Haplogroup X2a: Kennewick man

From Dienekes blog,

Kennewick Man was a Native American
Nature (2015) doi:10.1038/nature14625

The ancestry and affiliations of Kennewick Man

Morten Rasmussen, Martin Sikora, Anders Albrechtsen, Thorfinn Sand Korneliussen, J. Víctor Moreno-Mayar, G. David Poznik, Christoph P. E. Zollikofer, Marcia S. Ponce de León, Morten E. Allentoft, Ida Moltke, Hákon Jónsson, Cristina Valdiosera, Ripan S. Malhi, Ludovic Orlando, Carlos D. Bustamante, Thomas W. Stafford Jr, David J. Meltzer, Rasmus Nielsen & Eske Willerslev

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)1. 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 permitted2. 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 Americans2. 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 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 genomic-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.

Dienekes Anthropology blog

From the paper

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).

Ancestry and Affiliations of Kennewick man

Link to figures

a reply to: punkinworks10

You beat me to it. So now we have it, not even a descendant of the same group that gave rise to the Ainu. Guess it's time to turn the remains over now?

originally posted by: theantediluvian
a reply to: punkinworks10

You beat me to it. So now we have it, not even a descendant of the same group that gave rise to the Ainu. Guess it's time to turn the remains over now?

But, with him being HgX2a, we are back to his phenotype being Caucasoid, or more importantly west Eurasian, which is the ultimate origin for HGx.

But, with him being HgX2a, we are back to his phenotype being Caucasoid, or more importantly west Eurasian, which is the ultimate origin for HGx.

the split occurred sometime in the Palaeolithic and the current hypothesis has several X haplogroups moving into Siberia with only X2A making it to the Americas while the rest in Siberia died out,

a reply to: punkinworks10

The ultimate origin of X2a doesn't seem to be as important as the fact that it's present in northern North American indigenous groups with highest frequencies among Algonquian peoples (like 25% ?). Interestingly, it's found among Altai in Siberia and IIRC, the prevailing hypothesis is that it's not from recent admixture which means it's been preserved for several thousands of years.

Meanwhile, his Y-DNA is Q-M3 which is found predominantly among indigenous populations of the Americas and to a much lesser extent in Siberia.

Wikipedia - Genetic History of Indigenous Peoples of the Americas

Haplogroup Q-M3 (Y-DNA) is defined by the presence of the rs3894 (M3) (SNP).[3][31][35] The Q-M3 mutation is roughly 15,000 years old as that is when the initial migration of Paleo-Indians into the Americas occurred.[36][37] Q-M3 is the predominant haplotype in the Americas, at a rate of 83% in South American populations,[38] 50% in the Na-Dené populations, and in North American Eskimo-Aleut populations at about 46%.[30] With minimal back-migration of Q-M3 in Eurasia, the mutation likely evolved in east-Beringia, or more specifically the Seward Peninsula or western Alaskan interior. The Beringia land mass began submerging, cutting off land routes.[39][30][40]

From the paper:

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 Americans

ATS is being dodgy right now

a reply to: theantediluvian


Lets try this again,


here is good study on HgX

Clade X2e, defined by the synonymous substitution at 15310, encompasses all haplogroup X sequences in the Altaians (fig. 2). Among the nine Altaian X sequences, eight harbor the founder HVS-I motif of X2e, and seven of these eight also carry the HVS-II founder motif. As a result, a very low haplotype diversity of haplogroup X (0) in the Altaian region was obtained, making it significantly different from the haplotype diversities for haplogroups C and D (0.835 and 0.943, respectively) in the same region. Moreover, the nine Altaian mtDNAs do not harbor any nucleotide difference between nps 16090 and 16365. Therefore, under the assumption that these sequences are a random sample of the Altaian haplogroup X, an estimated ρ value

a reply to: punkinworks10

WOW its all of a sudden truncating posts

Clade X2e, defined by the synonymous substitution at 15310, encompasses all haplogroup X sequences in the Altaians (fig. 2). Among the nine Altaian X sequences, eight harbor the founder HVS-I motif of X2e, and seven of these eight also carry the HVS-II founder motif. As a result, a very low haplotype diversity of haplogroup X (0) in the Altaian region was obtained, making it significantly different from the haplotype diversities for haplogroups C and D (0.835 and 0.943, respectively) in the same region. Moreover, the nine Altaian mtDNAs do not harbor any nucleotide difference between nps 16090 and 16365. Therefore, under the assumption that these sequences are a random sample of the Altaian haplogroup X, an estimated ρ value

MODS what happened today on ATS, cant post more than a paragraph

this is really annoying

Clade X2e, defined by the synonymous substitution at 15310, encompasses all haplogroup X sequences in the Altaians (fig. 2). Among the nine Altaian X sequences, eight harbor the founder HVS-I motif of X2e, and seven of these eight also carry the HVS-II founder motif. As a result, a very low haplotype diversity of haplogroup X (0) in the Altaian region was obtained, making it significantly different from the haplotype diversities for haplogroups C and D (0.835 and 0.943, respectively) in the same region. Moreover, the nine Altaian mtDNAs do not harbor any nucleotide difference between nps 16090 and 16365. Therefore, under the assumption that these sequences are a random sample of the Altaian haplogroup X, an estimated ρ value

a reply to: punkinworks10

The interpreter is choking on the less than symbol, let's try inserting some white space. Here's the rest of your excerpted text:

< 0.33 (P < .05) was obtained. This value corresponds to a time depth of < 6,700 years (Forster et al. 1996), and it would suggest that Altaians have acquired haplogroup X2 only relatively recently. This scenario is supported by the concomitant presence in the Altaians of a wide range of other West Eurasian haplogroups (H, J, I, T, U1, U4, and U5) that comprise ∼27% of their mtDNAs. Indeed, any recent migration (for example, from the [southern] Caucasus region) that might have carried X2e mtDNA sequences to the Altai region would also explain the presence of the other West Eurasian mtDNA haplogroups in modern Altaians.

From the same paper, Origin and Diffusion of mtDNA Haplogroup X:

Further northeast of the Altai area, haplogroup X sequences were detected in the Tungusic-speaking Evenks, of the Podkamennaya Tunguska basin (Central Siberia). In contrast to the Altaians, the Evenks did not harbor any West Eurasian mtDNA haplogroups other than X. However, neither of the two Evenk X haplotypes showed mutations characteristic of the Native American clade X2a. Instead, one sequence was a member of X2b and the other of X2* (fig. 2). Thus, one possible scenario is that several X haplotypes arrived in Siberia from western Asia during the Palaeolithic, but only X2a crossed Beringia and survived in modern Native Americans. Alternatively, the presence of two phylogenetically different haplogroup X mtDNA sequences in this particular subpopulation of Evenks might be due to recent gene flow.

What I'm not understanding is what bearing this has on the dispute over the remains? If members of the tribes within the confederation that were suing for the return of the remains are descended from the same group that the Kennewick Man was a member of (allowing for admixture in the intervening time of course), then their claim seems validated.

a reply to: theantediluvian
Thanks,
For that , it's been a bad coding day , issuse with the workstation , issues with machine control software and ATS is being dodgy

originally posted by: punkinworks10
a reply to: theantediluvian
Thanks,
For that , it's been a bad coding day , issuse with the workstation , issues with machine control software and ATS is being dodgy

No problem, I've got a bunch of code to write myself — that I'm supposed to be demonstrating tomorrow (ugh). One of these days I'm going to get around to not procrastinating so much. Then again, it seems like I always do my best work under pressure.