May 18, 2014

13,000 years old Mexican remains confirm genetic continuity from Paleoamericans

New ancient mtDNA from an underwater cave in Yucatan confirmed that there are no obvious differences between the so-called Paleoamericans and modern Native Americans.

James C. Chatters et al., Late Pleistocene Human Skeleton and mtDNA Link Paleoamericans and Modern Native Americans. Science Magazine 2014. Pay per viewLINK [doi:10.1126/science.1252619]


Because of differences in craniofacial morphology and dentition between the earliest American skeletons and modern Native Americans, separate origins have been postulated for them, despite genetic evidence to the contrary. We describe a near-complete human skeleton with an intact cranium and preserved DNA found with extinct fauna in a submerged cave on Mexico’s Yucatan Peninsula. This skeleton dates to between 13,000 and 12,000 calendar years ago and has Paleoamerican craniofacial characteristics and a Beringian-derived mitochondrial DNA (mtDNA) haplogroup (D1). Thus, the differences between Paleoamericans and Native Americans probably resulted from in situ evolution rather than separate ancestry.

The Hoyo Negro girl, whose skeleton was preserved underwater for millennia, after she apparently fell into the cave and died as consequence, belonged to haplogroup D1, one of a handful found in modern Native Americans (all them within A, B, C, D and X2). 

The radiocarbon date for the skeleton is c. 12,800 BP, while the upper limit of her death (inferred from calcite formation on the bones, dated via thermoluminiscence) is of c. 12,000 BP. 

Overall there are already four mtDNA and two Y-DNA Paleoamerican sequences from the 13-10,000 BP bracket, all of which fit perfectly with modern Native American DNA. See map to the right.

This underlines that anthropometric estimates are not really reliable to determine ancestry, at least in the long run, because there has been much speculation about these not supporting continuity between the first settlers of America (Paleoamericans) and modern Native Americans, however ancient DNA consistently supports continuity. 

One thing is the genotype and another the phenotype. And although they are somehow related for the greatest part, this relationship is not always straightforward, at least with our current knowledge.

See also: Ancient DNA from Clovis culture is Native American (also Tianyuan affinity mystery


  1. Hello Maju! Where did you get that C1? How old is it? I would be interested to learn more on that find!

    1. Sent you a copy of the study. It's listed in it. All four sequences mentioned in the map are listed in the Chatters paper with references for the three that are from previous studies.

    2. It's c. 12.5 Ka old. Only the On Your Knees Cave (Alaska) is a bit more recent: c. 10 Ka.

  2. Thank you very much Maju!
    I tried to google for more information and found out something interesting:
    In this book's+beach+cave%22+and+%22C1%22&source=bl&ots=naeTSXFNgN&sig=eFWrEdVTeQb7KwGMhSLsYkjXin8&hl=fi&sa=X&ei=APh5U5z7M4TbygPDkYCwCA&ved=0CDcQ6AEwAQ#v=onepage&q&f=false
    There is a summary on page 165 on the earliest occurrences of native American mtDNA haplogroups:
    C1d has been found in Wizard’s Beach, Nevada, age 9500 BP (am I right that here, a different age is given compared to this new paper)
    B2 has been found in Hourglass Cave Colorado, age 8000 BP
    X2a has been found in Windower, Florida, age 7400 BP
    A2 has been found in Big Bar Lake, British Columbia, age 4975 BP
    M has been found in China Lake, British Columbia, 4959 BP
    D2 has been found in On Your Knees Cave, Alaska, age ?

    Then I found more information on Wizard's Beach Man, Arlington Springs Woman and Buhl Woman.
    Wizard's Beach Man: NV, 10,560–10,250 BP
    ”Wizard's Beach Man was craniometrically matched to modern Native Americans, DNA testing revealed that he possessed the Asian/Native American haplogroup C.

    Arlington Springs Woman, CA, USA 13,010–12,710
    Arlington Springs Woman HAD NO CRANIA to test, but DNA testing revealed she had the Asian/Native American haplogroup B. I even know a Chumash woman (the tribe in whose territory ASW was found) with the same haplogroup

    Buhl ID, USA 10,675 12,740–12,420 BP
    Buhl Woman was craniometrically matched to modern Native Americans. (No DNA test conducted.)

    It is nice that all Native American haplogroups are confirmed in ancient finds, although not all finds are equally old.

    In Perego et al, 2009, they argue that ”Phylogeographic analyses at the highest level of molecular resolution (69 entire mitochondrial genomes) reveal that two almost concomitant paths of migration from Beringia led to the Paleo-Indian dispersal approximately 15–17 kya. Haplogroup D4h3 spread into the Americas along the Pacific coast, whereas X2a entered through the ice-free corridor between the Laurentide and Cordilleran ice sheets … X2a expansion in America occurred in the Great Plains region, where the terminal part of the glacial corridor ended”.

    You surely remember our long discussion about Baraba steppe a-mtDNA. Recently, I came across a paper in which they said that ”The only two Siberian groups with an almost Amerindian combination are late third to early second millennium BC populations from Okunev and Sopka, southern Siberia. The multivariate analysis of five nonmetric facial traits and ten facial measurements in 15 cranial series reveals two independent tendencies. One of them shows a contrast between prehistoric Siberian Caucasoids and modern Siberian Mongoloids; the second one sets Amerindians apart from others. Prehistoric people who lived west of Lake Baikal and modern Uralic speakers are intermediate between Siberian Caucasoids and Siberian Mongoloids; Eskimos, Aleuts, and Chukchi are intermediate between Siberian Mongoloids and Amerindians; and Okunev and Sopka are intermediate between Siberian Caucasoids and Amerindians. Our results suggest that people of Okunev and Sopka are collateral relatives of Amerindians with some Caucasoid admixture.”

    In the oldest Sopka cemetery you find 3xU2e, 1xU5a1, 1xU4, 1xD, 4xC, 2xA, 4xZ. On the basis of Kozintsev’s analysis, people bearing Sopka haplotypes of C, A and Z were not like Northern Mongoloids but resembled Amerinds.

    1. Ok, Wizard's Cave - I confused it with the Alaskan site in my comment above.

      Interestingly A, which is the last documented lineage by the moment, is the less common of the four major NA matrilineages in South America (the other three are well represented), although it's very common, even tending to hegemony, in Central and North America.

  3. ... I managed to see the text:
    The most significant fact that emerges, though, is that Okunev and Sopka are clearly intermediate not between Caucasoids and Siberian Mongoloids but between Caucasoids and Amerindians. The cluster analysis even joins Okunev with Eskaleuts and Chukchi as well as Sopka with Amerindians. This should not be taken to imply any direct links, of course, but the tendency is evident.
    It does appear, then, that people of Okunev culture and Sopka are so far the only likely candidates for the role of collateral relations of Amerindians in Siberia. It remains to be seen whether new archaeological and ethno-graphic data such as those presented by Lipsky (1969) would support our finding.

    Cranial evidence suggests, however, that people of Okunev and Sopka, unlike Amerindians, had absorbed a considerable Caucasoid admixture. Archaeologically, Okunev culture includes both aboriginal Siberian elements and those which can be explained only by migrations from Europe (Savinov, 1997). The within-group skeletal heterogeneity of Okunev populations speaks in favor of
    incipient hybridization (Gromov, 1997).

    Okunev culture, the Upper Yenisei, late third or early second millennium BC (142).
    Measurements are published in Gromov (1997).

    1. Those are probably ancient Yeniseian peoples, ancestors of the Kets and such.

    2. ... and the astonishing thing is that Finns do not seem to be more East Asian shifted than Germans, French, Ukrainians, Spanish or Italians!

    3. Did you get the first part? If yes, do not post this comment twice!

      As for Finn and Saami, I find this figure exciting

      It was taken from this discussion:
      "If we zoom on the European panel we see as expected that especially Saamis, Mordovians and Vologda Russians pulls left toward the common East-Asian, Siberian and Native American dimension 2. Note that Finns doesn't show the same level of pull towards left as the Saamis, Mordovians and Vologda Russians.

      However if looking at dimension 3 /(vertical) we clearly see Saamis and Finns pulling towards the Native Americans dimension at about same level of intensity. It appears to be lacking among Vologda Russians and Mordovians who pull toward the common East-Asian, Siberian and Native American dimension 2 (horizontal). This seem to suggest (also noted by commentators of this blog from ealier posts) that there is different influences from the East in Europe."

    4. I think I'm missing some reference here. Maybe one of your comments did not get through?

      The graph seems from Anders, right? His results often collide with other results, maybe because he oversamples so much Northern Europe (sample strategy matters a lot when dealing with autosomal genetics). But, well, whatever is worth...

    5. Probably it is from him.

      I do not have the competence to judge his methods, but before La Braña, Olalde et al. was published in 2014, he correctly predicted that Swedes and Finns have the highest affinity with La Braña individual.

    6. I'm fine with Anders. What really bothers me is his hyper-high resolution images, which block my computer and make me near impossible to follow his work but otherwise he makes a decent job regarding Northern Europe details (but maybe not so much capturing the big picture). In any case I wouldn't assert anything autosomal without looking at it from different angles.

      Where in Olalde 2014 does it appear that "Swedes and Finns have the highest affinity with La Braña individual" (by the way it's two individuals, not one)? All I see is a PCA where Bra1 is totally off the mark.

      Also this kind of Nordic or NE European pseudo-affinity of Epipaleolithic peoples has been noticed by other bloggers such as Dienekes. For D. Bra has a more NW slant. The one who made the best work however was Davidski recently, who could practically prove with a simple PCA that Braña1 is way off the mark relative to modern Europeans, including Northern and Eastern ones:

      He says: "it's now an established fact that Mesolithic hunter-gatherers, like La Brana-1, were clearly outside the range of modern European, and indeed West Eurasian, genetic variation."

      Sadly I can't follow Anders (too large graphics for my PC) because his work is sometimes much more nuanced and he has, I know from references, recently found that while overall genetic affinity of Bra1 and other Epipaleolithic HGs is towards NE Europe long IBD affinity is stronger towards Basques or other Iberians (don't recall which ones, maybe both). This is a similar case to the one of Lochsbour, discussed here, which shows greatest overall affinity to Danes but more direct ancestry (long IBDs) to French.

      Autosomal DNA has many nuances. In this case it seems to imply that the most direct descendants of Western HGs like Lochsbour or La Braña are SW Europeans. However, as these are very significantly mixed with West Asian (and some African) Neolithic inputs, while NE Europeans are not, these appear in basic analysis as closer to Western HGs but that is only because Eastern HGs were closer to Western HGs (same Auriñaco-Gravettian origins) than West Asian peoples and Eastern Europeans descend mostly from Eastern HGs, including the Siberian (Mal'ta-like or NA-like element, missing in Western HGs).

      So, in synthesis: there's no direct Magdalenian link to NE Europe: it is a confounding factor caused by dominance of Eastern Gravettian ancestry.

    7. I agree with your analysis! If you follow that link, you can open a Power Point image in which it appears that La Braña 1 is closest to Finns and one LV (Latvian?). The image is from Olalde paper.

    8. This comment has been removed by the author.

  4. Genetic continuity, of course, while resolving one question, still doesn't explain how the Paleoindian phenotype disappeared and was replaced by the modern Native American phenotype.

    1. Is there a "Paleoindian" phenotype, a "modern Native American" single unified phenotype? I don't think so, really. For example Andeans often sport prominent narrow noses that are not matched even by the more "nosy" of West Eurasian individuals. Some NA populations are more "Mongoloid" but others sport a variety of less clearly defined phenotypes. There are even bearded Native Americans with curly hair somewhere in Amazonia.

      Actually their typology looks more like SE Asians than more standard "Mongoloids" in most cases, although of course all comparisons are inexact and they may also sport Siberian affinities, etc. To my eyes they are pretty much diverse.

  5. I am more and more convinced that groups of people have been moving around a lot, back and forth, and probably more in the north than in the south, and mixing with each other all the time, with new interactions boosting selection. Then, it seems that haplotypes may spread very fast and replace other haplotypes, and this replacement may have been even faster in the north, let alone in the arctic, were population numbers were lower than in the south. As for that haplogroup A in America, it may well be more recent, as the coalescence ages of hg B, D and C are older than coalescence ages of X and A, and X probably arose in a more western location than A.
    B Soares 38.100 – 63.800
    D Soares 35.600 – 61.400
    M8’CZ Soares 31.000 – 54.900
    X Soares 19.700 – 44.600
    A Soares 19.100 – 39.800
    It is fascinating that autosomal DNA is more stable. When I say this I have in mind for example La Braña which is said to share DNA with North Europeans, although his yDNA C has (almost?) disappeared and there were surely a lot of genes flowing to the north from the East, South and West later on. It seems that haplogroups may change completely but something always remains in the autosomal DNA. Of course, La Braña’s mtDNA, U5b, is still quite frequent in Europe, but yDNA is not, and it seems that it is precisely yDNA that can change very quicly, although people do not change autosomally so very much. I think that many people are speculating if there has been a yDNA replacement in the America from Palaeoindian times to later periods and wondering what that lost y line could be. On the basis of La Braña, it is not impossible.

    1. Actually autosomal DNA is not more stable. Recently Davidski run Bra1 freely (i.e. not "projecting") together with modern Europeans and he was just extreme.

      On PC1 he was like Northern Russians, probably owing to similar lack of "Neolithic" ancestry (i.e. both were equally opposite to Sardinians on that axis) and on PC2 he was like hyper-mega-ultra-Basque, much more extremely opposed to Adigeys than Basques (never mind other more average Europeans). So obviously in Bra1, as in other WHG samples, there is some of that pre-Neolithic "Europeanness", that those polarities suggest but it is way too diluted and/or derived in modern populations and that makes ancient HGs to be actually very extreme compared to us.

      So they are both telling us the same story by mean of different details. It is the "projection" method what causes a false appearance of similitude.

      Of course when sex-biased admixture happens then different markers, especially Y-DNA, may well be quite different from the others. But mtDNA tends to be the more stable of all genetic markers, I understand, unless mass resettling happened naturally.

      In any case, the main Paleolithic lineage detected so far in Europe (remember that the sample is small, irregular and has many blanks), which is I2, is still quite important in any case. Notably it seems to have "hijacked" the Neolithic expansion process and become quite important in Mediterranean Europe from Yugoslavia to the Basque Country, curiously the area where the sound ɲ (~ny) is universally found in all languages (further north only scatteredly: Irish, Dutch, Norwegian, Latvian, Ukranian).

  6. I am lineage C - the Walker River sample :) I am Northern Paiute too and raised 75 miles away. I have hundreds of cousins in the area.


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