA study might—but only might—bring finality to the debate over the "Ancient One." Danish researchers have concluded that he was Native American, they report in Nature. The results could sway the Army Corps of Engineers to turn over the remains to Native American groups for burial. Scientists want the bones kept available for study, and they have pushed against allowing Native Americans to bury the remains ever since they were found about 20 years ago in Washington state. One reason: The skull doesn't resemble those of Native Americans. The corps promises to review the study and make a decision "as quickly as possible," reports the Washington Post. “It’s very clear that Kennewick Man is most closely related to contemporary Native Americans,” a geneticist at the University of Copenhagen and lead author of the study tells the New York Times. “In my view, it’s bone-solid.” A skeptical Smithsonian scientist, however, tells AP that the results aren't conclusive enough to tie Kennewick Man—a "traveler" who lived about 8,500 years ago—to modern tribes. Either way, the study author points out an ironic twist: The DNA tests suggesting Native American heritage—and thus opening the door to burial—were made possible by court victories won by scientists seeking to keep the remains available for study. Still, Native American groups aren't expecting a quick resolution. “We expect to have a fight," says a member of the Confederated Tribes of the Colville Reservation, "but we would like to see him buried very respectfully in a resting place where he should be."