India is one of the most popular countries in the world. It is home to the most diverse assemblages of people with different ethnic identities, languages, religions, castes, and customs. However, the country has been underrepresented in whole genome sequencing studies.
But finally, scientists have revealed the most detailed look yet of how this population took shape. In South Asia’s largest-ever modern whole-genome analysis, scientists have generated 2,762 high-coverage genomes from India, including individuals from most geographic regions, speakers of all major languages, and tribal and caste groups.
According to scientists, the study could offer a comprehensive survey of genetic variation in India.
Indians are primarily believed to be a mixture of three ancestral populations:
- Hunter-gatherers who lived on the land for tens of thousands of years.
- Farmers with Iranian ancestry who arrived sometime between 4700 and 3000 B.C.E.
- Herders from the central Eurasian steppe region swept into the area sometime after 3000 B.C.E., perhaps between 1900 and 1500 B.C.E.
In a recent study, Priya Moorjani and her team from the University of California, Berkeley, confirmed those ancestral groups’ identities. Using data from the Longitudinal Aging Study in India–Diagnostic Assessment of Dementia (LASI-DAD), they examined over 2700 Indian people’s DNA, covering many regions, languages, tribes, and social groups.
Using ancient DNA from Iranian-rooted groups, the researchers were able to piece together the history of the Iranian farmers who migrated to India. After that, they ran simulations to find whose genes most closely resembled those of modern Indians. The closest match they discovered were farmers from Sarazm, an ancient farming center in what is now Tajikistan. These farmers kept livestock, farmed wheat and barley, and traded throughout Eurasia.
Intriguingly, one of the ancient Sarazm residents had Indian ancestry, while another was buried wearing bracelets resembling those from ancient India. This indicates a relationship between the two cultures and suggests that Sarazm and India mingled.
Michael Frachetti, an archaeologist, believes that this discovery is important. He thinks Sarazm greatly aided the introduction of farming, livestock, and DNA into Kashmir and northwest India.
Still, certain aspects of ancestry remain unclear, such as those originating in the steppe. Gyaneshwer Chaubey, a biological anthropologist, believes that to comprehend all of the source groups fully, we need additional ancient DNA samples from India.
Moorjani and her colleagues made some unexpected findings regarding prehistoric migrations. It’s been debated whether stone tools discovered in India approximately 80,000 years ago were created by humans and whether they left genetic traces in contemporary individuals. It’s been challenging to determine for sure without remnants.
According to current research, these early toolmakers did impact extant communities. Based on population changes and genetic mutation calculations, the researchers estimate that the ancestors of current Indians originated from a single migration out of Africa about 50,000 years ago.
Additionally, they discovered that, like Europeans, modern Indians may trace between 1% and 2% of their lineage back to Neanderthals and Denisovans. However, compared to other global populations, Indians possess a greater variety of these old genes.
The 2700 Indian genomes contained over 90% of all known Neanderthal genes that have infiltrated human populations. That is roughly half of what was found in a comparable study that examined over 27,000 genomes and found Neanderthal DNA in Icelanders. It’s too early to determine what evolutionary advantages the descendants of Neanderthals and Denisovans may have enjoyed. Still, the researchers have discovered several new candidates for genes carried by these extinct species.
Moorjani says ancient humans might have encountered and mated with a relatively large, genetically diverse population of our archaic cousins living on the subcontinent—although no fossils of those archaic cousins have been found. Another possibility is that India’s vast geographical boundaries and close kin–marrying traditions preserved different segments of Neanderthal DNA than on other continents.
Journal Reference:
- Elise Kerdoncuff, Laurits Skov, Nick Patterson, Wei Zhao, Yuk Yee Lueng, Gerard D. Schellenberg, Jennifer A. Smith, Sharmistha Dey, Andrea Ganna, AB Dey, Sharon L.R. Kardia, Jinkook Lee, Priya Moorjani. 50,000 years of Evolutionary History of India: Insights from ∼2,700 Whole Genome Sequences. BioRxiv. DOI: 10.1101/2024.02.15.580575