Genome of 12,600 year-old boy from Clovis culture confirms origin of Amerindians

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Rasmussen et al. tested the entire genome of a boy from the Clovis culture who died 12,600 years ago in Anzick, Montana. The results shows that all indigenous people in both North an South America seem to be descended from the same group of ancestors as those of the Clovis culture, which started c. 13,250 years ago. Clovis people are thought to have arrived to the Americas by crossing the land bridge from Siberia some 15,000 years ago.

The researchers compared the Anzick boy's genome with DNA samples from various Eurasian populations and 52 South American, Central American and Canadian tribes and found it to be most closely related to Central and South American populations, followed by Canadian tribes. The boy belonged to mtDNA haplogroup D4h3a, common among modern Amerindians. His Y-DNA is Q1a2a1 (L54, xM3), which is ancestral for Q1a2a1a1 (M3), the paternal lineage of modern Native Americans.

The Anzick genome was compared to that of the 24,000 year-old Mal'ta boy from Lake Baikal, to the 4,000 year-old Saqqaq Paleo-Eskimo from Greenland, as well as to the contemporary genomes of Karitiana and Mayan individuals. The Anzick-1 boy showed once again closer similarities with modern Native American (NA) populations than with the Mal'ta boy. Interestingly the Saqqaq Greenlander was intermediary between other NA and East Asians, and in fact closer to the Han Chinese to to the Anzick boy.

Unfortunately this genome won't give us an answer to the question of whether Europeans settled the Americas first during or immediately before or after the Last Glacial Maximum (26,000-19,000 years ago).

The earliest possible colonisation of the American continent might have taken place 30,000 years ago. The oldest skeletons in the Americas look distinctly more Europoid in their traits. Mongoloid features, present in modern Native Americans, suddenly replaced them from the time of the Clovis culture. This study confirms that Clovis was mongoloid and therefore also related to the modern Y-haplogroup Q1a and mt-haplogroups A, B, C and D of Native Americans.

It has been assumed that mtDNA haplogroup X2a, found exclusively in North America, was the last trace of the earlier European or Middle Eastern colonisation of the Americas. Y-DNA R1* has also been proposed, although there are only unconfirmed rumours of its existence among Native North Americans.

Notwithstanding the laudable accomplishment of sequencing a full ancient genome, it would have been far more interesting to choose a pre-Clovis sample to confirm the European, Middle Eastern or Siberian/East Asian identity of the first colonisers. I suppose that they started by the Clovis culture to avoid offending Native Americans by telling them that they are not descended from the Palaeolithic Americans.

The only solace I find is a hint of Irano-Gedrosian admixture in the Anzick-1 sample's K=11 admixture. The Anzick boy has nearly 100% of Native American admixture, 0% of Siberian, 0% East Asian (Chinese, Japanese), BUT 1 or 2% of the admixture that peaks in the Kalash, and is also found at high frequency in the Hazara, Sindhi, Balochi, Burusho, Persians, etc., and at a lower (10-15%) frequency in all Caucasian and European populations, except the Sardinians. This part of the original admixture of Y-DNA R, and could confirm that R1* was indeed present alongside X2a in the Upper Palaeolithic North American population that was replaced by the Clovis people.
 
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His Y-DNA is Q1a2a1 (L54, xM3), which is ancestral for Q1a2a1a1 (M3), the paternal lineage of modern Native Americans.

M3 isn't the only paternal lineage of modern Native Americans, however, and indeed L54+ M3-, namely Q L54>Z780, is present among a lot of modern Native Americans. Unfortunately, the supplementals don't indicate whether or not Z780 was tested on Anzick-1.

Unfortunately this genome won't give us an answer to the question of whether Europeans settled the Americas first during or immediately before or after the Last Glacial Maximum (26,000-19,000 years ago) - the so-called Solutrean hypothesis.

The earliest possible colonisation of the American continent might have taken place 30,000 years ago. The oldest skeletons in the Americas look distinctly more Europoid in their traits. Mongoloid features, present in modern Native Americans, suddenly replaced them from the time of the Clovis culture. This study confirms that Clovis was mongoloid and therefore also related to the modern Y-haplogroup Q1a and mt-haplogroups A, B, C and D of Native Americans.

But it directly contradicts the Solutrean hypothesis, which states that there is a connection between the Solutrean culture and Clovis in particular. What's of interest is the similarities between Solutrean and Clovis industries, and now there's some genetic evidence (admittedly only 1 sample and we still don't have a true Solutrean sample) that there's no Solutrean-Clovis genetic connection. It doesn't disprove Solutrean entirely, but it's very strong evidence against it.

Notwithstanding the laudable accomplishment of sequencing a full ancient genome, it would have been far more interesting to choose a pre-Clovis sample to confirm the European, Middle Eastern or Siberian/East Asian identity of the first colonisers. I suppose that they started by the Clovis culture to avoid offending Native Americans by telling them that they are not descended from the Palaeolithic Americans.

I would've thought that they chose Clovis because it's the most well-studied and is very interesting, and perhaps easier than older ones to get a good sample from. I really doubt they knew the results ahead of time and wanted to protect people's sensibilities. But I'd also like to see it compared to pre-Clovis samples as well.
 
Thank you for that interesting and helpful summary, Maciamo. But what do you think about the theory that the Solutreans and the Clovis folk could both be descended from a Siberian population, with part of the Siberian population striking out for Europe and another part staying in Siberia for a while before migrating across the Bering Strait. That idea seems more workable to me than the Solutrean Hypothesis, partly because the Bering Strait would be easier to cross than a lengthy stretch of Atlantic arctic ice and partly because of the time difference between the Solutreans and Clovis.
 
Interesting to note.
So is he not that far from being eskimo like
 
R1 YDNA and X2 MtDNA is not European but Siberian when it is 15000 years old behind.
R1 and blood puts together B is indeed found not negligible among am?rindians flood and blackfeet.
Clovis would therefore be closer to Navajos or commanches (langage atabascan) and also cheyennes (langage algonquin); but different from Sioux or blacfeet.

Indeed they could not keep the possible Europe because any puts together that siberian, Mongolian and austranesian is found at am?rindiens; and that the only real passages are the volcanic barrier of the Japan / islands Aleutes and the passage of the d?troit of Bering, because neither planes, nor liners or caravels were available at this time there.
 
@martiko unlikely. To me it looks more and more like R* is the original component of the Irano-Gedrosia-Kalash component. the whole landscape from Central Asia to Northeast Asia must have been different than nowadays. I remember back than when I used to say on Dienekes blog that North European appears to me like northern shifted Gedrosia. In the past people thought the Kalash are basically an extremely "inbreed" version of Punjabi or Pashtuns. But it gets more and more clear that Kalash are rather a source population, remnants of an ancient people.

By the way I myself have 2.3% Amerindian compared to the average of ~0.9% in my people. Also noteworthy is that I have 0% (average 0.7%) Siberian and close to 0% East Asian but 0.7% Arctic(average 0.1%) in Globe 13.

This must be the common origin of R* and Q* and the ancient connection of Irano_Kalash/North Euro on one side and Amerindian on the other.
 
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M3 isn't the only paternal lineage of modern Native Americans, however, and indeed L54+ M3-, namely Q L54>Z780, is present among a lot of modern Native Americans. Unfortunately, the supplementals don't indicate whether or not Z780 was tested on Anzick-1.

That's right. Some Native Americans do possess L54+ M3-. These seem to be found mainly in Mexico.

But it directly contradicts the Solutrean hypothesis, which states that there is a connection between the Solutrean culture and Clovis in particular. What's of interest is the similarities between Solutrean and Clovis industries, and now there's some genetic evidence (admittedly only 1 sample and we still don't have a true Solutrean sample) that there's no Solutrean-Clovis genetic connection. It doesn't disprove Solutrean entirely, but it's very strong evidence against it.

I suppose that different people have different Solutrean hypotheses. The one you mention seem to be solely based on similarities in spear points and stone tools. I have read about pre-Clovis North Americans having Caucasoid traits, which were replaced by Mongoloid traits from the Clovis culture onward. I wrote about it three and a half years ago. My hypothesis is therefore based on skeletons, not stones. I have never thought once that Europoid Americans were related to the Clovis culture.
 
Thank you for that interesting and helpful summary, Maciamo. But what do you think about the theory that the Solutreans and the Clovis folk could both be descended from a Siberian population, with part of the Siberian population striking out for Europe and another part staying in Siberia for a while before migrating across the Bering Strait. That idea seems more workable to me than the Solutrean Hypothesis, partly because the Bering Strait would be easier to cross than a lengthy stretch of Atlantic arctic ice and partly because of the time difference between the Solutreans and Clovis.

It's a strange question since any people in the Americas would inevitably be descended from people who came from Siberia. There is no other route. Well some people suggested a colonisation from Polynesia, and there has been evidence recently that Polynesians did indeed reach Chile. But that was fairly recently, since Polynesia was not settled by humans until the last 1000 years.

If you are referring to the suggestion by Raghavan et al. that the Mal'ta boy was a hybrid of European, South Asian and Siberian populations, I completely disagree and have explained why it is in fact the opposite : the Palaeolithic Siberian tribes related to Mal'ta were in all likelihood the source population from which modern Central-South Asians (R1, R1a, R1b, R2) and Europeans (R1a, R1b) are descended. This is also evident when one looks at this paper's admixtures. If one were to read the K11 admixtures without using critical thinking, Anzick-1 could look like a blend of 70% Native Andean, 14% Native Arizonan, 5% Native Alaskan, 5% Native Brazilian, 4% Native Costa Rican and 2% Kalash. But that is obviously not the case. Clovis people are ancestral to modern Amerindians, not a blend of many of them. I was utterly shocked that Raghavan et al., who consist of population geneticists from assorted European and American universities, could think that the Mal'ta boy was such a blend. I was even more dismayed when the scientific press meekly repeated those absurdities without thinking.
 
It's a strange question since any people in the Americas would inevitably be descended from people who came from Siberia. There is no other route. Well some people suggested a colonisation from Polynesia, and there has been evidence recently that Polynesians did indeed reach Chile. But that was fairly recently, since Polynesia was not settled by humans until the last 1000 years.

If you are referring to the suggestion by Raghavan et al. that the Mal'ta boy was a hybrid of European, South Asian and Siberian populations, I completely disagree and have explained why it is in fact the opposite : the Palaeolithic Siberian tribes related to Mal'ta were in all likelihood the source population from which modern Central-South Asians (R1, R1a, R1b, R2) and Europeans (R1a, R1b) are descended. This is also evident when one looks at this paper's admixtures. If one were to read the K11 admixtures without using critical thinking, Anzick-1 could look like a blend of 70% Native Andean, 14% Native Arizonan, 5% Native Alaskan, 5% Native Brazilian, 4% Native Costa Rican and 2% Kalash. But that is obviously not the case. Clovis people are ancestral to modern Amerindians, not a blend of many of them. I was utterly shocked that Raghavan et al., who consist of population geneticists from assorted European and American universities, could think that the Mal'ta boy was such a blend. I was even more dismayed when the scientific press meekly repeated those absurdities without thinking.

the colonization come from Australia and New Zealand arrived by Japan then Al?outes islands: A?nus, Esquimaud, Al?outes, am?rindians Lakota, Or?noques, Patagons. This theory of the road by the south Pacific is also unreliable as that by Atlantic-north.
And they cannot consider an accident to be the occupation of the island of P?ques as a generality, unless considering that the survivors are organized colonizers.
 
It's a strange question since any people in the Americas would inevitably be descended from people who came from Siberia. There is no other route. Well some people suggested a colonisation from Polynesia, and there has been evidence recently that Polynesians did indeed reach Chile. But that was fairly recently, since Polynesia was not settled by humans until the last 1000 years.

If you are referring to the suggestion by Raghavan et al. that the Mal'ta boy was a hybrid of European, South Asian and Siberian populations, I completely disagree and have explained why it is in fact the opposite : the Palaeolithic Siberian tribes related to Mal'ta were in all likelihood the source population from which modern Central-South Asians (R1, R1a, R1b, R2) and Europeans (R1a, R1b) are descended. This is also evident when one looks at this paper's admixtures. If one were to read the K11 admixtures without using critical thinking, Anzick-1 could look like a blend of 70% Native Andean, 14% Native Arizonan, 5% Native Alaskan, 5% Native Brazilian, 4% Native Costa Rican and 2% Kalash. But that is obviously not the case. Clovis people are ancestral to modern Amerindians, not a blend of many of them. I was utterly shocked that Raghavan et al., who consist of population geneticists from assorted European and American universities, could think that the Mal'ta boy was such a blend. I was even more dismayed when the scientific press meekly repeated those absurdities without thinking.

I'm not sure why it's a strange question. Perhaps I wasn't clear. I certainly wasn't suggesting that Mal'ta Boy was a hybrid - he was obviously a member of the source population. But the Solutrean hypothesis would require him to be a hybrid since, according to the Solutrean hypothesis, people associated with the Solutrean culture migrated from ice age Europe to North America across the arctic ice of the Atlantic, bringing their methods of making stone tools with them and providing the basis for the later Clovis technology that spread throughout North America. The hypothesis is based on proposed similarities between European Solutrean and Early American Clovis lithic technology. The presence of mtDNA X2 in Native American populations has also been mentioned in support of the hypothesis. My own suggestion was that Mal'ta Boy could have been part of a source population for both the Solutreans and Clovis, but it doesn't require Clovis to be actually descended from the Solutreans, just distant cousins who moved from Siberia across the Bering Strait.
 
To clarify, I was suggesting that, even if Clovis tools and Solutrean tools were made by related people, that doesn't require the Solutreans to be ancestral to the Clovis people, IMO. I think they were more likely cousins from the same Siberian source who moved in opposite directions geographically, which is a somewhat different argument than the Solutrean hypothesis.
 
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I have never thought once that Europoid Americans were related to the Clovis culture.

But that's exactly what the Solutrean hypothesis is all about. And that's why I don't agree with it, even if there is a connection between the Solutreans and the Clovis culture.
 
Alan
why do you want to be Kalash R? while Kalash present as many G Iranian and Indian as many L, I do not have the idea come to me to choose what people referring to R but I'd take tchuvash or even missing in the worst Siberian Tatars for R and Q
 
I'm neutral on Solutrean or variations, but I wouldn't consider it a crank theory, especially with two European Mesolithic individuals belonging to similar haplogroups as common in Native America.
(Admittedly a much different clade of C and undetermined Q).
Also, Clovis may have only been a much more mature phase of the much older Buttermilk Creek Culture (15kbp) in Texas. http://en.wikipedia.org/wiki/Buttermilk_Creek_Complex
An Alaskan migration is much more likely, but excluding other possibilities seems premature also. Who would have guessed La Brana was Haplogroup C?


What's puzzling though is the apparent lack of haplotype diversity in the Indian genome given what must have been multiple migrations into the Americas, and I doubt Anzick-1 represents the "complete indian"/

Culturally and technologically, there must have been at least one other introgression of peoples from Siberia approximately 5500 b.c. Ceramic pottery, farming practices, metallurgy, burial practices and a host of
cultural aspects speak to this, and sorry they weren't independent innovations. The only other possibility is that all of these cultural attributes, such as ceramic pottery, are much much older than currently believed.
 
I have a question about the last sentence of the abstract - what are they referring to with this statement? "Finally, we find evidence of a deep divergence in Native American populations that predates the Anzick-1 individual." Is it that they found a divergence in modern or ancient samples compared to Anzick-1? Does it mean that Anzick-1 population is one of many that entered the Americas 12,000 years ago and contributed autosomally to modern Native Americans, or if they meant ancient Native American (Paleo-Indian) samples were different than Anzick-1, and were replaced by Anzick-1 and it's decedents (modern Native Americans)? I want to read it as modern Native Americans are closely related to Anzick-1, but also contain deep divergence that is older than Anzick-1 a possible relec from earlier migrations in the genome.
 
Alan
why do you want to be Kalash R? while Kalash present as many G Iranian and Indian as many L, I do not have the idea come to me to choose what people referring to R but I'd take tchuvash or even missing in the worst Siberian Tatars for R and Q

And this is exactly why, Kalash are a good source population. L is not Indian nor is G exclusively Iranian. Ultimately L, R, H and J have ultimately one ANE origin. People are so excited about the R* found in the Mal'ta individual while they completely forget that Kalash have 7% of R* and 2.5% R1* themselves.
 
That 8,000-year-old Motala12 sample from Southern Sweden that was sequenced late last year was 19 percent ANE. What I'd like to see is a comparison of the ANE component of this new Anzick-1 boy with the ANE component of Motala12. And if it turns out they are more closely related to each other than they are to the ANE components of other samples, such as Afontova Gora-2 or the Mal'ta boy, then maybe a new component could be isolated from those two genomes.
 
But that's exactly what the Solutrean hypothesis is all about. And that's why I don't agree with it, even if there is a connection between the Solutreans and the Clovis culture.

The things I wanted to confirm are:

1) Were there really Caucasoid or Europoid people living in North America before the Clovis culture, notably between 15,000 and 30,000 years ago ? Were these people replaced by another migration bringing Y-haplogroup Q and mtDNA haplogroup A, B, C and D ?

2) How did X2a get to North America and where did it come from ? Was it European, Middle Eastern, Central Asian ?

3) What paternal lineage was linked to X2a ? (really crucial question for understanding the origins of haplogroup X2) Was it R1* as has been suggested ?


Call it Solutrean hypothesis or whatever you like, I still strongly believe that Caucasoid people came to North America during the Solutrean (22-17 kya) or Gravettian (32-22 kya) periods. I only use those terms to define periods in time. I do not mean that these people came from Western Europe. Actually, my hunch is that the first inhabitants of North America were related to the Mal'ta boy and belonged to Y-haplogroup R* or R1* and mt-haplogroups U (including perhaps U2 and U4), X2 and perhaps even C (presumably C4 or C5). In terms of admixture, these people would have carried ANE and Kalash-like autosomal DNA.

I don't care much about similarities in stone tools. It could have happened by pure coincidence or have been learned from other people, maybe even by the remnants of Caucasoid Palaeolithic North Americans.
 
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I'm neutral on Solutrean or variations, but I wouldn't consider it a crank theory, especially with two European Mesolithic individuals belonging to similar haplogroups as common in Native America.
(Admittedly a much different clade of C and undetermined Q).
Also, Clovis may have only been a much more mature phase of the much older Buttermilk Creek Culture (15kbp) in Texas. http://en.wikipedia.org/wiki/Buttermilk_Creek_Complex
An Alaskan migration is much more likely, but excluding other possibilities seems premature also. Who would have guessed La Brana was Haplogroup C?

While you are mentioning haplogroup C, two remarks:

1) La Brana's C1f cannot be related to the C3 found mostly in western Canada and Alaska. C1 and C3 diverged too long ago (over 50,000 years) to be thought of as cousins. In fact haplogroups I1 and J1 are more closely related than C1 and C3. Don't be fooled by appellations.

2) That brings us to the unresolved issue of the origin of C3 in north-western America. Its distribution suggests that it came after Q1a, probably as an expansion from Mongolia throughout Northeast Asia. What is odd is that no particular mtDNA haplogroup has been associated so far with this late migration of C3. They surely possessed different subclades of A, B, C and D than other Native Americans. But I would also expect to find at least some other Northeast Asian haplogroups like F, G, M7, M9, N9, Y or Z. If the migration happened from the Bronze Age onwards, it is even possible that European maternal lineages be found among C3 populations in North America. These would be assumed to have resulted from admixture with European colonists in recent centuries, but it is not necessarily the case. Likewise, if a Bronze Age expansion from Mongolia to Canada did happen, then even Y-DNA R1a and R1b could be present in trace frequencies among Native American lineages. Any R1b found in western North American tribes that is negative for L11, U106 or P312 should be considered as potentially Native American. All this said, I doubt that C3 was brought during or after the Bronze Age, for the simple reason that bronze technologies and horses were not found among Native North Americans. They could have been lost on the way, but it is still more reasonable to assume that C3 migrated to America some time between 10,000 and 5,000 years ago.
 

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