Harvard team helps Tamil Nadu lab with ancient DNA extraction and analysis

Konthagai is the burial site of Keeladi, the urban habitation site that is believed to have existed between 800 BCE to 300 CE as per the ASI

Tamil Nadu’s first Ancient DNA Lab at the Madurai Kamaraj University has opened its doors for a team from the world-renowned David Reich Lab to assist it in extracting DNA from 30 human samples collected from burial urns unearthed during excavations with “minimal damage” as part of the efforts to provide scientific evidence to archaeological findings.

The team led by Kendra Sirak, Senior Staff Scientist at David Reich Lab of the prestigious Harvard Medical School, US, is camping in the temple town of Madurai since February 13 to help the new lab analyse the samples collected from Konthagai, Sivagalai, Adichanallur, Mayiladumparai, and Kodumanal.

Konthagai is the burial site of Keeladi, the urban habitation site that is believed to have existed between 800 BCE to 300 CE as per a recent report submitted by Archaeological Survey of India (ASI) on the first two phases of the digging between 2014 and 2016. The new date derived by the ASI pushes the Sangam Era behind by another 500 years than it was earlier thought to be.

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The lab, which was inaugurated in November 2022, has begun preliminary work on conducting ancient DNA analysis on human, animal, and plant samples collected by the Tamil Nadu State Department of Archaeology (TNSDA) and ASI.

“We have begun the dry run. The samples are expectedly contaminated because they remained buried deep for centuries together. We are now being assisted by the Harvard team in extracting DNA from the human samples with minimal damage,” Professor G Kumaresan, Head, Department of Genetics, School of Biological Sciences, MKU, told DH.

“The team is helping us with the techniques they have successfully followed so far,” Kumaresan added. Sirak, who has so far analysed 500 DNA samples, is an expert in extracting DNA without disturbing the skull much and lessons from her will only help those at the MKU lab learn the tricks of the trade.

DNA is extracted mainly from teeth and petrous bones of the human samples which is used as the primary input. “DNA is generally extracted Calculus bone and from the root of the teeth. The extracted portion is then processed and computationally analysed. We will then compare the data of ancient DNA with global data to understand migration (of people) and the linkages with global populations,” Kumaresan added.

Sirak said her team was excited to collaborate with MKU team to study DNA from people who lived in Tamil Nadu long ago. “We will combine our expertise in hopes to generate authentic ancient DNA sequences that will help us to learn more about this very important part of India,” she told DH.

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The results of the DNA analysis generated by the MKU lab will be cross-checked by the Harvard team to ensure that the findings are right and questions are not raised over them since the samples are contaminated with bacterial DNA.

The results will then be compared with thousands of ancient and modern human genomes across the globe to explain in detail the ancient human migration and will be corroborated with Sangam Literature wherever possible.

Apart from ancient DNA, the MKU team is also exploring the proteins from skeletal remains and organic molecules from the potsherds of the offering pots. Some of the molecules retrieved so far includes Floxuridine (rice), Orotic Acid (milk), Myristic Acid (myristica), Ricinoleic Acid (castor) and cholesterol (animal fats).

The MKU lab has already sequenced about 1500 millions of DNA fragments from 20 samples of humans, animals, and plants. The DNA collected from the samples will help understand the agricultural and trade practices, while the organic molecular analysis would reveal the agricultural, cultural, and social practices in Tamil Nadu during 500 BC – 2500 BC.

The retrieval of rice is significant as pollen analyses of samples from the first phases of excavations in Keeladi found that excess production of rice contributed to the growth of the urban city while fertile land played “an active role” for the evolution of the habitation. The excess production of rice prompted the settlers to set sail in the seas to far-away land that are chronicled in several literature, the ASI report, which is yet to be made public, says.