Early DNA from this ancient civilization reveals the ancestry of modern South Asians

Long before climate change forced them to abandon their thriving towns, a group of hunter-gatherers settled in the Indus Valley as farmers, leading to the creation of one of world’s first large-scale urban societies, with booming economies and long-distance trade.

The Harappan civilization, which peaked around 2600 to 1900 BCE, boasted pioneering town planning, elaborate drainage systems, and granaries. They were a multicultural society and even had their own standardized system of weights and measures. But what prompted these people to drastically change their homelessness habits?

“A common view is that agriculture came to South Asia through the large-scale westward movement of Iranian farmers,” geneticist David Reich of Harvard University told ScienceAlert.

Hints of Iranian ancestry among modern South Asians have led scholars to suspect that when these ancient Iranians emigrated from fertile crescent in the Middle East (where the first traces of agriculture were found), they took with them their new agricultural way of life.

But a team of researchers led by archaeologist Vasant Shinde of Deccan College in India has just turned the timeline of this scenario upside down.

For the first time, the team has successfully sequenced the genome of an individual found buried in the remains of this ancient civilization, in a cemetery at the Rakhigarhi site in Haryana, India.

(Vasant Shinde Postgraduate Research Institute/Deccan College)

Above: Globular jar found near the head of the skeleton which yielded ancient DNA.

Although this site has long attracted interest, the warm climate of South Asia provides ideal conditions for degrading biological material, leaving little intact DNA to extract. But the team managed to find enough DNA in the 4,000-5,000-year-old remains by resampling the skeleton more than 100 times and pooling the results.

Their analysis showed that the genes associated with this individual’s Iranian ancestry came from before the time when farmers and hunter-gatherers in the region separated from each other. This individual’s Iranian ancestors left before agriculture spread across Iran, Reich said.

“Our study indicates that agriculture originated in South Asia either through local invention or adoption of ideas from Western neighbors (cultural communication) or a combination,” he said.

By comparing the genome of this individual with those of another study about to be Posted in Sciencethe team also provided some information on trade and movement between these ancient civilizations.

Eleven of 523 individuals genetically sampled from Gonur in Turkmenistan and Shahr-i-Sokhta in Iran belonged to the same genetic group as the South Asian individual.

“This suggests that these 11 people were recent migrants or descendants of migrants from the Indus Valley Civilization,” Reich said, which is supported by the cultural connections observed between the sites.

Map of the Indus Valley Civilization and other important Harappan sites.  (Shinde et al. Cell, 2019)Map of the Indus Valley Civilization and other important Harappan sites. (Shinde et al. Cell2019)

“The Harappans were one of the earliest civilizations of the ancient world and a major source of Indian culture and traditions, and yet it is a mystery how they related both to later peoples and to their contemporaries”, Shinde explained.

While we now know them through their urban remnants and 4,000-year-old relics, this newly sequenced genome has revealed that the ancient Harappan civilization has a far greater legacy.

“This individual buried in an Indus Valley Civilization cemetery was part of a population that is the greatest source of ancestry for nearly all South Asians today,” Reich explained.

Of course, there isn’t much to learn from an individual’s genome, so the researchers hope the technique they used will allow them to study the genomes of many other individuals from the Harappa civilization to create a broader picture of this rich history.

“We also want to study individuals from other time periods and geographic locations in South Asia,” Reich said, “particularly just before and after the advent of agriculture to understand to what extent genetic change accompanied these economic changes”.

Their findings were Posted in Cell.