mtDNA haplogroup V7 from ~5,000-year old kurgan of the Novosvobodnaya culture

I am not sure that the finding of a single mtDNA V7 sample suggest "a role of the TRB culture in the development of the Novosvobodnaya culture", or, indeed with the labeling of the TRB as "Indo-European". In any case, it's good to see some ancient DNA from the North Caucasus.

Acta Naturae. 2014 Apr-Jun; 6(2): 31–35.

Analysis of the Mitochondrial Genome of a Novosvobodnaya Culture Representative using Next-Generation Sequencing and Its Relation to the Funnel Beaker Culture

A. V. Nedoluzhko et al.

The Novosvobodnaya culture is known as a Bronze Age archaeological culture in the North Caucasus region of Southern Russia. It dates back to the middle of the 4th millennium B.C. and seems to have occurred during the time of the Maikop culture. There are now two hypotheses about the emergence of the Novosvobodnaya culture. One hypothesis suggests that the Novosvobodnaya culture was a phase of the Maikop culture, whereas the other one classifies it as an independent event based on the material culture items found in graves. Comparison between Novosvobodnaya pottery and Funnelbeaker (TRB) pottery from Germany has allowed researchers to suggest that the Novosvobodnaya culture developed under the influence of Indo-European culture. Nevertheless, the origin of the Novosvobodnaya culture remains a matter of debate. We applied next-generation sequencing to study ~5000-year-old human remains from the Klady kurgan grave in Novosvobodnaya stanitsa (now the Republic of Adygea, Russia). A total of 58,771,105 reads were generated using Illumina GAIIx with a coverage depth of 13.4x over the mitochondrial (mt) DNA genome. The mtDNA haplogroup affiliation was determined as V7, suggesting a role of the TRB culture in the development of the Novosvobodnaya culture and supporting the model of sharing between Novosvobodnaya and early Indo-European cultures.

Link

Analysis of Maikop crania (Kazarnitsky 2010)

From the paper, first a survey of other studies:

The Maikop cranium from Mandzhikiny I in Kalmykia was measured by A.A. Khokhlov. In his view, it resembles the previously published Maikop and Novosvobodnaya specimens. Khokhlov pointed to certain features common to the Maikop and Novosvobodnaya people and opposing them to the Pit Grave people. He questioned the resemblance between the Maikop crania from Evdyk I and those from Syezzheye and Zadono-Avilovsky; and he believed the former to resemble crania from the Caucasus, the Near East, and Southwestern Central Asia, being closest to those from Samtavro, Georgia, and Ginchi, Dagestan (Khokhlov, 2002).   

In a brief note, M.M Gerasimova, D.V. Pezhemsky, and L.T. Yablonsky (2002) described several Maikop crania from burial grounds on the Kalaus River in the Stavropol Region. The series is diverse and, judging by the results of multivariate analysis, is closest to the Chalcolithic group from Khvalynsk in the Samara Region.    

T.I. Alekseyeva (2004) measured a male skull from mound 13 burial 5 at Nezhinskaya near Kislovodsk (the plastic reconstruction of this individual’s appearance was made by L.T. Yablonsky), as well as two crania (male and female) from mound 70 burial 1 at Zamankul in Northern Ossetia. All these crania came from “Maikop– Novosvobodnaya” burials and were attributed to the Mediterranean variety of the Southern Caucasoid type which was distributed in Armenia, Georgia, Iran, and Mesopotamia during the Chalcolithic and Early Bronze Age. The heterogeneity of the Maikop group in Alexeyeva’s opinion may be due to individual variability, but also to admixture with the natives of the southeastern European steppes (Alekseyeva, 2004). 

Later, Gerasimova, Pezhemsky, and Yablonsky (2007) published a large article where crania from burial grounds on the Kalaus River were described in detail. They noted that the Maikop series is heterogeneous but on average it represented the Eastern Mediterranean trait combination. The latter is quite dissimilar to the Cromagnoid combination typical of certain Bronze Age groups of the Eastern European steppes. The idea that at least some Maikop people were descendants of immigrants from the Near East was deemed probable; however the role of the steppe admixture, possibly accounting for a somewhat greater robustness of Maikop crania compared to Mediterranean ones, was not excluded either.

And the author's own conclusions:

In sum, the results of the multivariate analysis suggest that Maikop people are distinct from all the contemporary and later Eastern European groups of the steppe and forest-steppe zones. This provides an additional argument in favor of the hypothesis that Maikop burials in Kalmykia attest not merely to the cultural impact of the Maikop community on the steppe tribes (Munchaev, 1994: 168); rather, they were left by a separate group which was unrelated to the local Pit Grave population by origin. The Southern Caucasoid trait combination revealed by the Maikop series is somewhat similar to that shown by the contemporaneous groups of the Northern Caucasus and southern Turkmenia. Clearly, this does not imply a direct connection with any of these regions.  

The Near Eastern parallels are no less suggestive (Bunak, 1947: 77). Thus, a small series from Al-Ubaid in southern Mesopotamia, dating from the 4th millennium BC, is characterized by dolichocrany (cranial index, 72.6), a high face, medium wide, high and sharply protruding nose, and wide palate (Keith, 1931: 239–241). Regrettably, the number of measurements is too small to warrant a reliable comparison with the Maikop series. However, the isolated position of the Maikop group in Eastern Europe, its vague resemblance to the Southern Caucasoids of the Caucasus and Southwestern Central Asia, and the Near Eastern cultural affinities of Maikop and Novosvobodnaya (Munchaev, 1994: 170) indirectly point to Near Eastern provenance.

It would certainly be interesting to obtain DNA from some of these specimens.

Related:

• The Maikop Singularity
• Origins of the Maykop phenomenon
• Uruk migrants in the Caucasus

Archaeology, Ethnology and Anthropology of Eurasia
Volume 38, Issue 1, March 2010, Pages 148–155

THE MAIKOP CRANIA REVISITED

Abstract Measurements of crania of people associated with the Early Bronze Age Maikop culture of the Northern Caucasus are analyzed. Data on Maikop males, new and previously published, were compared with those concerning chronologically and geographically related people using the canonical variate analysis. The Maikop series turned out to be isolated and no close parallels to it were found among the Bronze Age groups, either from the steppe and forest-steppe zones of Eastern Europe or from the Caucasus and Southwestern Central Asia. While certain parallels seem to point to the Near East, they are too few to warrant definite conclusions.

Link

The Maikop Singularity

From The Maikop Singularity: The Unequal Accumulation of Wealth on the Bronze Age Eurasian Steppe? by Philip L. Kohl (in Social Complexity in Prehistoric Eurasia)

The Maikop parallels with northern Mesopotamia or, more broadly, with the ancient Near East, and the seemingly consistent and growing number of calibrated radiocarbon determinations (currently more than 40 such dates; E. N. Chernykh personal communication) not only date the Maikop phenomenon more securely but also suggest some connections -albeit hard to specify- with larger historical processes, such as the north Mesopotamian, and later Uruk expansion into eastern Anatolia. The calibrated radiocarbon dates suggest that the Maikop culture seems to have had a formative influence on kurgan burial rituals and what now appears to be the later Pit-Grave (Yamnaya) culture on the Eurasian steppe (Chernykh and Orlovskaya 2004a: 97). 

... 

In other words, the fact that such a symbolic Mesopotamian practice is attested in the richest known "royal," or chiefly, Maikop burial must have significance not only for the earlier dating of the Maikop culture, but also for determining aspects of its cultural affiliation and formation. 

Other scholars have focused on the northern steppe component of the Maikop culture. ... V. A. Trifonov (2004: 58-60) in a reappraisal and comparison of the so-called royal tomb at Arslantepe with the Novosvobodnaya-phase Maikop burials, reverses the arrow of cultural transmission and borrowing and argues for an eastern Anatolian Chalcolithic origin of the Novosvobodnaya tombs, such as documented at Korucutepe. Thus, if Trifonov is correct, and if the calibrated radiocarbon dates securely place Maikop chronologically before the emergence of the Pit-Grave (Yamnaya) horizon, then somewhat counterintuitively, the origins of raising large barrows or kurgans above the broad, flat expanse of the steppes may not have been indigenous but may have been derived from eastern Anatolia or the northern periphery of the greater ancient Near East. 

... 

It is probably futile to seek a single source from which the Maikop culture emerged.

Related:

• Uruk migrants in the Caucasus 
• Origins of the Maykop phenomenon

Origins of the Maykop phenomenon

Unfortunately this is in German, so I can only read it with a lot of effort and the help of Google Translate. Anyway, it seems to argue against the "Uruk expansion from Mesopotamia" hypothesis and point towards Central Asia, with the author finding parallels of the Maykop culture in the Kura valley and Lake Urmia area. That would certainly fit the bill of a more "eastern" PIE homeland as I mention in one of my posts below -if we accept, as many do- an IE identity for at least elements within the Maikop culture.

It would be great if ancient DNA was ever able to shed some light on archaeological controversies such as this. It has already done so in Europe, where the discovery of a Mediterranean-like TRB farmer in Sweden destroyed theories of "acculturation" in the diffusion of the Neolithic economy into that continent, and I'm sure that similarly interesting things were taking place during prehistory in other parts of the world.


A couple of related recent posts:

• Stanislav Grigoriev's "Ancient Indo-Europeans"
• Uruk migrants in the Caucasus

Praehistorische Zeitschrift. Volume 87, Issue 1, Pages 1–28

Kaukasus und Orient: Die Entstehung des „Maikop-Phänomens“ im 4. Jahrtausend v.Chr.

Mariya Ivanova

[English abstract] Graves and settlements of the 5th millennium BC in North Caucasus attest to a material culture that was related to contemporaneous archaeological complexes in the northern and western Black Sea region. Yet it was replaced, suddenly as it seems, around the middle of the 4th millennium BC by a “high culture” whose origin is still quite unclear. This archaeological culture named after the great Maikop kurgan showed innovations in all areas which have no local archetypes and which cannot be assigned to the tradition of the Balkan-Anatolian Copper Age. The favoured theory of Russian researchers is a migration from the south originating in the Syro-Anatolian area, which is often mentioned in connection with the socalled “Uruk expansion”. However, serious doubts have arisen about a connection between Maikop and the Syro-Anatolian region. The foreign objects in the North Caucasus reveal no connection to the upper reaches of the Euphrates and Tigris or to the floodplains of Mesopotamia, but rather seem to have ties to the Iranian plateau and to South Central Asia. Recent excavations in the Southwest Caspian Sea region are enabling a new perspective about the interactions between the “Orient” and Continental Europe. On the one hand, it is becoming gradually apparent that a gigantic area of interaction evolved already in the early 4th millennium BC which extended far beyond Mesopotamia; on the other hand, these findings relativise the traditional importance given to Mesopotamia, because innovations originating in Iran and Central Asia obviously spread throughout the Syro-Anatolian region independently thereof.

Link

Uruk migrants in the Caucasus

From the paper:

The period between the 4th and 3rd millennia B.C. was the time of great cataclysmic events in the Caucasus; its cultural advances were influenced by changes within its boundaries as well as interactions with the outside world. 

The most significant occurrence of this epoch was the appearance of a large number of peoples of Mesopotamian cultural identity who contributed to speeding up the rhythm of its cultural development, adding “explosive” character to its progress. 

...  

During this period the South Caucasus experienced two powerful waves of Middle Eastern expansion: the first at the time of Late Neolithic culture of Sioni in the 4th-5th millennia B.C., and the second at the period of Tsopi culture in the Late Neolithic Age, at the end of the 5th and the first half of the 4th millennium B.C., which is known as the Uruk expansion era. Later, in the second half of the 4th and throughout the 3 rd millennium B.C., during the Early Bronze Age the Kura-Araxes culture of the Caucasus spread throughout the greater part of the Caucasus, Eastern Anatolia, northern parts of Iran, Middle East and even Europe. 

...

In this context, recent archaeological finds in the Southern and Northeastern Caucasus gave yet another, entirely new nuance to scientific researches into the ancient past of the Caucasus. They made it clear that incursion of these peoples into the Caucasus was not a onetime event, but continued for a significantly long period. Reasoning by the topography of the archaeological finds in Mesopotamia, it becomes clear that large masses of migrant settlers from that area did not move straight along the route to Transcaucasia in order to reach the destination faster. Actually, they settled down in every region of the Caucasus, in the mountains and flatlands, in areas where they could maintain a lifestyle familiar to them.     

... 

It seems obvious that from that period on, two cultures of the Caucasus that had been at different stages of development could coexist peacefully on the basis of their mutual participation in metallurgical manufacturing; it was this type of communal economy that gave impetus to a speedy development of the local culture. This is well illustrated by the metallurgical items of the Kura-Araxes culture, which is significantly more advanced in comparison with the preAeneolithic culture. 

...  

At present the situation has changed drastically. On the basis of a whole series of radiocarbon analyses, it has been proved [15; 82] that burial mounds of the ancient pit-grave culture are of a significantly later period in comparison with Maikop archaeological sites. This allows scholars to assume that the tradition of building this type of burial mounds emerged precisely in the Maikop culture. Its ties with Levant and Mesopotamian antiquities point to its earlier origin [15: 97]. At the same time, a whole range of chronological data obtained with radiocarbon analysis has established that the settlements and burial mounds of the South Caucasus containing Uruk artefact are coexistent with the Maikop culture [13: 149-153] and, accordingly, the ancient pit-grave culture and its burial mounds belong to a later period. Therefore, today we cannot possibly ascribe the emergence of this kind of burial mounds in the Maikop culture as well as similar contemporaneous sites in the South Caucasus to the influence of the steppe zone cultures. Moreover, there were no adverse conditions that would have prevented emergence of this type of burial mounds in the Caucasus itself  

UPDATE: Also relevant a book chapter on The Caucasus - donor and recipient of materials to and from the ancient near east, and a talk by EN Chernykh in a recent conference on the topic of Caucasus as the Bridge Between the Settled Farming and the Pastor.

BULLETIN OF THE GEORGIAN NATIONAL ACADEMY OF SCIENCES, vol. 6, no. 2, 2012

Uruk Migrants in the Caucasus

Konstantine Pitskhelauri

ABSTRACT. At the end of the 5th and in the 4th millennia B.C. large masses of Uruk migrants had settled in the South, and later in the North Caucasus. Assimilation of cultures of the newcomers and residents, as a result, caused their “explosive” development paving the way to the formation of the Maikop culture in the North Caucasus and the Kura-Araxes culture in the South Caucasus. © 2012 Bull. Georg. Natl. Acad. Sci.

Link (pdf)

The Indo-European invasion of the Baltic

In some recent posts, I showed that South Asian populations (North Indian Brahmins, South Indian Brahmins) can be seen as mixtures of West Eurasian and South Indian populations, but also that West Eurasians (Bulgarians, Greeks, Armenians, and French) can be seen as mixtures of South Asian and Sardinian populations.

This may seem strange, but can be explained if we understand how f3-statistics and rolloff actually work. These methods do not require pure or unadmixed ancestral populations, but exploit allele frequency differences in the reference populations together with either (i) allele frequencies in the mixed population, in the case of f3-statistics, or (ii) admixture linkage disequilibrium in the mixed population, in the case of rolloff.

If a and b are allele frequencies in two ancestral populations A and B that mix, then:

• The frequency of a will shift towards b if A experiences gene flow from B
• The frequency of a will randomly shift if A experiences gene flow from an "outgroup" population
• The frequency of a will shift towards b if A experiences gene flow from a third population that is geographically and genetically intermediate between A and B

An application to the Europe-South Asia cline

I took the following set of populations, and calculated all 1,365 possible f3-statistics:

"FIN30"         "Lithuanians"   "Russian"       "Pathan"        "Balochi"       "North_Kannadi" "Polish_D"      "Russian_D"     "Mixed_Slav_D"  "Bulgarian_D"   "Serb_D"        "Ukrainian_D"   "Belorussian"   "Bulgarians_Y"  "Ukranians_Y"

In the following table, I report the lowest Z-scores for each target population (third column). So, for example, Polish_D can be seen as a mixture of Lithuanians and Balochi. Only negative scores are indicative of admixture. I highlight in bold the significant negative scores (Z less than -3)


Lithuanians North_Kannadi FIN30 0.001606 0.000259 6.193 280043
Ukrainian_D Belorussian Lithuanians 0.00078 0.000299 2.614 268493
Lithuanians North_Kannadi Russian -0.002738 0.000248 -11.045 279965
North_Kannadi Polish_D Pathan -0.006959 0.000229 -30.344 280220
North_Kannadi Bulgarians_Y Balochi -0.003636 0.000246 -14.781 281604
Pathan Ukrainian_D North_Kannadi 0.033802 0.000623 54.237 271858
Lithuanians Balochi Polish_D -0.001171 0.000178 -6.581 279519
Lithuanians Pathan Russian_D -0.001829 0.000166 -11.026 280658
Lithuanians Pathan Mixed_Slav_D -0.001715 2e-04 -8.594 277635
Lithuanians Balochi Bulgarian_D -0.001247 0.000313 -3.979 272342
Lithuanians Balochi Serb_D -0.00091 0.000377 -2.416 270807
Lithuanians Balochi Ukrainian_D -0.002222 0.000358 -6.211 270399
Lithuanians Balochi Belorussian -0.000897 0.00027 -3.325 273076
Balochi Polish_D Bulgarians_Y -0.001198 0.000185 -6.481 279632
Lithuanians Balochi Ukranians_Y -0.001727 0.000187 -9.236 278677

It is clear, that what I have described holds here: European populations appear like mixtures of Lithuanians and South Asians; conversely, South Asian populations appear like mixtures of Europeans and North Kannadi.

This does not mean that the populations that appear unadmixed (FIN30, Lithuanians, North_Kannadi, and Serbs) are in fact so, for at least two reasons:

1. The f3 statistic confirms, but does not reject the presence of admixture; in particular, it fails to find real admixture in highly drifted populations
2. The f3 statistics exploits allele frequency correlations between populations: but the North Kannadi and Lithuanians/Finns occupy opposite ends of the studied cline, so their lack of signal of admixture may be due to the non-existence of populations that are even more unadmixed than themselves.

In the case of South Indians, we are completely sure that this is the case. Reich et al. (2009) managed to show this not because there are any unadmixed Ancestral South Indians (ASI) left, but because they exploited the existence of the Onge, an isolated group from the Andaman Islands that was a sister group to the ASI. So, we can be fairly sure that southern Indians themselves have West Eurasian-like admixture, even the ones that are at the end of the West Eurasia-South India cline on its southern end.

The problem is: there is no isolated group of unadmixed Europeans left in existence that might serve a similar proxy function as the Onge did for South Asians.

Enter Pickrell et al. (2012) to the rescue. In that paper, the authors studied admixture in the Khoe-San of South Africa. Now, many of the Khoe-San sub-groups appeared to be admixed, but the "Juj'hoan North" population appeared to be at the "end of the cline": it's impossible to detect admixture in them using alelle frequency differences, because, quite simply, there are no populations that are less unadmixed than them: they're as pure descendants of "Ancestral Bushman" as exist on the earth today.

But, the clever thing is, that we don't have to detect admixture only using allele frequency differences, but also using admixture LD, i.e., by exploiting the correlation between linkage disequilibrium (the co-inheritance of physically separated markers on a chromosome) and allele frequency differences between populations. Pickrell el al. were able to do this not by conjuring up a more unadmixed population than the "Juj'hoan North" one available to them, but by splitting up that population, and using one half to find allele frequency differences, and the other half to detect admixture LD.

Admixture LD signal in Lithuanians

Using the aforementioned idea, I set out to see whether Lithuanians, who occupy the European end of the Europe-South Asia cline present such a signal of admixture LD. I used the Lithuanian_D sample from the Dodecad Project and the Balochi HGDP sample as reference populations (to calculate allele frequency differences), and the Behar et al. (2010) Lithuanians for admixture LD. There were only ~300k SNPs usuable in this set, but sufficient to detect the signal of admixture LD:

The admixture time estimate is 200.350 +/- 61.608 generations, or 5,810 +/- 1790 years. This is not very precise, probably because of the small number of SNPs and individuals used, but it certainly points to the Neolithic-to-Bronze Age for the occurrence of this admixture. The date is certainly reminiscent of the expansion of the Kurgan culture out of eastern Europe, or, the later Corded Ware culture of northern Europe.

So, it may well appear that at least some of the people participating in these groups of cultures, were indeed influenced by the Indo-Europeans as they expanded from their West Asian homeland. These intruders mixed with eastern Europeans who vacillated during the late Neolithic between a northern Europeoid pole akin to Mesolithic hunter gatherers from Gotland and Iberia, and a widely dispersed Sardinian-like population that is in evidence at least in the Sweden-Italian Alps-Bulgaria triangle. The gradual appearance of non-mtDNA U related lineages in Siberia and Ukraine is most likely related to this phenomenon.

It would seem that the Proto-Indo-Europeans mixed with different substrata in the four directions of their expansion: Sardinian-like people in southern Europe, Lithuanian-like people in northern Europe, South Indian-like people in South Asia, and East Eurasians in Siberia and east central Asia. Extant groups are descendants of divergent Neolithic population groups, brought closer together (genetically) because of variable admixture with the PIE population and its early offshoots.

Conclusion

There are mutual signals of admixture across a Europe-South Asia cline: Europeans appear to be mixed with South Asians, and South Asians appear to be mixed with Europeans. The simplest explanation for this pattern involves expansion of a third, geographically and genetically intermediate population that affected both Europe and South Asia. We can use the signal of admixture LD to prove that this expansion affected some of the most unadmixed populations in Europe (e.g., Lithuanians), just as it did the most unadmixed populations of India (e.g., Dravidians).

It will be interesting to use these techniques to study signals of admixture in other "end of the line" populations such as Sardinians, South Indians, etc.

UPDATE I (rolloff analysis of Poles):

I have carried out rolloff analysis of my 25-strong Polish_D sample using Lithuanians and Pathans as references:

The signal is fairly distinct, and corresponds to 149.296 +/- 38.783 generations or 4330 +/- 1120 years. I am guessing that either the different reference population (Pathans vs. Balochi), or, more likely the increased number of target individuals (25 vs. 10) have contributed to the narrowing down of the uncertainty. It will be interesting to explore this signal further with more population pairs.

UPDATE II (rolloff analysis of Finns):

I have also used the 1000 Genomes Finnish sample (FIN) in a similar manner as Lithuanians, using 15 individuals to estimate allele frequency differences, and 15 ones for admixture LD, and using the Pathans as a South Asian reference population. There is a clear signal of admixture:

This dates to 104.967 +/- 14.797 generations, or 3,040 +/- 430 years. Finland came under the influence of both Europeans (and likely Indo-Europeans) during the Bronze Age period (a mixture of Battle Axe with local Comb Ceramic seems to have occurred), as well as likely non-European (and likely Uralic) intrusions during the same time frame, as part of the Seima-Turbino phenomenon. It will be interesting to repeat this analysis with an East Eurasian reference population to isolate potential signals of admixture dating to either the Comb Ceramic or Seima-Turbino episodes of migration.

(Note; added Oct 14): I carried out rolloff analysis using Nganassans as suggested in the above paragraph here.

UPDATE III (rolloff analysis of Ukrainians):

I have used the Yunusbayev et al. sample of Ukrainians, and estimated its admixture time using Lithuanians and Balochi as reference populations:

The admixture time estimate is 191.078 +/- 35.079 generations, or 5,540 +/- 1,020 years. It seems very similar to that in Lithuanians, with a smaller standard error, perhaps on account of either the larger number of SNPs or larger number of individuals.

It is tempting to associate this admixture signal with the Maikop culture which appeared at around this time. Assuming that North_European/West_Asian (or Lithuanian-like and Balochi-like) gene pools existed north and south of the Pontic-Caspian-Caucasus set of geographical barriers, then the Maikop culture which shows links to both the early Transcaucasian culture and those of Eastern Europe would have been an ideal candidate region for the admixture picked up by rolloff to have taken place. There are, of course, other possibilities.

UPDATE IV (rolloff analysis of Lithuanians with Pathan reference):

I repeated the first analysis of this post, but this time, I used Pathans, rather than Balochi as a reference population:

The admixture time estimate of 217.501 +/- 51.170 generations, or 6,310 +/- 1,480 years appears to be similar with the original estimate of 5,810 +/- 1790 years, so it does not appear that the use of Balochi or Pathan as a reference population much affects this result.

The Caucasus revisited (Yunusbayev et al. 2011)

This is another treasure trove of a paper, and together with Balanovsky et al. (2011) we now have a very clear picture of genetic variation in this most interesting of world regions.

Here is the ADMIXTURE analysis:

The authors also post results up to K=10 in the supplementary material, which show Druze/Bedouin/Basque-centered component. It is actually possible to push the analysis higher than K=7 without such problem components appearing, by retaining non-closely related individuals (using --genome in PLINK and then iteratively removing individuals from pairs with PI_HAT greater than some value).

Nonetheless, the components emerging from this analysis will be familiar to followers of the Dodecad Project. In terms of Dodecad v3:

• light yellow "North East Asian"
• orange "South East Asian"
• brown "Neo African" or "Sub_Saharan", as there are no African hunter-gatherers
• dark blue "North European", as there is no split of east/west Europe at this level
• middle blue "West Asian"
• light blue "Southwest Asian"
• green "South Asian", but anchored on Sindhi, a population from Pakistan, due to the lack of more southern populations from India

The labels of new populations sampled in this study can be seen in brown. I particularly hope that the substantial new autosomal data will become publicly available, so that I can use them in the Dodecad Project. It will be an invaluable new resource, filling some "holes" in the Eurasian landscape (e.g., east of the Caspian; Bulgarians; several new Caucasus populations) in the Li et al. (HGDP), and Behar et al. data.

(to be continued)

UPDATE I (Y-chromosomes):

Some observations:

• C has a concentration in the Turkic Nogays
• The presence of D this far west is very surprising, again in the Nogays. This haplogroup has a relic distribution, with particular concentrations in Tibet, Mongolia, Japan, and Andaman Islanders. In all likelihood its presence here is linked to the Nogays' eastern origin
• E and its subclades occurs at a very low frequency here
• G2a has a clear West Caucasus (both north and south) concentration
• I seems to have a mainly West Caucasus distribution as well; this is a common European haplogroup; it has quite elevated frequencies among the Andis and Kara Nogays. It would be interesting to discover some historical correlate for the presence of I in Kara Nogays but not Kuban Nogays and in Andis but not in most of the NE Caucasus
• J1 has the expected Northeast Caucasus nexus. This haplogroup is bimodal, with a mode in Arabians and a secondary mode in NE Caucasus. Note the paucity of J1e-P58, the reverse of the situation of Arabians; I've noted before the likely association of the P58 clade with Semitic languages.
• The extreme concentration of J2 in Chechens and Ingush are probably associated with low variance. Apart from these atypical populations, a substantial presence of this haplogroup can be found in the NW/S Caucasus in different populations and in the form of different subclades.
• The new LT mystery clade has its usual low-frequency wide distribution
• N occurs in Nogays as expected, and, like C, also in the NW Caucasus. This probably also represents an eastern influence, probably associated not only with the Nogays but also with various Tatar influences on the Caucasus.
• Q occurs widely in the NW Caucasus but only in 1 Nogay. Perhaps this is more of a Tatar marker, although a finer-scale resolution of this haplogroup is really necessary.
• R1a-related lineages occur less frequently here among eastern Slavs, a main reason for the disconnect between the Eastern European plain and the Caucasus. There does, however, appear to be good diversity here, with the presence of R1a*, R1a1-M198*, Note again how the Iranic Ossetians (both North and South) have almost no R1a1 compared to both their NW Caucasian and S Caucasian neighbors, again, suggesting that this may not have been an important Alan or steppe Iranian lineage, at least during the late antique time horizon. The occurrence of R1a1f-M458 may represent Slavic influence in the NW Caucasus.
• R1b-related lineages seem ubuiquitous in the Caucasus. R-M73 occurs substantially in Kara Nogays and Balkars, an apparent link with Central Asia where this haplogroup occurs frequently.

UPDATE II (Caucasus-Eastern Europe discontinuity)

The authors of this paper highlight the genetic discontinuity between the eastern European plain and the Caucasus. This was also apparent in the Balanovsky et al. (2011) paper, and was also a major conclusion of the Dodecad Project, with Caucasians exhibiting a high percentage of the "West Asian" component, while eastern Slavs low "West Asian" and high "East European".

The interpretation of this discontinuity is more difficult. There are surely parts of the Caucasus region that are mountainous and pose an ecological contrast to the flatlands of eastern Europe. That is consistent with a different type of population living in either region for a long time, despite the well-attested archaological contacts (e.g., Maikop or the settlement of steppe nomads such as Alans or Sarmatians).

On the other hand, the eastern Slavic population can, at least in part, have expanded more recently, in the medieval period, as part of the early Slavic dispersals, as well as the push to the north and east of the Russians. These appear to have partly displaced Turkic groups from the north Pontic region, with all of the above having displaced historical Scythian (Iranic) nomads, who, in turn, displaced the mysterious Cimmerians. If the discovery of east Eurasian mtDNA C in Neolithic and Bronze Age Ukraine stands up, there will be another layer of population replacement, as mtDNA C is quite rare in the broader region today. On the other hand, the Caucasus itself may have been affected from population movements from the Near East, as Balanovsky et al. suggest.

So, in conclusion, the discontinuity is a fact that emerges from different types of analyses, but its causes remain uncertain, and it is not clear when and how it was first established.

Mol Biol Evol (2011) doi: 10.1093/molbev/msr221

The Caucasus as an asymmetric semipermeable barrier to ancient human migrations

Bayazit Yunusbayev et al.

Abstract

The Caucasus, inhabited by modern humans since the Early Upper Paleolithic and known for its linguistic diversity, is considered to be important for understanding human dispersals and genetic diversity in Eurasia. We report a synthesis of autosomal, Y chromosome and mitochondrial DNA (mtDNA) variation in populations from all major subregions and linguistic phyla of the area. Autosomal genome variation in the Caucasus reveals significant genetic uniformity among its ethnically and linguistically diverse populations, and is consistent with predominantly Near/Middle Eastern origin of the Caucasians, with minor external impacts. In contrast to autosomal and mtDNA variation, signals of regional Y chromosome founder effects distinguish the eastern from western North Caucasians. Genetic discontinuity between the North Caucasus and the East European Plain contrasts with continuity through Anatolia and the Balkans, suggesting major routes of ancient gene flows and admixture.

Link

Genes and Languages in the Caucasus

If there was ever a paper that was the equivalent of a box of candy, this is probably it. I will update this post with my comments.

UPDATE I (Genealogical rate, Gene-language concordance, Ossetes): I seriously don't know where to begin with this paper. So, given the serendipitous appearance of an abstract on Y-chromosome mutation rates, here is a major new pro-genealogical rate quote from the new paper:

We found that “evolutionary” estimates of most clusters fall far outside the range of the respective linguistic dates, while “genealogical” estimates gave a good fit with the linguistic 23 dates. At least two population events in the Caucasus are documented archaeologically, which allows additional comparison with these “historical” dates. In both cases, the historical (archaeological) date is similar to a genetic estimate based on the “genealogical” mutation rate (Supplementary Note 2).

And, here's a comparison of the linguistic and genetic (based on Y-chromosomes) trees from the paper:

The correspondence seems remarkable; the only major discrepancy is for Iranic (Indo-European) Ossetes who group with NW Caucasians genetically, which makes sense as the Ossetes are probably to a large extent NW Caucasians that underwent a language shift at the influence of the Alans.

Speaking of the Ossetes, their negligible R1a1-M198 frequency (0.4-0.8%) should be a warning that Iranic steppe nomads _does not equal_ R1a1. While a limited contribution of Alans to the Ossetes is expected, it is not expected that Ossetes will have two of the lowest M198 frequencies in the Caucassus: in all probability R1a1 was not particularly important among Alans, and, by implication (?) Sarmatians.

UPDATE II (4 haplogroups for 4 language families):

The most interesting discovery in this paper is, of course, the correspondence between Y-chromosome haplogroups and language groups, thanks to the very large number of individuals tested and the deep phylogenetic resolution of the haplogroups:

Overall, the most frequent haplogroups in the Caucasus were G2a3b1-P303 (12%), G2a1a-P18 (8%), J1*-M267(xP58) (34%), and J2a4b*-M67(xM92) (21%), which together encompassed 73% of the Y chromosomes, while the other 24 haplogroups identified in our study comprise the remaining 27% (Table 2). ... haplogroup G2a3b1-P303 comprised at least 21% (and up to 86%) of the Y chromosomes in the Shapsug, Abkhaz and Circassians ... haplogroup G2a1a-P18 comprised at least 56% (and up to 73%) of the Digorians and Ironians (both from the Central Caucasus Iranic linguistic group), while not being found at more than 12% (average 3%) in other populations... haplogroup J2a4b*-M67(xM92) comprised 51-79% of the Y chromosomes in the Ingush and three Chechen populations (North-East Caucasus, Nakh linguistic group), while, in the rest of the Caucasus, its frequency was not higher than 9% (average 3%) ... haplogroup J1*-M267(xP58) comprised 44-99% of the Avar, Dargins, Kaitak, Kubachi, and Lezghins (South-East Caucasus, Dagestan linguistic group) but was less than 25% in Nakh populations and less than 5% in the rest of Caucasus.

Interestingly, G2a3 is one of the lineages of early Central European farmers, and 2 medieval German knights. G2 is also, curiously, one of the West Eurasian lineages that are found in very small quantities in India, especially among upper caste Hindus. We are beginning to make connections across space and time, even though the patterns are far from clear yet.

The prevalence of J1*-M267(xP58) in Dagestan is well known (or suspected) from previous studies. Notice that J-P58, if we use the genealogical rate has an age of ~5.4ky in Semitic groups, and this is in concordance with the 5,750 years ago origin of Semitic languages based on Bayesian phylogenetics. So, it is clear that part of haplogroup J1 was prevalent in ancient Semitic groups, another, disjoint part in ancient Dagestani groups.

To make things more interesting, the Nakh groups (Ingush and Chechens) have J2a4b*-M67(xM92) as their modal haplogroup. Nakh is also a Northeast Caucasian language subfamily, like Dagestani, and indeed NE Caucasian is also called Nakho-Daghestanian. What did the early speakers of this family look like?

It would be tempting to think that Proto-Nakho-Dagestanians were J1-dominated, as J1 exists in both Nakh (16-25%) and Dagestani (58-99%) groups, whereas J2a4b-M67 (the Nakh modal haplogroup) is nearly completely absent in Dagestanians.

UPDATE III (No European influence):

Another interesting discovery of this study is the lack of European influence in the populations of the North Caucasus.

It seems that both R1a1a-M198 and I2a-P37 have a major barrier eastward in the Don river. Please note that the former is not strictly a European haplogroup, but it nonetheless experiences a massive drop in frequency, and is negligible everywhere except in Abkhaz-Circassians (NW Caucasus; 10.3-19.7%), with an outlier in Dargins (22%).

This seems to put a limit on the origin of any hypothetical movements across the Eurasian steppe east of the Don river, as haplogroup I2a-P37 is largely absent in Central Asia, and occurs 3 times in 1,525 individuals in this sample. So, while there have been proposals of a Central European origin of some steppe pastoralist groups, these are hard to reconcile with this picture.

UPDATE IV (Haplogroup G):

Two of the modal haplogroups in this paper are G2a1a-P18 (Iranic, 56-73%) and G2a3b1-P303 (NW Caucasians, 21-86%). Battaglia et al. (2008) also found a high frequency of G2a* in Georgians and Balkars (~30%, also modal in both populations). It appears that G2a is a mainly West (both NW and SW) Caucasian phenomenon within the context of this region.

UPDATE V (Starostin and Language depth)

The authors applied the methodology of the late Sergei Starostin to the problem of language time depth:

The present work employs Starostin’s methodology, and we made special efforts to create the high-quality linguistic databases required for this analysis. Thus, based on significantly extended and revised linguistic databases, we have applied a glotto-chronological approach to the North Caucasian languages. As a result, our study provides a unique opportunity to make direct comparisons of linguistic and genetic data from the same populations. Lexico-statistical methods have also been applied to a number of language families using a Bayesian approach to increase the statistical robustness of language classification (Gray and Atkinson, 2003; Kitchen et al., 2009; Greenhill et al., 2010). Using these methods with the Caucasus languages under

study here will be the focus of future work.

It will certainly be interesting to see Bayesian phylogenetic methods applied to the Caucasus languages in the future, using the linguistic datasets developed here. The concordance of genetic-linguistic results in this paper, in addition to the many successes of the G&A approach, is making it increasingly difficult for those who doubt our ability to estimate the age of language families in a manner similar to that with which biologists estimate the age of genetic variation.

See also Tower of Babel project and the Evolution of Human Languages project at the Santa Fe Institute.

UPDATE VI (Haplogroup J2a)

I have recently speculated about a possible link between the Caucasus region and India based on the appearance of a "Dagestan" component in India, the clear West Asian origin of Ancestral North Indians, as well as a possible linguistic link between Northeast Caucasian, Hurrian, and Indo-European.

A problem with that theory is that the high J1*(xP58) frequency in Dagestan has no counterpart in South Asia. The current study, however, adds data on the Nakh part of the Nakho-Dagestanian (Northeast Caucasian) family, showing this to be J2a4b-M67 dominated. So, while I think that J1*(xP58) may have been present among Proto-Northeast Caucasians, these must have interacted with J2a folk.

J-M67 is clearly intrusive into the Central Caucasus, from the South where a much greater variety of J2a-related lineages is observed among Armenians, North Iranians, and Anatolian Turks.

We now have good coverage of J2a in the entirety of the West Asian region, with the exception of Azerbaijan, and a few patterns are beginning to emerge:

1. The center of the J2a world is somewhere between eastern Turkey, Armenia, Azerbaijan, Iran, and Syria
2. The Caucasus is a northern extension of this world, just as Greece and Italy are its main western extensions, with a strong extension into Central Asia as far as Xinjiang, and well into South Asia all the way to upper caste South Indian Hindus.
3. In the Caucasus itself J-M67 is dominating Nakh speakers, but with little other J2a related variation.
4. In comparison to Nakhs, J2a seems more varied in Georgians, among Ossetes, and among NW Caucasian speakers

It is hard to make any pronouncements on how J2a spread northwards from its Transcaucasian cradle, but I would think that the Kura-Araxes and Maikop cultures are fairly good candidates for that spread, with the former being J2a dominated, and the latter being more G2a dominated. I would not, however, dismiss a more recent spread of J2a into the region.

UPDATE VII (Absence of E1b1b1):

This haplogroup has a more Mediterranean distribution and is conspicuously absent in the North Caucasus. Unfortunately no downstream markers were typed, but (a) its presence in small amounts in NW Caucasians (1-1.7%) together with a similar low frequency (1.5%) in Georgians, (b) its absolute absence among Nakho-Dagestanians, except for one Lezghin, suggest to me that it arrived to the region from the west, and is probably a low-frequency trace of Ancient Greek colonies of the Black Sea, just as it is associated with Greek colonists in the West Mediterranean and Sicily.

UPDATE VIII (Haplogroups L and T):

There is a little haplogroup L in the North Caucasus. L-M27 and L-M317 seems concentrated in the Northwest, while L-M357 is found only in Nakh speakers. The detection of L-M357 in North but not South Iran may be related with this population, and also the L-rich population of Syria, especially from the eastern inland area.

Haplogroup T has been the subject of a major recent paper. In this region, it is found in 2 NW Caucasians, 1 Ossete and a couple of Lezgins, but unfortunately with no fine phylogenetic resolution.

Mol Biol Evol (2011) doi: 10.1093/molbev/msr126

Parallel Evolution of Genes and Languages in the Caucasus Region

Oleg Balanovsky1,2,*, Khadizhat Dibirova1,*, Anna Dybo3, Oleg Mudrak4, Svetlana Frolova1, Elvira Pocheshkhova5, Marc Haber6, Daniel Platt7, Theodore Schurr8, Wolfgang Haak9, Marina Kuznetsova1, Magomed Radzhabov1, Olga Balaganskaya1,2, Alexey Romanov1, Tatiana Zakharova1, David F. Soria Hernanz10,11, Pierre Zalloua6, Sergey Koshel12, Merritt Ruhlen13, Colin Renfrew14, R. Spencer Wells10, Chris Tyler-Smith15, Elena Balanovska1 and The Genographic Consortium16

We analyzed 40 SNP and 19 STR Y-chromosomal markers in a large sample of 1,525 indigenous individuals from 14 populations in the Caucasus and 254 additional individuals representing potential source populations. We also employed a lexicostatistical approach to reconstruct the history of the languages of the North Caucasian family spoken by the Caucasus populations. We found a different major haplogroup to be prevalent in each of four sets of populations that occupy distinct geographic regions and belong to different linguistic branches. The haplogroup frequencies correlated with geography and, even more strongly, with language. Within haplogroups, a number of haplotype clusters were shown to be specific to individual populations and languages. The data suggested a direct origin of Caucasus male lineages from the Near East, followed by high levels of isolation, differentiation and genetic drift in situ. Comparison of genetic and linguistic reconstructions covering the last few millennia showed striking correspondences between the topology and dates of the respective gene and language trees, and with documented historical events. Overall, in the Caucasus region, unmatched levels of gene-language co-evolution occurred within geographically isolated populations, probably due to its mountainous terrain.

Link