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

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.”