Early Indians

by Tony Joseph

  The only region that could provide such a platform is the Middle Ganga region, where at Lahuradewa in the Sant Kabir Nagar district of Uttar Pradesh in the Upper Ganga plain there is indeed evidence for rice harvesting, sedentary settlement and ceramics dating back to about 7000 BCE. The chronology of the transition from harvesting wild rice to cultivating domesticated rice is not yet certain, but there is no doubt that Lahuradewa indicates experiments in agriculture were happening at several places in south Asia around the same time and that Mehrgarh was not alone. The only thing inhibiting its connection or comparison with Mehrgarh is the fact that the harvested plant/crop in Lahuradewa is rice, and not wheat or barley as in Mehrgarh, which later on became the mainstay of the Harappan Civilization.

  Why didn’t the Lahuradewa experiments lead to a rice-cultivation-based civilization of its own in the Middle Ganga region at this time? It is quite possible that for ecological or other reasons Lahuradewa could not develop a full agricultural package, with multiple crops and many domesticated animals as in Mehrgarh or west Asia. It could also be that the variety of rice that was grown at Lahuradewa was yet to reach its full productivity potential, which may have happened after hybridization with japonica rice which arrived from east Asia much later (see chapter 3, p. 157).

  What about similarities with west Asia? Jarrige has this to say: ‘In spite of some obvious differences, for instance the progressive predominance of the breeding of Zebu (Bos indicus), the full setting of the farming economy at Mehrgarh displays evident similarities with what had been noticed in the case of the early Neolithic settlements in the hilly regions forming the eastern border of Mesopotamia.’

  For example, at the Ganj Dareh and Ali Kosh sites in the Deh Luran region of Iran at the foothills of the Zagros mountains, dated to around 7900 BCE, archaeologists have found the same kind of quadrangular houses built with narrow bricks about sixty centimetres long with finger marks for keying the mortar as was seen in Mehrgarh. Circular firepits filled with burnt pebbles that were found at Mehrgarh were also common at all these early settlements, and so were the traces of red paint found on the walls of the structures in Mehrgarh. Polished stone axes made in black diorite are found only in the upper levels of Period 1 in Mehrgarh and, similarly, in Ali Kosh, they are found only in the later phases, along with stone vessels. Only a few graves have been exposed at Ali Kosh, but they show skeletons placed in positions similar to those at Mehrgarh. Other similarities include ornaments made of seashells and semi-precious stones such as turquoise, a few beads in copper, baskets coated with bitumen and oblong-shaped cakes of red ochre.

  The most striking parallels, however, could be the sequential slab construction method by which the earliest ceramics were made in Mehrgarh and at the foothills of the Zagros mountains and the building of big, multicellular granaries. Jarrige says the similarities between the sites on the eastern border of Mesopotamia – such as Ganj Dareh and Ali Kosh – and on the western margins of the Indus Valley – such as Mehrgarh – are ‘significant’. He uses the phrase ‘a sort of cultural continuum’ to describe the relationship between the two regions in terms of the geographical context and the evolution of the sites over time.

  It is, therefore, difficult to escape the conclusion that there were very close connections between the Mehrgarh Neolithic and west Asian Neolithic, but that should not take away from the fact that Mehrgarh had its own strong and striking characteristics, quite separate from those of west Asia. The domestication of the zebu cattle and possibly an indigenous goat variety, the early discovery and use of cotton, the dentistry and the profusion of craft activities and the quality of their work, all stand out and perhaps suggest ‘an earlier, local background’ as Jarrige puts it, that is yet to be fully understood. There is also little doubt that the water buffalo, as important a part of south Asia’s food economy as the zebu cattle, was also domesticated in India, though whether this was done at Mehrgarh or somewhere in Gujarat is open to debate.

  Similarities between two regions can occur either because of migrations or because of cultural diffusion, mediated perhaps by nomadic groups. So which one could it have been in Mehrgarh? That Mehrgarh was a little bit behind the developments in west Asia in chronological terms shows that, on current evidence, the flow of ideas in the early stages is more likely to have been from the west to the east, rather than from the east to the west. But that still does not answer the question whether the Neolithic transformation of Mehrgarh was accompanied by migrations of people. And there is only one way to settle this issue: DNA evidence, especially ancient DNA.

  The story that DNA tells

  There are three ways in which you can use DNA evidence to probe affinities between different populations and to trace migrations: analysis of uniparental DNA (Y-chromosome or mtDNA) of present-day populations, whole genome sequencing of present-day populations and DNA analysis of ancient human remains. Let us go through them one by one and see what they have to say about whether there was a migration of Iranian agriculturists into south Asia.

  Uniparental DNA analysis looks at the haplogroups present in a population and analyses their family tree or phylogeny, and also maps their geographical distribution. As mentioned earlier, haplogroups identify a single line of descent either through the paternal line, from father to son to his son and so on (Y-chromosome), or through the maternal line, from mother to daughter to her daughter and so on (mtDNA).

  Since mutations happen at a fairly predictable rate, these lines of descent branch out over time, forming clear family trees with the mutations being the nodes from where new branches sprout. These branches and sub-branches are called macro-haplogroups, haplogroups or subhaplogroups or clades and they are named separately for Y-chromosome and mtDNA lineages. Geneticists have worked out Y-chromosome and mtDNA family trees that cover most of the modern human population based on current knowledge, and these are updated and expanded as new data comes in. Therefore, a geneticist can analyse the uniparental DNA of a person and decipher the macro-haplogroup, haplogroup and clade or subclade that he or she belongs to and, therefore, the family tree that he or she is part of. This is what happens, for example, when you hand over your DNA to a company that specializes in decoding your ancestry. (If two persons belong to the same mtDNA haplogroup, it means that they share a common female ancestor, and if two people belong to the same Y-chromosome haplogroup, it means that they share a common male ancestor, going back to the time when that haplogroup originated.)

  And it’s not just the family tree that can be worked out. Based on available data, we can also work out the ‘phylogeography’ of different haplogroups, which tells you not just to which branch of what family tree you belong, but also how that particular branch is distributed around the world today geographically and also how old a particular haplogroup or its subclade is. For example, we know that mtDNA haplogroup M2 is the most ancient haplogroup in the Indian subcontinent, that it arose around 60,200 years ago and that it is rarely found outside of South Asia.

  The first method: Y-chromosome and mtDNA

  The first method of getting an approximate idea of migrations is by accessing data on the distribution of various mtDNA and Y-chromosome haplogroups within a population and analysing their phylogeography. There are two pieces of data that could give clues about where a particular haplogroup or its subclade originated and how it spread: the relative frequency, or popularity, of the haplogroup in the different regions in which it is present and the variance within the haplogroup. Variance measures the diversity of subclades that a haplogroup has, and this is usually a function of the age of the haplogroup in a particular region and the population size. The higher the frequency and variance of a haplogroup in a particular region, the higher the likelihood that this region was a centre from which the haplogroup spread. Many such studies have been done in India, giving us some idea of the extent to which migrations may have shaped our demography.

  For example, as mentioned earlier, we now know that 70 to 90 per cent of m
tDNA haplogroups in Indian populations can trace their origin to the First Indians who arrived in India some 65,000 years ago. This means that only about 10 to 30 per cent of mtDNA lineages in the country are the result of later migrations. But the picture is radically different on the Y-chromosome side: as mentioned earlier, only 10 to 40 per cent of the Y-chromosome haplogroups in various Indian populations are descendant lineages of the First Indians. That means over 60 per cent of Y-chromosome haplogroups in the country are the result of later migrations. (There is a reason for this difference, which we will get into in chapter 4.)

  We also know which haplogroups are likely to owe their origin to the First Indians and which ones are likely to be the result of later migrations. The 2017 paper by Marina Silva and others identified mtDNA haplogroups K2a5, U1a3a, H13a2a and R0a2 as Neolithic period migrations from west Asia, meaning they could be the mtDNA groups that came to India as part of farming-related migrations. The same study mentioned Y-chromosome haplogroups J2, L1a and L1c as the ones most likely to be associated with the spread of agriculture from west Asia.

  But wait, as we discussed in chapter 1 (pp. 23–24), uniparental chromosomes mtDNA and Y-chromosome capture only a small part of the entire genome of individuals. So can we do whole genome analysis and see if those results too support the results of the uniparental DNA analysis? Yes, we can, as we shall find out now.

  The second method: Whole genome data

  There are two studies, one published in 2009 and the other in 2013, that did extensive sampling of present-day Indian population groups and used whole genome sequencing to reconstruct India’s population history. Both papers had David Reich of the Harvard Medical School, K. Thangaraj and Lalji Singh of CCMB and Nick Patterson of the Broad Institute of Harvard and MIT as co-authors, among others.

  The first paper was titled ‘Reconstructing Indian Population History’ and the second was titled ‘Genetic Evidence for Recent Population Mixture in India’. Both studies emphasized one fact: everyone in India today is a mix, in different proportions, of ancestry related to at least two groups: the First Indians and west Eurasians.6 The term west Eurasian includes west Asians such as people of the Fertile Crescent and Iran, as well as those from central Asia, the Caucasus and Europe. The studies showed that all population groups in India today have some amount of west Eurasian ancestry, varying from 20 per cent to 80 per cent, depending on the group. (Whole genome sequence data of present-day populations give us a general picture of affinities between different groups, though not a granular picture of how that affinity came about or who moved from where to where.)

  But there were some twists in the story before this research conclusion was put to paper and it is worth following these twists to understand the political context of the discussions about migrations. The suggestion that modern Indians carry a significant amount of west-Eurasian-related ancestry was unpalatable to many, probably because it seemed to support the long-standing theory that it was a migration of Steppe pastoralists from central Asia sometime within the last 4000 years that brought Indo-European languages, including an early version of Sanskrit, and related cultural practices and concepts to India. These Indo-European-language speakers called themselves Aryans, and for many in the right wing the idea that they came to India from elsewhere is unacceptable because they believe it would dethrone Sanskrit and the Vedas as the singular and fundamental source of Indian culture, as it would mean that the mighty Harappan Civilization that has left an indelible impression on Indian history and culture would have preceded their arrival.

  Reich describes the reaction to the findings of the research in his 2018 book, Who We Are and How We Got Here:

  The tensest twenty-four hours of my scientific career came in October 2008 when my collaborator Nick Patterson and I travelled to Hyderabad to discuss these initial results with Singh and Thangaraj.

  Our meeting on October 28 was challenging. Singh and Thangaraj seemed to be threatening to nix the whole project. Prior to the meeting, we had shown them a summary of our findings, which were that Indians today descend from a mixture of two highly divergent ancestral populations, one being ‘West Eurasians’. [The other being the First Indians.] Singh and Thangaraj objected to this formulation because, they argued, it implied that West Eurasian people migrated en masse into India. They correctly pointed out that our data provided no direct evidence for this conclusion. They even reasoned that there could have been a migration in the other direction, of Indians to the Near East7 and Europe . . .

  The cultural resonances of our findings gradually became clear to us. So we groped toward a formulation that would be scientifically accurate as well as sensitive to these concerns.

  The next day, the full group reconvened in Singh’s office. We sat together and came up with new names for ancient Indian groups. We wrote that the people of India today are the outcome of mixtures between two highly differentiated populations, Ancestral North Indians (ANI) and Ancestral South Indians (ASI), who before their mixture were as different from each other as Europeans and east Asians are today. The ANI are related to Europeans, central Asians, Near Easterners and people of the Caucasus, but we made no claim about the location of their homeland or any migration.

  According to the study, the ASI were the descendants of the First Indians.

  In essence, instead of stating that today’s Indians are descendants of both the First Indians and west-Eurasian-related populations as the research suggested, the published paper created two new theoretically constructed population groups and said that today’s Indians are the result of a mixture of two highly differentiated groups, ANI and ASI, with the ANI being closely related to west Eurasians. This was a scientifically defendable framework to understand the population structure of South Asia and to avoid a political controversy, but the cost of the compromise was that it made it easier to misinterpret the study. For instance, it left room for uninformed and false commentary in the news media that the ANI was a homogeneous and very ancient population group of India, like the ASI, which had settled here tens of thousands of years ago. This, despite the study itself stating clearly that the ANI could be a mixture of populations resulting from multiple migrations and may not be a homogeneous group, thus leaving open the possibility that some migrations could be as recent as within the last 4000 years.

  Even with this formulation, the paper improved our understanding of Indian population formation, because it provided genetic evidence for a mixing of the descendants of the First Indians and other population groups who were closely related to the current-day populations of west Asia, Europe, the Caucasus and central Asia.

  But this still left a problem, as those ideologically not ready to accept the idea of migrations into India could still assert that the direction of migration was from India to the rest of the world and this is what accounts for the close relationship between some population groups of India and those of west Asia, Europe, the Caucasus and central Asia. Whole genome data can prove affinity between population groups, but it cannot necessarily prove the direction of migration. As for uniparental data, large-scale population movements or natural calamities and epidemics that may have happened in the past could make it difficult to interpret the current-day distribution, frequency and variance data of haplogroups. So in addition to the two methods we have already discussed – uniparental DNA analysis based on present-day mtDNA and Y-chromosome lineages and whole genome sequencing of present-day populations – we need to look for a third method to settle the argument about the direction of migration, and there is, in fact, such a method: DNA analysis of ancient human remains. And to this we turn now.

  The third method: Ancient DNA

  Ancient DNA can settle questions about the direction of movement of peoples for the simple reason that with samples of DNA taken from ancient human skeletons at different time periods in a particular location, we can see how populations moved, on the ground, in the past. For example, if we see that ancient DNA from location X before 2000 BCE shows
no evidence whatsoever for, say, any central Asian or Steppe lineage, and then from 1000 BCE onward we start seeing lots of evidence for that lineage, then we can clearly conclude that there was an influx of people with Steppe lineage into location X sometime between 2000 BCE and 1000 BCE.

  The science of ancient-DNA took off only in the past five years or so. And since then, it has been rewriting history as we know it in continent after continent. The beauty of this process is that as more and more ancient DNA gets analysed across regions and continents, it is as if the pieces of a global historical puzzle are rapidly falling in place. The more the global migration picture gets filled, the more difficult it becomes to overturn the scientific consensus on how each region got populated.

  The new ancient-DNA-based study that would settle long-standing questions about Indian prehistory was titled ‘The Genomic Formation of South and Central Asia’ and was posted on the preprint server for biology, bioRxiv, in March 2018. It was co-authored by ninety-two scientists from around the world and was co-authored and co-directed by David Reich, who runs a lab that currently has no equal in its ability to sequence and analyse DNA at scale and speed.

  Notably, among the ninety-two co-authors were scientists from different disciplines who are stars in their own fields, such as James Mallory, archaeologist and author of the classic book In Search of Indo-Europeans: Language, Archaeology and Myth, and David Anthony, anthropologist and author of the ground-breaking book The Horse, the Wheel and Language: How Bronze-Age8 Riders from the Eurasian Steppes Shaped the Modern World. Other well-known co-authors included the archaeobotanist Dorian Fuller and the archaeologist Nicole Boivin, who are familiar names in India owing to the work they have done in the country; Vasant Shinde, vice chancellor of the Deccan College, India’s premier institution for archaeology; and Thangaraj of the CCMB, who was a co-director of the study as well. Niraj Rai of the Birbal Sahni Institute of Palaeosciences, Lucknow, Priya Moorjani of the University of California and Ayushi Nayak of the Max Planck Institute for the Science of Human History, Germany, were also co-authors. The study was lead-authored by Vagheesh Narasimhan of the Department of Genetics, Harvard Medical School.