West-East admixture in Mongolian Altai in the Bronze Age

This new study found West-East Eurasian admixture in Mongolian Altai before the Iron Age. This finding partly contradicts previous data by González-Ruiz 2012 that suggested a strict genetic divide until the Iron Age.

Clemence Hollard et al., Strong genetic admixture in the Altai at the Middle Bronze Age revealed by uniparental and ancestry informative markers. FSI Genetics 2014. Pay per view → LINK [doi:10.1016/j.fsigen.2014.05.012]

The new data comes from two kurgan burial sites in Westernmost Mongolia: Tsagaan Asga and Takhilgat Uzuur-5 (abbreviated as TA and TU respectively).

In both sites mtDNA lineages have dual origins, although in TU (close to the Russian and Khazakh border) there is some prevalence of Western matrilineages (3/5), while in TA (somewhat farther East) the opposite is true instead (3/7 Western matrilineages), suggesting some clinality. 

On the other hand Y-DNA is totally dominated by Western lineages with a single exception (C), although these Western lineages (Q and R1a) are of Central Asian/Siberian type without exception. Of course, Q variants have been lingering in Central Asia, Siberia and some parts of East Asia almost certainly since Aurignacian, being part of the early genesis of Native Americans (see here for a more in-depth discussion and here for China's Neolithic Y-DNA, which includes some Q), while R1a-Z93 seems a more recent arrival, maybe Epipaleolithic or Neolithic (see here), but both seem to have their origins in or near Iran, judging on basal diversity. 

There is no trace of European-specific inflows on the Y-DNA side, even if some of the mtDNA lineages may be thought as having this origin (H1, H7, U4).

The Eastern ancestry is all typical of NE Asia. I would pay particular attention to mtDNA D, which seems to have spread in the Taiga with the Seima-Turbino phenomenon, which inaugurated the Bronze Age in that area and is believed to originate in Altai.

So, as conclusions, we can say that:

1. There was incipient East-West admixture in parts of Altai already in the Bronze Age, the main actor of this admixture were females.
2. Patrilineal ancestry was essentially "Western" of the kind that must have been in Altai since the Neolithic or earlier (i.e. not European but Central Asian of West Asian affinities/origins)
3. The cultural context is Kurgan, strongly suggesting Indoeuropean language (of the Tocharian branch probably).
4. The Seima-Turbino link however suggests some sort of affinity with carriers of the mtDNA D lineage in the Taiga in that same period, lineage not found further West in Altai. These Siberian Bronze Age vector people were very likely of Tungusic ethnicity. Although early Turkic connections cannot be totally ruled out, in general Turkic peoples seem more associated to the steppe instead and the roots of their expansion were probably forged some centuries later, already in the Iron Age. 
5. Both in the expansion of Indoeuropean eastwards and later in that of Altaic languages and ethnic affiliation westwards, the Altai region seems to have played a key pivotal role. However modern Altaians, even if Turkic by language, retain almost integrally the same Y-DNA genetic signature as the Bronze Age peoples mentioned here, what underlines their capacity to cross ethno-linguistic lines once and again while keeping their patrilineal ancestry nearly unaffected. They are therefore a good example of how populations can change ethno-linguistic ascription without significant genetic flow in such a key factor as the patrilineages. Surely many other peoples did the same in many other geographies. Ancestry and language need not to be linked, even if they sometimes are.

Nearly complete sequence of a Neanderthal from Altai

A 99.9% complete Neanderthal genome from a toe bone found at Denisova Cave (Altai, Southern Siberia).

Documents at Max Plank Institute for Evolutionary Anthropology, Department of Evolutionary Genetics.

A high-quality Neandertal genome sequence

The genome sequence was generated from a toe bone discovered in Denisova Cave in southern Siberia in 2010. The bone is described in Mednikova (Ethnology & Anthropology of Eurasia 2011. 39: 129-138).

DNA sequences were generated on the Illumina HiSeq platform and constitute an average 50-fold coverage of the genome. 99.9% of the 1.7GB of uniquely mappable DNA sequences in the human genome are covered at least ten times.
Contamination with modern human DNA, estimated from mitochondrial and nuclear DNA sequences, is around 1%.

The figure shows a tree relating this genome to the genomes of Neandertals from Croatia, from Germany and from the Caucasus as well as the Denisovan genome recovered from a finger bone excavated at Deniosva Cave. It shows that this individual is closely related to these other Neandertals. Thus, both Neandertals and Denisovans have inhabited this cave in southern Siberia, presumably at different times. 

One may wonder: how can they know it is a Neanderthal and not a "Denisovan"? Because of the close genetic affinity with other Neanderthals from Europe:

It is still possible, considering its position in the tree that the Altai Neanderthal had minor "Denisovan" admixture. But it would be very minor in any case. 

33,000 years old dog from Altai is directly related to modern dogs

The 33,000 Ka old dog

Ancient mtDNA from the oldest known dog remains (ref. of its discovery in 2011) places it unmistakably in the dog subspecies. This does not just confirm that domestic dogs existed do far back in time but also that modern domestic dogs have such deep origins.

Anna S. Druzhkova et al., Ancient DNA Analysis Affirms the Canid from Altai as a Primitive Dog. PLoS ONE 2013. Open access → LINK [doi:10.1371/journal.pone.0057754]

Abstract

The origin of domestic dogs remains controversial, with genetic data indicating a separation between modern dogs and wolves in the Late Pleistocene. However, only a few dog-like fossils are found prior to the Last Glacial Maximum, and it is widely accepted that the dog domestication predates the beginning of agriculture about 10,000 years ago. In order to evaluate the genetic relationship of one of the oldest dogs, we have isolated ancient DNA from the recently described putative 33,000-year old Pleistocene dog from Altai and analysed 413 nucleotides of the mitochondrial control region. Our analyses reveal that the unique haplotype of the Altai dog is more closely related to modern dogs and prehistoric New World canids than it is to contemporary wolves. Further genetic analyses of ancient canids may reveal a more exact date and centre of domestication.

The Altaian Upper Paleolithic dog belongs to clade A, the most common one among modern dogs, including some pre-Columbian lineages from America and such different breeds as the Siberian Husky, the Irish Setter, the Dachshund, the Toy Poodle or the Pug, just to mention a few (see Supp. Table 2 for a longer list).

The authors also compared the lineage with Upper Paleolithic wolf remains from Altai, which are not closely related. 

Figure 2. Consensus Neighbour Joining tree (1,000 bootstrap steps) built assuming the Tamura-Nei substitution model, the best fit model for the dataset comprising complete mitochondrial genomes from coyotes (Coyotes), wolves (OWW, NWW – Old and New World wolves, respectively) and dogs combined with partial control region sequences from the Altai specimen (Altai dog) and additional prehistoric canids (pre-Columbian dogs, eastern Beringian wolves).
We highlighted all clades containing modern dogs in light blue and enlarged Clade A for better visibility. The position of the Altai specimen is marked with a light blue arrow in the enlargement. Bootstrap values are shown with an asterisk whenever larger than 50.

Surely the presence of four different generic Canis lupus mtDNA clades in modern dogs indicates the domestication of at least four different wolf females, either in the same or different places. 

Gravettian dog with bone (ref)

This finding puts to rest the Neolithic hypothesis of the origin of modern dogs (alleged second domestication, because UP dogs were known) and is at least consistent with my favorite hypothesis of dog domestication in SE Asia (ref 1, ref 2) within the context of the early expansion of Homo sapiens in Eurasia-Australasia in the late Middle Pleistocene, with backflow via South Asia to the West, where dogs may have played a decisive role in the long-term competition with the strong and intelligent Neanderthals.

Mitochondrial snapshots from an East-West encounter in Altai

Ukok Plateau landscape
(CC by Kobsev)

The Iron Age Pazyryk culture of Ukok Plateau (Altai Mountains, Central Asia) are generally considered to be related to Scythians or other Indoeuropean peoples of Western affinity. However the affiliation of Pazyryk peoples remains controversial. A new Catalan study may help to shed some light to the matter:

Mercedes González Ruiz et al., Tracing the Origin of the East-West Population Admixture in the Altai Region (Central Asia). PLoS ONE, 2012. Open access ··> LINK [doi:10.1371/journal.pone.0048904]

Abstract

A recent discovery of Iron Age burials (Pazyryk culture) in the Altai Mountains of Mongolia may shed light on the mode and tempo of the generation of the current genetic east-west population admixture in Central Asia. Studies on ancient mitochondrial DNA of this region suggest that the Altai Mountains played the role of a geographical barrier between West and East Eurasian lineages until the beginning of the Iron Age. After the 7th century BC, coinciding with Scythian expansion across the Eurasian steppes, a gradual influx of East Eurasian sequences in Western steppes is detected. However, the underlying events behind the genetic admixture in Altai during the Iron Age are still unresolved: 1) whether it was a result of migratory events (eastward firstly, westward secondly), or 2) whether it was a result of a local demographic expansion in a ‘contact zone’ between European and East Asian people. In the present work, we analyzed the mitochondrial DNA lineages in human remains from Bronze and Iron Age burials of Mongolian Altai. Here we present support to the hypothesis that the gene pool of Iron Age inhabitants of Mongolian Altai was similar to that of western Iron Age Altaians (Russia and Kazakhstan). Thus, this people not only shared the same culture (Pazyryk), but also shared the same genetic east-west population admixture. In turn, Pazyryks appear to have a similar gene pool that current Altaians. Our results further show that Iron Age Altaians displayed mitochondrial lineages already present around Altai region before the Iron Age. This would provide support for a demographic expansion of local people of Altai instead of westward or eastward migratory events, as the demographic event behind the high population genetic admixture and diversity in Central Asia.

Surely the most interesting finding of this study is that, unlike all other studies so far in the area, Bronze Age burials¹ from westernmost Mongolia carried 100% (3/3) Eastern Asian haplogroups (all D). Only one sample from the same wider region and period had ever before produced some Eastern lineages but as minority (9%, Southern Siberia, Turbat 2005), all others producing instead 100% Western haplogroups.

Instead Iron Age burials produced a much more mixed picture (n=16):

• Eastern haplogroups: 8 (50%)
• A: 1
• C: 2
• D: 4
• G2a: 1
• Western haplogroups: 8 (50%)
• HV6: 1
• J: 1
• K: 3
• U5a1: 2
• T1: 1

This process however does not just imply penetration of Western lineages in the Mongolian part of Altai but also, as can be inferred in other studies' data, an extension of Oriental ones to the Western parts of Central Asia. The contrast between a well defined East-West genetic divide in the Bronze period and almost total blur in the Iron one instead is dramatically captured by these maps:

Figure 2. Spatial frequency distribution maps of East Eurasian lineages.

A- Pre-Iron Age period; B- Iron Age period. Frequency values and detailed information for populations 1–8 are shown in table 3. 1- Mongolia (Altai), 2- Gorny Altai, 3- West Kazakhstan, 4- Central Kazakhstan, 5- South Kazakhstan, 6- East Kazakhstan, 7- SW Siberia, 8- Mongolia (Egyin Gol).

The authors conclude:

The Pazyryk groups analysed so far appear to be genetically homogeneous and they did not present significant genetic differences to current Altaians. These results suggest that roots of the current genetic diversity and admixture of the Altai region in Central Asia could be traced back to the Iron Age.

______________

Note: 

¹ Text minimally edited long after original publication because the Bronze Age burials from the region do not belong to Pazyryk culture (which only spans part of the Iron Age), as I wrongly said first.