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Ancient DNA Studies Untangle Genetic History of Indus River Valley Civilization

NEW YORK – Two new ancient DNA studies have provided a refined look at historical population dynamics in parts of Asia and the Middle East, particularly involving the Indus Valley or Harappan civilization — a group centered in the northwestern portion of South Asia some 3,900 to 4,600 years ago that contributed significant ancestry to present-day South Asians.

"The Harappans were one of the earliest civilizations of the ancient world and a major source of Indian culture and traditions, and yet it has been a mystery how they related both to later people as well as to their contemporaries," Deccan College archaeologist Vasant Shinde said in a statement. 

Shinde was co-first author on a study appearing online today in Cell. There, he and his colleagues successfully sequenced one individual from the Indus Valley Civilization (IVC), comparing it to other ancient and modern samples.

Their results revealed ancestry from an ancient Iranian population and a group of hunter-gatherers from Southeast Asia in the IVC representative. That individual appeared to be genetically similar to a several ancient individuals sequenced for another study published today from sites in Iran and southcentral Asia. The individuals in that cluster did not have significant ancestry from Steppe pastoralists or Anatolian farmers, providing still more clues about populations that did — or did not — contribute to IVC genetics.

That analysis also offered clues to the advent of agriculture in South Asia, suggesting it first arose there when hunter-gatherers took on farming practices through cultural transmission or by developing it independently, rather than appearing in the region as a result of migration from the Fertile Crescent.

"[S]ampled ancient genomes from the Iranian plateau and IVC descend from different groups of hunter-gatherers who began farming without being connected by substantial movement of people," Shinde and his co-authors wrote.

To overcome poor DNA preservation caused by the region's hot climate, the team started by using error rate reduction strategies, enrichment, and targeted short read sequencing to screen for usable DNA in 61 skeletal samples from the Rakhigarhi cemetery site in India. From there, the group focused in on a subset of libraries, which were enriched at more than 1.2 million SNPs before being subjected to additional sequencing.

Using this approach, the researchers generated sequences from dozens of libraries from a skeleton known as I6113, providing information at more than 208,111 SNPs. After quality control steps, they were left with 31,760 informative SNPs that were used in their subsequent analyses.

"While each of the individual datasets did not produce enough DNA, pooling them resulted in sufficient genetic data to learn about population history," co-senior author David Reich, a genetics researcher affiliated with Harvard Medical School and the Broad Institute, said in a statement.

Along with other analyses of I6113, the team found that the ancient individual had a large ancestry component from Iran, while clustering with 11 samples from Iran and Turkmenistan that Reich, Shinde, and their colleagues sequenced for a study published online today in Science.

For that analysis, a team from Harvard, the Broad Institute, Washington University, and other centers around the world sequenced 523 ancient samples, including 182 samples from Iran and Central Asia, 209 Steppe samples from Kazakhstan and Russia, and 132 northern Pakistan samples. It also did additional sequencing on 19 ancient individuals analyzed previously to improve the quality of those genome profiles.

Together, the genetic data made it possible for researchers to tease out sources of ancestry in individuals living in South Asia today. In southern India today, for example, the researchers saw signs of ancestry stemming from the IVC, and from populations found further southeast that IVC descendants encountered. Another ancestral population appeared to include individuals descended from IVC individuals who met and mixed with Steppe pastoralists.

That data suggested that "after the fall of the IVC, several migrations into South Asia led to the formation of two distinct populations therein, one more ancestral to modern North Indians and the other more ancestral to modern South Asians," University of California at Santa Cruz ecology and evolutionary biology researchers Beth Shapiro and Nathan Schaefer, who were not involved in the studies, wrote in a related perspectives article in Science. "The ancestry of most present-day Indians is probably composed of these two populations along with a handful of others."

Because the Iranian ancestry component appears to come from an ancient population that split from other Iranian populations more than 12,000 years ago — before farming was established in the Fertile Crescent — authors of the new studies reasoned that farming probably did not arrive in India as a result of migration by farming groups, but likely arose in parallel as previously reported in parts of Europe.

"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," authors of the Cell study explained. "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 in these regions."

The researchers also explored the relationships between the population migrations reflected in the ancient genetic and archeological data and the transmission of prominent language groups in South and Central Asia and beyond, hinting that well-known Indo-European languages may have arrived in South Asia with populations from Eastern Europe and Central Asia rather than moving into the region with Anatolian farmers, who do not seem to have contributed significant ancestry to the IVC.

"These studies speak to two of the most profound cultural transformations in ancient Eurasia — the transition from hunting and gathering to farming and the spread of Indo-European languages, which are spoken today from the British Isles to South Asia — along with the movement of people," Vagheesh Narasimhan, a postdoctoral fellow in Reich's lab and co-first author on the Cell and Science papers, said in a statement.

Despite the information gleaned from the 12 ancient individuals with ties to the IVC, though, the authors warned that additional analyses are needed to complement the current findings, given the importance and complexity of the civilization.