R1ans still at large (or, the story of India)

Ten ago, in the pre-ancient DNA "Dark Ages" a big debate raged on about the origin of R1a  men in India. The stage had been set even earlier, by the pioneering Eurasian heartland paper which was the first (to my memory) to link M17 with steppe migrations and Indo-Iranians. Yet, there was pushback as the distribution of M17 was better described, and people started using Y-STRs to try to date and place phylogeographically its migrations.

The two poles of the debate were the "Out-of-India", which relied primarily on Y-STR based time estimates that seemed very old (even Paleolithic, if one used the wrong mutation rate) in India, and the "Into-India" which thought that the R1a distribution pointed to its being brought into India by the Indo-Aryans in the conventional ~3,500BC time frame of the "Aryan Invasion Theory" (AIT).

AIT has been much maligned because it has been received as a Western colonialist imposition on Indian history: a way to claim that Indian civilization was not native but European in origin. Europeans were certainly guilty of misusing AIT: for British colonials it represented a precedent for their colonization of India; for German National Socialists it was evidence for the greatness of the Aryan race and its past expansions eastward. It also played into internal Indian politics, espoused by some as a means of furthering their superiority as either descendants of "Aryan conquerors" or as oppressed victims of the same.

Of course, a misuse of a theory does not mean it is wrong, and if a new preprint based on ancient and modern DNA is correct, it means that AIT was basically correct: Indo-Aryans did come to India in the Late Bronze Age, via the steppe, and ultimately from central Europe.

The opposing Out-of-India theory is all but dead, although failed theories often have a long half-life, especially if they are espoused for psycho-political reasons. I would argue that Out-of-India was dead for thousands of years before it was conceived, since even in Homer's time it was known that "India" was not "one thing" but was peopled by Indians in the north and "Eastern Ethiopians" in the south (which differed from their western "actual" Ethiopians of Africa by their possession of straight rather than curly hair). These were the "Ancestral North Indians" and "Ancestral South Indians" that modern science has revealed. Out-of-India is little more than a nationalistic myth functioning as an antidote to this basic dichotomy, a way to imbue India's diverse citizens with a myth of common origins.

Yet, proponents of AIT (who have a non-trivial overlap with R1an enthusiasts) are also scratching their heads because of the 27 ancient South Asian males from South Asia studied in the preprint there is exactly one R1a, who also happened to live after the time of the Buddha and not during the Bronze Age.

Both OIT enthusiasts (who expected copious and abundant R1a in India and its environs since the Paleolithic) and AIT/R1an enthusiasts (who expected to see it come in c. 3,500BC) are bound to be disappointed.

Perhaps the R1a Indo-Aryans did come to South Asia in a conventional AIT time frame and they haven't been sampled. Or, maybe they were, indeed, there, but were not R1ans. Or, maybe both sides missed the bigger story which is that the Indo-Aryans (so closely associated with India today) were simply not there as early as people have thought. 

bioRxiv: doi: https://doi.org/10.1101/292581

The Genomic Formation of South and Central Asia

Vagheesh M Narasimhan, Nick J Patterson et al.

The genetic formation of Central and South Asian populations has been unclear because of an absence of ancient DNA. To address this gap, we generated genome-wide data from 362 ancient individuals, including the first from eastern Iran, Turan (Uzbekistan, Turkmenistan, and Tajikistan), Bronze Age Kazakhstan, and South Asia. Our data reveal a complex set of genetic sources that ultimately combined to form the ancestry of South Asians today. We document a southward spread of genetic ancestry from the Eurasian Steppe, correlating with the archaeologically known expansion of pastoralist sites from the Steppe to Turan in the Middle Bronze Age (2300-1500 BCE). These Steppe communities mixed genetically with peoples of the Bactria Margiana Archaeological Complex (BMAC) whom they encountered in Turan (primarily descendants of earlier agriculturalists of Iran), but there is no evidence that the main BMAC population contributed genetically to later South Asians. Instead, Steppe communities integrated farther south throughout the 2nd millennium BCE, and we show that they mixed with a more southern population that we document at multiple sites as outlier individuals exhibiting a distinctive mixture of ancestry related to Iranian agriculturalists and South Asian hunter-gathers. We call this group Indus Periphery because they were found at sites in cultural contact with the Indus Valley Civilization (IVC) and along its northern fringe, and also because they were genetically similar to post-IVC groups in the Swat Valley of Pakistan. By co-analyzing ancient DNA and genomic data from diverse present-day South Asians, we show that Indus Periphery-related people are the single most important source of ancestry in South Asia — consistent with the idea that the Indus Periphery individuals are providing us with the first direct look at the ancestry of peoples of the IVC — and we develop a model for the formation of present-day South Asians in terms of the temporally and geographically proximate sources of Indus Periphery-related, Steppe, and local South Asian hunter-gatherer-related ancestry. Our results show how ancestry from the Steppe genetically linked Europe and South Asia in the Bronze Age, and identifies the populations that almost certainly were responsible for spreading Indo-European languages across much of Eurasia.

Link

Y chromosome super-fathers

This is a very exciting paper. Most of these lineages are so young that there are good chances that their founders were figures from history or mythology.

The most interesting one is DC2 which was also found in south Siberian Kurgans, belongs to haplogroup R1a1 and is given an age of 3,284 years by the authors (with some almost impossibly wide confidence intervals). Based on its distribution, and if a Bronze Age date is right, it is difficult to see in it anything other than a patrilineage that was present in Proto-Indo-Iranians.

European Journal of Human Genetics advance online publication 14 January 2015; doi: 10.1038/ejhg.2014.285

Y-chromosome descent clusters and male differential reproductive success: young lineage expansions dominate Asian pastoral nomadic populations

Patricia Balaresque et al.

High-frequency microsatellite haplotypes of the male-specific Y-chromosome can signal past episodes of high reproductive success of particular men and their patrilineal descendants. Previously, two examples of such successful Y-lineages have been described in Asia, both associated with Altaic-speaking pastoral nomadic societies, and putatively linked to dynasties descending, respectively, from Genghis Khan and Giocangga. Here we surveyed a total of 5321 Y-chromosomes from 127 Asian populations, including novel Y-SNP and microsatellite data on 461 Central Asian males, to ask whether additional lineage expansions could be identified. Based on the most frequent eight-microsatellite haplotypes, we objectively defined 11 descent clusters (DCs), each within a specific haplogroup, that represent likely past instances of high male reproductive success, including the two previously identified cases. Analysis of the geographical patterns and ages of these DCs and their associated cultural characteristics showed that the most successful lineages are found both among sedentary agriculturalists and pastoral nomads, and expanded between 2100 BCE and 1100 CE. However, those with recent origins in the historical period are almost exclusively found in Altaic-speaking pastoral nomadic populations, which may reflect a shift in political organisation in pastoralist economies and a greater ease of transmission of Y-chromosomes through time and space facilitated by the use of horses.

Link

The place of Armenian in the Indo-European language family

Journal of Language Relationship • Вопросы языкового родства • 10 (2013) • Pp. 85—137

The place of Armenian in the Indo-European language family: the relationship with Greek and Indo-Iranian*

Hrach Martirosyan

The main purpose of this paper is to present lexical correspondences that unite Armenian with Greek and/or Indo-Iranian. They include shared innovations on the one hand, and isolated lexemes on the other. These two lexical corpora — lexical innovations on an inherited basis and isolated words — can be placed within the same temporal and spatial framework. After the Indo-European dispersal Proto-Armenian would have continued to come into contact with genetically related Indo-European dialects. Simultaneously, it would certainly also have been in contact with neighbouring non-Indo-European languages. A word can be of a substrate origin if it is characterized by: (1) limited geographical distribution; (2) unusual phonology and word formation; (3) characteristic semantics. The material presented here, albeit not exhaustive, allows to preliminarily conclude that Armenian, Greek, (Phrygian) and Indo-Iranian were dialectally close to each other. Within this hypothetical dialect group, Proto-Armenian was situated between Proto-Greek (to the west) and Proto-Indo-Iranian (to the east). The Indo-Iranians then moved eastwards, while the Proto-Armenians and Proto-Greeks remained in a common geographical region for a long period and developed numerous shared innovations. At a later stage, together or independently, they borrowed a large number of words from the Mediterranean / Pontic substrate language(s), mostly cultural and agricultural words, as well as animal and plant designations. On the other hand, Armenian shows a considerable number of lexical correspondences with European branches of the Indo-European language family, a large portion of which too should be explained in terms of substrate rather than Indo-European heritage.

Link (pdf)

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

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.

...

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.

...

“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.

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.