Indus Valley people did not have genetic contribution from the steppes: Head of Ancient DNA Lab testing Rakhigarhi samples

By HARTOSH SINGH BAL | 27 April 2018

Niraj Rai, the head of the Ancient DNA Laboratory at Lucknow’s Birbal Sahni Institute of Palaeosciences (BSIP), where the DNA samples from the Harappan site of Rakhigarhi in Haryana are being analysed, has revealed that a forthcoming paper on the work will show that there is no steppe contribution to the DNA of the Harappan people. This result comes close to settling one of the most important outstanding issues regarding the Indian past—the question concerning the possible migration of Indo-European language speakers from the Pontic steppe in Central Asia into north-west India.

“It will show that there is no steppe contribution to the Indus Valley DNA,” Rai said. “The Indus Valley people were indigenous, but in the sense that their DNA had contributions from near eastern Iranian farmers mixed with the Indian hunter-gatherer DNA, that is still reflected in the DNA of the people of the Andaman islands.” He added that the paper based on the examination of the Rakhigarhi samples would soon be published on bioRxiv (pronounced “bio-archive”), a preprint repository of papers in the life sciences.

The Rakhigarhi samples belonged to individuals who lived approximately 4,600 years ago, during the peak of the Indus Valley Civilisation. The absence of steppe DNA markers in the samples indicates that, at that point in time, there had been no intermingling between the steppe pastoralists and the population of the Indus Valley Civilisation.

The bones of four people were excavated in Rakhigarhi. According to Rai, three samples from Rakhigarhi were morphologically well preserved, but the DNA that was extracted from them was highly degraded. “But we were able to obtain a good sample,” he said. The excavation and extraction of samples has been carried out under Vasant Shinde, a senior archaeologist who is the vice-chancellor at the Deccan College Post Graduate and Research Institute in Pune. The Rakhigarhi study, Rai said, provides direct evidence for the claims of a paper published in preprint on bioRxiv in March 2018, which outlines a comprehensive model for the settlement of different populations within the subcontinent.

Shinde and Rai are among 91 co-authors of this March 2018 paper, titled “The Genomic Formation of South and Central Asia.” The study was carried out at the laboratory for ancient DNA at the Harvard Medical School, which is run by David Reich, a geneticist and a professor in the college’s department of genetics. The model proposed in the paper elaborates on a 2009 paper from the lab that suggests the current population of India is largely an admixture in varying proportion of two older populations—the Ancestral North Indians (ANI) and the Ancestral South Indians (ASI).


The March 2018 paper posits two migrations into South Asia—the first, by Iranian farmers less than 9,000 years ago, and the second, by the steppe pastoralists less than 5,000 years ago. The first migration mingled with the pre-existing hunter-gatherer population of South Asia and gave rise to what the authors’ term the Indus Periphery People—the latest study clarifies that this represents the population of the Indus Valley Civilisation, and not another distinct population. The second migration of steppe people, which coincided with the decline of the Indus Valley Civilization, around 4,000 years ago, mixed with the Indus Periphery People to give rise to the ANI population. Simultaneously, the Indus Periphery People also migrated southward and further mixed with the indigenous hunter-gatherers who lived in the area to give rise to the ASI population. Most Indians today are the subsequent admixture of the ANI and the ASI populations.

The paper, however, does not include a study of any ancient DNA from the Indus Valley people, a lacuna that will be filled only when the paper Rai referred to becomes available. In its absence, the study that was published in the March 2018 paper used a stand-in population, whose DNA was based on that of three outlier samples of ancient DNA from between 4000 and 5000 years ago, which were found in the eastern Iranian region, and whose DNA profile resembles that of 41 other samples from the Swat site of the Indus Valley from a millennium later, after its decline.

Rai said that he and his team at the BSIP agreed to be a part of the March 2018 paper “after two years of intense discussion and analysis of our own data sets.” He continued, “There is no question of the model being flawed. It is a most solid piece of work—no new study will overturn it. Our own work which will be out very soon provides solid evidence for the model.”

Rai had earlier told Open magazine that the male “Y chromosome R1a genetic marker is missing in the Rakhigarhi sample.” The R1a is seen as a marker of Indo-European speakers, but its absence in a single sample is not significant—it is the wider analysis of the entire genome that is important in the context of this sample.

The work by Rai and his team will provide direct evidence for the model proposed by the March 2018 paper from the Reich Lab, which has bearing on a number of questions of great interest pertaining to the Indian past. The preprint states, “Our results also shed light on the question of the origins of the subset of Indo-European languages spoken in India and Europe. It is striking that the great majority of Indo-European speakers today living in both Europe and South Asia harbor large fractions of ancestry related to … Steppe pastoralists … suggesting that ‘Late Proto-Indo-European’—the language ancestral to all modern Indo- European languages—was the language” of the steppe pastoralist population.

In other words, the preprint observes that the migration from the steppes to South Asia was the source of the Indo-European languages in the subcontinent. Commenting on this, Rai said, “any model of migration of Indo-Europeans from South Asia simply cannot fit the data that is now available.”

Hartosh Singh Bal is the political editor at The Caravan, and is the author of Waters Close Over Us: A Journey Along the Narmada. He was formerly the political editor at Open magazine.


48 thoughts on “Indus Valley people did not have genetic contribution from the steppes: Head of Ancient DNA Lab testing Rakhigarhi samples”

andaman people got isolated and indian genes got evovled a lot after ”andaman hunter gatherers” stage. this study just proves that people make their own conclusions based on their own biases.

I think one major error in the interpretation of these results could be the assumption that the migration of R1a indicates the spread of IE languages. This may not be true, given that Subhash Kak has already shown that Brahmi script evolved out of the Indus script (there are numerous other lines of evidence to show that IVC was Vedic). So the question is, how did IE spread, if not through R1a migration. The answer might be I1a migration, which took place out of India, via sea and coastal routes. This paper makes a case for the same:

No, he means the “out of India” migration model for profiling the past of the Indo-European speakers, which is the favourite model for Hindutvists.

Why is Rai deliberately trying to link events that have no link? Indus Valley and Steppes migration are not linked. The Rakhigarhi DNA is from 2500 BC. The widely agreed dates for the Aryan migration are 2000 BC earliest. That is a full 500 years AFTER the DNA of Rakhigarhi samples.

@Ajay Joshi “In other words, the preprint observes that the migration from the steppes to South Asia was the source of the Indo-European languages in the subcontinent. Commenting on this, Rai said, “any model of migration of Indo-Europeans from South Asia simply cannot fit the data that is now available.”””

It means that Migration from out of india into india cannot fit this current data…That means Aryan invasion is myth

The concern I have is this whole study and interpretations are based on DNA derived from one sample skeleton. If so, how much reliable and accurate are these results and interpretations? All most all other related studies published are based on tens of samples.

One of the co-author, VS Shinde has published an article (1) very recently (2018), According to this article, 46 sets of complete or partial skeletal remains were excavated at Rakhigarhi cemetery. Out of these 46 samples, there were 9 individuals with more than half of the skull preserved, 14 individuals with pelvic bones remained and fully 12 cases were indeterminate due to skeletal incompleteness or poor preservation. Why couldn’t they try more than 3 samples? DNA contamination? Hopefully, we will be able to see more details in the article when it is published.

1. Shinde VS, Kim YJ, Woo EJ, Jadhav N, Waghmare P, Yadav Y, et al. (2018) Archaeological and anthropological studies on the Harappan cemetery of Rakhigarhi, India. PLoS ONE 13(2): e0192299. doi:10.1371/journal.pone.0192299


Here is one question. The study reported by mscientists from the University of Cambridge have shown that lactose tolerant associated mutation, 13910T, that is present in high frequency in India are originally found in Europeans. Interestingly, this mutation is more prevalent in North and West Indians than South and Northeast Indians, who are more lactose intolerant. This mutation is originated in Europe some 7,500 years ago. This study has also found that in addition to the mutation, the nearby genetic regions of the mutation has the same origin as that found in Europeans. Thus, the data from this study shows there was migration between Europe and India (1). What would be relevance of this study to the current report that contradicts the smresukts If the Cambridge University study and similar studies by other groups?
Low prevalence of lactase persistence in Neolithic South-West Europe. –
Mol Biol Evol. 2012 Jan;29(1):249-60.

So here is my conclusion. I know this is very politically charged, but truth is more important. Iranians and Indigenous hunter gatherer people mixed together forming the IVC. Later the Steppe pastoral people came at the end of IVC. A branch of Ivc people moved south and other branch spread out in north India. The north Indian IVC group mingled more with the Steppe pastorals who came later, while the south Indian IVC branch mingled more with the Indigenous/SA hunter gatherers.

This is the most objective take on this issue. Did pastoral people bring Vedic culture etc are just assumptions. you can spin it in any direction as for now. This is the tip of iceberg & first researches of its kind, in coming years this will be more clear.

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