DNA analysis of Harappan skeleton from Rakhigarhi: Thin evidence

The scientific paper on the DNA analysis of the Harappan skeleton from Rakhigarhi claims that there was no Aryan invasion and no Aryan migration and that all the developments right from the hunting-gathering stage to modern times in South Asia were done by indigenous people. An agenda-setting for indigeneity of populations, ideas and civilisational traits may be embeded in the paper.

Published : Oct 01, 2019 06:00 IST

Prof. Vasant Shinde and Dr Niraj Rai during the release of the results of the DNA analysis to the media in New Delhi on September 6.

Prof. Vasant Shinde and Dr Niraj Rai during the release of the results of the DNA analysis to the media in New Delhi on September 6.

IN early September, the newspapers reported with considerable excitement the publication of a scientific paper on the DNA analysis on an individual skeleton found in the Harappan site of Rakhigarhi in Hisar district of Haryana. The analysis was conducted by a fairly large group of geneticists and a few archaeologists. The deceptive titles of some of these news reports, particularly the reference to the “Aryan invasion theory” being debunked, has caught the eyes of the interested public. I, and I am sure historians, too, received phone calls asking for comments. I have been told there is much social media traction for this story. I am neither a geneticist nor an archaeologist like the 28 authors of the scientific paper on gene analysis, but as a historian familiar with the debates and the issues involved, I find it necessary to address some concerns that have been raised by several academics. It appears that to separate the wheat from the chaff, we first need to critically look at the paper and then at the media reports.

The report in The Economic Times (published on September 6) has quoted Professor Vasant Shinde, the lead author of the paper in the scientific journal Cell (September 5, 2019), as saying: “The paper indicates that there was no Aryan invasion and no Aryan migration and that all the developments right from the hunting-gathering stage to modern times in South Asia were done by indigenous people.”

It is indigeneity that seems to be the catchword and the great new discovery that the scholar seems to be excited about. I wonder whether the next step will be to go back to the issue of polygenesis of modern humans, to debunk the “out of Africa” thesis.

Let us move to the paper published in Cell titled “An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers”. The main arguments in this paper may be summed up as follows: excavations at the site of Rakhigarhi have revealed a Mature Harappan context dated to about 2800-2300 BCE; the sampling of the skeletal remains was done at this site, of what appears to be a woman with the genetic identification code I6113 and the archaeological skeletal code RGR7.3, BR-01, HS-02. the principal-component analysis technique involving a comparison with similar data from 11 other skeletal remains in two sites [Gonur (3) and Shahr-i-Sokhta (8)] was undertaken. Cutting through the details of techniques and analysis, it appears that “this individual is not only significantly different in ancestry from the primary ancient populations of Bronze Age Gonur and Shahr-i-Sokhta but also does not fall within the variation of present-day South Asians”, according to the authors of the study.

We are further told that the 11 samples that were chosen for comparison were from among 44 individuals because of a distinctive ancestry profile, where the Indus Periphery Cline (IPC) saw a match with the Indus Valley Cline (IVC). (Cline refers to a gradual change of a phenotype over a long period of time in a region due to environmental variability, from the Greek meaning “to lean”.) Hence, the authors postulated the possibility that there was outward migration from the IVC to Iran and Turkmenistan, as the 12 skeletal remains were seen as belonging to the same cline.

Iranian and Steppe ancestry

Further, it was found that the I6113 ancestry was closely linked to Iranian ancestry and not at all to Steppe ancestry. Since modern populations of Iran and South Asia have a high component of Steppe ancestry and almost none of the ancient Iranian one, this reveals a significant change post the IVC period. There are two things that immediately strike one in this argument: the authors seem to be aware that the IVC reveals a flourishing cosmopolitan urban culture. The assumption that one individual would represent the whole population of that city, and indeed the entire civilisation, seems distinctly at odds with the otherwise painstaking methodology and genetic analysis. At best, it may be extrapolated from the data that a section of the population in Rakhigarhi (estimated IVC population at its peak is about four to six million) had links with a section (only 11 of 44 match the type from Rakhigarhi) in the IPC.

Linked to this, the issue of movement out of the IVC is quite surprising and seems to be beyond the brief of the data analysis and analysts. Enough is known about the close trading contacts between Mesopotamia and the Indus civilisations, and several artefacts attesting to this have been found. There is also written evidence from Mesopotamia to corroborate this. So, instead of presuming that the IPC received out-migration from the IVC, why can we not suggest the reverse?

A second line of argument draws from the comparison of the Iranian ancestry in terms of DNA data from c.10,000-8,000 BCE. It has been argued that there is a closer match with the data from the earlier date, implying that the ancestors of the IVC cline were hunter-gatherers rather than farmers. The second postulation, hence, is that farming began in the IVC independently from the West Asian experience. Where the Anatolian farmer-related ancestry is present (negligible but present, we are told), it came in via the Steppe ancestry in the post-IVC period, which became the dominant strain in modern South Asians.

These results are significant not because they are conclusive, or even convincing as they stand, but because they reveal the complexity of social and cultural human evolution in prehistoric times. The data pool used in the paper generating all this excitement is too limited as the ancient DNA is lacking in a substantive sense. Where earlier we were informed in a synthetic study by the well-known geneticist David Reich (one of the lead authors of this study as well) that the Iranian movement into the east occurred around 9,000 years ago (2018), the scholars of the Cell article are trying to establish that the movement of people from the Near East actually occurred around 12,000 years ago. This is striking because Reich in his interesting book Who Are We, and How We Got Here , published in 2018, points out that his Indian collaborators (and mind you the latter are geneticists, not archaeologists or historians) were strongly opposed to his understanding of the movement of west Eurasians into the Indian subcontinent. They apparently suggested that such a revelation could be politically explosive. He also mentions that his collaborators were making the opposite proposition—migration “of Indians to the Near East and Europe”—without any evidence whatsoever. Reich’s silence in newspaper reports on this shift in his understanding may be taken as his new-found agreement of the model propounded by his Indian collaborators as far back as 2008, unless he tells us otherwise. Since he strongly expressed his feeling at the time that political considerations were coming in the way of important patterns of people’s movements and intermixing being revealed, do we deduce that he changed his mind owing to the political views (he had earlier mentioned that perhaps one should be more “sensitive”), or is it a purely academic opinion based on the arguably thin evidence as cited in the research article?

The article in question does allow for ambiguities, as seen in the concluding discussion: “These findings suggest that in South Asia as in Europe, the advent of farming was not mediated directly by descendants of the world’s first farmers who lived in the Fertile Crescent. Instead, populations of hunter-gatherers—in Eastern Anatolia in the case of Europe… and in a yet-unsampled location in the case of South Asia—began farming without large-scale movement of people into these regions. This does not mean that movements of people were unimportant in the introduction of farming economies at a later date; for example, ancient DNA studies have documented that the introduction of farming to Europe after 6500 BCE was mediated by a large-scale expansion of Western Anatolian farmers who descended largely from early hunter-gatherers of Western Anatolia.... It is possible that in an analogous way, an early farming population expanded dramatically within South Asia, causing large-scale population turnovers that helped to spread this economy within the region. Whether this occurred is still unverified and could be determined through ancient DNA studies from just before and after the farming transitions in South Asia ” (emphasis added throughout).

So, all the hullaballoo about outward migration or the indigenous development of farming is hanging by a thread. Also, some important studies on the transitional hunter-gatherer Natufian cultural sites in the Fertile Crescent region like Ain-Mallaha have indicated that the knowledge of agriculture/cultivation was older than generally believed, although its manifestation as a primary subsistence strategy may have occurred later. The hunter-gatherer societies were aware of the value of specific flora, the evidence of it being the lunate tools with plant stains that have been found, the pestles and mortars, and storage pits and baskets. That these proto-cultivation efforts are what led to the sustained use and development of agricultural knowledge and technique is an accepted argument. Also, recent researches have suggested a revised chronology for the Pre-Pottery Neolithic in the Levant going as far back as 12,000 years ago. So, even if we accept the Eurasian migration occurring at an early date, it does not necessarily mean these were not agriculturists, or those who knew the value of agriculture.

The final paragraph of the Cell paper is where many newspaper reports and WhatsApp messages seem to be getting their titles from—the reference to languages spreading to India via Central Asia in the early second millennium BCE. Again, the research paper carefully avoids using the term Aryan or even Indo-Aryan, even though it does refer to Indo-European, Indo-Iranian and Balto-Slavic language families. The distinctive genetic compass of Ancestral North Indians (ANI) and Ancestral South Indians (ASI) studied by several geneticists over the past decades has indicated several complex mixtures occurring within and across these groups in deep time, is elided here.

Also, the rigorous linguistic analysis of the Avesta, the Vedas and other texts that have lent weight to the language family theory is missing. Hence, the complexity of the issue is missed—people may carry languages but they also imbibe them; further, synthetic language evolution, marked by mixing of language traditions, is something that is clearly out of the domain of discussion here.

In a separate paper in the journal Science on September 6, authored by most of the same set and including around 70 more, the issue missing above is foregrounded. Vagheesh M. Narasimhan et al in “The Formation of Human Populations in South and Central Asia” draw our attention to their analysis of 523 individuals “mostly from Central Asia and northern-most South Asia.” The diverse temporal and spatial range involved sampling from the past 8,000 years DNA of populations living in 19 sites in Iran and Turan (c. 12,000-1 BCE), two sites of western Siberia (c. 6400-3900 BCE), 56 sites from the Central Steppes (3400-800 BCE), and 12 sites in northern-most South Asia, and Swat and Chitral regions of Pakistan, corresponding to the map of north and north-western British India (c. 1200 BCE-1700 CE). The main arguments in this paper are as follows: the ancestry in the region broadly known as South Asia in the Holocene was characterised by at least three genetic gradients;one of these was the IPC consisting of people with different proportions of Iranian farmer and ancient ASI-related ancestry; the IPC had an affinity with the IVC before 2000 BCE; the ASI derived from this cline after 2000 BCE; between 2000 and 1000 BCE, the Central-Steppe-Middle and Late Bronze Age ancestry expanded towards South Asia; a mixture of CS-MLBA with the IPC led to the formation of the Steppe Cline; the ANI developed from the Steppe Cline at this time on the basis of the Swat Valley evidence; subsequently there is diverse and variable intermixing of ANI and the ASI in South Asia. Important observations made include, “these results show that neither of the two primary source populations of the Modern Indian Cline, the ANI or ASI, was fully formed before the turn of the second millennium BCE”; and “through formal modelling, we demonstrate that it is this contribution of Indus Periphery Cline people to later South Asians, rather than westward gene flow bringing an ancestry unique to South Asia onto the Iranian plateau , that explains the high degree of shared ancestry between present-day South Asians and early Holocene Iranians.”

Some authors who have been going to the press regarding the findings may reread this, for clearly this statement suggests that there is no westward gene flow from South Asia. They may also look up the term “indigenous”, as their public statements and the discussion mentioned above are at variance.

The cline (pun intended) in this article is towards movements and assimilations, big and small, that go into the making of the genetic map of the Indian subcontinent. Further, there is little to warrant the rather irresponsible statements being made in newspaper reports about Aryans/Aryan invasions. Much has been said about how flawed such theories were, since the 1950s. I seriously doubt that the main contributors to these scholarly papers would wish to be embroiled in what is a wasteful and unwarranted discussion. The spread of Indo-European languages is clearly discussed as an occurrence coinciding in South Asia with the post-2000 BCE movements and mixtures. Surprisingly, there is no mention of the remarkable work of linguists and Sanskritists such as Michael Witzel, Fritz Staal and Stephanie Jamison, who have contributed immensely to our understanding of the Indo-Aryan language culture through a close reading of the Vedic texts, nor of the historians R.S. Sharma, Romila Thapar and D.N. Jha and archaeologists such as J.P. Mallory who have analysed the contexts in which the Vedas appear to have been composed. The deliberate silence on certain issues such as the correspondence materially and in other ways with the Bactro Margiana Arachaeological Complex, or overplaying of continuity on the basis of the study of genetic data seems suspect. It is inexplicable how the geneticists’ toolkit can, without the disciplinary insights, independently include linguistic and contextual analysis to make such sweeping generalisations.

It is suggested in the Science article that non-IPC ASI ancestors were the carriers of the proto-Dravidian language from within peninsular India. Is all of this discussion new? No, these have been a part of vehement discussions by archaeologists, historians, linguists and anthropologists for several decades now.

tentative findings

Archaeologists such as Jonathan M. Kenoyer, Shereen Ratnagar and Rita P. Wright have made important contributions to the study of the Harappan civilisation, but they do not even find a place in the bibliography, and the linguists and historians mentioned above are also missing. Are the findings conclusive? No. The findings here are tentative to say the least. They do suggest that people were moving, not necessarily as invaders or in hordes, and that they carried certain cultural traits that may have been assimilated. On the other hand, it is obvious that even without significant movements, traits and ideas, including subsistence strategies, could have travelled. Here, palynologists need to be brought to the table, as the zooarchaeological and archaeobotanical records reveal very important traces of movements and harnessing of cultigens, germane to the discussions about the origins of farming. Further, the work of scholars in the non-English-speaking world, particularly from Russia and China, must also be accessed to make better sense of the entire issue. In fact, the pioneering work of Elena Kuzmina, which is now available in English translations, should be seriously studied by those interested in the Indo-European language family and the Steppe cultures.

Is there anything at all important in these studies for those studying the subcontinent’s history? Reich humorously refers to the geneticists as the barbarians who arrived late on the scene in the studies and discussion on the human past. What then is different and significant about the present discussion and debate is the letting of the barbarians into the room, and finding that there are interesting possibilities that they proffer with regard to who we are. But if we are looking for definitive answers, my understanding would be that the muddied waters have got muddier, though there are also present some new avenues for solution of questions that have remained vexed up until now. To see the genetic evidence as clinching is reductive and does not take into consideration cultural accretion and contextual transformations.

An agenda-setting for indigeneity of populations, ideas and civilisational traits may be embedded in these studies. But by themselves these are meaningless for the analysis of sociocultural development, and we can only hope that in the future, even as we have more valid substantial and substantive genetic data, the trivialisation of the issues of historical development cease to find so much traction.

Dr R. Mahalakshmi is Professor at the Centre for Historical Studies

in Jawaharlal Nehru University, New Delhi.

Sign in to Unlock member-only benefits!
  • Bookmark stories to read later.
  • Comment on stories to start conversations.
  • Subscribe to our newsletters.
  • Get notified about discounts and offers to our products.
Sign in


Comments have to be in English, and in full sentences. They cannot be abusive or personal. Please abide to our community guidelines for posting your comment