Back to the Beginning

THE ANCIENT SETTLEMENT of Sarazm, located on the Samarkand plain, is a remote location in what is today northwestern Tajikistan. But during the third millennium BCE, this area thrummed with life. It sat at what researchers call a three-way point of inter­section between the ancient Iranian world of Hissar, Khinaman, Shahdad, Tepe Yahya and Susa on one side, Central Asia on the other, and the Indus Valley further below. A key location for trade and commerce between these regions, everything from ex­otic goods like carved stoneware, carnelian coppers and beads, and many precious stones and minerals, to agricultural products and technology, including domestic seeds, passed through this urban centre. Some have even suggested that farming could have spread from here further south into South Asia.

A new genetic study seeking to trace the earliest sources of the Indian subcontinent’s ancestry has now found that a significant part of our past probably comes from this ancient location.

Genetic studies in recent years have shown that Indians today carry the genes of not just an indigenous group of South Asian hunter-gatherers and a group of people from the Yamnaya region of Central Asia (the Eurasian Steppes, that is said to have arrived sometime between 1900 and 1500 BCE), but also an ancient Irani­an group that precedes the arrival of the people from the Steppes. The researchers of this new study pulled the threads of this Irani­an-related gene flow and tried to piece together the jigsaw puzzle of where this particular part of our ancestry could have come from. They compared the Iranian-related aspect of our ancestry to those of previously extracted ancient DNA from groups with Iranian ancestry that predated the gene flow into South Asia and found that the people who lived in Sarazm provided the best fit. “Most Indians derive ancestry from three ancestral groups re­lated to ancient Iranian farmers, Eurasian Steppe pastoralists and South Asian hunter-gatherers. While we understand the source of the latter two, it remains unclear what the source or timing of the Iranian-related ancestry in India is. We systematically exam­ined the ancestry across diverse groups in India, [analysing the genes of] ancient Iranian-related individuals from the Neolithic to the Iron Age. We show the common source of ancient Iranian-related ancestry linked to early Neolithic samples from Sarazm in Ancestral North Indians (ANI), Ancestral South Indians (ASI), Austroasiatics-related and East Asian-related individuals in In­dia,” says Priya Moorjani, the population geneticist from the Uni­versity of California, Berkeley, who is one of the authors of this study. When this gene flow spread to India, however, is unclear, she says, and a topic for future research. “Notably, archaeological evidence supports direct connections between Sarazm and South Asia, including connections with agriculture sites of Mehrgarh and early Indus Valley Civilisation [IVC],” she adds.

Not only have connections with places like Mehrgarh, in present-day Pakistan, and early IVC sites, been established, but as the researchers write, one individual at Sarazm (referred to as Sarazm_EN_1 in the paper) was found with shell bangles that are identical to the ones found at sites in Pakistan and India such as Shahi-Tump in Makran and Surkotada in Gujarat. When its ancestry was analysed, the researchers found that this individual also carried a substantial South Asian hunter-gatherer-related ancestry, suggesting that it wasn’t just people from this area pos­sibly moving into the Indian subcontinent and mixing with the population there. The reverse also took place.

Not everyone however is convinced by the argument that Indians derive their ancestry from the three primary groups of ancient Iranians, people from the Eurasian Steppes, and indig­enous South Asian hunter-gatherers. Gyaneshwer Chaubey, a biological anthropologist at Banaras Hindu University who has been involved in several gene studies conducted in India, says it is difficult to reach any type of consensus because of the lack of ancient genome samples from South Asia. “The lack of ancient genome samples from South Asia is a big drawback. Right now, the researchers use [ancient] genome samples from other regions [with links to South Asia] as a proxy for samples from here. Unless we get samples from here, we will be missing the complete story.”

Moorjani has been among a group of geneticists that has made many significant discoveries in recent years. Back in 2013, she was part of a team that showed how the mixing that characterised the ancestors of modern-day Indians suddenly stopped about 1,900 years ago, suggesting, possibly, the start of the caste system. A couple of years ago, she was also the senior author of a paper that showed how common “founder events” have been in human history. Such an event occurs when a small number of ancestral individuals gives rise to a large fraction of the population. This could happen because of war, famine or disease, which could have drastically reduced the larger popu­lation, or because of geographic isolation, such as groups being cut off on islands, or because of cultural practices where people marry within the same community. More than half of the 460 groups Moorjani and her colleagues had analysed experienced a population bottleneck somewhere in the last 10,000 years or so.

Of particular interest to her lab is the concept of disease mapping. South Asians, it is believed, have severe found­er events in many groups, because of the shift from population mixture to endogamy, leading to a decrease in ge­netic diversity and an increase in inci­dences of recessive hereditary diseases. Niraj Rai, the head of the Ancient DNA Lab at Birbal Sahni Institute of Palaeo­sciences in Lucknow, talks about various disorders seen in India—from a rare aberration in a protein, MYBPC3 (cardiac myosin binding protein C) which correlates with a high risk of heart failure, found in about 4 per cent of those with Indian ancestry, to the presence of butyrylcholinesterase deficiency in the Vysya community in Andhra Pradesh, where patients experience neuromuscular blockade and muscle paralysis when administered with some muscle relaxants—to point to what he calls the genetic burden in India. “Because of the wide practice of endogamy, Indians suffer from many genetic-based diseases,” he says.

In disease mapping, researchers try to identify genetic variants that cause such diseases. Moorjani and her colleagues are cur­rently working on such an exercise among South Asians. “In the LASI-DAD study [Longitudinal Ageing Study in India-Diagnostic Assessment of Dementia; whose samples the researchers also used in the current paper] in collaboration with groups from the University of Michigan and University of Southern California, we aim to identify genes associated with Alzheimer’s disease and ageing in India. We are also studying other diverse groups in India to study how evolutionary history, in particular, founder events, has shaped the disease burden across groups.”

THE CURRENT PAPER, published as a preprint recently on bioRxiv, is said to be the largest ever whole-genome analysis from India. Using the samples from the LASI-DAD study, Moorjani and her colleagues sequenced the genomes of more than 2,700 modern Indians from 18 different states. These individuals, representing nearly every geographic region, spoke different languages (from Indo-European and Dravidian to the Tibeto-Burman family of languages), and belonged to different caste and tribal groups, providing, according to the researchers, the most comprehensive snapshot of genetic diversity in India.

The researchers however didn’t just stop to look at the com­position of our ancestry a few thousands of years ago. They used the data to go much further back, and discovered that modern-day Indians de­rive their ancestry from a single group of Homo sapiens that migrated out of Africa about 50,000 years ago, and—quite star­tlingly—that Indians today carry quite a substantial amount of Neanderthal and Denisovan genes. According to the researchers, Indians derive around 1 to 2 per cent of their ancestry through gene flow from these two archaic human spe­cies. The Neanderthal DNA here in fact is more varied than in any other modern population known today. And, according to the researchers, it is possible to recon­struct about 90 per cent of the known Ne­anderthal genome just from the genomes of modern-day Indians. “We show that there is a large diversity in Neanderthal and Denisovan ancestry among Indians. Notably, 90 per cent of the Neanderthal ancestry segments segregat­ing in all non-Africans are seen in Indians, and Indians have the larg­est amount of population-specific Neanderthal ancestry segments. Indians also harbour the largest variation in Denisovan ancestry among Eurasian populations,” Moorjani says.

These discoveries, as fascinating as they are, raise more ques­tions. If Indians derive their ancestry from a group of modern humans (Homo sapiens) that moved out of Africa 50,000 years ago, then who were the individuals who left behind the many advanced stone tools we find from much earlier periods in some parts of India? Could these have been Neanderthals or Deniso­vans, whose range so far hasn’t been known to have extended to South Asia, or did the ancestors of the modern humans who settled in South Asia encounter these species elsewhere and bring their genes with them? “The most detailed archaeological work [on Neanderthals] has been done in Europe, and so it is assumed that’s predominantly where the Neanderthals lived, though their range could have extended further south and east,” Moorjani says, adding that she hopes the results of her paper will lead to a revalu­ation of the fossil evidence in India and beyond.

Ravi Korisettar, a well-known archaeologist from Karnatak University in Dharwad, thinks it is unlikely that the Neanderthals or Denisovans could have been living in some parts of South Asia. “You cannot rule out the possibility. But archaeolog­ically, so far, there is no evidence to suggest this might be the case. In fact, we know there were other hominin species here,” he says.

A few years ago, Korisettar was part of a team that had discov­ered around 78,000-year-old Middle Palaeolithic tools in Jwala­puram in Andhra Pradesh. Who invented the Middle Palaeolithic has been a source of many palaeoarchaeology dustups. According to some researchers, this radical change in stone tools, from primi­tive and bulky hand-axes and cleavers, and heavy-cutting core stone tools, to sophisticated stone tools that were smaller, more pointed and sharper, is reflective of the kind of abstract thinking that points to the evolution of our own species—Homo sapiens. According to this theory, Homo sapiens invented this new technology in Africa and introduced it to other species when they encountered them after they moved out of Africa. Oth­ers argue that different human species independently arrived at this new tech­nological breakthrough. Since the dis­covery in Jwalapuram, researchers have discovered even older Middle Palaeolithic tools in India—from 385,000-year-old stone tools in Attirampakkam in Tamil Nadu, to 247,000-year-old stone tools elsewhere in Hanumanthunipadu in Andhra Pradesh.

So, if modern-day Indians derive their ancestry from a single group of Homo sa­piens that migrated out of Africa about 50,000 years back, who were the cre­ators of these tools? When asked in an earlier interview to Open, Shanti Pappu, who along with Akhilesh Kumar of the Sharma Centre for Heritage Education in Chennai discovered the 385,000-year-old stone tools in Attirampakkam in Tamil Nadu, refused to be drawn into questions about which species could have made these tools, citing the lack of fossil discoveries in India. To her, simplistic explanations of population migrations or dif­fusion of technological ideas do not hold. “We must attempt to understand the complexities involved in these processes. Our re­search reflects on the complexity of understanding the evolution of new technological and behavioural strategies adopted during the Indian Middle Palaeolithic Age. We argued, in our paper, that the processes of change from the preceding Acheulean were slow and complex, and thereby needed new theoretical approaches to interpret,” she had said.

This latest genetic study, Korisettar points out, does not rule out that Homo sapiens had reached the Indian subcontinent long before 50,000 years ago. “It just means those individuals did not pass down their genes. Perhaps they died before. Who knows?” he says. Interestingly, Korisettar points out that while older Middle Palaeolithic sites are being discovered, researchers are also finding that the earlier, more crude Acheulean tools are being found to last longer across several sites in south India. This could mean, he says, two distinct ancient hominin species in this area. “We see this late survival of Acheulean and a parallel evolution of Middle Palaeolithic in many places. For instance, we see Acheulean tools in Andhra Pradesh surviving up to 140,000 years, and Middle Pal­aeolithic tools in the same region going back 240,000 years. These may be two different hominins,” he says.

If the modern humans who settled in South Asia encountered Neanderthals and Denisovans and carried their genes with them to this region, what explains the sheer diversity of these genes and their preservation among modern Indians today? According to re­searchers, it is possible that there could be environmental factors that push these sequences to remain in the genomes of populations in different regions across India. “Let’s say in the Ne­anderthal genome, there is a mutation in a particular chromosome that helps an individual fight with some [disease] pathogen, mostly prevalent in northern India. So, you will find this gene among northern Indians, but you may not find it among people in the south. So, even though there was a common Neander­thal genome, the pressure would be very different in different regions. This could be one reason why the Neanderthal ge­nome has survived in different popula­tions [within India] in a different way,” says Chaubey. It is probably too early to tell whether or not genes inherited from archaic species bestow people in South Asia with any evolutionary advantages, but there is a good chance this could be the case. “Previous analysis in mainly Europeans has shown that archaic ancestry has had a major impact on human adaptation and fitness, impacting numerous traits from high-altitude adaptation to disease sus­ceptibility like diabetes,” Moorjani says. “In India, we also find that Neanderthal ancestry has impacted several immune genes, including a gene cluster on chromosome 3 that impacts response to SARS-CoV-2. A striking signal of enrichment of Denisovan an­cestry is seen on chromosome 6 at the MHC locus which plays an important role in immune function. At this locus, the frequency of Denisovan ancestry is 100-fold higher than the genome-wide average and there are an unusually high number of variants shared with Denisovans [and not in other archaic groups]. Previ­ous analyses have shown that genes in this region are candidates for balancing selection across worldwide populations.”

In the paper, the researchers ask, “When did people first mi­grate to India from Africa? What is the contribution and legacy of archaic gene flow from the Neanderthals and Denisovans to Indians? How have recent technological innovations like Neo­lithic farming and the spread of languages impacted variation in India?” We still do not know a lot, but the study provides some tantalising clues.

Genetic Profilinghuman migrationhuman raceIndiansIranian roots