The largest-ever genome analysis of South Asians uncovered a number of surprising revelations—including the variety of Neanderthal genes in our genetic makeup.
The lead image: is one of the most detailed reconstructions of an ancient Indus gateway in the Harappan civilisation by artist Chris Sloan.
The genome study: The basic deets
A team of researchers—led by Berkeley geneticist Priya Moorjan—analysed 2,762 genomes. These were taken from a genetic database of older Indians—collected for the Longitudinal Aging Study in India—Diagnostic Assessment of Dementia (LASI-DAD). The scientists included “people from nearly every geographic region, speakers of every major language group, and all tribes and castes.”
Why this is a very big deal: Genome sequencing studies in the West have mostly ignored Indian ancestry—or given it minimal attention:
While some recent genomic studies have included Indian populations, they’ve typically sampled very few people or focused on Indian people living outside of India, thus representing only a narrow range of the genetic diversity seen within the country today, the authors write. As a result, researchers have only a limited understanding of India’s genetic history.
This is the largest and most diverse genome study to focus on India.
Key point to note: Although the results of the study are making headlines, its findings have not been peer-reviewed. So this is very interesting and important—but not proven.
Revelation #1: The Harappan debate
First, defining ‘Aryan’: Contrary to the colonialist use of the word—greatly beloved to fascists—Aryans in the context of human history refers to Bronze Age herders who migrated out of the steppes (or grasslands) of Central Asia some 4,000 years ago.
The great Aryan question: The origins of Vedic culture has been a source of controversy—ever since the discovery of the Indus Valley Civilisation in the 1920s. British colonialists claimed that the civilisation was a pre-Vedic society destroyed by Aryan invaders (nicely mirroring and justifying their own imperialism). These mighty Aryans brought the elements of Hindu culture that the British admired—such as the Vedas, shastras etc. In later decades, historians debunked the invasion theory—but they maintained the thesis that the arrival of Aryans—perhaps as migrants—marked the beginning of Vedic culture.
The established timeline: looks something like this:
One: The first Indians came out of Africa and can be traced back to the Andamans. They are known as either Andamanese Hunter Gatherers or Ancient Ancestral South Indians (AASI).
Two: Ancient Ancestral South Indians moved north and mixed with settlers from Iran—who arrived 9,000 years ago. The result is referred to as the Indus Periphery People. They likely spoke an early Dravidian language. They also built the Harappan civilisation. The remains found in Harappan ruins show no trace of the so-called ‘Aryan’ gene–suggesting they had no contact with those steppe herders, who came much later.
Three: When the Harappan civilisation declined after 2000 BCE, many of its descendants moved south-east to mix with those ‘first Indians’—and formed the Ancestral South Indian (ASI) population, most of whom live in South India today.
Four: Around the same time, we witnessed a huge influx of settlers from the Central Asian Steppes (hello, Aryans!)—either due to invasion or migration. The remaining Harappans mixed with them to form the Ancestral North Indian (ANI) population.
The Hindu nationalist thesis: Hindu ideologues like MS Golwalkar have long railed against the Aryan invasion/migration theory—because it suggests that the most hallowed Hindu traditions were “imported.” It was—and still is—very important to establish Vedic culture as indigenous to India—not brought by outsiders. Hindu nationalists instead claim that the Indus Valley Civilisation as its birthplace.
To this end, they have mustered their own posse of experts who claim that “Harappan people are the same as Vedic people.” Geneticists like Niraj Rai go even further: “We are suggesting an out-of-India migration theory”—and that the “Harappans had taken Vedic culture to other parts of the world.” And this explains the common roots of Indo-European languages.
What the new study reveals: For starters, it confirms the three ancestral sources of our genes:
Most Indians are primarily 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., and herders from the central Eurasian steppe region who swept into the region sometime after 3000 B.C.E., perhaps between 1900 and 1500 B.C.E.
Genetic sequencing has also helped us identify those Iranian farmers—by comparing Indian genes with ancient DNA from groups with Iranian ancestry. What they found:
The best fit came from farmers from an ancient agricultural centre called Sarazm in the northwest of what today is Tajikistan. Farmers here grew wheat and barley and kept cattle, and traded extensively throughout Eurasia. Interestingly, one ancient individual from Sarazm also carried traces of Indian ancestry; another was buried with ceramic bracelets similar to those made in ancient India. “That really helped directly connect the two cultures, and it showed that it wasn’t just one-way mixing,” Moorjani says.
But, but, but: The genome study doesn’t weigh in on the highly debated chronology—or the origins of Vedic culture. It is also hazy on the details of the genetic contributions of those steppe dwellers aka Aryans.
Revelation #2: The Ancient Indians debate
Disagreement over Toba: Around 74,000 years ago, Mount Toba erupted on the Indonesian island of Sumatra. The ash fell on the Indian subcontinent—and on a species that fashioned tools out stones. Scientists cannot agree as to whether these were early homo sapiens—in which case the migration out of Africa happened way earlier than we think. Or were these tools made by some other kind of early human—such as Neanderthals or Denisovans?
The problem: is that there are no human fossils from this period. Scientists have only found “thousands of stone flake tools used for cutting and scraping.” In fact, remains of ancient human species have not been uncovered in India so far.
What the study found: One to two percent of Indians’ genes comes from Neanderthals and Denisovans—which is the same percentage as Europeans. Africans have a lower 0.5% because there were no Neanderthals on the continent. Humans migrated out of Africa and encountered our ancient human cousins—and mated with them. The presence of their genetic material suggests they were present on the subcontinent when the ancient hunter gatherers arrived—even though there is no fossil record.
The most striking revelation: 90% of all known Neanderthal genes were found in 2,700 Indian genomes. For perspective: “That’s about 50% more than was recovered in a similar study of Neanderthal DNA in Icelanders that analysed more than 27,000 genomes.” Even more surprising: Nearly 12% of the Neanderthal gene sequences identified haven’t been found anywhere else in the world. This is especially intriguing: since no fossils of these ancient humans have been found in India—raising questions about “how these genes got there—and why they stuck around.”
On the migration debate: The study doesn’t offer any comfort to those who argue for an earlier migration out of Africa: “The study also reveals that most of the overall genetic variation in Indian people stems from a single major migration out of Africa that occurred around 50,000 years ago.” If there were any modern humans on the subcontinent before their arrival, those genes have not survived—unlike those of Neanderthals and Denisovans.
The bottomline: The Indian genome suggests that the history of ancient humans is far from complete. It contains mysteries that may yet upend our understanding of our ancestors. And that’s truly cause for excitement.
Reading list
The original study is here—and a more concise summary is available on Smithsonian. Science has two good stories—a detailed piece on the study and the debate over human life on the subcontinent during Toba eruption. New Scientist looks at why this is exciting for research into the Neanderthal genome. We did an excellent Big Story on ancient Indian humans—looking at the Harappan excavations in the 1960s. For more on the debate over the origins of Vedic culture, read BBC News. We also looked at the Denisovans in this Big Story—and we laid out the latest findings on human evolution in this Big Story on the Dragon Man. Either is a good read if you want to get the difference between the various kinds of humans straight.
