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NEW DELHI: The timeline of how and when modern humans populated India is somewhat sketchy. While most Indians can trace their ancestry to more than one lineage, the origin of some of these ancient populations remains unclear, with India largely underrepresented in whole genome sequencing studies worldwide.
A new study, currently on a preprint server, has now reconstructed part of the evolutionary history of Indians after examining 2,762 genomes representing diverse population groups. Among its conclusions:
* All Indians have 1-2% Neanderthal and Denisovan ancestry, but it is not clear if and when these pre-human species ever populated India.
* Today, most Indians derive their ancestry from three groups: South Asian hunter-gatherers, farmers with Iranian ancestry (sometime between 4700 and 3000 BCE) and herders from the central Eurasian steppe region (around 3000 BCE).
* Much of the genetic variation in Indians stems from a single major migration out of Africa, around 50,000 years ago.
* While examining the ancestry derived from Iranian farmers, genetic links pointed to an ancient region called Sarazm. Interestingly, one individual from Sarazm had Andamanese-related ancestry, indicating a possible gene flow in the other direction too.
“We are slowly building the timeline of India and both present-day and ancient DNA samples have transformed our understanding,” said the study’s lead author, Dr Priya Moorjani, a molecular and cell biologist at the University of California, Berkeley.
Humans and hominins
Neanderthals, whose fossils were first discovered in Germany in 1856, lived in Europe and Western Asia starting around 400,000 years ago, and went extinct 30,000 years ago. Denisovans, a species discovered in 2008 in Siberia, are believed to have walked Eurasia around the same time as the Neanderthals, and coexisted with humans before going extinct.
In research that won him the Nobel Prize for Physiology or Medicine in 2022, the Swedish geneticist Svante Pääbo identified Denisovans as a distinct species, besides showing that Neanderthals interbred with humans during the time they coexisted.
It is not yet clear if Neanderthals coexisted with the earliest humans in India, but modern Indians do carry most of the Neanderthal genes that exist in other human populations.
“We infer that all Indians have 1-2% Neanderthal and ~0.1-0.2% Denisovan ancestry. Notably, a majority of the Neanderthal ancestry that exists today in present-day individuals (e.g., East Asians, Europeans, Oceanians and South Asians) is found in India, while other worldwide populations retain only a subset of this variation,” Moorjani said.
“Indians also harbour the most Denisovan ancestry among Eurasian populations. This may suggest that Neanderthals and Denisovans lived in India… though without direct fossil evidence, it remains an open question,” she said.
What makes the question all the more intriguing is the discovery of ancient stone tools in Attirampakkam village of Tamil Nadu. In 2018, a paper published in Nature (Akhilesh et al) dated these tools to 3.85 lakh—1.72 lakh years ago. With no human fossils found in the vicinity, however, it is unclear who made those tools.
Were the toolmakers human, in which case Homo sapiens would have been present in India in that period, which is much earlier than when migration out of Africa is believed to have happened? Or were these perhaps the work of a hominin species such as Neanderthals?
Moorjani, who was not involved in that study, said its findings have led to suggestions that different groups, e.g., modern humans, Neanderthals and Denisovans may have inhabited India around this time. “However, without a revaluation of human fossils in India, this question remains unclear.”
What her study did do is estimate when modern humans settled in India. Using a mathematical model based on the amount of genetic mutation that takes place over time, her group dated it to around 50,000 years. “Moreover,” she said, “we find that majority of the genetic variation in Indians stems from a single major migration out of Africa that occurred around 50,000 years ago, with minimal contribution from earlier migration waves.”
The Iranian connection
To identify the potential source of Iranian farmer ancestry in India, the researchers investigated 15 ancient Iranian groups. They found a common source of Iranian-related ancestry from early Neolithic cultures of Central Asia (Sarazm) into the ancestors of several groups in India: Ancestral South Indians, Ancestral North Indians, Austro-Asiatic-related and East Asian-related.
“What was very interesting to us was also that archaeological studies have also documented trade connections between Sarazm and South Asia, including connections with agriculture sites of Mehrgarh and early Indus Valley Civilisation,” Moorjani said.
“Moreover, one of the Sarazm individuals had Andamanese-related ancestry and was discovered with shell bangles that are identical to ones found at sites in Pakistan and India such as Shahi-Tump, Makran and Surkotada, Gujarat,” she said.
More to learn
What has been constructed so far is not the complete timeline “There are many open questions remaining, in particular about who was inhabiting India 50,000 years ago,” Moorjani said.
“Did the range of Neanderthals and Denisovans extend to South Asia? Did modern humans encounter Neanderthals and maybe Denisovans further east in Eurasia than widely believed? In future, combined with insights from other fields like archaeology and linguistics, I hope the fine-scales story of our evolutionary past will become clearer.”
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