Major admixture in India took place ~4.2-1.9 thousand years ago (Moorjani et al. 2013)

A new paper on the topic of Indian population history has just appeared in the American Journal of Human Genetics. In previous work it was determined that Indians trace their ancestry to two major groups, Ancestral North Indians (ANI) (= West Eurasians of some kind), and Ancestral South Indians (ASI) (= distant relatives of Andaman Islanders, existing today only in admixed form). The new paper demonstrates that admixture between these two groups took place ~4.2-1.9 thousand years ago.

The authors caution about this evidence of admixture:

It is also important to emphasize what our study has not shown. Although we have documented evidence for mixture in India between about 1,900 and 4,200 years BP, this does not imply migration from West Eurasia into India during this time. On the contrary, a recent study that searched for West Eurasian groups most closely related to the ANI ancestors of Indians failed to find any evidence for shared ancestry between the ANI and groups in West Eurasia within the past 12,500 years3 (although it is possible that with further sampling and new methods such relatedness might be detected). An alternative possibility that is also consistent with our data is that the ANI and ASI were both living in or near South Asia for a substantial period prior to their mixture. Such a pattern has been documented elsewhere; for example, ancient DNA studies of northern Europeans have shown that Neolithic farmers originating in Western Asia migrated to Europe about 7,500 years BP but did not mix with local hunter gatherers until thousands of years later to form the present-day populations of northern Europe.15, 16, 44 and 45

This is of course true, because admixture postdates migration and it is conceivable that the West Eurasian groups might not have admixed with ASI populations immediately after their arrival into South Asia. On the other hand, a long period of co-existence without admixture would be against much of human history (e.g., the reverse movement of the Roma into Europe, who picked up European admixture despite strong social pressure against it by both European and Roma communities, or the absorption of most Native Americans by incoming European, and later African, populations in post-Columbian times). It is difficult to imagine really long reproductive isolation between neighboring peoples.

Such reproductive isolation would require a cultural shift from a long period of endogamy (ANI migration, followed by ANI/ASI co-existence without admixture) to exogamy ~4.2-1.9kya (to explain the thoroughness of blending that left no group untouched), and then back to fairly strict exogamy (within the modern caste system). It might be simpler to postulate only one cultural shift (migration with admixture soon thereafter, with later introduction of endogamy which greatly diminished the admixture.

The authors cite the evidence from neolithic Sweden which does, indeed, suggest that the neolithic farmers this far north were "southern European" genetically and had not (yet) mixed with contemporary hunter-gatherers, as they must have done eventually. But, perhaps farmers and hunters could avoid each other during first contact, when Europe was sparsely populated. It is not clear whether the same could be said for India ~4 thousand years ago with the Indus Valley Civilization providing evidence for a large indigenous population that any intrusive group would have encountered. In any case, the problem of when the West Eurasian element arrived in India will probably be solved by relating it to events elsewhere in Eurasia, and, in particular, to the ultimate source of the "Ancestral North Indians".

It is also possible that some of the ANI-ASI admixture might actually pre-date migration. At present it's anyone's guess where the original limes between the west Eurasian and ASI worlds were. There is some mtDNA haplogroup M in Iran and Central Asia, which is otherwise rare in west Eurasia, so it is not inconceivable that ASI may have once extended outside the Indian subcontinent: the fact that it is concentrated today in southern India (hence its name) may indicate only the area of this element's maximum survival, rather than the extent of its original distribution. In any case, all mixture must have taken place somewhere in the vicinity of India.

A second interesting finding of the paper is that admixture dates in Indo-European groups are later than in Dravidian groups. This is demonstrated quite clearly in the rolloff figure on the left. Moreover, it does not seem that the admixture times for Indo-Europeans coincide with the appearance of the Indo-Aryans, presumably during the 2nd millennium BC: they are much later. I believe that this is fairly convincing evidence that north India has been affected by subsequent population movements from central Asia of "Indo-Scythian"-related populations, for which there is ample historical evidence. So, the difference in dates might be explained by secondary (later) admixture with other West Eurasians after the arrival of Indo-Aryans. Interestingly, the paper does not reject simple ANI-ASI admixture "often from tribal and traditionally lower-caste groups," while finding evidence for multiple layers of ANI ancestry  in several other populations.

My own analysis of Dodecad Project South Indian Brahmins arrived at a date of 4.1ky, and of North Indian Brahmins, a date of 2.3ky, which seems to be in good agreement with these results.

The authors also report that "we find that Georgians along with other Caucasus groups are consistent with sharing the most genetic drift with ANI". I had made a post on the differential relationship of ANI to Caucasus populations which seems to agree with this, and, of course, in various ADMIXTURE analyses, the component which I've labeled "West Asian" tends to be the major west Eurasian element in south Asia.

Here are the estimated admixture proportions/times from the paper:

Sadly, the warm and moist climate of India, and the adoption of cremation have probably destroyed any hope of studying much of its recent history with ancient DNA. On the other hand, the caste system has probably "fossilized" old socio-linguistic groups, allowing us to tell much by studying their differences and correlating them with groups outside India.

Coverage elsewhere: Gene Expression, HarappaDNA
Related podcast on BBC.

AJHG doi:10.1016/j.ajhg.2013.07.006

Genetic Evidence for Recent Population Mixture in India

Priya Moorjani et al.

Most Indian groups descend from a mixture of two genetically divergent populations: Ancestral North Indians (ANI) related to Central Asians, Middle Easterners, Caucasians, and Europeans; and Ancestral South Indians (ASI) not closely related to groups outside the subcontinent. The date of mixture is unknown but has implications for understanding Indian history. We report genome-wide data from 73 groups from the Indian subcontinent and analyze linkage disequilibrium to estimate ANI-ASI mixture dates ranging from about 1,900 to 4,200 years ago. In a subset of groups, 100% of the mixture is consistent with having occurred during this period. These results show that India experienced a demographic transformation several thousand years ago, from a region in which major population mixture was common to one in which mixture even between closely related groups became rare because of a shift to endogamy.

Link

Indo-European homeland and migrations: half a century of studies and discussions (Gamkrelidze & Ivanov 2013)

An extensive English summary of an article in Russian by Gamkrelidze and Ivanov almost 30 years since the publication of their original book. There are other articles in the volume of the JOLR presenting different views (unfortunately most behind a paywall).

Indo-European homeland and migrations: half a century of studies and discussions [In Russian with English summary]

The problem of the initial place from which the original Indo- European dialects spread over Eurasia has been studied by several generations of scholars. Few alternative points of view have been proposed: first an area near the North Sea (in the works of some scholars of the border of the 19th and 20th centuries), then the North coast of the Black Sea (an old idea of Schrader revived by Maria Gimbutas and her followers) or an area closer to the more eastern (Volga-Ural) parts of Central Eurasia. 40 years ago we suggested first in a talk at a conference, then in a series of articles and in a resulting book (published in Russian in 1984) that the Northern part of the Near East (an area close to North-East Syria and North Mesopotamia) may be considered as a possible candidate for the Indo-European homeland; similar suggestions were made by C. Renfrew and other scholars in their later works. Recent research on these topics has brought up additional evidence that seems to prove the Near Eastern hypothesis for the time that had immediately preceded the dispersal of the Indo-European protolanguage. Indirect evidence on the early presence of Indo-Europeans in the areas close to the Near East can be found in the traces of ancient contacts between linguistic families in this part of Eurasia. Such contacts between Proto-Indo-European and Proto-Kartvelian have been suggested in the work of T. Gamkrelidze and G. Mach’avariani more than 60 years ago. The following studies have established a number of important loanwords from Proto-Indo-European in Proto-Kartvelian. Particularly interesting discoveries in this field were made by the late G. A. Klimov. He has found many new common elements of the two families in addition to a relatively long list in our joint work. The main difficulty in interpreting the results of his investigations is connected to the problem of a possible common Nostratic origin both of Proto-Indo-European and of Proto-Kartvelian. If these two linguistic families were originally cognate, then some part of the correspondences found by Klimov and other scholars might be traced back to the early period of Proto-Nostratic (more than 10 000 years ago). Only those words that were not inherited from this ancient time are important as a proof of the later presence of Proto-Indo-European in the area close to the Proto-Kartvelian (to the southwest of the Transcaucasian area in which the latter spread in the historic time). In our book, published in 1984, we suggested some common terms shared by these languages, explaining them as possible traces of later Indo-European (probably Indo-Iranian) migrations through the Caucasus. The study of this problem has been enriched through the recent research on Proto-North Caucasian. S. L. Nikolaev and S. A. Starostin have compiled a large etymological dictionary of this family, furthering the comparative studies started by Prince N. S. Trubetzkoy. Starostin has gathered a large collection of the terms of material culture common to North Caucasian and Indo-European. They include many names of domestic animals and animal body parts or products of cattle-breeding, plants and implements. In a special work on this subject Starostin suggested that all these terms were borrowed in the area of the Near East to the South of Transcaucasia in the early 5th mil. BC. Although we still use the traditional term “North Caucasian”, it is not geographically correct even if applied to such living languages as Abkhaz and to the extinct Ubykh (spoken originally at the southern part of the South-West Transcaucasian area). Since both Hurro-Urartian and Hattic (two ancient dialects of this linguistic group) were spoken in the regions to the South of Transcaucasia already in the 3rd mil. BC, it becomes possible to pinpoint the homeland of the whole family (which at that time was not North Caucasian) in the same area close to the supposed Proto-Indo-European and Proto-Kartvelian homelands. The fricative š in the Hurrian name for ‘horse’, eššə, and an affricate *č (> š) in the forms of the other North Caucasian dialects correspond to the Proto-Indo-European palatal stop *k’ that has become an affricate *č and then a fricative š /s in the Indo-European languages of the satəm type. Similar changes are present in the other borrowings discussed by Starostin. He supposed that the common words discovered by him were mostly borrowed from Proto-North Caucasian (or from a dialect of it) into Proto-Indo-European. The opposite direction of borrowing from an Indo-European dialect of a satəm type can be suggested due to the typologically valid laws of sound change. But no matter which direction of the borrowing should be chosen, the existence of these loanwords is beyond doubt. They clearly point to the location of the Indo-European homeland. In our monograph we suggested that several words shared by Semitic and Indo-European (such as the ancient term for ‘wine’, Hittite wiyana­) can be considered Proto-Indo-European borrowings (as distinct from the rest of the most ancient old Semitic or Afro-Asiatic loanwords in Proto-Indo-European). S. A. Starostin suggested that a large number of (mainly West) Semitic words that did not have correspondences in the other Afro-Asiatic languages had been borrowed from Proto-Indo-European. He came to the conclusion: “the original Indo-European (Indo-Hittite) homeland was somewhere to the North of the Fertile Crescent from where the descendents of Indo-Hittites could have moved in two directions (starting with early 5th millennium BC) to the South where they came into the contact with the Semites, and indeed could have driven a part of them further to the South, and to the North (North-East) whence they ultimately spread both to Europe and to India”. The interference of the early dialects of Proto-Indo-European, Proto-Semitic and Proto-Kartvelian to which the early Proto-“North” Caucasian can be added might have led to the formation of a sort of linguistic zone (Sprachbund) that not only shared many words pertaining to a new farming economy, but also had several phonological and grammatical features in common. After we had published our hypothesis on the Near Eastern homeland of the Indo-Europeans, several scholars asked us why, at a time when writing had already been invented, there were no written documents testifying to the presence of Indo-Europeans in these areas. It seems that now there are several possible answers to the question. The great specialist on Iranian, W. B. Henning, who had worked for many years on the problem of the name of Tocharians, suggested in a posthumous article that their early ancestors were Gutians who had invaded Mesopotamia in ca. 2350—2200 BC. In an article written after we had already published our book, we have developed Henning’s idea (based mainly on the etymological links of Near Eastern Guti and Tukri and Central Asian names of corresponding Indo-European Kuchean and Tocharian ethnic groups), also paying attention to the possible explanation of some names of Gutian kings preserved in Sumerian texts. Recently it has been suggested that an unknown “Pre-Sumerian” language, reconstructed on the basis of the phonetic values of many cuneiform signs, was an archaic “Euphratic” Indo-European dialect spoken in Southern Mesopotamia in the second half of the 4th mil. BC. According to this hypothesis, the phonetic values of approximately one hundred of the early signs that are different from the Sumerian ones go back to the Euphratic words. A large number of Anatolian personal names (of a very archaic Indo-European type) have been found in the Old Assyrian texts from trade colonies in Asia Minor. The continuation of the excavations in Kanish that have yielded more than 23000 cuneiform tablets has made it possible to discover in them many Anatolian Indo-European names and loanwords. The Old Assyrian documents in Kanish are encountered in the archaeological levels II and Ib dated by the first centuries of the 2nd mil. BC (on the base of the recently found lists of eponyms); they precede Old Hittite texts for ca. 250 years. At that time the two Anatolian groups of dialects — a Northern (Hittite) one, displaying centum dialect features, and a Southern (Luwian), partly similar to the satəm languages — were already quite distinct. From the very beginning, the idea of the Indo-European homeland in the Near East was connected to the discovery of a possible link between the appearance of speakers of Indo-European dialects in Europe and the spread of the new farming technology. This trend of thought has been developed in the archeological works of Sir Colin Renfrew. Subsequent attempts to support this hypothetical connection were made by comparing genetic data on the time and space characteristics of the European population. The farming terms common to Indo-European and other linguistic families discussed above show that the innovations were not restricted to one group of languages and were transmitted and exchanged between different ethnic formations. The area of the interference of these families coincides with the kernel of the rising farming in the Near East. That process of global (multilingual and multicultural) change had led to the diffusion of the results of the Neolithic revolution. The main directions of this diffusion coincide with the trends of the Indo-European migrations, but the new objects might have been introduced earlier than some of their Indo-European names and the latter might precede the coming of those who coined the terms. The spread of Near Eastern innovations in Europe roughly coincides with the split of Proto-Indo-European (possibly in the early 5th mil. BC), but some elements of the new technology and economy might have penetrated it much earlier (partly through the farmers close to the Tyrrhenian population as represented 5300 years ago by the genome of the Tyrolean Iceman). The diffusion took several thousand years and was probably already all over Europe ca. 3550 BC. At that time Indo-European migrations were only beginning. The speakers of the dialects of Proto-Indo-European living near the kernel of the technological revolution in Anatolia should have acquired the main results of this development. The growth of farming economy in Europe became more active with the split of the proto-language and the dispersal of the Indo-Europeans. The astonishing scope and speed of that process were afforded by the use of the domesticated horse and wheeled vehicles. The Indo-Europeans did not have to be pioneers in this field, but they were probably skillful in spreading other peoples’ innovations. Recent work on the Botai culture of North Kazakhstan makes it possible to suppose a contribution of the Proto-Yeniseian people to the development of horse domestication. For approximately fifteen hundred years serious preparatory work on horse domestication and the use of wheeled vehicles had been going on in different parts of Eurasia. Then, almost suddenly, the results are witnessed. On the border of the 3rd and 2nd mil. BC both of these important innovations appear together, usually in a context implying the presence of Indo-Europeans: traces of Near East-type chariots and the ritual use of the horse are clear in (probably Ancient Iranian) Margiana (Gonur), we see chariots on the Anatolian type of seals in Kanish; Hurrian sculptures and other symbols of horse abound in Urkeš as if foretelling the future Mespotamian-Aryan and Hurrian excellent training of horses in Mitanni (as later in Urartu). One of the first examples of the sacrificial horses used together with chariots in an archaic ritual was found in Sintashta; the following studies of the cities of the Transuralian Sintashta-Arkaim area made it clear that some Indo-European (and maybe Iranian as well) elements were at least partly present there. The movement of Indo-Europeans to the north of the Caspian Sea in the northeast direction documented in the Sintashta-Arkaim complex led them much farther to the Altai-Sayany area where recent genetic investigations found traces of a Caucasoid element. Another Indo-European group moving in a parallel eastward direction using the South Silk Road caused the presence of a similar anthropological group among the population of Central Asia. It may be supposed that the Caucasoid anthropological type of the Iranian and/or Tocharian population of Eastern Turkestan, attested in the mummies recently found there as well as in the contemporary images of the native people, should be considered as the result of these migrations from the West to the East. The problem whether the boats played a role comparable to that of chariots at the time of early migrations is still to be decided by maritime archaeology. It seems that before the efficient use of chariots and horses, long-term mass movements were hardly possible. The first changes in the geographical position of separate dialects, e.g. when the Anatolians separated the Greeks from the rest of the East Indo-European group (that included the Armenians and Indo-Iranians), were caused by rather small-scale migrations close to the original homeland in the Near East.

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

Sakha origins

An interesting quote from the paper:

Although the genetic heritage of the native populations of Sakha is mostly of East Asian ancestry, analyses of autosomal SNP data as well as haploid loci also show a minor West  Eurasian genetic component. The patchy presence of the “European” (blue) component in the  ADMIXTURE plot (Figure 6), most pronounced in Yukaghirs, probably testifies to recent  admixture with Europeans. In addition, the presence of European-specific paternal lineages  R1a-M458, I1 and I2a among Yakuts, Dolgans, Evenks and Yukaghirs likely points to a  recent gene flow from East Europeans. Although only individuals with self-reported unadmixed ancestry for at least two generations were included in the study of haploid loci,  mistakes in ethnic self-identification cannot be entirely excluded. One of the main sources of  gene flow has likely been Russians who accounted for 37.8% of the population of Sakha in  2010 [61]. The migration of Russians (at first mainly men) to eastern Siberia started already  in the 17th century, when Yakutia was incorporated into the Russian Empire [62]. 

But:

The mtDNA haplogroup J detected in the remains from a Yakut burial site dated to the  beginning of the 17th century [41], long before the beginning of the settlement of Russian  families in the 18th century [63], clearly points to more ancient gene flow from western  Eurasia. The presence of haplogroups H8, H20 and HV1a1a among the Yakuts, Dolgans and  Evenks (Figure 1) also suggests gene flow other than from Russians, because these  haplogroups are rare (H8 and H20) or even absent (HV1a1a) among Russians [64-67], but are  common among southern Siberian populations as well as in the Caucasus, the Middle and  Near East [19,68-70]. Moreover, the HVSI haplotypes of H8, H20a and HV1a1a in our  sample exactly match those in the Buryats from the Buryat Republic [19]. Similarly, the Ychromosome haplogroup J in Dolgans and Evens very likely testifies to gene flow through  South Siberia, as it is present among native South Siberian populations [47,71]. The scenario  of ancient gene flow from West Eurasia is supported by ancient DNA data, which show that  in the Bronze and Iron Ages, South Siberia, including the Altai region, was an area of  overwhelmingly predominant western Eurasian settlement [72,73], and the Indo-European  migration even reached northeastern Mongolia [74]. To summarize, the West Eurasian  genetic component in Sakha may originate from recent admixture with East Europeans,  whereas more ancient gene flow from West Eurasia through Central Asia and South Siberia is  also probable. 

BMC Evolutionary Biology 2013, 13:127 doi:10.1186/1471-2148-13-127

Autosomal and uniparental portraits of the native populations of Sakha (Yakutia): implications for the peopling of Northeast Eurasia

Sardana A Fedorova et al.

Abstract (provisional)

Background

Sakha -- an area connecting South and Northeast Siberia -- is significant for understanding the history of peopling of Northeast Eurasia and the Americas. Previous studies have shown a genetic contiguity between Siberia and East Asia and the key role of South Siberia in the colonization of Siberia.

Results

We report the results of a high-resolution phylogenetic analysis of 701 mtDNAs and 318 Y chromosomes from five native populations of Sakha (Yakuts, Evenks, Evens, Yukaghirs and Dolgans) and of the analysis of more than 500,000 autosomal SNPs of 758 individuals from 55 populations, including 40 previously unpublished samples from Siberia. Phylogenetically terminal clades of East Asian mtDNA haplogroups C and D and Y-chromosome haplogroups N1c, N1b and C3, constituting the core of the gene pool of the native populations from Sakha, connect Sakha and South Siberia. Analysis of autosomal SNP data confirms the genetic continuity between Sakha and South Siberia. Maternal lineages D5a2a2, C4a1c, C4a2, C5b1b and the Yakut-specific STR sub-clade of Y-chromosome haplogroup N1c can be linked to a migration of Yakut ancestors, while the paternal lineage C3c was most likely carried to Sakha by the expansion of the Tungusic people. MtDNA haplogroups Z1a1b and Z1a3, present in Yukaghirs, Evens and Dolgans, show traces of different and probably more ancient migration(s). Analysis of both haploid loci and autosomal SNP data revealed only minor genetic components shared between Sakha and the extreme Northeast Siberia. Although the major part of West Eurasian maternal and paternal lineages in Sakha could originate from recent admixture with East Europeans, mtDNA haplogroups H8, H20a and HV1a1a, as well as Y-chromosome haplogroup J, more probably reflect an ancient gene flow from West Eurasia through Central Asia and South Siberia.

Conclusions

Our high-resolution phylogenetic dissection of mtDNA and Y-chromosome haplogroups as well as analysis of autosomal SNP data suggests that Sakha was colonized by repeated expansions from South Siberia with minor gene flow from the Lower Amur/Southern Okhotsk region and/or Kamchatka. The minor West Eurasian component in Sakha attests to both recent and ongoing admixture with East Europeans and an ancient gene flow from West Eurasia.

Link

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.

mtDNA haplogroup H and the origin of Europeans (Brotherton et al. 2013)

Panel b is particularly interesting, as it clearly shows the Iberian-ness of Bell Beaker mtDNA (BBC), and the South-Eastern-ness of LBK.

From the paper:

From around 2800 BC, the LNE Bell Beaker culture emerged from the Iberian Peninsula to form one of the first pan-European archaeological complexes. This cultural phenomenon is recognised by a distinctive package of rich grave goods including the eponymous bell-shaped ceramic beakers. The genetic affinities between Central Europe’s Bell Beakers and present-day Iberian populations (Fig. 2) is striking and throws fresh light on long-disputed archaeological models3. We suggest these data indicate a considerable genetic influx from the West during the LNE. These far-Western genetic affinities of Mittelelbe-Saale’s Bell Beaker folk may also have intriguing linguistic implications, as the archaeologically-identified eastward movement of the Bell Beaker culture has recently been linked to the initial spread of the Celtic language family across Western Europe39. This hypothesis suggests that early members of the Celtic language family (for example, Tartessian)40 initially developed from Indo-European precursors in Iberia and subsequently spread throughout the Atlantic Zone; before a period of rapid mobility, reflected by the Beaker phenomenon, carried Celtic languages across much of Western Europe. This idea not only challenges traditional views of a linguistic spread of Celtic westwards from Central Europe during the Iron Age, but also implies that Indo-European languages arrived in Western Europe substantially earlier, presumably with the arrival of farming from the Near East41.

It does seem increasingly likely that there was a major Out-of-Iberia episode which may very well have involved a population of relative newcomers (R1b males, undetected in Europe in the pre-5ka period) interacting with an "Iberian" matrilineal substratum and then exporting both R1b and the "Iberian" type of H into most of Western Europe with the Bell Beaker phenomenon. It's hard to think of the Bell Beakers as ultimately descended from the first farmers alone, both because of their distinctive physical type, and also because of the aforementioned absence of R1b in early farmers. More ancient DNA work will certainly help solve many of the remaining puzzles.

Also from the paper:

The demographic reconstruction, which is based on direct calibration points, has major implications for understanding post-glacial human history in Europe. Our new estimate is incompatible with traditional views that the majority of present-day hg H lineages were carried into Central, Northern and Eastern Europe via a post-glacial human population expansion before the Holocene (12 kya)13. Our data complement a recent study, based on present-day mt genomes, which describes a pronounced population increase at ~7000 BC (interpreted as a Neolithic expansion into Europe), but followed by a slow population growth until the present day26. By including ancient DNA data from across the critical time points in question, our skyride plot corrects for missing temporal data and suggests substantial growth of hg H from the beginning of the Neolithic and continuing throughout the entire Neolithic period. This emphasizes the role of farming practices and cultural developments in the demographic expansions inferred in subsequent time periods, which have not yet been explored genetically.

Nature Communications 4, Article number: 1764 doi:10.1038/ncomms2656

Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans

Paul Brotherton et al.

Haplogroup H dominates present-day Western European mitochondrial DNA variability (>40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this ‘real-time’ genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current estimates for human mitochondria.

Link

Indo-Europeans galore

A whole bunch of papers in a journal I hadn't heard of before, but written by some of the best known people in this field. I see lots of "Buy pdf" links to accompany them, so if you want to spare me the expense, feel free to e-mail me a copy.

Anyway, here's a list of titles for reference:


Anthony, David Two IE phylogenies, three PIE migrations, and four kinds of steppe - p. 1-21
Balanovsky, Oleg; Utevska, Olga; Balanovska, Elena Genetics of Indo-European populations: the past, the future - p. 23-35
Blazek, Vaclav Indo-European zoonyms in Afroasiatic perspective - p. 37-54
Burlak, Svetlana Languages, DNA, relationship and contacts - p. 55-67
Dybo, Anna Language and archeology: some methodological problems. 1. Indo-European and Altaic landscapes - p. 69-92
Dybo, Vladimir Dialectal variation of Proto-Indo-European in the light of accentological research - p. 93-108
Gamkrelidze, Tamaz; Ivanov, Vyacheslav Indo-European homeland and migrations: half a century of studies and discussions - p. 109-136
Kullanda, Sergey Early Indo-European social organization and the Indo-European homeland - p. 137-144
Mallory, J.P. Twenty-first century clouds over Indo-European homelands - p. 145-154
Kornienko, Tatiana 'Archaeological Research in Northern Mesopotamia and North Caucasus' [Chronicle] - p. 155-162
Korovina, Eugenia 'Problems of the Indo-European Homeland' [Chronicle] - p. 163-166

UPDATE: Someone sent me the Anthony paper. Here is the main figure which suggests a correspondence between the linguistic phylogeny of Ringe et al. and the archaeological reconstruction of out-of-steppe movements of its author:

One of the weakest points of the steppe model is its treatment of Anatolians. Movement marked #1 perhaps takes some populations in an indistinct way into the east Balkans, but does not take them all the way to Anatolia.

The steppe model must propose some kind of early round-the-Black Sea mechanism to bring the Anatolians to their historical seats. This is not trivial; it might seem like a small jump from Thrace (where the endpoint of the first migration, marked with 1 is placed) to Anatolia, but it is in fact in the southern parts of the peninsula that we first find the Anatolian speakers. And, Anatolian place names are also recorded in Greece and its immediate environs, and not at all in the proposed migration route. Thus, the arrow must take the Anatolians further west (to account for the evidence from the Aegean, and then bring them south and east). I don't find this very plausible.

Estimating the date of composition of the Homeric epics

This might be an interesting way of dating literary works for which there are no/conflicting traditions about their date of composition.

Bioessays DOI: 10.1002/bies.201200165

Linguistic evidence supports date for Homeric epics

Eric Lewin Altschuler et al.

The Homeric epics are among the greatest masterpieces of literature, but when they were produced is not known with certainty. Here we apply evolutionary-linguistic phylogenetic statistical methods to differences in Homeric, Modern Greek and ancient Hittite vocabulary items to estimate a date of approximately 710–760 BCE for these great works. Our analysis compared a common set of vocabulary items among the three pairs of languages, recording for each item whether the words in the two languages were cognate – derived from a shared ancestral word – or not. We then used a likelihood-based Markov chain Monte Carlo procedure to estimate the most probable times in years separating these languages given the percentage of words they shared, combined with knowledge of the rates at which different words change. Our date for the epics is in close agreement with historians' and classicists' beliefs derived from historical and archaeological sources.

Link

“Mismodelling Indo-European Origins” Talk

Martin Lewis and Asya Pereltsvaig have been critical of the recent paper on Indo-European origins on the GeoCurrents blog, and they recently gave a talk at Stanford on the topic.



Some relevant past posts:

• U7 in Rostov Scythians
• The Indo-European invasion of the Baltic
• IE-speaking West Europeans are West Asian-admixed relative to Non-IE speaking Basques
• Indo-European genetic signatures in an Orcadian and a Lithuanian
• The Bronze Age Indo-European invasion of Europe
• Assessment of ancient European DNA with 'globe13'

I think that the Indo-European question has been debated for more than two centuries without any clear resolution. Over the next few years, I think that either of two things will occur:

• A clear unambiguous pattern of expansion mimicking the IE dispersal will appear in ancient DNA, providing the "smoking gun" for one of the different hypotheses.
• No such Eurasian-wide pattern will emerge, and it will turn out that Indo-Europeanization was effected with minimum dispersal of populations.

I suspect the former will be the case, but it will nonetheless be interesting to see how the different parties coming from archaeology and linguistics will react to the (archaeo)genetic avalanche that will doubtlessly provide us with new information about the prehistoric past.

U7 in Rostov Scythians

I found it quite interesting that in terms of mtDNA, the Rostov Scythians studied by der Sarkissian resembled closely the Shugnans of Tajikistan, who speak an eastern Iranian language. The author finds links between the Scythians and the "Central Asian Corridor", in particular with respect to mtDNA haplogroup U7.

This "Central Asian Corridor" sensu der Sarkissian (Iraq, Iran, Pakistan, India) seems to touch Frachetti's Inner Asian Mountain Corridor (shown below) in the region of the Pamirs.

Interestingly, the Sughnans belong, anthropologically to the Pamir-Ferghana type, which was also called Central Asian interfluvial type, the rivers in question being the Oxus and Jaxartes (Amu Darya and Syr Darya). And, of course, between these two rivers was the heartland of the Bactria Margiana Archaeological Complex, which I have previously linked with the Indo-Iranians.

Wells et al. studied Y-chromosomes of Sughnans, Yagnobis and other Iranic survivals of Tajikistan more than 10 years ago, and it will be very well worth revisiting them with newer methods. The area east of the Caspian and west of the IAMC intersects so much history, that any data from from it (new or ancient) would be extremely useful.

In my own experiments there has been an unambiguous "South Asian" genetic component in almost all Iranic peoples, even the westernmost Kurds. While the interpretation of this component is not easy, it does point to a genetic relationship between its possessors and Central/South Asia, with notable contrasts between Kurds/Iranians and their non-Iranic Armenian/Anatolian/Caucasian neighbors.

The occurrence of mtDNA haplogroup U7 in the Rostov Scythians is also consistent with a link between the Iranian nomads who penetrated into Europe with the area east of the Caspian, and it is also, of course, consistent with the narrative of Herodotus who recorded the migration of the Scythians into Europe.

There is a widely held theory that the origin of the Indo-Iranians are to be sought in eastern Europe. That theory appears inconsistent both with the "South Asian" autosomal signal in Iranic groups, and with the mtDNA evidence. Consider, again, the evidence of der Sarkissian:

Now, if Rostov Scythians were primarily descended from Mesolithic West Eurasians or even Bronze Age ones, then we would expect them to cluster at the "top", approaching the northern Europeoid extrema of PWC and Bronze Age Altai (ALT-BA). On the contrary, their position is well to the "south" of all European Bronze Age groups, and intermediate between Europeans and Iron Age Asian groups from south Siberia and Kazakhstan (KUR-IA, KAZ-IA). Again, this is compatible with an east-west migration during the Iron Age.

It might be worth speculating on the possible autosomal history of the steppe, for which the mtDNA evidence complements others: I offer that the long-term trend will be one of diminishing "North European", increasing "West Asian" and "East Eurasian" influences across the Neolithic-Bronze-Iron Age boundaries. At the western end of the steppe, there may also be "Mediterranean"/Sardinian-like infusions from the Balkans and Central Europe, although these clearly did not influence Inner/South Asia (where Mediterranean components shrink to non-existence), and Europe proper was mostly the recipient rather than the emitter of populations to Asia. Hopefully, autosomal data to test this conjecture will be made available in the coming years.

Swat valley cemetery

A lost civilisation: 3,000-year-old cemetery discovered in Swat

The Italian Archaeological Mission on Wednesday discovered an ancient cemetery dating back thousands of years at Odigram, Swat — a site experts believe was built between 1500 BC to 500 BC.

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A total of 23 graves have been excavated at the site that seems to be an ancient cemetery, indicating that they belonged to the pre-Buddhist era.

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“It clearly indicates that Swat Valley was thickly populated at that time. Most probably they were the Dards (a group of people defined by linguistic similarities and not a common ethnic origin, predominantly found in Eastern Afghanistan) and in my view these Dards were somehow linked culturally to the people presently living in Kohistan and Kalash valleys,” revealed Massimo Vidale, a professor of Archaeology at University of Padua. “They probably spoke the Indo-European languages. We can say that the present culture of Kalash and Kohistan in Chitral valley can be linked with the ancient culture of Swat,” Vidale explained.

Ancient European DNA assessment with 'globe4'

In a previous experiment, I showed that ADMIXTURE at K=4 tracks the same signal of Amerindian-like admixture detected with f-statistics. I encapsulated that analysis in the globe4 calculator over at the Dodecad Project blog, and decided to use it to assess a few ancient European autosomal samples:

Please note that a very variable number of SNPs was extracted from these various samples. These results should be viewed as indicative of possible patterns that might be confirmed by a more thorough analysis. Also, please consult the globe4 post for more details on the methodology behind it, and the interpretation of the 4 components.

With these various caveats, I would say that these results seem to make some sense and to be fairly consistent with the scenario of Patterson et al. (2012):

• Oetzi and Gok4, the "farmers" seem to lack the Amerindian component
• Ajv52, and Ajv70, the northern hunter-gatherers seem to possess it
• Bra1, the Mesolithic Iberian seems to lack it as well

Bra1 also happens to be the most limited sample in terms of available SNPs. Nonetheless, this would appear broadly consistent with the idea that the "Amerindian"-like admixture in Europeans emanated from north-eastern Europe. Today, all continental Europeans seem to possess some of it, but this can be explained by migration of Ajv-like individuals and their mixtures into Western and Southern Europe from central or northern Europe for which there is ample historical and archaeological evidence (e.g., Italo-Celts, Germans, and Slavs, in addition to other, earlier phenomena).

A broader context

The absence of the Amerindian-like admixture in South Indian Brahmins and Armenians, and its paucity Kurds and Iranians might indicate that this type of ancestry was not represented in ancient Armenians and Indo-Iranians. Indeed, all these populations possess less of this admixture than those of the North Caucasus. Cypriots possess none of it as well, where the Greek_D sample, a small 2.5% portion. In a previous analysis, I estimated a historical-era estimate of North European admixture in Greeks, and this admixture presumably incorporates the signal of Amerindian-like admixture. Additionally, an Iron Age individual from Bulgaria will soon be announced as being Sardinian-like.

The sum of these factors leads me to believe that the signal of Amerindian-like admixture did not play an important role in the formation of the Graeco-Phrygians (and their Armenian relatives) and the Indo-Iranians, or at least did so to an insignificant degree. As the former expanded westward from the PIE homeland, and the latter eastward, they would have had little opportunity to encounter this type of admixture; rather, they would have admixed with Sardinian-like individuals in the west, and Ancestral South Indian (ASI)-like or East Asian individuals in the east.

On the other hand, as Indo-European groups expanded into eastern Europe, setting off a chain of events that would eventually transform most of the northern part of the continent, and, in historical times, much of the rest of it, they would have met with Ajv-like individuals carrying the signal of Amerindian-like admixture, as well as the Oetzi/Sardinian-like farmers that had spread all the way to Scandinavia by the late Neolithic. The population formed by this mixture would have carried with it the signal of Amerindian-like ancestry, and would then transpose it across the continent. The signal would become increasingly muted westward and southward, and indeed this is what we observe.

UPDATE: It is interesting to see that South Indian Brahmins (both the Metspalu et al. sample, and my Iyer_D and Iyengar_D samples) lack this admixture, while Uttar Pradesh Brahmins do not, given the rolloff evidence for a more recent admixture of the latter. This is consistent with a historical admixture event, after the migration of Brahmin groups southwards, as described in that post.

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.

3D laser scan of Stonehenge reveals axehead graffiti

Stonehenge up close: digital laser scan reveals secrets of the past

The first complete 3D laser scan of the stone circle has also revealed tool marks made 4,500 years ago, scores of little axehead graffiti added when the enormous slabs were already 1,000 years old, and damage and graffiti contributed by Georgian and Victorian visitors. 

...

Long after the monument was built, when Bronze Age burial mounds rich in grave goods began to be scattered across the plain around Stonehenge, and the archaeological evidence suggests those who could make or trade in metal goods had an almost shamanic status, people carved little images of daggers and axes, many now invisible to the naked eye, into the stones. Scores more have been revealed by the scan, including 71 new axe heads, bringing the total to 115 – doubling the number ever recorded in Britain.

"It is wonderful to have discovered so many more, but what is fascinating is that they are carved without regard to the importance or the siting of the stones – almost as if the people who carved them could no longer quite remember the significance of the monument and how it worked," Greaney said.

They probably could no longer remember, because they were Indo-European newcomers, and not the same people as the Megalithic folk who built Stonehenge.

A little history:

Craniologists of the time used a ratio based on length and width measurements, known as the cranial index, to divide skulls into two basic types: 'dolichocephalic', long and narrow in shape, and 'brachycephalic', broad and round in shape. Based on his observations at sites like Belas Knap, Thurnam established his famous axiom, 'long barrows, long skulls; round barrows, round skulls'. The long skulls were found in long barrows and never in association with metallic artefacts, while round skulls were found in round barrows sometimes with metalwork. 

... 

Thurnam's and Rolleston's theories gained considerable credibility in the late Victorian period and survived well into the earlier 20th century. Such racist theories failed to stand up, however, in the face of Gordon Childe's arguments for the definition of an archaeological culture based on shared social characteristics and material culture rather than race or biological type. In addition, the considerable moral repugnance felt towards Victorian anthropology and its role in the rise of fascist ideology in the 1930s caused the argument over long and round skulls to be sidelined and eventually dismissed. The identification of the Bronze Age incomers based on their material culture, including metalwork and Beaker pottery vessels, remained a more acceptable alternative.
In the 1990s, however, the archaeologist Neil Brodie took a fresh look at the craniological evidence and concluded that there was undeniably a difference between the shape of skulls from Neolithic long barrows and Bronze Age round barrows. A trend from long to round skull shape was clearly shown. 

The differences, he argued, could be caused by cultural practices, such as the binding of infants' heads, as well as by diet and a range of climatic or environmental factors. Looking at the totality of human history, he showed that head shape fluctuates in populations over long periods of time, and that extremes of head types occur in successive prehistoric populations as a matter of historical chance.

We don't have DNA evidence from British round barrows yet, but Beaker burials from Germany show the first R1b ever found, while Neolithic Western Europe shows a mix of I2a and G2a. Difference in material culture? check. Difference in physical anthropology? check. Difference in time of appearance? check. Difference in genetics? preliminary check.

So, it seems like a good bet that the people who carved axehead graffiti on Stonehenge were simply invaders who took over the site from the previous inhabitants, and, as is so often the case, used it for their own purposes.

rolloff analysis of North Indian Brahmins as Orcadian+North Kannadi

In a previous experiment, I tested the Dodecad Project South Indian Brahmin sample (Iyer and Iyengar) using Orcadians and North Kannadi as reference populations. In the current one, I use the same references to investigate admixture in the Uttar Pradesh Brahmins included in the Metspalu et al. (2011) dataset. A total of 473,837 SNPs are used in this experiment.

I first verified that f3(Brahmins_from_Uttar_Pradesh_M; Orcadian, North_Kannadi) is negative, using qp3Pop:

 Source 1 Source 2 Target f_3 std. err Z SNPs
 result: Orcadian North_Kannadi Brahmins_from_Uttar_Pradesh_M -0.007882 0.000359 -21.951 463297

The exponential fit can be seen below:

The estimated age is 79.706 +/- 9.197 generations, or 2,310 +/- 270 years.

This is about a thousand years younger than the signal observed for the South Indian Brahmin group. A possible explanation has to do with the fact that South Indian Brahmins migrated to South India, and hence did not intermarry with successive waves of invaders into India in historical times. Uttar Pradesh, on the other hand, received multiple invasions from the direction of Central Asia:

Most of the invaders of North India passed through the Gangetic plains of what is today Uttar Pradesh. Control over this region was of vital importance to the power and stability of all of India's major empires, including the Maurya (320–200 BC), Kushan (100–250 CE), Gupta (350–600 CE), and Gurjara-Pratihara (650–1036 CE) empires.[11] Following the Huns invasions that broke the Gupta empire, the Ganges-Yamuna Doab saw the rise of Kannauj.[12] During the reign of Harshavardhana (590–647 CE), the Kannauj empire reached its zenith.[12]

It will be interesting to see whether a young admixture signal also exists in my 5-strong sample of Jatts, since that population has traditions of "Scythian" origins.

rolloff analysis of South Indian Brahmins as Armenian+Chamar

The first analysis of this population showed that there were negative f3(Brahmin; X, Y) signals when X were a variety of West European, Balkan, and West Asian population, and Y either the Chamar or North Kannadi. In the first analysis I used Orcadians and North Kannadi. I have now carried out a new rolloff analysis on 470,559 SNPs, using Armenians_Y and Chamar_M as the reference populations.

The exponential fit can be seen below.

The admixture date is 142.814 +/- 15.010 generations, or 4,140 +/- 440 years, which seems to correspond quite well with commonly accepted dates for the formation of Indo-Iranian.

I have previously observed that:

These patterns can be well-explained, I believe, if we accept that Indo-Iranians are partially descended not only from the early Proto-Indo-Europeans of the Near East, but also from a second element that had conceivable "South Asian" affiliations. The most likely candidate for the "second element" is the population of the Bactria Margiana Archaeological Complex (BMAC). The rise and demise of the BMAC fits well with the relative shallowness of the Indo-Iranian language family and its 2nd millennium BC breakup, and has been assigned an Indo-Iranian identity on other grounds by its excavator. As climate change led to the decline and abandonment of BMAC sites, its population must have spread outward: to the Iranian plateau, the steppe, and into South Asia, reinforcing the linguistic differentiation that must have already began over the extensive territory of the complex.

Quite possibly, as the West Asian element began mixing with the Sardinian-like population in Greece, another branch of the Indo-Europeans made its appearance east of the Caspian, in the territory of the BMAC, admixing with South Asian-like populations. Thus, it might seem that the Graeco-Aryan clade of Indo-European broke down during the Bronze Age, with one branch heading off to the Balkans, and another to the east. 

This scenario would also explain how the likely J2-bearing population associated with the earliest Proto-Indo-Europeans may have acquired the contrasting pattern I have previously described: the western (cis-Caspian) population would have admixed with R1b-bearers who occupy the "small arc" west and south of the Caspian, while the eastern (trans-Caspian) populations would have admixed with R1a-bearers who occupy the "large arc" in the flatlands north and east of the Caspian. It would also explain how the "western" branch (Graeco-Armenian) would have picked up Sardinian-like "Atlantic_Med" admixture, which is absent in the "eastern" Indo-Iranian branch.

At the same time, this scenario would explain the lack of "North European" admixture in the "western" branch (since this was shielded by the Caucasus and Black Sea from the northern Europeoids who may have lived north of these barriers), and explain it in the "eastern" branch (since the BMAC agriculturalists were in contact with presumably northern Europeoid groups inhabiting the steppelands, unhindered by any major physical barriers). (The relative absence of this admixture in the Graeco-Armenian branch may be advanced on the strength of its absence in Armenians, the evidence of a Sardinian-like Iron Age individual from Bulgaria, and the historical-era timing of admixture for the Greek population.)

It would be interesting to carry out similar experiments on Iranian groups, to see if they, too, present a similar pattern of admixture.

Armenians as Phrygian colonists, or, rolloff analysis of Armenians as a mixture of Sardinians+Balochi

I analyze the Yunusbayev et al. Armenians_Y sample in a similar manner as the South Indian Brahmins. The 30 lowest f3 statistics are:

Sardinian Velamas_M Armenians_15_Y -0.00349 0.000264 -13.23 239451
Sardinian Piramalai_Kallars_M Armenians_15_Y -0.003213 0.00028 -11.484 239389
Sardinian GIH30 Armenians_15_Y -0.002983 0.00023 -12.986 241310
Balochi Sardinian Armenians_15_Y -0.002837 0.000193 -14.681 241698
Sardinian Sindhi Armenians_15_Y -0.002794 0.000203 -13.757 241928
Sardinian Muslim_M Armenians_15_Y -0.002761 0.000295 -9.351 238639
Indian_D Sardinian Armenians_15_Y -0.002743 0.000224 -12.226 241916
Sardinian Kanjars_M Armenians_15_Y -0.002727 0.000281 -9.722 239240
Iyer_D Sardinian Armenians_15_Y -0.002718 0.000263 -10.322 238943
Brahui Sardinian Armenians_15_Y -0.002715 0.000196 -13.882 241885
Sardinian Dusadh_M Armenians_15_Y -0.002666 0.000281 -9.502 238994
Sardinian INS30 Armenians_15_Y -0.00265 0.000237 -11.162 240965
Iyengar_D Sardinian Armenians_15_Y -0.002624 0.000297 -8.847 238564
Sardinian Dharkars_M Armenians_15_Y -0.002501 0.000267 -9.359 239505
Sardinian North_Kannadi Armenians_15_Y -0.002463 0.000288 -8.545 239278
Sardinian Chamar_M Armenians_15_Y -0.002445 0.000275 -8.904 240102
Sardinian Kshatriya_M Armenians_15_Y -0.002372 0.000267 -8.897 239047
Pathan Sardinian Armenians_15_Y -0.00224 0.000199 -11.264 241759
Sardinian Brahmins_from_Uttar_Pradesh_M Armenians_15_Y -0.002189 0.00025 -8.774 239395
Jatt_D Sardinian Armenians_15_Y -0.001806 0.000273 -6.608 238465
Cypriots Kanjars_M Armenians_15_Y -0.001699 0.00026 -6.547 238237
Cypriots Velamas_M Armenians_15_Y -0.001642 0.000275 -5.965 238392
Cypriots Muslim_M Armenians_15_Y -0.001618 0.000279 -5.798 237762
Cypriots Dusadh_M Armenians_15_Y -0.001611 0.000279 -5.779 238096
GIH30 Cypriots Armenians_15_Y -0.001608 0.000223 -7.216 239819
Iyer_D Cypriots Armenians_15_Y -0.001562 0.000251 -6.217 238012
Sindhi Cypriots Armenians_15_Y -0.001544 0.000209 -7.383 240276
Cypriots North_Kannadi Armenians_15_Y -0.001464 0.000276 -5.298 238273
Cypriots Kshatriya_M Armenians_15_Y -0.001438 0.00026 -5.534 238076

I carried out rolloff analysis using the Balochi and Sardinians as references, for a total of 510,844 SNPs. Note that the Burusho were not used in this experiment, because they were culled due to more than 5% East Eurasian admixture, as per the followed procedure. 

The Balochi are very similar to the Burusho otherwise, and this also gives me the opportunity to see a Sardinian+Balochi population pair to complement a previous analysis of French as Sardinian+Burusho, which presented an f3 signal of quite similar intensity. The exponential fit is seen below.

The jackknife gives an age estimate of 113.194 +/- 14.674 generations, or 3,280 +/- 430 years, assuming a generation length of 29 years.

I had somewhat expected the Armenians to show a more recent signal of admixture than the French, as they lived much closer to the boundary of Europe and Asia, and may have had more opportunity to admix between Sardinian-like populations of Europe and "West Asian"-like populations of Asia.

But, the inferred date also raises another possibility. Herodotus says of the Armenians who were part of the army of King Xerxes:

the Armenians were equipped like Phrygians, being Phrygian colonists" (7.73)

Now, the Phrygians became masters of Central Anatolia during the tumultuous events near the end of the Bronze Age (12th century BC), following the collapse of the Hittite Empire. And, their ancestral homeland was in Thrace. And, there is fairly good evidence that Armenian is the closest language related to Greek within the Indo-European language family. And, we have some tantalising evidence that even during the Iron Age, the population of Thrace was Sardinian-like. And, the Armenians do contrast with their Caucasian neighbors in possessing ~10% of the Sardinian-like Atlantic_Med component that South and Northeast Caucasians lack.

All of the above combine to make a pretty compelling story. Could it be that Armenians preserve a legacy of admixture between a linguistically Indo-European speaking, genetically Sardinian-like population, which arrived in Asia Minor from the Balkans at the end of the Bronze Age, finally settling in the Armenian Highlands, and mixing with the local people they encountered?

The plot thickens. And, this is, certainly, a question that can be answered by ancient DNA research, e.g., by comparing the genomes of historical Phrygians and Armenians with those from Hittite-era, or earlier Anatolians.