Kennewick Man

Note: Polynesian is a term that the Albino people have applied to Pacificans/Austronesians who have significant "White Mongol/European" admixture. They reserve the term Melanesian for the original "Pure Black" Pacificans/Austronesians who have resisted admixture.

Quote: This clay facial reconstruction of Kennewick Man was carefully sculpted around the morphological features of his skull, and lends a deeper understanding of what he may have looked like nearly 9,000 years ago.

So what about the other reconstruction in the previous photograph, which looks nothing like this reconstruction, who does that one look like? Albino lies!

Colville

The Colville tribe is a Native American tribe of the Pacific Northwest. The name Colville comes from association with Fort Colville, named after Andrew Colvile of the Hudson's Bay Company. Earlier, outsiders often named the Colville Scheulpi or Chualpay; the French traders called them Les Chaudières ("the Kettles") in reference to Kettle Falls.

The tribe was originally located in eastern Washington on the Colville River and the area of the Columbia River between Kettle Falls and the town of Hunters.[1] The tribe's history is tied with Kettle Falls, an important salmon fishing resource,[2] and an important post of the Hudson's Bay Company, which brought the advantages and disadvantages of contact with people of European heritage. In 1846, the Jesuit St. Paul's Mission was established. Through its influence nearly all the upper Columbia tribes were Christianized.[2] In 1872, the Colville tribe was relocated to the Colville Indian Reservation,[2] an Indian reservation in eastern Washington, inhabited and managed by the Confederated Tribes of the Colville Reservation, which is a federally recognized tribe comprising twelve bands. The twelve bands are the Methow, Okanogan, Arrow Lakes, Sanpoil, Colville, Nespelem, Chelan, Entiat, Moses-Columbia, Wenatchi, Nez Perce, and Palus.
Mooney (1928) estimated the number of the Colville at 1,000 as of 1780, but Lewis and Clark placed it at 2,500, a figure also fixed upon by Teit (1930). In 1870, there were 616; in 1900, 298;[2] in 1904, 321; in 1907, 334; and in 1937, 322.

Quote from the study above: Here we analyse genome-wide data to show that some Amazonian Native Americans descend partly from a Native American founding population that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans.

BELOW IS WHAT THE FIRST AMERICANS LOOKED LIKE!

Chinese (Han)

The Han Chinese are an ethnic group native to East Asia. They constitute approximately 92% of the population of Mainland China, 93% of the population of Hong Kong, 92% of the population of Macau, 98% of the population of Taiwan, 76.2% of the citizen population of Singapore, 24.5% of the population of Malaysia, and about 19% of the entire global human population, making them the largest ethnic group in the world. The Han Chinese are often referred to as "Chinese" or "ethnic Chinese" in English. They are regarded as a subset of the Chinese nation (Zhonghua minzu). They sometimes refer to themselves as Yan Huang Zisun, meaning the "descendants of (god-emperors) Yan and Huang"

Because the Chinese are such a homogenous group (like Europeans) they have very little (as compared to Blacks) genetic diversity: Y-chromosome haplogroup "O" is the common DNA marker in most Han Chinese.

Phylogeographic Differentiation of Mitochondrial DNA in Han Chinese: phylogenetic analysis of 263 Han mtDNAs shows that 94% of the lineages can be allocated to specific subhaplogroups of the Eurasian founder haplogroups M, N, and R (which is itself a subhaplogroup of N shared between Europe and East Asia).

Japan:

The Jomon and Ainu were the original Black inhabitants of Japan.

Jomon

Analysis of mitochondrial DNA of Jomon skeletons from Hokkaido indicates that haplogroups N9b and M7a may reflect maternal Jomon contribution to the modern Japanese mtDNA pool.
Y-dna haplogroup D-M55

Ainu

Genetic testing has shown them to belong mainly to Y-haplogroup D-M55. Y-DNA haplogroup D2 is found frequently throughout the Japanese Archipelago including Okinawa. The only places outside Japan in which Y-haplogroup D is common are Tibet in China and the Andaman Islands in the Indian Ocean.
Based on analysis of one sample of 51 modern Ainus, their mtDNA lineages have been reported to consist mainly of haplogroup Y (21.6%), haplogroup D (17.6%), haplogroup M7a (15.7%), and haplogroup G1 (15.7%).

Modern Japanese:

At about 350 B.C. a Chinese Mongol group called the "Yayoi" will break-off from China and invade, conquer and destroy the Black native Jomon and Ainu civilizations of Japan. These Yayoi are the progenitors of modern Japanese - many having Jomon and Ainu admixture.

Y-chromosome DNA
A 2005 study by Michael F. Hammer reports. Of the 259 Japanese males samples tested: belong to Haplogroup D-(34.7%).

Mitochondrial DNA
According to an analysis of the 1000 Genomes Project's sample of Japanese from the Tokyo metropolitan area, the mtDNA haplogroups found among modern Japanese include D (72%), B (23%), M7 (10.2%), G (10.2%), N9 (8.5%), F (7.6%), A (6.8%), Z (3.4%), M9 (2.5%), and M8 (1.7%).

Korea

The earliest known Korean pottery dates back to around 8000 BC, and evidence of Mesolithic Pit-Comb Ware culture or Yungimun Pottery is found throughout the peninsula. An example of a Yungimun-era site is in Jeju-do. Jeulmun or Comb-pattern Pottery is found after 7000 BC, and pottery with comb-patterns over the whole vessel is found concentrated at sites in west-central Korea, where a number of settlements such as Amsa-dong existed. Jeulmun pottery bears basic design and form similarities to that of Mongolia, and the Amur and Sungari river basins of Manchuria and the Jōmon culture in Japan.

The predominant view is that the Korean people of today are not the ethnic descendants of the Paleolithic inhabitants.

Y-DNA haplogroups
Korean males display a high frequency of Haplogroup O-M176 (O2b), a subclade that probably has spread mainly from somewhere in the Korean Peninsula or its vicinity, and Haplogroup O-M122 (O3), a common Y-DNA haplogroup among East Asians in general. Haplogroup O2b occurs in approximately 30% (ranging from 20% to 37%) of all Korean males, while haplogroup O3 has been found in approximately 40% of sampled Korean males. Korean males also exhibit a moderate frequency (approximately 15%) of Haplogroup C-M217.

mtDNA haplogroups
Studies of Korean mitochondrial DNA lineages have shown that there is a high frequency of Haplogroup D4, Haplogroup B, which occurs very frequently in many populations of Southeast Asia, Polynesia, and the Americas, is found in approximately 10%. Haplogroup A has been detected in approximately 7% of Koreans. Haplogroup A is the most common mtDNA haplogroup among the Chukchi, Eskimo, Na-Dene, and many Amerind ethnic groups of North and Central America. The other half of the Korean mtDNA pool consists of an assortment of various haplogroups, each found with relatively low frequency, such as G, N9, Y, F, D5, M7, M8, M9, M10, M11, R11, C, and Z.

OVERVIEW OF ANALYSIS AND RESULTS

We provide an overview of our key analysis steps and results here. The technical details of the
precise methods and settings we used are listed in the appendix.
Terminology. In the presentation that follows we use the term “Native Americans” to refer
to the indigenous peoples of North, Central, and South America. The human genetics research
community understands there to be shared genetic signatures among these peoples relative to
other populations in the globe, and we refer to people carrying these signatures as having “Native
American ancestry”. Finer levels of genetic structure exist within Native Americans, and as a
result, we at times distinguish between Native American groups or populations. When we use the
term population, we do not imply any level of genetic differentiation, we simply mean a collection
of individuals with a defining characteristic (usually because they inhabit a particular geographic
area or have a specific group/tribal affiliation).

Obtaining data. To begin the analysis we acquired the Kennewick Man sample raw sequence
read data from the Short Read Archive (Accession # SRS937952). We also acquired the Colville
Tribe sample genotypes from Morten Rasmussen (personal communication). For reference samples,
we used the publicly available sequence phase 3 data from the 1000 Genomes Project
Consortium (2015) and a recent large-scale survey of Native American variation (Raghavan et al.
2015).

Processing of sequence reads. To process the Kennewick sequence data, we trimmed the
adapters from the raw reads and mapped the remaining read data to the human reference genome
(hg19). The read-mapping is the most time-consuming computational step as the original input has
6 billion reads (specifically this step took 16,104 CPU hours to complete). After removing PCR
duplicates and reads with low mapping quality or short length, the read number reduces to 54.3
million reads. This number differs somewhat from the Rasmussen et al. paper, in which their
pipeline produced 60 million reads, since we apply a slightly more stringent filter for fragment
length. We observe 1x average coverage as a result, which also agrees with the Rasmussen
et al. analysis. Of the input reads, on average 6.69% of the reads map to the reference human
genome. This fraction of endogenous DNA is within the range of other archaeological samples
that have been successfully analyzed.

Assessment of chemical damage pattern typical of ancient DNA. DNA molecules experience
a post-mortem degradation process, leading to a set of chemical modification patterns typical
of ancient DNA (aDNA). First, aDNA molecules are typically short in length, often < 100 base pairs
(bps). Second, cytosine deamination occurs with higher frequency near the end of molecules and
generates an increasing level of C-to-T substitution at the 5-end of a read and corresponding Gto-
A substitution pattern at the 3-end. Lastly, loss of a purine base (A or G) induces a break on the
3-side of the depurinated site, leading to an excess of purines at the genomic positions preceding
the 5-end of molecules and a corresponding increase in the proportion of pyrimidines (C or T)
following the 3-end.

We assessed the size distribution and damage patterns of inserted molecules using uniquely
mapped, non-duplicate reads with the mapDamage2 program (J ´onsson et al.. 2013). The sequence
reads for the Kennewick sample clearly show these patterns: short molecule length (median
length 49 bp, Figure 1), increase in C-to-T substitutions at 50 and 30 ends of reads from
single-stranded libraries, and C-to-T substitutions at 50 ends and G-to-A substitutions at 30 ends
of reads from double-stranded libraries (Figure 2), and the signature of a loss of purines next to
depurinated sites (Figure 3).

Assessment of contamination from modern humans. Estimating the level of contamination
from modern human DNA via various sources, such as contact with those who conducted
excavation or sequencing experiments or prepared laboratory reagents, is a critical step in aDNA
analysis. We estimated the level of contamination from exogenous human sources in the Kennewick
sequence data based on a method implemented in the contamMix program (Fu et al..
2013).

In brief, this program uses the majority-based mitochondrial DNA (mtDNA) consensus sequence
as a representative of the endogenous sequence, assuming that sequence coverage is
high enough to accurately call a consensus sequence given presence of some contaminant reads
and sequencing errors. Then, it models observed sequence reads as a sample from a mixture
of mitogenomes, including the endogenous one and potential contaminants, as represented by
311 contemporary human mitogenomes. The probability of reads drawn from the endogenous
mitogenome, and its 95% confidence interval, is estimated through a Markov chain Monte Carlo
algorithm. From this we obtained an estimate of 7.3% contamination (with a 92.5%–97.5% credible
interval of 6%–8.8%). In Rasmussen et al., they report a 95% confidence interval ranging from
3.7–7.1%.

The level of mtDNA contamination does not necessarily reflect the level of nuclear DNA contamination.
To assess contamination in the nuclear DNA genome, we took advantage of the fact
that a male is hemizygous for the X chromosome and that no mismatches in the X chromosome
sequence reads are expected. By evaluating the minor allele mismatch reads on the X chromosome
relative to allele frequencies of alleles in the European population, we obtain contamination
estimates of 3–3.2% depending on which method is used. These are slightly higher than the 2.5%
reported in the Rasmussen et al. manuscript.

Mitochondrial DNA (mtDNA) haplogroup. The mtDNA haplogroup an individual carries is
indicative of ancestry and relatively easy to observe from aDNA as mtDNA is more abundant in
cells than autosomal DNA. Using the consensus sequence of the mtDNA reads obtained, we find
the mtDNA haplotype to be haplogroup X2a. This haplogroup has only been observed in Native
Americans (Reidla et al. 2003). Rasmussen et al. report the same haplogroup for the sample.

D and f-stat analyses.

To measure genetic similarity between populations in a form that is
robust to observation error we use an “f3-outgroup” statistic which measures how much shared
similarity two populations have with each other relative to a third. We calculated the f3-outgroup
statistic between the Kennewick sample and each population in the Rhagavan dataset using the
Yoruban population (West Africa) as an outgroup. We find the Kennewick sample has the highest
shared similarity to Native American populations with the highest values observed being with
populations from South America (Figure 7), in line with the observations from Rasmussen et al.
We also use the D-statistic which provides a test of whether four populations (numbered 1 to
4 arbitrarily) can be arranged into a tree structure in which Population 1 and 2 are most closely
related and 3 and 4 are most closely related, with no secondary gene flow between members
of 1 and 2 with 3 and 4. The D-statistic is normalized to produce a Z-score which can be used
to reject the tree hypothesis for large magnitude values (e.g. jZ-scorej > 3). We find any tree
hypothesis with Kennewick grouped with other Native American populations is not rejected, and
relevant alternatives are rejected (Table 1).

We did not have access to Ainu or Polynesian data so we use Japanese and Solomons Island population data as a surrogate.

Rare variant analysis. To further assess the ancestry of the Kennewick man, we take a novel
approach that is based on the geographic distribution patterns of rare variants. Most rare variants
are the result of recent mutation events and as a result they are geographically clustered to single
regions of the globe and are highly indicative of ancestry. Here, we tabulate the geographic distribution
of the rare variants carried by the Kennewick man. This approach requires the use of global
sequence data to define the rare variants. As a reference set we use the 1000 Genomes phase3
data. This dataset does not contain Native Americans from North America. However, it contains
samples with Native American ancestry; specifically Peruvians from Lima (PEL), Mexicans from
Los Angeles (MXL), Colombians from Medellin (CLM). These individuals exhibit varying degrees
of admixture between Native American, European, and African ancestries. The Peruvians from
Lima are known from previous studies to contain the most Native American ancestry (>75%, de
Moura et al. 2016).

We find 60 globally rare variants pass our QC filters and are found in the Kennewick Man.
Figure 8 shows the number which are present in each 1000 Genomes population. The plot shows
that rare variants present in the 1000 Genomes and carried by the Kennewick man are predominantly
found among individuals with Native American ancestry. Specifically, there is the highest
sharing with Peruvians from Lima (PEL). Previous studies estimate the PEL have 1.42–1.95-fold
more Native American ancestry than Mexicans from Los Angeles (MXL) (de Moura et al. 2016),
and this likely explains the nominally elevated sharing (44 vs 42 shared rare alleles in PEL vs
MXL). A correction for the differing levels of Native American ancestry would likely show the MXL
as having the highest level of sharing.

To provide a positive and negative control for this procedure, we also show sharing profiles for
a Neolithic European sample (Lazaridis et al. 2014) and the Anzick-1 Clovis sample (Rasmussen
et al. 2014) (Figures 9 and 10). For the Neolithic European sample the sharing is elevated
with European populations (Tuscans from Italy (TSI), Spanish (IBS), CEPH study families from
Utah (CEU), Great Britain (GBR). For the Anzick-1 sample, the profile is largely similar to that of
Kennewick. (Note: the raw numbers are higher for these samples than the Kennewick sample
because of differences in coverage).

Though most analyses tout Kennewick Mans similarity with the Karitiana people of Brazil: the graph clearly shows that Kennewick man is MUCH MORE SIMILAR to the Arara People of Brazil.

The Arara people, also called Arara do Pará are an indigenous people of Brazil, living in the state of Pará, Brazil. They are known for both their prowess in warfare and trophy-keeping practices. They maintained a nomadic existence and frequently intermarried with other tribes. The largest Arara settlement is Laranjal village. The Arara have been in contact with non-native peoples since the 1850s. They had peaceful encounters with outsiders along the Xingu and Iriri Rivers. From 1889 to 1894, they were harassed by rubber tappers. Arara people speak the Arára language, also known as the Ajujure language, which is a Karib language.

DISCUSSION OF RESULTS

The analyses carried out in the original Rasmussen et al. study use methods that are widely
applied in the field of population genetics, and as such, the main concern in re-evaluating their
work is to rule out the possibility of an error in the implementation of their analysis pipeline. Given
the numerous steps that take place in a population genetic analysis, there is some probability of
implementation errors. One prominent recent example of this is provided in the publication of a
claim of back gene flow into Sub-Saharan Africa from outside of Africa on the basis of analysis of
ancient DNA from an Ethiopian sample (Gallego Llorente et al. 2015). This claim has since been
refuted as it apparently arose due to a bioinformatic error in the merging of data files (Callaway
2016). Thus, one of our main contributions here has been to carry out the major analysis steps of
the Rasmussen et al. study independently.

Based on our results, we found no reason in any stage to suspect errors in the analysis pipeline
carried out by Rasmussen et al. The precise numeric values we find in some cases differ but the
differences are, to our judgement, small and in line with the variance expected due to different
parameter choices in the initial read mapping steps and subsequent analyses. The analyses we
re-implemented from Rasmussen et al. are all consistent with the Native American ancestry of the
Kennewick Man.

One minor criticism may be the use by Rasmussen and colleagues of a filter on sequence
read length of 30 bp. Several published analyses use a still more stringent criterion of a  35
bp length threshold. Using longer read length thresholds can be beneficial because it removes
reads that are possibly coming from microbes associated with the archaeological sample and/or
reads that are human but map to the reference genome poorly. On the other hand, using longer
length thresholds plausibly throws out informative reads and enriches the sample for potential
contaminants, as modern human DNA reads are usually less damaged and hence longer in size
(>100 bp). Here we used a threshold of >30 bp.

The choices regarding read lengths may explain the discrepancy among the contamination
estimation numbers. We obtained nuclear genome contamination estimates of 3-3.2% while the
Rasmussen et al. study obtained a nuclear estimate of 2.5%. For the mtDNA based estimates, we
found a 95% credible interval of 6–8.8%, and Rasmussen et al provide an interval of 3.7–7.1%.
Some variance between the nuclear and mtDNA contamination estimates is expected because of
their distinct molecular properties (mtDNA exists in much higher copy number per cell than nuclear
DNA, has a distinct structure, and is carried in mitochondrial organelles as opposed to the
nucleus).

For the difference between studies, the discrepancy is relatively small and likely reflects
the read length threshold used by the original study and our follow-up. The X-chromosome based
estimation of contamination is designed such that having more microbial reads included (as might
be expected with the less stringent threshold of  30bp) would bias the estimated contamination
rate downwards, consistent with the difference observed. The mtDNA-based estimation of contamination
should be unaffected by the inclusion of additional microbial reads. A second effect is
that because short reads are more likely to be endogenous rather than contaminant, shorter read
length thresholds should result in read collections that have a lower proportion of contaminating
reads. This should cause both the X-based and mtDNA-based contamination estimates to move
downwards when shorter reads are included, as observed.

As we carried out our analysis we were especially wary to rule out that modern Native American
DNA has contaminated the sample. Such contamination would be more challenging to detect
than contamination from more distant sources such as from Europeans. For this reason, the assessment
of whether the bulk of the reads truly represent ancient DNA is important. The damage
patterns we observed are typical of aDNA and, together with the analyses of mtDNA and X chromosome
reads, argue against the possibility of extensive modern Native American contamination
driving the results.

To add a new dimension to the assessment of the Kennewick sample’s ancestry, we assessed
rare variant sharing patterns. This analysis identifies globally rare variants and asks which ones
are carried by the Kennewick Man. These variants are typically informative of ancestry because
rare variants cluster geographically. These are also not typically included on genotyping arrays
and so would have little impact in the PCA, admixture, f3, and D-statistic analyses. While our
implementation of this approach relied on the 1000 Genomes data, which unfortunately contains
poor representation of Native American populations from North America, the patterns of rare variant
sharing we found are consistent with Native American ancestry. For example, the profile seen
for Kennewick is similar to that seen in the Anzick sample and distinct from that seen in ancient
European samples.

Taken together our analysis of mtDNA, variants that overlap genotyping arrays (PCA, admixture,
f3, and D-statistic analyses) and rare variants provide evidence of ancestry from 3 nonoverlapping
subsets of the sequence read data. Each is consistent with Native American ancestry.
In sum, our analyses here, based on the human sequence reads associated with the Kennewick
Man provided in the Short Read Archive, all point to the Native American ancestry of the
sample. Our results mitigate any concern over errors by Rasmussen et al. because, while we used
some of the same software used by Rasmussen to process and analyze the data, the pipelines
used here were independently established. We also added a new method based on rare variants
and again found evidence for Native American ancestry.

Kennewick Man

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 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).

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.

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.
Methods

Main• Methods• Accession codes• References• Acknowledgements• Author information• Extended data figures and tables• Supplementary information

We extracted DNA from a 200-mg bone fragment from Kennewick Man, and built both single and double stranded DNA libraries, which were sequenced on the Illumina HiSeq platform (Supplementary Information sections 1, 2). We performed DNA damage analyses and estimated decay rates to verify authenticity; additionally we estimated contamination on both nuclear and mitochondrial DNA (Supplementary Information sections 2, 3, 4). For the nuclear contamination we developed a model to identify the most likely source population (Supplementary Information section 4). Both mitochondrial and Y-chromosome haplogroup were determined (Supplementary Information sections 2, 5). To resolve the ancestry of Kennewick Man, we performed PCA, outgroup f3- and D-statistics, as well as ADMIXTURE analyses on a panel of published SNP array data that was collected and curated from worldwide populations with suggested relationship to Kennewick Man (Supplementary Information sections 6, 7), in addition to data generated from members of the Colville Tribe (Supplementary Information section 1). Individual and tribal consent was obtained for all study participants, and the National Committee on Health Research Ethics in Denmark had no comments on the design (H-3-2012-FSP21). We tested if Kennewick Man belonged to a population ancestral to the Colville Tribe and estimated their divergence time (Supplementary Information section 8). Lastly, we reanalysed the craniometric data for Kennewick Man, and compared it to both individual samples and population mean data (Supplementary Information section 9).

Background

The U.S. Army Corps of Engineers (USACE or Corps), Northwestern Division, controls the collection from site 45BN495, which includes the skeletal remains of Kennewick Man. The collection is presently housed at the Burke Museum of Natural History and Culture on the University of Washington campus. The skeleton was discovered on July 28, 1996, by two young men walking along the Columbia River near Kennewick, Washington. The discovery was reported to the police who called a local archaeologist, James Chatters, to investigate and collect the remains. Upon determination that the site was located on federal property (USACE, Walla Walla District), the Corps was notified. While the physical characteristics of the remains led to an initial belief that the remains were from an early European settler, the discovery of a stone projectile point embedded in the hip bone suggested a much earlier time period. Initial radiocarbon dating placed the skeleton between 8,340 and 9,200 years old.

Based on the presence of the projectile point and the age of the remains, USACE took control of the remains and made a determination that the custody of the remains should be transferred to a group of claimant tribes pursuant to NAGPRA. The claimant tribes included four federally recognized Indian tribes (the Confederated Tribes of the Colville Reservation; the Confederated Tribes of the Umatilla Indian Reservation; the Confederated Tribes and Bands of the Yakama Nation; and the Nez Perce Tribe), and one federally unrecognized tribe (the Wanapum Band). Subsequent to the transfer decision, the following events occurred:

• The decision to transfer was challenged in October 1996 by eight scientists who wanted to study the remains.
• In 1997, the District Court of Oregon found the Corps had acted before it had all required evidence and remanded the case to the Corps for further consideration.
• In March 1998, the Corps entered into an agreement with the Department of the Interior (DOI) whereby DOI would decide whether the remains were “Native American” under NAGPRA and the Corps would determine their proper disposition.

• After two years of examination, analysis, and study, DOI determined the remains to be Native American in January 2000 and culturally affiliated with the claimant tribes in September of that same year.
• The Corps again made a determination that the custody of the remains should be transferred to the claimant tribes. This was again challenged by the scientists in 2001.
• In August 2002, the District Court of Oregon found DOI’s decision that the remains were Native American to be arbitrary and capricious. The Court held that the remains were not “Native American” as defined by the statute, nor could they be culturally affiliated with the claimant tribes.
• The Court ordered the Corps to grant access to the plaintiff scientists to study the remains subject to “reasonable terms and conditions.”

• In September 2002, the tribes intervened for purposes of the appeal to challenge the District Court’s decision.
• In October 2002, The United States appealed the “Native American” decision to the Ninth Circuit Court of Appeals.
• In April 2004, the Ninth Circuit Court of Appeals affirmed the District Court of Oregon’s decision and remanded the case.

• Following the Ninth Circuit decision, the plaintiffs submitted a study plan to the Corps along with subsequent study requests. The Corps approved the majority of these requests, allowing the plaintiffs to have access the collection to perform a series of studies, as ordered by the Court. Terms and conditions were placed on each of these studies to protect and preserve the research potential of the collection. The Corps has responded to all requests from the plaintiff scientists and the plaintiffs completed all approved studies.

• One of the members of the plaintiff’s team also requested access to conduct ancient DNA (aDNA) analysis on already sampled portions of the skeleton, which was approved by the Corps in August 2011.
• In September 2014, results of the plaintiffs’ studies were published in Kennewick Man: The Scientific Investigation of an Ancient American Skeleton, edited by Douglas W. Owsley and Richard L. Jantz, Texas A&M University Press.
• On June 18, 2015, the results of aDNA testing of the skeleton were published in “The Ancestry and Affiliations of Kennewick Man,” by Morten Rasmussen et al., in the Journal Nature.
• In April of 2016, the Rasmussen results of aDNA testing were independently validated by John Novembre et al. in a technical report titled, “Assessment of the genetic analyses of Rasmussen et al. (2015).”

Legal Standard
NAGPRA became federal law in 1990. It provides for the disposition and repatriation of "Native American" human remains and certain cultural items that have been either inadvertently discovered on federal lands or curated in museums receiving federal funding. 25 U.S.C. §§ 3001-3013. ''Native American" is a specifically defined term that triggers the applicability of the statute. The definition is "of, or relating to, a tribe, people, or culture that is indigenous to the United States." 25 U.S.C. § 3001(9). The statutory definition of ''Native American" has been determined to be unambiguous in its meaning. Bonnichsen v. United States, 217 F. Supp. 2d 1116, 1136 (D. Or. 2002) (Bonnichsen I); Bonnichsen v. United States, 367 F.3d 864, 875-76 (9th Cir. 2004) (Bonnichsen II). The Ninth Circuit determined that to be Native American under the statute, human remains and cultural items must "bear some relationship to a presently existing, tribe, people, or culture." Bonnichsen II, 367 F.3d at 875.

The Ninth Circuit acknowledged that NAGPRA does not specify precisely what kind, or how strong, a relationship is required in order to make a Native American determination, but the court was clear that age alone is not a sufficient basis for determining that remains are Native American, although it can be a factor that is considered. A Native American determination must be made on a finding that substantial evidence supports the agency's decision. Bonnichsen II, 367 F.3d at 779-80. Substantial evidence is more than a mere scintilla of evidence. It means such relevant evidence as a reasonable mind might accept as adequate to support a conclusion, even if it is possible to draw two inconsistent conclusions from the same evidence. See Bonnichsen II, 367 F.3d, at fn. 19, fn. 20; Richardson v. Perales, 402 U.S. 389, 401 (1971); Landes v. Royal, 833 F.2d 1365, 1371 (9th Cir. 1987).

Determining remains to be Native American is, therefore, distinct from determining cultural affiliation. Cultural affiliation, the second step of the NAGPRA process, is required before transfer may occur. See Bonnichsen II, 367 F.3d at 875 (the first inquiry asks "whether the human remains are Native American" and the second inquiry asks "which American Indians or Indian tribe bears the closest relationship to Native American remains"). This determination does not address cultural affiliation nor does it propose a transfer of custody of the remains.

To establish cultural affiliation, there must be a preponderance of evidence that there is a "relationship of shared group identity which can be reasonably traced” between a present day Indian tribe and an identifiable earlier group. 25 U.S.C. § 3001(2); see also 25 U.S.C. § 3005(a)(4). First, substantial evidence is a lower threshold of proof than preponderance of the evidence. Substantial evidence is essentially a reasonableness standard ("such evidence as a reasonable mind might accept as adequate to support a conclusion"), whereas preponderance of the evidence requires the conclusion being drawn as being more likely than not true. Second, to be Native American under NAGPRA, there needs to be merely a connection to a presently existing tribe, people, or culture. For cultural affiliation, there needs to be shared group identity with a tribe. A tribe, people, or culture is significantly broader than only a tribe; likewise a "connection" is more ephemeral than a "shared group identity."

The District Court clarified that it is “not the role of the court to determine whether Kennewick Man is or is not ‘Native American’ under the terms of NAGPRA….The court is simply concluding that the record will not support the Secretary’s affirmative finding that the remains are ‘Native American.’” Bonnichsen I, 217 F. Supp. 2d at 1139, fn. 41.
My decision here centers on the recently published information, which provides sufficient and substantial evidence that will now support a Native American determination, as outlined below.

Original Native American Determination and Studies
This Native American determination is based on significant new evidence that was not available until recently and not considered in the original Native American determination. The Corps is required to continue to uphold is responsibilities under both NAGPRA and the Archaeological Resources Protection Act and evaluate all new evidence. The prior court rulings inform the Corps responsibilities under these laws.

On January 11, 2000, the Department of the Interior determined that there was “sufficient information to determine that [the Kennewick skeletal] remains should be considered ‘Native American’ as defined by NAGPRA.” Memorandum from Francis P. McManamon to Assistant Secretary, Fish and Wildlife and Parks, Determination That the Kennewick Human Skeletal Remains are “Native American” for the Purposes of the Native American Graves Protection and Repatriation Act [hereafter January 2000 DOI Memo]. DOI used primarily age and geography to indicate Native American ancestry. Additional radiocarbon dating of the bones by DOI at three separate laboratories confirmed that the remains were older than 6,000 years (January 2000 DOI Memo). The chronological age obtained through radiocarbon dating was further confirmed and refined by DOI through geomorphologic and sedimentary investigations of the river bank (Huckleberry et al. 1998; Wakeley et al. 1998), analysis of the remains themselves (Powell and Rose 1999), comparison of sediments adhering to the remains and in the river bank profile (Huckleberry and Stein 1999), and information from the analysis of the lithic artifact lodged in the ilium (Fagan 1999). In all, information derived using the methods and techniques of archaeology, geomorphology, physical anthropology, sedimentology, and other scientific disciplines supported a determination that the remains were probably between 8,500 and 9,500 years old (January 2000 DOI Memo).

The DOI study also identified morphological characteristics that are considered Native American, including a large malar tubercle, blurred nasal sill, zygomatic posterior tubercle, slight nasal depression, moderate prognathism, elliptical dental arcade, straight palatine suture, and what appeared to be an angled zygomaticomaxillary suture (Powell and Rose 1999). However, morphological studies completed also indicated that Kennewick Man’s cranium was unlike any modern Native American group and more like crania from the south Pacific and Polynesia (Powell and Rose 1999).

When the Corps recovered the remains in 1996, Dr. David Glenn Smith was attempting to perform a series of DNA extractions to determine the presence or absence of certain haplogroups. Affidavit of David Glenn Smith (Bonnichsen v. United States), May 19, 1997, at ¶ 4. In subsequent correspondence, Dr. Smith stressed that DNA studies are important to demonstrate that there is a direct ancestor/descendant relationship between modern Native Americans and Paleoindians. E.g., Letter from David Glenn Smith to Colonel Donald R. Curtis, dated May 29, 1997.

DNA testing, therefore, became a critical component of DOI’s analysis of Kennewick Man in 2000. As indicated by DOI, “DNA analysis will be useful to the Department in determining if a shared group identity or cultural affiliation can be made between these very ancient remains and Indian tribes that have historically inhabited the Upper Plateau region in Washington State.” DOI Press Release, dated February 18, 2000. In a report to DOI, scientists looked at the potential for DNA analysis of the Kennewick remains (Tuross and Kolman 2000). At the time, despite expressing concerns over low levels of human bone collagen and possible complexities in extracting the DNA, the report stated that it was also “possible that mitochondrial DNA analyses of the skeleton will allow assignment of the skeleton to the biological grouping of American Indian (Tuross and Kolman 2000:4).”

DOI, therefore, incorporated DNA testing into its study plan for determining cultural affiliation of the Kennewick remains. DOI developed a plan for conducting DNA testing with the goal of extracting, amplifying, analyzing, and interpreting ancient DNA from the remains “to determine the mitochondrial DNA haplogroup and Y-chromosome genetic characteristics of the individual.” See United States, Federal Defendant's Submission of Work Plan for DNA Analysis, submitted to District Court of Oregon on April 10, 2000, at Exhibit 1, Attachment 1, page 1]. DOI worked with independent scientists on implementation of the plan, while other scientists assured that appropriate samples were extracted and were tied to other examinations of the remains, such as the broader taphonomic studies. Id. The selected laboratories were unable to isolate uncontaminated DNA from the Kennewick remains at that time (Kaestle et al. 2000; Merriwether et al. 2000; Smith et al. 2000).

The Court noted the reliance on age (over 8,000 years old) and geography (Columbia Plateau) in the determination of Native American ancestry. “The decision [that Kennewick Man was Native American] was premised on only two facts: the age of the remains, and their discovery site within the United States.” Bonnichsen I, 217 F. Supp. 2d at 1130. The Court found that some relationship between remains or cultural items and an existing tribe, people, or culture that is indigenous is necessary for a Native American determination. Id. at 1136. The Court reviewed the results of craniometric studies of Kennewick Man and other early Holocene crania, none of which appear similar to modern Native Americans. Id. at 1137-1139.

“The physical features of the Kennewick Man appear to be dissimilar to all modern American Indians…that does not preclude the possibility of a relationship between the two. However, absent a satisfactory explanation for those differences, it does make such a relationship less likely, and suggests that the Kennewick Man might have been part of a group that did not survive or whose remaining members were integrated into another group.” Id. at 1146. The Court reviewed the administrative record for information that would provide evidence of a relationship and found that “a thorough review does not reveal the existence of evidence from which that relationship may be established.” Id. at 1138.

The Ninth Circuit affirmed these conclusions, finding that the “[t]he administrative record contain[ed] no evidence, let alone substantial evidence, that Kennewick Man’s remains are connected by some special or significant genetic or cultural relationship to any existing indigenous tribe, people, or culture.” Bonnichsen II, 367 F.2d at 880.

Lacking DNA evidence comparing Kennewick Man’s genetics to modern Native Americans and other modern populations, the courts instead used cranial morphology to reflect genetics—“differences in appearance may reflect genetic differences between ancient samples and more recent American Indians and northern Asian populations.” Bonnichsen I, 217 F. Supp. 2d at 1137. Because Kennewick Man’s cranial morphology did not reflect modern Native American morphology and because the court found no other evidence of a relationship with a present-day tribe people or culture indigenous to the United States, the court concluded that the “Secretary did not have sufficient evidence to conclude that the Kennewick Man remains are “Native American” under NAGPRA.” Id. at 1138; see also Bonnichsen II, 367 F.2d at 880.

New Evidence for Native American Determination Over the last two years, published scientific analyses of Kennewick Man’s skeleton have provided new evidence informing on the ancestry and lifestyle of Kennewick Man (Owsley and Jantz 2014). Primarily, there have been significant advances in the extraction and sequencing of ancient DNA, and Kennewick Man’s DNA has been analyzed (Novembre et al. 2016; Rasmussen et al. 2015). The Corps has reviewed this new evidence, along with all previously completed studies, in order to determine if the new evidence supports a determination that Kennewick Man is Native American.

Craniometric and Skeletal Evidence
Recently published studies of Paleoindian1 crania, describe difficulties in interpreting population affinities for a single specimen such as Kennewick Man. Craniometric studies of Kennewick Man and other Paleoindian human remains reaffirm that their cranial morphology is distinct from historic Native Americans (Hackenberger 1999; Jantz and Owsley 1997; Jantz and Spradley 2014; Powell and Rose 1999; Spradley et al. 2014; Rasmussen et al. 2015). Overall, Paleoindian crania do not look like modern Native American crania. Recent studies, however, warn against an oversimplification of the complexities of microevolution over time and space and the role played by genetic drift on morphological changes (Edgar 2007; Powell 2005; Powell and Neves 1999).

Thomas and Larsen (2015:782) point to the “voluminous experimental, epidemiological, and skeletal biological record” that show the importance of biocultural circumstances on skeletal plasticity. Behavioral, cultural, and environmental circumstances can influence morphology over generations (e.g., For the purposes of this document, “Paleoindian” refers to the earliest inhabitants of North and South America dating to before 8,000 years ago. Armelagos and Van Gerven 2003; Auerbach 2012; Jantz and Meadows Jantz 2000). Expecting cranial remains that are over 8,000 years apart to look exactly the same ignores these types of changes (Auerbach 2012). As noted by Edgar et al. (2007:106), “the ultimate cause for the dissimilarity between Paleoindians and contemporary Native Americans is time—Paleoindian and other post-Pleistocene humans are simply not contemporary, which one might imagine is a source for diversity from a variety of evolutionary factors,” over thousands of years and many generations (id.).

In addition to the fact that the morphology of a population changes over time, scientists have recently challenged the validity of the interpretations of ancestor-descendant relationship using a single specimen such as Kennewick Man—“Stating a fossil is similar to a particular recent group is not the same as saying the fossil belongs to that group. It is simply a statement of similarity” (Jantz and Spradley 2014:475). “Morphological similarity can arise not only through shared descent but also through convergent evolution or phenotypic plasticity coupled with similar environments” (Skoglund et al. 2015:104).

The use of a single specimen to infer ancestor-descendant relationships was reviewed by Rasmussen et al. (2015). They analyzed the worldwide modern human data set that was used for the initial comparisons to Kennewick Man (including Howells’ 1973, 1989 and 1996 data for prehistoric and modern populations [hereafter Howells’ Data Set]). Rasmussen et al. found that while the craniometric analysis shows similarity to Polynesians and Ainu, “Kennewick Man’s pattern of craniometric affinity falls well within the range of affinity patterns evaluated for individual Native Americans” (Rasmussen et al. 2015:458). The authors conclude that a reliable reconstruction of the biological population affinities for Kennewick Man cannot be completed because there are not enough independent phenetic markers and within group population variation is too large to produce reliable results. Kennewick Man is “part of the male Amerind craniometric variation” (Rasmussen et al. 2015, Supplementary Information: 13); he just might not look like the “average” modern Native American. Therefore, Kennewick Man should not be ruled out as a Native American because his cranial morphology differs from the average modern Native American.

Jantz and Spradley (2014:474) point out that Howells’ Data Set has poor representation of Native American crania stating that “such a limited comparative set could in no way adequately reflect the morphometric diversity of North America.” Tasa and Vogel (2016) also observed that Howells’ Data Set has poor representation of Native American crania from the Pacific Northwest, the geographic location of Kennewick Man. Tasa and Vogel used measurements from 179 late pre-contact to contact period known Pacific Northwest Native American crania to determine if Howells’ Data Set would identify these individuals as Native American using discriminant function analysis. Using the least stringent level of typicality (likelihood that the individual belongs to the selected group), only 21 of the Native American individuals (12%) were reliably classified as Native Americans. Using the most stringent typicality, only 4 (2%) of the Pacific Northwest Native American individuals were reliably classified as Native American. The results show that Howells’ samples are insufficient to make assignments for more recent Native American skeletons, let alone for a cranium such as Kennewick Man that is over 8,000 years old.

Finally, Kennewick Man exhibits traits that can reasonably be considered Native American, as was originally noted by Powell and Rose (1999) during the DOI studies. These morphologies include a large malar tubercle, blurred nasal sill, zygomatic posterior tubercle, slight nasal depression, moderate prognathism, elliptical dental arcade, straight palatine suture, and what appeared to be an angled zygomaticomaxillary suture. Additional analysis has also shown Kennewick Man exhibits coalition (union) between the third metatarsal and third cuneiform (two normally separate foot bones) in both feet.

This trait occurs in higher frequencies among Native American groups than among individuals of European or African ancestry, and shows good evidence of heritability (Case 2014). A reanalysis of the dentition shows that there is “no dental evidence to rule him out as a descendant of the Siberian Sinodonts who were direct ancestors of later Indians of North and South America” (Turner 2014:192). In addition, the short broad palate and great palatal depth exhibited by Kennewick Man are common among people of Eurasian origin and various Native American populations (Gill 2014:506).

In summary, the newest scientific data on Kennewick Man and skeletal analyses of Paleoindian skeletons support the following:

• Kennewick Man’s skeleton exhibits traits that can reasonably be considered Native American.
• Kennewick Man’s cranium falls within the range of affinity patterns for individual Native Americans.
• Significant biocultural factors influence changes in morphology over nearly 8,000 years, and expecting the crania of a population not to change over time is unreasonable.
• Comparing an individual cranium like Kennewick Man to population-mean data does not provide reliable results for ancestry relationships, and should not form a basis for excluding Kennewick Man from Native ancestry.
• The Howells’ Data Set cannot reliably assign known Pacific Northwest Native American crania to Native American populations, and should not be used to exclude Kennewick man from Native ancestry.
DNA Evidence for Native American Determination

Over the last ten to fifteen years, the field of paleogenomics has seen large growth due to the improvements in the extraction, isolation, sequencing, and analysis of ancient DNA (e.g., Carpenter et al. 2013; Chatters et al. 2014; Kempt and Schurr 2010; Paabo et al. 2004; Potter et al. 2014; Prufer et al. 2014; Rasmussen et al. 2010; Rasmussen et al. 2014; Smith et al. 2005; Shapiro and Hofreiter 2014; Tackney et al. 2015). Ancient DNA from the Americas continues to provide data for research on Native American population genetics, including the timing of the population of the Americas, migration patterns, and migration routes (e.g., Chatters et al. 2014; Goebel et al. 2008; Kaestle and Smith 2001; Kemp et al. 2007; Kitchen et al. 2008; Skoglund et al. 2015; Raghavan et al. 2015).

The Corps approved another attempt to extract aDNA from Kennewick Man in 2011, using a previously sampled section of hand bone. On June 18, 2015, the results of the analysis of DNA recovered from the hand bone were published (Rasmussen et al. 2015). The researchers extracted, amplified, and compared Kennewick Man’s DNA to modern populations. The results were based on autosomal DNA, mitochondrial DNA, and Y-chromosome data, as compared to worldwide genomic data (Rasmussen et al. 2015). To validate the results, the Corps contracted for an independent review of the 2015 DNA analysis (Novembre et al. 2016). That review concurred with the findings of Rasmussen et al. (2015).

Although the potential for contamination is often noted as a concern for any DNA study, including for aDNA studies, and for the Kennewick DNA studies in particular (e.g., Owsley and Jantz 2014:645), Rasmussen et al. (2015) and Novembre et al. (2016) both addressed this concern. Novembre et al. concluded that the “damage patterns we observed are typical of aDNA and, together with the analyses of mtDNA and X chromosome reads, argue against the possibility of extensive modern Native American contamination driving the results (Novembre et al. 2016:17).”

Geneticists use the term “Native American” to refer to indigenous peoples of North, Central, and South America. Finer levels of genetic structure exist within Native Americans, and as a result, it is possible to distinguish between Native American groups or populations that inhabit a particular geographic area or have a specific group/tribal affiliation (Novembre et al. 2016). For Kennewick Man to be considered “Native American” under NAGPRA, the genetic evidence should provide reasonable evidence of a connection to any North American Native American group from the United States.

First, the new genomic evidence rejects the hypothesis that Kennewick Man is more closely related to Ainu or Polynesians than to Native Americans (Rasmussen et al. 2015). Second, as reported by both Rasmussen and Novembre, the autosomal DNA, mitochondrial DNA, and Y chromosome data all consistently show that Kennewick Man is genetically closer to modern Native Americans than to any other population worldwide.

The mtDNA haplogroup for Kennewick Man is haplogroup X2a (Rasmussen et al. 2015; Novembre et al. 2016). This haplogroup has only been observed in Native Americans (Novembre et al. 2016). The Y-chromosome haplogroup was established to be hgQ-M3, “a lineage observed exclusively among Native Americans and in Northeast Siberia (Rasmussen et al. 2015, Supplemental Information: 8). Using methods to assess admixture proportions, the ancestry profile of Kennewick Man is most similar to that of living Native Americans from North America (Novembre et al. 2016; Rasmussen et al. 2015). Using a measure of genetic similarity, a few populations of living Native Americans from South American samples are also similar to the Kennewick sample (id.). This result is not unique to Kennewick and is seen in another ancient sample from North America (i.e., Anzick) (id.).

Additionally, the pattern observed in Kennewick Man is mirrored in the Colville Tribe (Rasmussen et al. 2015:456). “Among the groups for which we have sufficient genomic data, we find that the Colville…show close affinities to that individual [Kennewick Man] or at least to the population to which he belonged.” (Rasmussen et al. 2015:458). The Colville were one of the original claimant tribes. A comparative genetic sample was not available for the other claimant tribes, and therefore, there are no data available for their specific relationship to Kennewick Man.
These genetic results show that Kennewick Man is closely related to present-day Native North American populations, including those from the same geographic region, which implies some genetic continuity between ancient and modern populations in the Pacific Northwest and Columbia Plateau (Raghavan et al. 2015).

In summary, the newest genetic evidence supports the following:
• Kennewick Man is genetically related to contemporary Native Americans.
• Kennewick Man’s ancestry profile is most similar to several Native North American
populations, including the Colville Tribe.
• Kennewick Man is more closely related to Native Americans than to any other worldwide
population, including the Ainu or Polynesian groups.

Conclusion
The recent results provided by skeletal and statistical analyses of Kennewick Man and other Paleoindians, along with the DNA analysis has lead me to review the evidence for Kennewick Man’s Native American ancestry. This new evidence supports the following:
• Kennewick Man’s skeleton exhibits traits that can reasonably be considered Native
American.
• Kennewick Man’s cranium fits within the affinity patterns seen in individual Native
American crania.
• Genetic evidence establishes that Kennewick Man is more closely related to modern Native
Americans, including the Colville, than to any other group.
• Biocultural influences on morphology, genetic drift, mutation, and natural selection over
8,000 years impact the differences seen between all Paleoindian crania and modern Native
American groups.

• The original evidence used to exclude Kennewick Man from the Native American groups—
craniometric analysis—has been shown not be to be a reliable indicator of ancestry.
Based on this new skeletal, statistical, and genetic evidence, together with evidence previously considered by DOI, it is reasonable to conclude that Kennewick Man is "of, or relating to, a tribe, people, or culture that is indigenous to the United States." 25 U.S.C. § 3001(9). Therefore, I find that Kennewick Man is Native American and subject to the processes and procedures outlined in the Native American Graves Protection and Repatriation Act.
The Corps will next review the priority of custody pursuant to 43 C.F.R. § 10.6, including cultural affiliation. At present, there has been no decision to transfer the remains.

__________________________________________ Date_____________
Scott A. Spellmon
Brigadier General, US Army
Division Commander
2 Any additional and substantial evidence discovered during the review of the priority of custody that is relevant to this Native American determination will be addressed and included in the record.

Following up on the Karitiana - though the following quote is false.

Quote: The strongest relationship is between certain Amazonian tribes, such as the Karitiana, Surui, and Xavante, and the Indigenous Peoples of Papua New Guinea, two regions that are coincidentally among the most linguistically diverse in the world.

karitiana

Contact history

Very little is known about the history of the Karitiana prior to the start of the 20th century. The first reference to this group in the literature dates from 1909, in a report by Captain Manoel Teophilo da Costa Pinheiro, one of the members of the Rondon Commission. In 1910 Marshall Rondon himself mentions the Karitiana, then living close to the middle Jaci-Paraná river: this data was later used by Curt Nimuendajú on his Ethnohistorical Map. However, it seems that the first contacts with whites took place earlier, at the end of the 18th century, and intensified with the arrival en masse of rubber tappers and caucho rubber extractivists towards the close of the 19th century. Nonetheless, the Karitiana avoided systematic contact until the 1950s, the presence of whites becoming permanent from around the middle of this decade with the arrival of the SPI and Salesian missionaries.

The group seems to have been fairly mobile during the 20th century, possibly under pressure from the colonization fronts of the surrounding society. While Captain Manoel da Costa Pinheiro’s reference indicates the presence of the Karitiana on the Jaci-Paraná in 1909, a map sketched by J. Barboza in 1927 locates the Karitiana on the left shore of the middle and lower Candeias, between this river and the Jaci-Paraná. The area between the Candeias and Jamari rivers, important affluents of the right shore of the Madeira river, was declared the territory of the Arikém (Ariquême). In this same area, the records of the 9th Regional Inspectorate of the SPI from 1948 situate the Karitiana slightly further to the east. Between 1950 and 1953 they were located on the middle Candeias river in what appeared to be a new movement westwards; the group was probably visited by three Salesian priests in this location in 1958. Then in 1967-69 the Karitiana Indigenous Post was set up further west on the upper Das Garças river. Apparently some years later the group headed a little further westwards, eventually occupying the current site on the shores of the Sapoti river.

According to their historical narratives, the Karitiana experienced a brutal demographic decline after contact with the whites. Indeed Darcy Ribeiro considered them extinct in 1957. This situation led the group to adopt extreme measures to avoid their complete extinction. Firstly, an elderly leader, Antônio Morais, married various Karitiana women (7 or 10, depending on the different versions), including some women in principle interdicted by matrimonial rules. This event ended up generating a densely related population from the genealogical and genetic viewpoint: a study by the Federal University of Pará, in 1991, showed that the coefficient of average consanguinity – which measures the degree of genetic kinship of a population – of the Karitiana was 0.142 (between first-degree cousins, this figure is 0.125). Also according to the research, all the Karitiana below 16 years old descend from the chief Morais, very often by various genealogical lines.

The group led by the chief Morais lived on the middle Candeias, working for a rubber boss in exchange for industrialized goods. At some point, possibly around the 1930s or 40s, this group left the region, refusing any contact with the whites. They moved westwards, encountering another group – called Capivari or Joari, according to the different versions – from whom they had probably separated during the initial moments of contact at the start of the 20th century (when narrating the episode of the encounter, the Karitiana emphasize that communication was possible since the two groups spoke the same language). The two groups met in the area currently occupied by the Karitiana, which they today recognize as the former Capivari\Joari territory. In this region they entered into contact with the whites once again, at the end of the 1950s. Their historical traditions stress the vital importance of the meeting of these two groups: with the populations of both groups heavily reduced, the couples formed after the union proved to be fundamental to the subsequent demographic and cultural recovery of the people.

It is unknown why the group formed after the re-encounter of the Karitiana and Capivari/Joari kept the name of the former, but it is likely, judging by the memories of those alive today, that Antônio Morais had become a prodigious giver of women – since the Karitiana recount that Morais looked for men among the Capivari/Joari to marry his many daughters – and his prestige had grown enormously due to the many sons-in-law he brought to live with him. At the same time, Morais was already well-known as a leader in the region at the time of the first permanent contacts with whites, becoming a key intermediary between the latter and the Karitiana: in 1957 he was taken to Porto Velho with his son José Pereira, and the two became the first Karitiana to be baptized, according to the records held in the Cathedral in the city.

A subsequent DNA study by David Reich & Svante Pääbo titled: "An early modern human from Romania with a recent Neanderthal ancestor:" Terms the specimen "Oase-1" and re-dates it to 37,000–42,000-years-old. Oase-1 belongs to the Y-dna haplogroup F, which is carried by most males in Eurasia today. The Mtdna = N. Study quote: We then find that the Oase 1 individual shares equally as many alleles with early Europeans, as with present-day East Asians and Native Americans.