Notes: The Malta boy – When did Europeans arrive at Lake Baikal?

24,000 year old boy from Lake Baikal is ‘scientific sensation’

By The Siberian Times reporter
28 October 2013

Remains of the child suggest an ‘unknown European invasion of Siberia deep in ancient times’.

Geneticist Connie Mulligan of the University of Florida called the findings ‘jaw-dropping’. DNA from this ancient Siberian skeleton offers clues to the first Americans. Picture: The State Hermitage museum, St. Petersburg

New DNA findings, if confirmed, have stunning implications for our understanding of both pre-historic Siberians – and native Americans. They would suggest that, contrary to previous understanding, some indigenous populations are – in fact – European or West Asiatic in origin.

The Danish-US research was carried out on the bones of a Siberian boy whose remains were found near the village of Mal’ta close to Lake Baikal in the 1920s in a grave adorned with flint tools, pendants, a bead necklace and a sprinkling of ochre. The remains are held in the world famous Hermitage Museum in St Petersburg and analysis of a bone in one of his arms represents ‘the oldest complete genome of a modern human sequenced to date’, according to Science magazine.

‘His DNA shows close ties to those of today’s Native Americans. Yet he apparently descended not from East Asians, but from people who had lived in Europe or western Asia,’ said ancient DNA expert Eske Willerslev of the University of Copenhagen. ‘The finding suggests that about a third of the ancestry of today’s Native Americans can be traced to ‘western Eurasia’.’

The research may help explain why ‘European ancestry previously detected in modern Native Americans do not come solely from mixing with European colonists, as most scientists had assumed, but have much deeper roots’, said the report.

It may also raise a similar question about the ‘European look’ of some ancient Siberians – for example in the tattooed permafrost princess Ukok found in a burial chamber in the Altai Mountains, whose remains date from around 2,500 years ago.

Princess Ukok tattooes

‘Princess’ Ukok’s shoulder, tattoo of fantastic animal, and a drawing of it made by Siberian scientists. Picture and drawing:  Elena Shumakova, Institute of Archeology and Ethnography, Siberian Branch of Russian Academy of Science

Russian scientists reconstructed her to show what many were surprised to be a European face, unrelated to the modern day Altai tribes. The finding is confirmed by DNA analysis which showed her to be Pazyryk in origin. Her group was part of the Samoyedic family, with elements of the Iranian-Caucasian substratum’.

The four year old boy was found near the Belaya River close to the village of Mal’ta which is famed for the discovery of ancient art, some of it showing close links to European discoveries of the same period. Willerslev and co-author Kelly Graf of Texas A&M University ‘used a variety of statistical methods to compare the genome with that of living populations.

‘They found that a portion of the boy’s genome is shared only by today’s Native Americans and no other groups, showing a close relationship.

‘Yet the child’s Y chromosome belongs to a genetic group called Y haplogroup R, and its mitochondrial DNA to a haplogroup U. Today, those haplogroups are found almost exclusively in people living in Europe and regions of Asia west of the Altai Mountains, which are near the borders of Russia, China, and Mongolia.’

Until now it has been widely believed that Native Americans were linked to Eastern Siberian tribes, having crossed Beringia, a vast Ice Age land bridge.

The magazine report stated: ‘One expected relationship was missing from the picture – the boy’s genome showed no connection to modern East Asians.

‘DNA studies of living people strongly suggest that East Asians – perhaps Siberians, Chinese, or Japanese – make up the major part of Native American ancestors. So how could the boy be related to living Native Americans, but not to East Asians?’

Malta boy, map of Beringia

The Mal’ta boy was related to people who later migrated across Beringia to the Americas. Picture: G.Grullon/Science

Willerslev and his team propose that earlier than 24,000 years ago ‘the ancestors of Native Americans and the ancestors of today’s East Asians split into distinct groups.

‘The Mal’ta child represents a population of Native American ancestors who moved into Siberia, probably from Europe or west Asia. Then, sometime after the Mal’ta boy died, this population mixed with East Asians. The new, admixed population eventually made its way to the Americas.’

The timing is uncertain but ‘the deep roots in Europe or west Asia could help explain features of some Paleoamerican skeletons and of Native American DNA today’. Some of the traces of Eurasian genetic signatures in modern Native Americans do not come from colonial times when incoming Europeans mixed with the indigenous population.

‘Some of them are ancient,’ said Willerslev. Geneticist Connie Mulligan of the University of Florida called the findings ‘jaw-dropping’.

Yet perhaps the findings – the full details of which are due to be published soon in Nature journal – are not so surprising. Famed Russian archeologist Mikhail Gerasimov found art work at Mal’ta which show a close resemblance to European female figurines of the Upper Paleolithic period. The similarities extend to tools and dwelling structures.

From the Dienekes Anthropology Blog:

Ancient DNA from Upper Paleolithic Lake Baikal (Mal’ta and Afontova Gora)

The study I mentioned in a previous post has now been made available in Nature. Two Upper Paleolithic Siberians (24-17kya) have been sequenced at low coverage. The better quality (and older) Mal’ta (MA-1) sample belongs to Y-haplogroup R and mtDNA haplogroup U, and the younger (but poorer quality) Afontova Gora (AG-2) sample appears to be related to it.

Most interestingly, there is evidence for gene flow between the MA-1 sample and Native Americans, which makes sense as these are Siberians of the period leading up to the initial colonization of the Americas. The interesting thing is that MA-1 does not appear to be East Eurasian, as proven by the test D(Papuan, Han; Sardinian, MA-1) which is non-significant, so MA-1 is not more closely related to Han than to Papuans (which is true for modern native Americans). So, it seems that the gene flow between MA-1 and Native Americans was towards Native Americans from MA-1 and not vice versa.

It is fascinating that such a sample could be found so far east at so early a time. Both Y-chromosome R and mtDNA haplogroup U are very rare east of Lake Baikal which has been considered a limit of west Eurasian influence into east Eurasia. And, indeed, both these haplogroups are absent in Native Americans, so it is not yet clear how Native Americans (who belong to Y-chromosome haplogroups Q and C and mtDNA haplogroups A, B, C, D, X) are related to these Paleolithic Siberians. The obvious candidate for this relationship is Y-chromosome haplogroup P (the ancestor of Q and R). So, perhaps Q-bearing relatives of the R-bearing Mal’ta population settled the Americas.

In any case, this is an extremely important sample, as its position in “no man’s land” in the PCA plot (left) demonstrates, between Europeans and native Americans but close to no modern population.

Its closest present-day relatives are indicated in (c), with Native Americans (red) being the closest, and a scattering of boreal populations from the Atlantic to the Pacific (but not in the vicinity of Lake Baikal) next in line (yellow).

This distribution clearly related to the evidence for admixture in Europe adduced in two other recent papers, although the question of who went where and when remains to be resolved. Was MA-1 part of an intrusive western population encroaching  on east Eurasians? Or did MA-1 lookalikes arrive as first settlers in empty territory, later ceding this space to east Eurasians from, perhaps, China? Did the two mix in Siberia or did they arrive in the Americas in separate migrations and mix there? And, how does this all relate to events in Europe in the far west?

UPDATE: Razib makes an excellent point:

Also, can we now finally bury the debate when east and west Eurasians diverged? Obviously it can’t have been that recent if a >20,000 year old individual had closer affinity to western populations.

We already knew that Tianyuan was more Asian than European, so I think west Eurasians diverged from the rest >40 thousand years ago. But, Tianyuan was so early that its precise relationships to different Asian groups could not be determined. So, I’d say it’s a good guess that east-west split off before 40 thousand years in Eurasia.

Nature (2013) doi:10.1038/nature12736

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

Maanasa Raghavan, Pontus Skoglund et al.

The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians1, 2, 3, there is no consensus with regard to which specific Old World populations they are closest to4, 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-gatherers10, 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 Asians2, 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.


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