West_Asian in the flesh (hunter-gatherers from Georgia) (Jones et al. 2015)

Years ago, I detected the presence of a West_Asian genetic component (with dual modes in "Caucasus" and "Gedrosia") whose origins I placed in the "highlands of West Asia" and which I proposed spread into Europe post-5kya with Indo-European languages.

Earlier this year, the study by Haak et al. showed that steppe invaders after 5kya brought into Europe a 50/50 mix of "Eastern European Hunter-Gatherer" (EHG) ancestry/An unknown population from the Near East/Caucasus. The "unknown population" was most similar to Caucasians/Near Easterners like Armenians but did not correspond to any ancient sample.

A new paper in Nature Communications by Jones et al. finds this "missing link" in the flesh in Upper Paleolithic/Mesolithic hunter-gatherers from Georgia which they call "Caucasus Hunter-Gatherers" (CHG). From the paper:

The separation between CHG and both EF and WHG ended during the Early Bronze Age when a major ancestral component linked to CHG was carried west by migrating herders from the Eurasian Steppe. The foundation group for this seismic change was the Yamnaya, who we estimate to owe half of their ancestry to CHG-linked sources.

The authors also make the connection to South Asia:

In modern populations, the impact of CHG also stretches beyond Europe to the east. Central and South Asian populations received genetic influx from CHG (or a population close to them), as shown by a prominent CHG component in ADMIXTURE (Supplementary Fig. 5; Supplementary Note 9) and admixture f3-statistics, which show many samples as a mix of CHG and another South Asian population (Fig. 4b; Supplementary Table 9).

Also of interest:

Both Georgian hunter-gatherer samples were assigned to haplogroup J with Kotias belonging to the subhaplogroup J2a (see methods).

The paper is open access, so go ahead and read it for other details.

Nature Communications 6, Article number: 8912 doi:10.1038/ncomms9912

Upper Palaeolithic genomes reveal deep roots of modern Eurasians

Eppie R. Jones et al.

We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ~45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ~25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ~3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.

Link

Bronze Age mixing of multiple populations => Armenians (?)

As far as I can tell, the hypothesis of "several mixtures" comes from looking at many pairs of populations and seeing that different types of pairs seem like they mixed to make Armenians. Possibility (1) is that Armenians have multiple mixtures, and possibility (2) is that none of the sources work very well.

Hellenthal et al. did not find mixture in Armenians, but they worked with a different methodology and smaller sample size. Either, the N=173 sample size enabled detection of this admixture, or differences in methodology account for differences in conclusions. If true, the admixture dates in this paper would be some of the earliest discovered by looking at modern populations (without the help of ancient DNA).

The TreeMix analysis (Figure 4) is inconclusive about admixture from a population best represented by Neolithic Europeans. There is no plot of residuals in this figure, so this model with one migration event may not be adequate. Prior knowledge suggests that it isn't, as Pakistani and European populations have no admixture in Figure 4.

It's great that the authors will share their data!
ftp://ngs.sanger.ac.uk/scratch/project/team19/Armenian
As of this writing, the data is not "live"; it might appear when the paper is published.

bioRxiv doi: http://dx.doi.org/10.1101/015396

Genetic evidence for an origin of the Armenians from Bronze Age mixing of multiple populations

Marc Haber et al.

The Armenians are a culturally isolated population who historically inhabited a region in the Near East bounded by the Mediterranean and Black seas and the Caucasus, but remain underrepresented in genetic studies and have a complex history including a major geographic displacement during World War One. Here, we analyse genome-wide variation in 173 Armenians and compare them to 78 other worldwide populations. We find that Armenians form a distinctive cluster linking the Near East, Europe, and the Caucasus. We show that Armenian diversity can be explained by several mixtures of Eurasian populations that occurred between ~3,000 and ~2,000 BCE, a period characterized by major population migrations after the domestication of the horse, appearance of chariots, and the rise of advanced civilizations in the Near East. However, genetic signals of population mixture cease after ~1,200 BCE when Bronze Age civilizations in the Eastern Mediterranean world suddenly and violently collapsed. Armenians have since remained isolated and genetic structure within the population developed ~500 years ago when Armenia was divided between the Ottomans and the Safavid Empire in Iran. Finally, we show that Armenians have higher genetic affinity to Neolithic Europeans than other present-day Near Easterners, and that 29% of the Armenian ancestry may originate from an ancestral population best represented by Neolithic Europeans.

Link

A story of 69 ancient Europeans

A new study on the bioRxiv includes data on 69 ancient Europeans (remember when we got excited in anticipation for the single genome of the Iceman? that was only three years ago) and adds plenty of new info to chew on for those of us interested in prehistory. 

Two Near Eastern migrations into Europe

In 2011, I observed that West Eurasian populations were too close (measured by Fst) to allow for long periods of differentiation between them. By implication, there must have been a "common source" of ancestry uniting them, which I placed in a "womb of nations" of the Neolithic Near East. I proposed that migrations out of this core area homogenized West Eurasians, writing:

In Arabia, the migrants would have met aboriginal Arabians, similar to their next door-neighbors in East Africa, undergoing a subtle African shift (Southwest_Asians). In North Africa, they would have encountered denser populations during the favorable conditions of MIS 1, and by absorbing them they would became the Berbers (Northwest_Africans). Their migrations to the southeast brought them into the realm of Indian-leaning people, in the rich agricultural fields of the Mehrgarh and the now deserted oases of Bactria and Margiana. Across the Mediterranean and along the Atlantic facade of Europe, they would have encountered the Mesolithic populations of Europe, and through their blending became the early Neolithic inhabitants of the Mediterranean and Atlantic coasts of Europe (Mediterraneans). And, to the north, from either the Balkans, the Caucasus, or the trans-Caspian region, they would have met the last remaining Proto-Europeoid hunters of the continental zone, becoming the Northern Europeoids who once stretched all the way to the interior of Asia.

The new paper confirms the last two of these migrations. The remainder involve parts of the world from which no ancient DNA has been studied.

The first migration (early Neolithic) is already uncontroversial, but the paper includes data from Spanish early farmers that are also Sardinian- and LBK-like. The "Sardinian" Iceman was no fluke. It is now proven that not only the LBK but also the Spanish Neolithic came from the same expansion of Mediterranean populations which survives in Sardinia. The authors write:

Principal components analysis (PCA) of all ancient individuals along with 777 present-day West Eurasians4 (Fig. 2a, SI5) replicates the positioning of present-day Europeans between the Near East and European hunter-gatherers4,20, and the clustering of early farmers from across Europe with present day Sardinians3,4,27, suggesting that farming expansions across the Mediterranean to Spain and via the Danubian route to Hungary and Germany descended from a common stock.

The second migration went into eastern Europe:

The Yamnaya differ from the EHG by sharing fewer alleles with MA1 (|Z|=6.7) suggesting a dilution of ANE ancestry between 5,000-3,000 BCE on the European steppe. This was likely due to admixture of EHG with a population related to present-day Near Easterners, as the most negative f3-statistic in the Yamnaya (giving unambiguous evidence of admixture) is observed when we model them as a mixture of EHG and present-day Near Eastern populations like Armenians (Z = -6.3; SI7).

The EHG (Eastern European Hunter-Gatherers) are likely Proto-Europeoid foragers and the Yamnaya (a Bronze Age Kurgan culture) were a mixture of the EHG and something akin to Armenians.The "attraction" of later groups to the Near East is clear in the PCA: hunter-gatherers on the left side, the Near East (as grey dots) on the right side, and Neolithic/Bronze Age/modern Europeans in the middle. The second migration may very well be related to the Uruk expansion and the presence of gracile Mediterranoids and robust Proto-Europeoids in the Yamna:

The Yamna population generally belongs to the European race. It was tall (175.5cm), dolichocephalic, with broad faces of medium height. Among them there were, however, more robust elements with high and wide faces of the proto-Europoid type, and also more gracile individuals with narrow and high faces, probably reflecting contacts with the East Mediterranean type (Kurts 1984: 90).

The authors present a table of Fst values which confirms the homogenizing influence of migrations from the Near East. The WHG group has an Fst=0.086 with Armenians, but the LBK farmers have only 0.023. The EHG group has an Fst=0.067 with Armenians, but the Yamnaya steppe people have only 0.030. Someone might argue that it is the Armenians that are receiving genes from Europe, but the same pattern holds even for the Bedouins, for which admixture with Europeans seems far-fetched: 0.106 to 0.043 and 0.093 to 0.060. It is now clear that the "glue" that did not allow West Eurasian populations to drift very far apart were migrations from the Near East.

The (partial) demise of the farmers

It seems that the legacy of the early farmers suffered two hits, which is why only in Sardinia and (to a lesser degree) in southern Europe that they have persisted as the major component of ancestry. The first blow came during the Neolithic:

Middle Neolithic Europeans from Germany, Spain, Hungary, and Sweden from the period ~4,000-3,000 BCE are intermediate between the earlier farmers and the WHG, suggesting an increase of WHG ancestry throughout much of Europe.

And the coup de grâce after the 5kya mark:

We estimate that these two elements each contributed about half the ancestry each of the Yamnaya (SI6, SI9), explaining why the population turnover inferred using Yamnaya as a source is about twice as high compared to the undiluted EHG. The estimate of Yamnaya related ancestry in the Corded Ware is consistent when using either present populations or ancient Europeans as outgroups (SI9, SI10), and is 73.1 ± 2.2% when both sets are combined (SI10). [...] The magnitude of the population turnover that occurred becomes even more evident if one considers the fact that the steppe migrants may well have mixed with eastern European agriculturalists on their way to central Europe. Thus, we cannot exclude a scenario in which the Corded Ware arriving in today’s Germany had no ancestry at all from local populations.

Confirmation of the Bronze Age Indo-European invasion of Europe

In 2012 I had used the paltry data on a handful ancient DNA samples to observe that in ADMIXTURE modern Europeans had a West Asian genetic component (peaking in "Caucasus" and "Gedrosia") that pre-5kya Europeans didn't. I proposed that the Bronze Age migration of the Indo-Europeans spread this component:

But there is another component present in modern Europe, the West_Asian which is conspicuous in its absence in all the ancient samples so far. This component reaches its highest occurrence in the highlands of West Asia, from Anatolia and the Caucasus all the way to the Indian subcontinent. [...] Nonetheless, some of the legacy of the earliest Indo-European speakers does appear to persist down to the present day in the genomes of their linguistic descendants, and I predict that when we sample later (post 5-4kya) individuals we will finally find the West_Asian piece that is missing from the European puzzle.

This prediction is now confirmed:

This pattern is also seen in ADMIXTURE analysis (Fig. 2b, SI6), which implies that the Yamnaya have ancestry from populations related to the Caucasus and South Asia that is largely absent in 38 Early or Middle Neolithic farmers but present in all 25 Late Neolithic or Bronze Age individuals. This ancestry appears in Central Europe for the first time in our series with the Corded Ware around 2,500 BCE (SI6, Fig. 2b, Extended Data Fig. 1).

I was a little puzzled with the "Ancient North Eurasians" recently proposed as a "third ancestral population" for Europeans: it seemed to be a tertium quid that spread after 5kya, but very different geographically than the "West Asian" component. But:

These results can be explained if the new genetic material that arrived in Germany was a composite of two elements: EHG and a type of Near Eastern ancestry different from that which was introduced by early farmers (also suggested by PCA and ADMIXTURE; Fig. 2, SI5, SI6).

So, it seems that there is no contradiction after all and both EHG (which is related to "Ancient North Eurasians") and another type of Near Eastern ancestry (=West_Asian) arrived after 5kya.

1939 strikes back

It is amazing how well this was anticipated by Carleton Coon in 1939. Back then much of West Eurasia was an archaeological/anthropological terra incognita, there was no radiocarbon dating, no DNA, no computers, not even serious multivariate statistics. And yet:

We shall see, in our survey of prehistoric European racial movements, 8 that the Danubian agriculturalists of the Early Neolithic brought a food-producing economy into central Europe from the East. They perpetuated in the new European setting a physical type which was later supplanted in their original home. Several centuries later the Corded people, in the same way, came from southern Russia but there we first find them intermingled with other peoples, and the cul-tural factors which we think of as distinctively Corded are included in a larger cultural equipment. [...] On the basis of the physical evidence as well, it is likely that the Corded people came from somewhere north or east of the Black Sea. The fully Neolithic crania from southern Russia which we have just studied include such a type, also seen in the midst of Sergi's Kurgan aggregation. Until better evidence is produced from elsewhere, we are entitled to consider southern Russia the most likely way station from which the Corded people moved westward.

And in 2015:

Our results support a view of European pre-history punctuated by two major migrations: first, the arrival of first farmers during the Early Neolithic from the Near East, and second of Yamnaya pastoralists during the Late Neolithic from the steppe (Extended Data Fig. 5).

In 1939:

Linguistically, Indo-European is probably a relatively recent phenomenon, which arose after animals had been tamed and plants cultivated. The latest researches find it to be a derivative of an initially mixed language, whose principal elements were Uralic, called element A, and some undesignated element B which was probably one of the eastern Mediterranean or Caucasic languages. 5 The plants and animals on which the Somewhere in the plains of southern Russia or central Asia, the blending of languages took place which resulted in Indo-European speech. This product in turn spread and split, and was further differentiated by mixture with the languages of peoples upon whom it, in one form or other, was imposed. Some of the present Indo-European languages, in addition to these later accretions from non-Indo-European tongues, contain more of the A element than others, which contain more of the B. The unity of the original " Indo- Europeans," could not have been of long duration, if it was ever complete. 

In 2015:

These results can be explained if the new genetic material that arrived in Germany was a composite of two elements: EHG and a type of Near Eastern ancestry different from that which was introduced by early farmers (also suggested by PCA and ADMIXTURE; Fig. 2, SI5, SI6). We estimate that these two elements each contributed about half the ancestry each of the Yamnaya (SI6, SI9), explaining why the population turnover inferred using Yamnaya as a source is about twice as high compared to the undiluted EHG.

The EHG is still flimsy as it's only two individuals from Karelia and Samara who are very similar to each other. It's hard not to imagine that the hunter-gatherer from Russian Karelia (outside any proposed PIE homeland) would be speaking a similar language as his Samara counterpart. Did they both speak "element A" and was PIE formed when the "southern" steppe hunter-gatherers came into contact with "element B" people from the Caucasus? Short of a time machine, we can never say for sure. This might very well be an answer to the conundrum of Uralic/Proto-Kartvelian borrowings. There is simply no geographical locale in which these two language families neighbor each other: Northwest, Northeast Caucasian speakers and the pesky Greater Caucasus intervene. But, maybe there was no such locale, and these borrowings aren't due to some "PIE people" living adjacent to Uralic and Proto-Karvelian speakers but the "PIE people" being a mix of an element A (EHG) that was (or interacted with) Uralic and another element B (Armenian-like) that was (or interacted with) Proto-Kartvelian.

Urheimat (or not?)

The authors of the current paper are agnostic about the PIE homeland:

We caution that the location of the Proto-Indo-European9,27,29,30 homeland that also gave rise to the Indo-European languages of Asia, as well as the Indo-European languages of southeastern Europe, cannot be determined from the data reported here (SI11). Studying the mixture in the Yamnaya themselves, and understanding the genetic relationships among a broader set of ancient and present-day Indo-European speakers, may lead to new  insight about the shared homeland.

Whatever the ultimate answer will be, it seems that Coon was right that "The unity of the original " Indo- Europeans," could not have been of long duration, if it was ever complete." If PIE=EHG (as Anthony and Ringe suggest), then "from the crib", PIE got half its ancestry from a non-IE, Near Eastern source. Conversely, if PIE=Near East (as I suggested) then "from the crib", PIE got half of its ancestry from a non-IE, Eastern European source. The "Yamnaya" seems to max out in Norwegians at around half, which means that they are about a quarter Proto-Indo-European genetically, regardless of which theory is right.

These two possibilities (as well as the third one of PIE being neither-nor, but rather a linguistic mixture of the languages of the EHG and Near East) are testable. The Anthony/Ringe version of the steppe hypothesis predicts pre-Yamnaya expansions from the steppe. Whether these happened and what was their makeup can be tested: if they did occur and they did lack "Near Eastern" ancestry, then the steppe hypothesis will be proven. PIE in the Near East, on the other hand, predicts that some PIE languages (certainly the Anatolian ones) will be a "within the Near East" expansion. If such migrations did occur and they lacked "EHG" ancestry, then some variant of the Gamkrelidze/Ivanov model will be proven. Or, the truth might be that everywhere where Indo-Europeans arrive they carry a blend of "West Asian" and "EHG", supporting the third possibility. Time will tell.

In the interim, I am curious about how much Yamnaya ancestry existed in different parts of Europe (all of the post-5kya samples in this study come from Germany, with a couple from Hungary). In northern Europe, all populations seem to have less Yamnaya ancestry than the Corded Ware: there it must have declined. But, modern Hungarians have more than Bronze Age Hungarians: there it must have increased.

Germany and a slice of Hungary is a very narrow window through which to see the whole of Europe and these results must be tested by looking at samples from beyond the "heartland". I do hope that some kind of Moore's law operates in the world of ancient DNA, and in three more years we'll be reading studies about thousands of ancient individuals.

bioRxiv doi: http://dx.doi.org/10.1101/013433
Massive migration from the steppe is a source for Indo-European languages in Europe

Wolfgang Haak , Iosif Lazaridis , Nick Patterson , Nadin Rohland , Swapan Mallick , Bastien Llamas , GuidoBrandt , Susanne Nordenfelt , Eadaoin Harney , Kristin Stewardson , Qiaomei Fu , Alissa Mittnik , Eszter Banffy ,Christos Economou , Michael Francken , Susanne Friederich , Rafael Garrido Pena , Fredrik Hallgren , ValeryKhartanovich , Aleksandr Khokhlov , Michael Kunst , Pavel Kuznetsov , Harald Meller , Oleg Mochalov ,Vayacheslav Moiseyev , Nicole Nicklisch , Sandra L. Pichler , Roberto Risch , Manuel A. Rojo Guerra , ChristinaRoth , Anna Szecsenyi-Nagy , Joachim Wahl , Matthias Meyer , Johannes Krause , Dorcas Brown , DavidAnthony , Alan Cooper , Kurt Werner Alt , David Reich

We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost four hundred thousand polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of western and far eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ~8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary, and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ~24,000 year old Siberian6. By ~6,000-5,000 years ago, a resurgence of hunter-gatherer ancestry had occurred throughout much of Europe, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ~4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ~3/4 of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ~3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for the theory of a steppe origin of at least some of the Indo-European languages of Europe.

Link

Paternal lineages and languages in the Caucasus

An interesting new study on Y chromosome and languages in the Caucasus. The distribution of haplogroups is on the left. The authors make some associations of haplogroups with language families:

• R1b: Indo-European
• R1a: Scytho-Sarmatian
• J2: Hurro-Urartian
• G2: Kartvelian

Hum Biol. 2014 May;86(2):113-30.

Human paternal lineages, languages, and environment in the caucasus.

Tarkhnishvili D1, Gavashelishvili A1, Murtskhvaladze M1, Gabelaia M1, Tevzadze G2.

Abstract

Publications that describe the composition of the human Y-DNA haplogroup in diffferent ethnic or linguistic groups and geographic regions provide no explicit explanation of the distribution of human paternal lineages in relation to specific ecological conditions. Our research attempts to address this topic for the Caucasus, a geographic region that encompasses a relatively small area but harbors high linguistic, ethnic, and Y-DNA haplogroup diversity. We genotyped 224 men that identified themselves as ethnic Georgian for 23 Y-chromosome short tandem-repeat markers and assigned them to their geographic places of origin. The genotyped data were supplemented with published data on haplogroup composition and location of other ethnic groups of the Caucasus. We used multivariate statistical methods to see if linguistics, climate, and landscape accounted for geographical diffferences in frequencies of the Y-DNA haplogroups G2, R1a, R1b, J1, and J2. The analysis showed significant associations of (1) G2 with wellforested mountains, (2) J2 with warm areas or poorly forested mountains, and (3) J1 with poorly forested mountains. R1b showed no association with environment. Haplogroups J1 and R1a were significantly associated with Daghestanian and Kipchak speakers, respectively, but the other haplogroups showed no such simple associations with languages. Climate and landscape in the context of competition over productive areas among diffferent paternal lineages, arriving in the Caucasus in diffferent times, have played an important role in shaping the present-day spatial distribution of patrilineages in the Caucasus. This spatial pattern had formed before linguistic subdivisions were finally shaped, probably in the Neolithic to Bronze Age. Later historical turmoil had little influence on the patrilineage composition and spatial distribution. Based on our results, the scenario of postglacial expansions of humans and their languages to the Caucasus from the Middle East, western Eurasia, and the East European Plain is plausible.

Link (pdf)

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

4,000-year old chariot burial from Georgia

This would make it roughly contemporaneous to the chariot burials of the Sintashta-Petrovka culture of the European steppe.

4,000-Year-Old Burial with Chariots Discovered in South Caucasus

An ancient burial containing chariots, gold artifacts and possible human sacrifices has been discovered by archaeologists in the country of Georgia, in the south Caucasus.

The burial site, which would've been intended for a chief, dates back over 4,000 years to a time archaeologists call the Early Bronze Age, said Zurab Makharadze, head of the Centre of Archaeology at the Georgian National Museum.

Archaeologists discoveredthe timber burial chamber within a 39-foot-high (12 meters) mound called a kurgan. When the archaeologists reached the chamber they found an assortment of treasures, including two chariots, each with four wooden wheels. [See Images of the Burial Chamber & Chariots]

...

The burial dates back to a time before domesticated horses appeared in the area, Makharadze said. While no animals were found buried with the chariots, he said, oxen would have pulled them.

D4500 and the unity of early Homo

Science 18 October 2013:

Vol. 342 no. 6156 pp. 326-331

DOI: 10.1126/science.1238484

A Complete Skull from Dmanisi, Georgia, and the Evolutionary Biology of Early Homo

David Lordkipanidze et al.



The site of Dmanisi, Georgia, has yielded an impressive sample of hominid cranial and postcranial remains, documenting the presence of Homo outside Africa around 1.8 million years ago. Here we report on a new cranium from Dmanisi (D4500) that, together with its mandible (D2600), represents the world's first completely preserved adult hominid skull from the early Pleistocene. D4500/D2600 combines a small braincase (546 cubic centimeters) with a large prognathic face and exhibits close morphological affinities with the earliest known Homo fossils from Africa. The Dmanisi sample, which now comprises five crania, provides direct evidence for wide morphological variation within and among early Homo paleodemes. This implies the existence of a single evolving lineage of early Homo, with phylogeographic continuity across continents.

Link

Origin of Early Transcaucasian Culture (aka Kura-Araxes culture)

From the paper:

Akhundov (2007) recently uncovered pre-Kura-Araxes/Late Chalcolithic materials  from the settlement of Boyuk Kesik and the kurgan necropolis of Soyuq Bulaq in  northwestern Azerbaijan, and Makharadze (2007) has also excavated a pre-Kura-Araxes  kurgan, Kavtiskhevi, in central Georgia. Materials recovered from both these recent  excavations can be related to remains from the metal-working Late Chalcolithic site  of Leilatepe on the Karabakh steppe near Agdam (Narimanov et al. 2007) and from  the earliest level at the multi-period site of Berikldeebi in Kvemo Kartli (Glonti and Dzavakhishvili 1987). They reveal the presence of early 4th millennium raised burial  mounds or kurgans in the southern Caucasus. Similarly, on the basis of her survey work  in eastern Anatolia north of the Oriental Taurus mountains, C. Marro (2007)likens chafffaced wares collected at Hanago in the Sürmeli Plain and Astepe and Colpan in the eastern  Lake Van district in northeastern Turkey with those found at the sites mentioned above  and relates these to similar wares (Amuq E/F) found south of the Taurus Mountains in  northern Mesopotamia

... 

The new high dating of the Maikop culture essentially signifies that there is no
chronological hiatus separating the collapse of the Chalcolithic Balkan centre of
metallurgical production and the appearance of Maikop and the sudden explosion of  Caucasian metallurgical production and use of arsenical copper/bronzes. More than  forty calibrated radiocarbon dates on Maikop and related materials now support this high  chronology; and the revised dating for the Maikop culture means that the earliest kurgans  occur in the northwestern and southern Caucasus and precede by several centuries those of the Pit-Grave (Yamnaya) cultures of the western Eurasian steppes (cf. Chernykh and Orlovskaya 2004a and b). The calibrated radiocarbon dates suggest that the Maikop ‘culture’ seems to have had a formative influence on steppe kurgan burial rituals and what now appears to be the later development of the Pit-Grave (Yamnaya) culture on the Eurasian steppes (Chernykh and Orlovskaya 2004a: 97).   

...  

In other words, sometime around the middle of the 4th millennium BCE or slightly subsequent to the initial appearance of the Maikop culture of the NW Caucasus, settlements containing proto-Kura-Araxes or early Kura-Araxes materials first appear across a broad area that stretches from the Caspian littoral of the northeastern Caucasus in the north to the Erzurum region of the Anatolian Plateau in the west. For simplicity’s sake these roughly simultaneous developments across this broad area will be considered as representing the beginnings of the Early Bronze Age or the initial stages of development of the KuraAraxes/Early Transcaucasian culture. 

...  

The ‘homeland’ (itself a very problematic concept) of the Kura-Araxes culture-historical community is difficult to pinpoint precisely, a fact that may suggest that there is no single well-demarcated area of origin, but multiple interacting areas including northeastern Anatolia as far as the Erzurum area, the catchment area drained by the Upper Middle Kura and Araxes Rivers in Transcaucasia and the Caspian corridor and adjacent mountainous regions of northeastern Azerbaijan and southeastern Daghestan. While broadly (and somewhat imprecisely) defined, these regions constitute on present evidence the original core area out of which the Kura-Araxes ‘culture-historical community’ emerged.  

Kura-Araxes materials found in other areas are primarily intrusive in the local sequences. Indeed, many, but not all, sites in the Malatya area along the Upper Euphrates drainage of eastern Anatolia (e.g., Norsun-tepe, Arslantepe) and western Iran (e.g., Yanik Tepe, Godin Tepe) exhibit— albeit with some overlap—a relatively sharp break in material remains, including new forms of architecture and domestic dwellings, and such changes support the interpretation of a subsequent spread or dispersal from this broadly defined core area in the north to the southwest and southeast. The archaeological record seems to document a movement of peoples north to south across a very extensive part of the Ancient Near East from the end of the 4th to the first half of the 3rd millennium BCE. Although migrations are notoriously difficult to document on archaeological evidence, these materials constitute one of the best examples of prehistoric movements of peoples available for the Early Bronze Age.

Tel Aviv vol. 36, 2009 241–265

Origins, Homelands and Migrations: Situating the Kura-Araxes Early Transcaucasian ‘Culture’ within the History of Bronze Age Eurasia

Philip L. Kohl

This paper summarizes current understanding of the emergence, nature and subsequent southwestern and southeastern spread of the early Transcaucasian (eTC) or Kura-Araxes ‘culture-historical community’ (Russian: obshchnost’) and then places this complex cultural phenomenon in the context of the larger early Bronze Age world of the Ancient Near east and the western eurasian steppes.

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

Stanislav Grigoriev's "Ancient Indo-Europeans"

I had seen bits and pieces of SA Grigoriev's ideas in various publications, but it's nice to see this work in its entirety (although the reproduction of the maps doesn't seem to be very good). From the conclusion:

The Indo-European problem is a complex one, combining linguistic and archaeological evidence. In linguistics Gamkrelidze and Ivanov have suggested a system and a fundamental solution. Convincing linguistic models uniquely localising the Indo-European homeland in the Balkans, or even in the North Pontic area or Central Europe, are lacking. Often criticism of Gamkrelidze and Ivanov has been reduced to no more than a statement that archaeological evidence in favour of it is absent. As we see, this does not correspond to reality (and, by the way, did not correspond to reality before the publication of this book). There are a number of facts to prove the connections of North Eurasian and European cultures with the Near East, whilst convincing examples to demonstrate the reverse connections do not now exist. There is a purely historiographic tradition, not substantiated by facts. For the long years this tradition flourished it proved impossible to flesh it out with arguments, although skilled scholars attempted to do so. Therefore, hypotheses about the northern origin of the Indo-Europeans have practically nothing which can be used today in support, either linguistic or archaeological. The archaeological model suggested here is not complete in many respects. Many parallels may raise doubts, as it has not always been possible to back them up with completely identical artefacts. But in the consideration of distant migrations and subsequent cultural transformations, such complete similarity may be wanting. 

Interestingly, Grigoriev's reconstruction does not seem to agree with G&I's model in all its details, as the latter suggested the Halafian culture as the archaeological manifestation of the Proto-Indo-European community (picture from Wikipedia on the right).

For reasons of my own (i.e., finding the hiding place of the "West Asian" autosomal component which I believe was introduced to Europe by Indo-Europeans) it might be worth seeking a more "eastern" PIE homeland.

In any case it would be wonderful to get some archaeogenetic data from the Near East. Irrespective of one's opinion on the IE problem, most everyone would agree that this is a critical region for understanding the prehistory of Eurasia.

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)

Disentangling the histories of mtDNA haplogroups M1 and U6

mtDNA haplogroups M1 and U6 are often mentioned in terms of Eurasian back-migration in Africa. The former is the only clade of the Asian haplogroup M which occurs in Africa at all; the latter is the only clade of the West Eurasian haplogroup U that does the same. These haplogroups also tend to co-exist in North and East Africa, although they are largely absent in sub-Saharan Africa. Different ideas have been offered for their occurrence, including a "Paleolithic" spread or a more recent one associated with the spread of Afroasiatic languages.

The new paper offers useful new data on this debate. The most important conclusion is that despite their oft-mentioned association, these two haplogroups appear to have distinct histories. One argument for this is their separate geographic distribution:

M1 (on panel A) is much more common in Northeast Africa and the Near East (including the Caucasus), whereas U6 (panel B) is more confined in Africa, and has its stronger peak in NW Africa, being rare in NE Africa.

An interesting aside, is that all the mysterious M1 from the Caucasus belongs to subclade M1a, while the smaller M1b clade tends to co-occur with M1a in other parts of Africa and the Near East. This indicates a founder effect for the origin of Caucasian M1a, but leaves open the issue of the immediate origins of M1. Hopefully it will become possible to place this haplogroup within the broader M phylogeny in the future.

The Bayesian skyline plots also contrast M1 and U6 in terms of their demographic histories:

The authors argue that these histories are inconsistent with either a very early dispersal history with the Dabban industry, as well as a more recent spread with Afroasiatic. From the paper:

The transition from the Middle Palaeolithic to Upper Palaeolithic in North Africa is characterised by the appearance of the “Dabban”, an industry that is restricted to Cyrenaica in northeast Libya and represented at the caves of Hagfet ed Dabba and Haua Fteah [19]. Whilst a techno-typological shift occurred within the Dabban ~33 KYA [19], starker changes in the archaeological record occurred throughout North Africa and Southwest Asia ~23-20 KYA, represented by the widespread appearance of backed bladelet technologies. The appearance of these backed bladelet industries more or less coincides with the timing of the Last Glacial Maximum (LGM) (~23-18 KYA), including: ~21 KYA in Upper Egypt [20]; ~20 KYA at Haua Fteah with the Oranian [21]; the Iberomaurusian expansion in the Jebel Gharbi ~20 KYA [22]; and the first Iberomaurusian at Tamar Hat in Algeria ~20 KYA [23]. The earliest Iberomaurusian sites in Morocco appear to be only slightly younger ~18 KYA [24].

A disassociation of these haplogroups from the UP in North Africa might be consistent with my idea that the UP was in part a cultural revolution that spread not only with people, but often with ideas across a species that already had the "biological machinery" for behavioral modernity and was already established in both Africa and the Near East.

As for the connection to Afroasiatic, the authors detect a linguistic correlation with M1a, which, however, appears too old to have been involved directly in the spread of this language family:

Concerning haplogroup M1 individually, a significant correlation with languages was observed. Furthermore, within M1, it appears that the correlation is mostly due to M1a. However, given the small sample size of M1b, any potential signal correlating with language might not be detectable. Interestingly, M1a has a likely East African origin, but its coalescent age of ~21 KYA still largely predates that of the proto-AA. Maybe a sub-clade of M1a would still give a similar correlation, but there are not sufficient samples to allow splitting M1a into its various sub-clades, and to test for a correlation. Although we found a correlation, limited sample sizes do not allow drawing unambiguous connection between genes and languages. Furthermore, it is also possible that this putative sub-clade of M1 does not testify for the expansion of AA speaking people, but was already present among the people who inhabited the area before the spread of the AA languages.

Personally, I am in favor of an East African origin of Afroasiatic, as this makes sense of various lines of evidence, one of which is the African shift of the "Southwest_Asian" component that is modal in Semitic populations. I envision that M1 was geographically circumscribed in a NE African population after its much earlier arrival from Asia and piggy-backed onto the expansion of Afroasiatic speakers, thus explaining the observed correlation. A good analogy would be with the expansion of, say, haplogroup H in the Americas which piggybacked on the European colonization, even though the coalescence age of H predates the arrival of Europeans in the New World by many millennia.

BMC Evolutionary Biology 2012, 12:234 doi:10.1186/1471-2148-12-234


Divorcing the Late Upper Palaeolithic demographic histories of mtDNA haplogroups M1 and U6 in Africa

Erwan Pennarun et al.

Abstract (provisional)
Background
A Southwest Asian origin and dispersal to North Africa in the Early Upper Palaeolithic era has been inferred in previous studies for mtDNA haplogroups M1 and U6. Both haplogroups have been proposed to show similar geographic patterns and shared demographic histories.

Results
We report here 24 M1 and 33 U6 new complete mtDNA sequences that allow us to refine the existing phylogeny of these haplogroups. The resulting phylogenetic information was used to genotype a further 131 M1 and 91 U6 samples to determine the geographic spread of their sub-clades. No southwest Asian specific clades for M1 or U6 were discovered. U6 and M1 frequencies in North Africa, the Middle East and Europe do not follow similar patterns, and their sub-clade divisions do not appear to be compatible with their shared history reaching back to the Early Upper Palaeolithic. The Bayesian Skyline Plots testify to non-overlapping phases of expansion, and the haplogroups' phylogenies suggest that there are U6 sub-clades that expanded earlier than those in M1. Some M1 and U6 sub-clades could be linked with certain events. For example, U6a1 and M1b, with their coalescent ages of ~20,000-22,000 years ago and earliest inferred expansion in northwest Africa, could coincide with the flourishing of the Iberomaurusian industry, whilst U6b and M1b1 appeared at the time of the Capsian culture.

Conclusions
Our high-resolution phylogenetic dissection of both haplogroups and coalescent time assessments suggest that the extant main branching pattern of both haplogroups arose and diversified in the mid-later Upper Palaeolithic, with some sub-clades concomitantly with the expansion of the Iberomaurusian industry. Carriers of these maternal lineages have been later absorbed into and diversified further during the spread of Afro-Asiatic languages in North and East Africa.

Link

Investigating East Asian admixture in Balkans/Anatolia/Caucasus

I used ALDER with a dataset of populations from the Balkans, Anatolia, and Caucasus, using the She, Japanese, Miaozu, and Dai as East Asian references. A few caveats for this analysis:

1. Some populations may possess "South Asian" admixture which may be mistaken for East Asian
2. Populations differ in the number of SNPs used in the analysis; for example, the Armenian_D sample includes mostly Family Finder data which has a smaller overlap with the SNP set used
3. Populations differ in the number of individuals used, from a low of 5 (e.g., Turkish_Cypriot) to a high of 45 (Armenian_D)

I have also added the HGDP Europeans to the analysis. The results can be seen below; I have made bold those rows where all estimates are at least one standard error above zero, and bold/big those where the estimates are they are two standard errors above zero. I consider the latter to be the most reliable.

I have already discussed the Turkish signal of admixture at length elsewhere. I will note that the Iranian_D sample produces similar or younger admixture dates, which would make sense, given the fact that the Iranians came under control of the Mongols, while the successes of the latter in Anatolia were short-lived.

A very interesting signal is that of the North Ossetians which show admixture ~9-10 centuries ago. This seems to have occurred a little after the foundation of the kingdom of Alania, and I think it makes excellent sense to view it as the signal of Eurasian nomads (who must have carried some East Asian admixture at that time) intermingling with pre-Iranic local Caucasus populations, Two other populations from the Caucasus, the Georgians and Lezgins (and also the Abkhaz and Chechens) show earlier admixture signals that could very well date to the period of east-west Eurasian migrations inaugurated by the Huns, although a possible Sassanian origin of such influence cannot be overlooked.

The Kurds are another interesting case where the Dodecad sample and the Yunusbayev et al  sample produce very different dates. The different number of SNPs may be at play here, or it may be that some Dodecad participants have recent Turkish ancestry that cause the admixture date average to appear lower, although the globe13 analysis suggests that the "East Asian" found here may be in fact "South Asian".

It seems to me that with large, dense, and well-curated sample sets from several of these populations, their admixture dynamics will become more distinct.

Neandertals and modern humans may not have met in the southern Caucasus

There have been some recent indications that modern West Eurasians might not have precisely equal amounts of Neandertal ancestry, and that these differences may have been accented during prehistory. One possible explanation for this might be the fact that as modern humans expanded in Eurasia, they encountered different concentrations of Neandertals, and, in some places no Neandertals at all.

This hypothesis may be better resolved once a high coverage Neandertal genome is published, to complement the recent publication of the Denisova genome, as well as the new Altai Neandertals recently announced.

Journal of Human Evolution doi:dx.doi.org/10.1016/j.jhevol.2012.08.004

New chronology for the Middle Palaeolithic of the southern Caucasus suggests early demise of Neanderthals in this region

R. Pinhasi et al.

Neanderthal populations of the southern and northern Caucasus became locally extinct during the Late Pleistocene. The timing of their extinction is key to our understanding of the relationship between Neanderthals and anatomically modern humans (AMH) in Eurasia. Recent re-dating of the end of the Middle Palaeolithic (MP) at Mezmaiskaya Cave, northern Caucasus, and Ortvale Klde, southern Caucasus, suggests that Neanderthals did not survive after 39 ka cal BP (thousands of years ago, calibrated before present). Here we extend the analysis and present a revised regional chronology for MP occupational phases in western Georgia, based on a series of model-based Bayesian analyses of radiocarbon dated bone samples obtained from the caves of Sakajia, Ortvala and Bronze Cave. This allows the establishment of probability intervals for the onset and end of each of the dated levels and for the end of the MP occupation at the three sites.

Our results for Sakajia indicate that the end of the late Middle Palaeolithic (LMP) and start of the Upper Palaeolithic (UP) occurred between 40,200 and 37,140 cal BP. The end of the MP in the neighboring site of Ortvala occurred earlier at 43,540–41,420 cal BP (at 68.2% probability). The dating of MP layers from Bronze Cave confirms that it does not contain LMP phases.

These results imply that Neanderthals did not survive in the southern Caucasus after 37 ka cal BP, supporting a model of Neanderthal extinction around the same period as reported for the northern Caucasus and other regions of Europe. Taken together with previous reports of the earliest UP phases in the region and the lack of archaeological evidence for an in situ transition, these results indicate that AMH arrived in the Caucasus a few millennia after the Neanderthal demise and that the two species probably did not interact.

Link

rolloff analysis of Lezgins as Sardinian+Burusho

I have carried out rolloff analysis of Lezgins, a Northeast Caucasian population that is of particular interest due to it being modal for the "Dagestan" component whose long-distance relationships with Western Europe and South Asia have triggered a great deal of followup investigation on my part.

The Lezgins are also interesting for other reasons: they may be one of the populations related to the Kura-Araxes culture; they possess a high frequency of Y-haplogroup R1b, so they may be related to the migration that brought this haplogroup into Europe from West Asia.

In my previous analysis of the French using the same reference populations, I speculated that their signal of admixture may involve admixture between a Sardinian-like and a West Asian population in Asia itself circa 7,000 years ago, followed by a later expansion into Europe. And, in my analysis of Lithuanians and Ukrainians, I discovered a somewhat less "old" signal of admixture involving South Asian+North European references with a mean value of 5.5-6.3ky for the various population pairs.

The exponential fit for the Lezgins can be seen below:

The admixture time estimate is 198.773 +/- 70.649 generations or 5,760 +/- 2,050 years. This is not very precise, but seems consistent with the two phenomena described above. It also seems to contrast with the much younger signal for Armenians.

Ancient mtDNA haplogroup X2 from Central Europe

Davidski reminds me of a paper by Lee et al. I had posted the abstract of, but did not comment on. He highlights the fact that mtDNA haplogroup X2 has been detected at this site (3.6-2.8ky cal BC) but not in earlier LBK Neolithic Europeans. Furthermore, he attributes the arrival of X2 in Europe to "Northwest Eurasians":

Reading the quotes below, I can’t help thinking that X2 lineages in Europe might be associated with the arrival of the so called Northwest Eurasians of North/Central/East Europe and the North Caucasus, while X1 with the earlier migrations of the Sardinian-like Southwest Eurasians of Mediterranean Europe, North Africa and the Near East.

However, mtDNA haplogroup X2 seems to have originated in the Near East:

Finally, phylogeography of the subclades of haplogroup X suggests that the Near East is the likely geographical source for the spread of subhaplogroup X2, and the associated population dispersal occurred around, or after, the LGM when the climate ameliorated. The presence of a daughter clade in northern Native Americans testifies to the range of this population expansion.

Moreover, it occurs at a higher frequency in Southern Europeans than Northern Europeans and is well-represented in the Caucasus, Near East, and even Africa. These twin facts are inconsistent with it being related to "Northwest Eurasians", however that hypothetical people is defined.

Of related interest, mtDNA haplogroup X2b has been detected in Iron Age "princely burials" from the same location and by the same group. Also from Reidla et al.:

The sister groups X2b and X2c (X1 and X2, respectively, in the work of Herrnstadt et al. 2002) encompass one-third of the European sequences (excluding the samples from the North Caucasus). It is of interest that some North African sequences (from Morocco and Algeria) belong to X2b as well. Subhaplogroup X2b shows a diversity that is consistent with a postglacial population expansion in both West Eurasia and North Africa.

Fernandes et al. (2012) consider X2b to be of European origin. X2 has been discovered in a Megalithic long mound from France (4.2ky cal BP), and in abundance at Treilles (c. 3,000 BC), in the latter case associated with a predominantly Y-haplogroup G2a (with some I-P37.2) population. In Jean Manco's excellent compendium, X2b is also listed as being present in Neolithic Portugal (3,400 years BC), and X2j in Neolithic Germany (4625-4250 BC); the latter is said to be "North African" by Fernandes et al. (2012).

Therefore, we can probably reject Davidski's speculation...

So, X2 has been located at multiple late Neolithic sites in Central Europe, including the Corded Ware burial ground at Eulau, Eastern Germany. Of course, that’s also where Y-chromosome haplogroup R1a was found (see here). I suspect this wasn’t a coincidence and it’s likely these markers entered Europe together from the east, probably between 4,000 and 3,000 B.C.

X2 shows no association with northern Europeans at present, and occurs in ancient DNA samples from Western Europe that show no indication of being related to Y-haplogroup R1a at all, and even precede the hypothetical 4-3ky BC entry window.

Also of interest is that no X2 was mentioned in recent published data from Ukraine and West Siberia, and none of it was detected in Mesolithic Europeans. So, it seems that X2 variants entered Europe during the Neolithic, and there is no indication that they did so with Davidski's hypothetical R1a-bearing Northwest Europeans.

Differential relationship of ANI to Caucasus populations

The observation in Reich et al. (2009) that Ancestral North Indians (ANI) and CEU (HapMap White Utahns) form a clade to the exclusion of Adygei (a NW Caucasian HGDP population) has always puzzled me, because in my ADMIXTURE experiments, the dominant West Eurasian component in South Asia has always been one centered in the Caucasus rather than Europe, an observation also confirmed by Metspalu et al. (2011).

I have now used the qpDstat program of ADMIXTOOLS to calculate some D-statistics using a wide variety of West Asian populations that have appeared in the literature since 2009 (mainly Behar et al. 2010, and Yunusbayev et al. 2011), in addition to the Adygei. This analysis is based on 87,925 SNPs. I have kept SNPs included in the Rutgers map for Illumina chips, since most of the datasets merged with the Reich et al. (2009) dataset were genotyped on such chips, and applied a --geno 0.01 flag after merging the various datasets.

The following populations were considered:

North_Kannadi, Sindhi, Pathan, Kashmiri_Pandit, Brahmins_from_Uttar_Pradesh_M, Iyer_D, Iyengar_D, CEU30, Onge, Adygei, Lezgins, Georgians, Ukranians_Y, Abhkasians_Y, Chechens_Y, North_Ossetians_Y, Armenians_Y, Kurds_Y, Iranians_19, Romanians_14, Bulgarians_Y, Greek_D

I calculated D-statistics of the form:

D(CEU30, non-CEU West Eurasian; South Asian, Onge)

I report, for each South Asian population, the score for non-CEU West Eurasian being Adygei, and the most negative Z-score:

It is clear, that while CEU are more related to Indian cline populations than Adygei are, at least for the case of the Pathans, they are less related to them than Georgians are. The Georgian population is one of the modal populations of the West Asian autosomal component.

The full set of results can be found here. It appears that North Ossetians (who are also from the NW Caucasus) follow the Adygei pattern, while Abkhazians, Lezgins, and Armenians appear more related to ANI than CEU are, similar to the Georgian pattern.

Interestingly, D(CEU, Iranian; South Asian, Onge) appear positive, and this is probably not because CEU are more related to ANI than Iranians, but because Iranians also have ASI admixture.

Ukrainians do not appear more closely related to ANI than CEU are, rather the opposite. This is consistent with the recent f3-statistics analysis of South Indian Brahmins, in which the strongest signals of admixture involved populations from Western Europe, the Balkans, and West Asia, but not from eastern Europe.

All the available evidence suggests that ANI is most related to populations of the South and NE Caucasus, and not to those of the NW Caucasus like Adygei. To confirm this, I calculated some additional D-statistics (also included in the spreadsheet):

All in all, this seems to be very consistent with my working model of Eurasian prehistory. It is also in agreement with proposals for a genetic relationship between Indo-European and NE Caucasian/Hurrian and/or early contacts between it and Kartvelian. No such relationship, as far as I can tell, has been seriously advanced with respect to NW Caucasian languages.

A valuable lesson from this analysis is that now that multiple West Asian populations have been genotyped, caution must be exercised when using the HGDP Adygei, because they are clearly not representative of the different language families (NE/S Caucasian and Indo-European) present in West Asia. Surprises may lurk even at the sub-1000km scale in a region as diverse as the Caucasus.

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.