India 4: Where did Asian Indians come from? (v1.0)

Few studies had been conducted on a through genetic analysis of Indians in the Indian subcontinent. Global genetic sequencing efforts have largely ignored India. Recently, University of California, Berkley undertook such a study and has interesting results. South Asia is home to one of the world's most diversified populations where around 1.5 billion people, a mash-up of many ethnic identities, languages, religions, castes, and customs reside. 

The scientists have now revealed a thorough analysis of this population's evolutionary history. The team sequenced over 2700 modern Indian genomes using data from the Longitudinal Aging Study in India–Diagnostic Assessment of Dementia (LASI-DAD). These genomes included speakers of nearly every major language group, individuals from all tribes and castes, people from nearly every geographic region, and included both rural and suburban individuals. 

The researchers concluded that three ancestral populations make up the majority of Indians: hunters and gatherers similar to Andamanese who inhabited the area for tens of thousands of years, farmers with Iranian/Persian ancestry who arrived between 4700 and 3000 BCE, and herders from the central Eurasian steppe region who swept into the area sometime after 3000 B.C.E., perhaps between 1900 and 1500 B.C.E.

The proportion of people's ancestry associated with ancient Andamanese like hunter-gatherers, for example, was highest in the south and lowest in the north of India, and higher in certain language and caste groups.

To find out more about the identity of the Iranian/Persian-related farmers who entered the region thousands of years ago, the researchers also examined the previously retrieved ancient DNA from Iranian-ancestry groups that existed before the genetic pulse into India. Further, they carried out simulations to determine whose genes most closely matched the genetic patterns observed in modern Indians. Farmers from Sarazm, an old agricultural hub in the northwest of what is now Tajikistan, were the most compatible. These farmers reared livestock, farmed wheat and barley, and engaged in significant commerce with other countries in Eurasia. Sarazm would have been a crucial hub for the spread of domestic animals, farming, and human genes into Kashmir and northwest India. "A very important story is being told here. Most people underestimate how interconnected societies were throughout prehistoric times," A reviewer said. 

By using a different technique of estimating the amount of genetic mutation that occurs between generations and calculating how long it would have taken for India's modern population to reach its current state of variation, the researchers claimed that most of the varied settlers who gave rise to modern Indians were part of a single migration out of Africa approximately 50,000 years ago who over time drifted to India. 

The researchers also discovered that the modern people in the sample had 1% to 2% of their ancestry from Neanderthals and their close relatives, the Denisovans—about the same as Europeans. However, as compared to other global populations, Indians together possess an astounding diversity of these ancient genes. The 2700 Indian genomes contained over 90% of all known Neanderthal genes that have infiltrated human populations. That is roughly 50% more than what was found in a comparable study of Neanderthal DNA in Icelanders that analysed more than 27,000 genomes. The researchers also identified several new candidates for Neanderthal- and Denisovan-inherited genes that may have given their descendants some evolutionary advantage, though it’s too early to say what those boons might have been. 

One speculation is that the ancient humans might have encountered and mated with a relatively large, genetically diverse population of the archaic cousins living on the subcontinent—although no related fossils have been found. Another possibility is that India’s vast geographical boundaries and close kin–marrying traditions better preserved different segments of Neanderthal DNA than on other continents. Another study recently published puts forth a hypothesis on Neanderthal DNA variance across geographies. Mystery solved: How and why humans have Neanderthal DNA (msn.com)

Scholars have debated over the years whether modern humans were responsible for ancient stone age tools found in India and dated to approximately 80,000 years ago, and if so, whether they left a genetic legacy in modern populations. But with no remains associated with these tools, researchers haven’t been able to pin down their makers.

Still, other ancestral source populations, such as those from the steppe, remain somewhat “vague,” says biological anthropologist Gyaneshwer Chaubey at Banaras Hindu University. He says the relative paucity of ancient DNA samples from India means other, ancient source populations could be missing from the mix.