The Mal'ta aDNA findings

The recent sequencing of ancient DNA from the remains of a Central Siberian young boy, corresponding to the Gravettian site of Mal'ta, West of Lake Baikal, dated to c. 24,000 years calBP, has caught the interest of many anthropology enthusiasts. During my hiatus of more than two months, most people who asked me to retake blogging with an specific request, talked of these findings. Let's see:

Maanasa Raghavan et al., Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 2013. Pay per view → LINK [doi:10.1038/nature12736]

Abstract

The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians^{1, 2, 3}, there is no consensus with regard to which specific Old World populations they are closest to^{4, 5, 6, 7, 8}. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal’ta in south-central Siberia⁹, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date. The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers^{10, 11, 12}, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages⁵. Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians^{2, 13}. Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago¹⁴, revealed similar autosomal genetic signatures as MA-1, suggesting that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans.

Haploid lineages

The Mal'ta boy, MA-1, carried distinct yDNA R* and mtDNA U* lineages. While both are clearly related to those dominant in Europe and parts of Asia (West, South) nowadays, they are also distinct from any specific dominant lineage today.

R* (yDNA) is neither R1 nor R2 but another distinct branch of R. This kind of R(xR1, R2) is most rare today and found mostly in and around NW South Asia. Following Wikipedia, this "other R" is found in:

• 10.3% among the Burusho
• 6.8% among the Kalash
• 3.4% among the Gujarati

However I must say that I recall from old discussions that some R(xR1) is also found among Mongols and some North American Natives. I would have to find the relevant studies though (maybe in an update).

U* (mtDNA) is also quite rare today but has been found in Swabian Magdalenian hunter-gatherers, as well as in some Neolithic samples, although it may well be a totally different kind of U* (I could not discern the specific markers in the paper nor the supplementary materials and it must be reminded that the asterisk only means "others").

Autosomal DNA

The study also shows some statistical inferences from the autosomal (or nuclear) DNA of the Mal'ta boy:

Figure 1 [b & c]
b, PCA (PC1 versus PC2) of MA-1 and worldwide human populations for which genomic tracts from recent European admixture in American and Siberian populations have been excluded19.
c, Heat map of the statistic f3(Yoruba; MA-1, X) where X is one of 147 worldwide non-African populations (standard errors shown in Supplementary Fig. 21). The graded heat key represents the magnitude of the computed f3 statistics.

Here we can appreciate that MA-1 is closest to Native Americans but still rather intermediate between them and South and West Eurasians. Interestingly East Asians are quite distant instead, suggesting that MA-1 was still not too much admixed with that continental population, unlike what happens with Native Americans, who are essentially East Asian in the autosomal and mtDNA aspects. So this kid appears to be some sort of a "missing link" in the Paleolithic ethnogenesis of Native Americans.

Figure 2 | Admixture graph for MA-1 and 16 complete genomes. An admixture graph with two migration edges (depicted by arrows) was fitted using TreeMix21 to relate MA-1 to 11 modern genomes from worldwide populations22, 4 modern genomes produced in this study (Avar, Mari, Indian and Tajik), and the Denisova genome22. Trees without migration, graphs with different number of migration edges, and residual matrices are shown in Supplementary Information, section 11. The drift parameter is proportional to 2Ne generations, whereNe is the effective population size. The migration weight represents the fraction of ancestry derived from the migration edge. The scale bar shows ten times the average standard error (s.e.) of the entries in the sample covariance matrix. Note that the length of the branch leading toMA-1 is affected by this ancient genome being represented by haploid genotypes.

Even if I am not too keen of TreeMix, in this case the results seem consistent.

We can appreciate here that a sample of Native Americans (the Karitiana, maybe not as "pure" as the Xavantes but still very much so) show up in a different branch from MA-1, reflecting their overwhelmingly East Asian ancestry, mostly by the maternal side (mtDNA). MA-1 instead hangs from the South-West Eurasian branch, soon after the split between South Asians and West Eurasians. Both have extremely drifted branches, surely indicating the small size of their founder populations, typical of the Far North. 

In addition to this basic tree, two admixture events are signaled: one is the already known Denisovan (H. erectus?) weak one into Australasian Natives (represented by Papuans) and the other one, quite more intense, is the one hanging from upstream of MA-1 to Native Americans (Karitiana), reflecting the partial South-West Eurasian ancestry of Native Americans (noticeable also in their dominant paternal ancestry: haplogroup Q). 

The fact that the admixture signal stems from quite upstream of MA-1 indicates that this boy (or rather his relatives) were not direct ancestors of Native Americans in any significant way but rather a different branch from the same trunk. Probably proto-Amerindians were already in this period at the North Pacific coasts, not sure if in Beringia or around Okhotsk or what but certainly they had already separated from the Mal'ta population.

What did we know of Native American genesis before this finding?

There are three principal lines of evidence:

1. Y-DNA, which among Native Americans is essentially haplogroup Q (plus some C3, which is from NE Asia). By phylogenetically hierarchical diversity, haplogroup Q must have coalesced in West or Central Asia (or maybe South Asia?), very possibly in or near Iran. The NE Asian and Native American branches are clearly derived, even if more important numerically today.
2. mtDNA, which among Native Americans is essentially from NE Asia (A, C, D), middle East Asia (B) but also in a small amount from West Asia (X2). 
3. Archaeology: we can track, more or less directly, the proto-NAs by means of following the Upper Paleolithic sequence in Siberia and nearby areas. 
1. C. 47,000 years ago (calBP) H. sapiens with Aurignacoid technology (i.e. linked to West Eurasian earliest Upper Paleolithic) reached Altai, displacing the Neanderthals to the Northern fringes of the district.
2. C. 30,000 years ago, Upper Paleolithic ("mode 4") technology with roots in Altai reached other parts of Siberia, Mongolia and North China, from where it expanded eastwards and southwards gradually in a process of, probably, cultural diffusion. 
3. By c. 17,000 years ago they were already in North America and c. 15,000 years ago in South America. In the LGM they were probably in Beringia already (but this is only indirectly attested so far). 

So we already had a good idea about the origins of Native Americans: their ultimate roots, at least patrilineally, seem to be in Altai (where they were part of the wider West Eurasian colonization at the expense of Neanderthals with Aurignacian-like technology and dogs). Then, probably around 30,000 years ago they expanded eastwards through Siberia and maybe nearby areas, entering in intense and intimate contact with the already existent East Asian populations, with whom they admixed once and again, mostly by the female side. 

It would seem therefore that their society was already patrilocal because otherwise their patrilineages would have just got dissolved among the locals and would have never reached Beringia nor America in such dominant position.

Overall this is the quite clear notion that I have on Native American earliest genesis and for me there is no reasonable doubt about this narrative (except maybe in the fine details). However I must reckon that some individuals have reacted very negatively against it. But no matter how much they yell, I fail to see their arguments. 

How does this new finding affects this narrative?

It simply confirms it with further evidence. By 24,000 calBP the proto-NAs were surely already, as I said before, in NE Asia close to the Pacific coasts, so this Mal'ta population is a branch left behind in their migration (plus whatever new inflows from the West, which we can't evaluate). The very low affinity level with East Asians, in spite of its quite Eastern location, shows that early East Asians had not yet reached, at least in significant numbers, so far North. If they had, they probably did only at more eastern longitudes, probably near the sea, where resources were more plentiful.

In other words: the first Central Siberians were of South+West Eurasian stock and the current East Asian genetic and phenotype hegemony in that area reflects post-LGM flows, mostly lead by yDNA N1. 

Early Native Americans were the product of admixture of these earliest Siberians with NE Asians, admixture that surely happened East of Lake Baikal, although the exact details are still unclear. 

What does MA-1 say about the West?

His mtDNA is generally consistent with other common U-derived lineages found in West Eurasian Upper Paleolithic, so not much other than he was somehow related, what is confirmed by autosomal analysis. 

His yDNA is more interesting maybe, nonetheless because it is probably the oldest sequence of this kind but also because it belongs to haplogroup R. It certainly discards whatever "molecular clock" guesstimates for R that are shorter than this site's age but on its own it is not able to set a real age other than a bare minimum. 

So for example Eupedia's estimate of 29 Ka for R as such could still be valid, although I would say that extremely unlikely. 

Indirectly however it does say something by confirming the overall narrative of Native American origins as above and that means that Eupedia's estimate of a mere 24 Ka age for haplogroup Q is almost certainly wrong by a lot. 

Using that tree, we would have to at least double the age of Q in order to fit with the Altai narrative (which begins at c. 47 Ka ago), what, extrapolating, implies an age for R of at least 58 Ka. I have estimated some 48 Ka of age for R1 and 68 Ka for P, so it makes good sense after these so necessary corrections. The exact ages we may never know but the approximate ages should be something like these. 

And that's about all I can say. More in comments (and/or updates) if need be.



Update (Dec 6): R* and P* (and other rare clades) among Central Asians

A reader sent me copy of the study by Wei-Hua Shou et al. (2010) titled Y-chromosome distributions among populations in Northwest China identify significant contribution from Central Asian pastoralists and lesser influence of western Eurasians, published by Nature (doi:10.1038/jhg.2010.30).

While it is not the bit of info I was recalling above, it does add some information about unmistakable R(xR1,R2) and P(xQ,R) among Central Asian populations (from P.R. China territory). In detail:

• R* is found in 5/31 Tayiks, 1/41 Kazakhs and 1/50 Uyghurs.
• P* is found in 1/31 Tayiks and 1/43 Kirgizes. 

Also of interest should be the presence of:

• Q(xQ1) in  8/35 Dongxiang (a Mongol ethnicity), 1/45 Kirgizes and 1/50 Tu (another Mongol ethnicity).
• F(xG,H,I,J,K) in 2/32 Yugu (Yugurs, a distinct Uyghur sub-ethnicity), 2/41 Kazakh, 1/31 Tayiks and 1/50 Tu.
• K(xN,O,P) in  32/533 total (i.e. 6% in Easternmost Central Asia), among which are most notable: 9/50 Uyghurs, 6/23 Uzbeks, 6/27 Bao'an (another small Mongol ethnicity), 3/32 Xibo (a Tungusic ethnicity), 2/32 Yugu and 2/5 Mongols. I guess that it is possible that this is a distinct K subclade, although it can well be either part of MNOPS (NO*?) or also belong to LT (L?).
• R2 in 1/31 Tayiks and 2/27 Bao'an.