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, 523 (7561), 455-458

The Ancestry and Affiliations of Kennewick Man

Affiliations

The Ancestry and Affiliations of Kennewick Man

Morten Rasmussen et al. Nature.

Abstract

Kennewick Man, referred to as the Ancient One by Native Americans, is a male human skeleton discovered in Washington state (USA) in 1996 and initially radiocarbon dated to 8,340-9,200 calibrated years before present (BP). His population affinities have been the subject of scientific debate and legal controversy. Based on an initial study of cranial morphology it was asserted that Kennewick Man was neither Native American nor closely related to the claimant Plateau tribes of the Pacific Northwest, who claimed ancestral relationship and requested repatriation under the Native American Graves Protection and Repatriation Act (NAGPRA). The morphological analysis was important to judicial decisions that Kennewick Man was not Native American and that therefore NAGPRA did not apply. Instead of repatriation, additional studies of the remains were permitted. Subsequent craniometric analysis affirmed Kennewick Man to be more closely related to circumpacific groups such as the Ainu and Polynesians than he is to modern Native Americans. In order to resolve Kennewick Man's ancestry and affiliations, we have sequenced his genome to ∼1× coverage and compared it to worldwide genomic data including for the Ainu and Polynesians. We find that Kennewick Man is closer to modern Native Americans than to any other population worldwide. Among the Native American groups for whom genome-wide data are available for comparison, several seem to be descended from a population closely related to that of Kennewick Man, including the Confederated Tribes of the Colville Reservation (Colville), one of the five tribes claiming Kennewick Man. We revisit the cranial analyses and find that, as opposed to genome-wide comparisons, it is not possible on that basis to affiliate Kennewick Man to specific contemporary groups. We therefore conclude based on genetic comparisons that Kennewick Man shows continuity with Native North Americans over at least the last eight millennia.

Figures

Extended Data Fig. 1
Extended Data Fig. 1. Phylogenetic tree of mitochondrial haplogroup X including Kennewick Man
A median-joining network of Genbank sequences from haplogroup X was constructed as described in the supplemental material. Haplogroup names are indicated by bold dark grey boxes, sequences of Native American origin are in light green background. GenBank accession numbers are shown in boxes at branch tips.
Extended Data Fig. 2
Extended Data Fig. 2. Y-chromosome haplogroup
a, Phylogenetic tree including representative sequences of haplogroup P, the clade that includes haplogroups Q and R. Kennewick Man shares ancestry with orange branches. Each branch is labelled with an integer index and, in brackets, the number of SNPs that define it. b, Counts of SNPs from each branch of the tree, stratified by Kennewick Man genotype (ancestral in blue, derived in orange) and mutation type (C→T and G→A transitions coloured more lightly). Branch 19 was omitted to preserve scale; the Kennewick genotype was ancestral at all 145 sites for which read data were available.
Extended Data Fig. 3
Extended Data Fig. 3. D-statistic based test for Ainu and Polynesian affinity to Han Chinese and Native Americans
Test of the type D((CHB,Ainu/Polynesian),(X,Karitiana)), where X is an Arctic or Native American population, including Kennewick Man and Anzick-1. Values equal to 0, has population X being closer to Karitiana than either CHB or Ainu/Polynesian. Thick and thin whiskers represent 1 and 3 standard errors, respectively.
Extended Data Fig. 4
Extended Data Fig. 4. Similarity between Kennewick Man and Anzick-1 as well as Colville
Test of D((YRI,Kennewick/Anzick-1/Colville/Chipewyan),(X,Karitiana)), to illustrate similarities between Kennewick Man and Anzick-1, and the Colville tribe. Thick and thin whiskers represent 1 and 3 standard errors, respectively.
Extended Data Fig. 5
Extended Data Fig. 5. Affinity of Kennewick Man and Anzick-1 to Native American populations
Test of D((YRI,X),(Kennewick,Anzick-1)) to distinguish different affinities of the ancient samples, and D((YRI,CHB),(X,Karitiana)) to test for recent Asian gene-flow. Thick and thin whiskers represent 1 and 3 standard errors, respectively.
Figure 1
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 f3-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. c, admixture proportions for world-wide set of population, including masked Native American, Anzick-1 and Kennewick, shown at K=14.
Figure 2
Figure 2. Shared ancestry among samples within the Americas
Heat maps of f3-outgroup statistics testing (YRI; Native Americans, X), where X is Kennewick Man (a), Anzick-1 (b), Colville (c) or Chipewyan (d). Warmer colours indicate higher allele sharing.
Figure 3
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 neighboring tribes.

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