Who We Are and How We Got Here

by David Reich

  The Nazis’ interest in migrations and the spread of Indo-European languages has made it difficult for serious scholars in Europe to discuss the possibility of migrations spreading Indo-European languages.11 In India, the possibility that the Indus Valley Civilization fell at the hands of migrating Indo-European speakers coming from the north is also fraught, as it suggests that important elements of South Asian culture might have been influenced from the outside.

  The idea of a mass migration from the north has fallen out of favor among scholars not only because it has become so politicized, but also because archaeologists have realized that major cultural shifts in the archaeological record do not always imply major migrations. And, in fact, there is scant archaeological evidence for such a population movement. There are no obvious layers of ash and destruction around thirty-eight hundred years ago suggesting the burning and sacking of the Indus towns. If anything, there is evidence that the Indus Valley Civilization’s decline played out over a long period, with emigration away from the towns and environmental degradation taking place over decades. But the lack of archaeological evidence does not mean that there were no major incursions from the outside. Between sixteen hundred and fifteen hundred years ago, the western Roman Empire collapsed under the pressure of the German expansions, with great political and economic blows dealt to the western Roman Empire when the Visigoths and the Vandals each sacked Rome and took political control of Roman provinces. However, there so far seems to be little archaeological evidence for destruction of Roman cities in this time, and if not for the detailed historical accounts, we might not know these pivotal events occurred.12 It is possible that in the apparent depopulation of the Indus Valley, too, we might be limited by the difficulty archaeologists have in detecting sudden change. The patterns evident from archaeology may be obscuring more sudden triggering events.

  What can genetics add? It cannot tell us what happened at the end of the Indus Valley Civilization, but it can tell us if there was a collision of peoples with very different ancestries. Although mixture is not by itself proof of migration, the genetic evidence of mixture proves that dramatic demographic change and thus opportunity for cultural exchange occurred close to the time of the fall of Harappa.

  A Land of Collisions

  The great Himalayas were formed around ten million years ago by the collision of the Indian continental plate, moving northward through the Indian Ocean, with Eurasia. India today is also the product of collisions of cultures and people.

  Consider farming. The Indian subcontinent is one of the breadbaskets of the world—today it feeds a quarter of the world’s population—and it has been one of the great population centers ever since modern humans expanded across Eurasia after fifty thousand years ago. Yet farming was not invented in India. Indian farming today is born of the collision of the two great agricultural systems of Eurasia. The Near Eastern winter rainfall crops, wheat and barley, reached the Indus Valley sometime after nine thousand years ago according to archaeological evidence—as attested, for example, in ancient Mehrgarh on the western edge of the Indus Valley in present-day Pakistan.13 Around five thousand years ago, local farmers succeeded in breeding these crops to adapt to monsoon summer rainfall patterns, and the crops spread into peninsular India.14 The Chinese monsoon summer rainfall crops of rice and millet also reached peninsular India around five thousand years ago. India may have been the first place where the Near Eastern and the Chinese crop systems collided.

  Language is another blend. The Indo-European languages of the north of India are related to the languages of Iran and Europe. The Dravidian languages, spoken mostly by southern Indians, are not closely related to languages outside South Asia. There are also Sino-Tibetan languages spoken by groups living in the mountains fringing the north of India, and small pockets of tribal groups in the east and center that speak Austroasiatic languages related to Cambodian and Vietnamese, and that are thought to descend from the languages spoken by the peoples who first brought rice farming to South Asia and parts of Southeast Asia. Words borrowed from ancient Dravidian and Austroasiatic languages, which linguists can detect as they are not typical of Indo-European languages, are present in the Rig Veda, implying that these languages have been in contact in India for at least three or four thousand years.15

  The people of India are also diverse in appearance, providing visual testimony to mixture. A stroll down a street in any Indian city makes it clear how diverse Indians are. Skin shades range from dark to pale. Some people have facial features like Europeans, others closer to Chinese. It is tempting to think that these differences reflect a collision of peoples who mixed at some point in the past, with different proportions of mixture in different groups living today. But it is also possible to overinterpret physical appearances, as it is known that appearances can also reflect environment and diet.

  The first genetic work in India gave seemingly contradictory results. Researchers studying mitochondrial DNA, always passed down from mothers, found that the vast majority of mitochondrial DNA in Indians was unique to the subcontinent, and they estimated that the Indian mitochondrial DNA types only shared common ancestry with ones predominant outside South Asia many tens of thousands of years ago.16 This suggested that on the maternal line, Indian ancestors had been largely isolated within the subcontinent for a long time, without mixing with neighboring populations to the west, east, or north. In contrast, a good fraction of Y chromosomes in India, passed from father to son, showed closer relatedness to West Eurasians—Europeans, central Asians, and Near Easterners—suggesting mixture.17

  Some historians of India have thrown up their hands and discounted genetic information due to these apparently conflicting findings. The situation has not been helped by the fact that geneticists do not have formal training in archaeology, anthropology, and linguistics—the fields that have dominated the study of human prehistory—and are prone to make elementary mistakes or to be tripped up by known fallacies when summarizing findings from those fields. But it is foolhardy to ignore genetics. We geneticists may be the barbarians coming late to the study of the human past, but it is always a bad idea to ignore barbarians. We have access to a type of data that no one has had before, and we are wielding these data to address previously unapproachable questions about who ancient peoples were.

  The Isolated People of Little Andaman Island

  My research into the prehistory of India began in 2007 with a book and a letter.

  The book was The History and Geography of Human Genes, Luca Cavalli-Sforza’s magnum opus, in which he mentions the “Negrito” people of the Andaman Islands in the Bay of Bengal, hundreds of kilometers from the mainland. The Andaman Islands have remained isolated by deep sea barriers for most of the history of modern human dispersal through Eurasia, although the largest, Great Andaman, has been massively disrupted by mainland influence over the last few hundred years (the British used it as a colonial prison). North Sentinel Island is populated by one of the last largely uncontacted Stone Age peoples of the world—a group of several hundred people who are now protected from outside interference by the Indian government, and who are so not-of-our-world that they shot arrows at Indian helicopters sent to offer help after the Indian Ocean tsunami of 2004. The Andamanese speak languages that are so different from any others in Eurasia that they have no traceable connections. They also look very different from other humans living nearby, with slighter frames and tightly coiled hair. In one section of his book, Cavalli-Sforza speculated that the Andamanese might represent isolated descendants of the earliest expansions of modern humans out of Africa, perhaps having moved there before the migration that occurred after around fifty thousand years ago and that gave rise to most of the ancestry of non-Africans today.

  On reading this, my colleagues and I wrote a letter to Lalji Singh and Kumarasamy Thangaraj of the Centre for Cellular and Molecular Biology (CCMB) in Hyderabad, India. A few years earlier, Singh and Thangaraj had published a paper on mitochondrial and Y-chromosome D
NA from people of the Andaman Islands.18 Their study showed that the people of Little Andaman Island had been separated for tens of thousands of years from peoples of the Eurasian mainland. I asked them whether it would be possible to analyze whole genomes of the Andamanese, to gain a fuller picture.

  Singh and Thangaraj were excited to collaborate and quickly convinced me that there was a broader picture to paint involving mainland Indians as well. They offered us access to a vast collection of DNA. In the freezers at CCMB, they had assembled samples that represented the extraordinary human diversity of India—the last time I checked, the collection included more than three hundred groups and more than eighteen thousand individual DNA samples. These had been assembled by students from all over India who had visited villages and collected blood samples from people whose grandparents were from the same location and group. From the CCMB collection, we selected twenty-five groups that were as diverse as possible geographically, culturally, and linguistically. The groups were of traditionally high as well as low social status in the Indian caste system, and also included a number of tribes entirely outside the caste system.

  A few months later, Thangaraj came to our laboratory in Boston, bringing with him this unique and precious set of DNA samples. We analyzed them using a single nucleotide polymorphism (SNP) microarray, a technology that had just recently become available in the United States but was not yet available in India. For this reason, Thangaraj had been granted permission by the Indian government to take the DNA outside India. (There are Indian regulations limiting export of biological material if the research can be achieved within the country.)

  Figure 17a. People in the north primarily speak Indo-European languages and have relatively high proportions of West Eurasian–related ancestry. People in the south primarily speak Dravidian languages and have relatively low proportions of West Eurasian ancestry. Many groups in the north and east speak Sino-Tibetan languages. Isolated tribal groups in the center and east speak Austroasiatic languages.

  Figure 17b. Analysis of the primary patterns of genetic variation in South Asia shows that the majority of Indian groups form a gradient of ancestry, with Indo-European speakers from the north clustering at one extreme, and Dravidian speakers from the south at the other.

  A SNP microarray contains hundreds of thousands of microscopic pixels, each of which is covered by artificially synthesized stretches of DNA from the places in the genome that scientists have chosen to analyze. When a DNA sample is washed over the microarray, the fragments that overlap the artificial DNA sequences bind tightly, and the fragments that do not are washed away. Based on the relative intensity of binding to these bait sequences, a camera that detects fluorescent light can determine which possible genetic types a person carries in his or her genome. The SNP microarray that we analyzed was able to study many hundreds of thousands of positions in the genome that harbor a mutation carried by some people but not others. By studying these positions, it is possible to determine which people are most closely related to which others. The technique is much less expensive than sequencing a whole human genome since it zeroes in on points of interest—those that tend to differ among people and thus provide the greatest density of information about population history.

  To obtain an initial picture of how the samples were related to each other, we used the mathematical technique of principal component analysis, which is also described in the previous chapter on West Eurasian population history, and which finds combinations of single-letter changes in DNA that are most informative about the differences among people. Using this method to display Indian genetic data on a two-dimensional graph, we found that the samples spread out along a line. At the far extreme of the line were West Eurasian individuals—Europeans, central Asians, and Near Easterners—which we had included in the analysis for the sake of comparison. We called the non–West Eurasian part of the line the “Indian Cline”: a gradient of variation among Indian groups that pointed on the plot like an arrow directly at West Eurasians.19

  A gradient in a principal component analysis plot can be caused by several quite different histories, but such a striking pattern led us to guess that many Indian groups today might be mixtures, in different proportions, of a West Eurasian–related ancestral population and another very different population. Seeing that the southernmost groups in India—which also spoke Dravidian languages—tended to be farthest away from West Eurasians in the plot, we explored a model in which Indians today are formed from a mixture of two ancestral populations, and we evaluated the consistency of this model with the data.

  To test whether mixture occurred, we had to develop new methods. The methods that we applied in 2010 to show that mixture had occurred between Neanderthals and modern humans20 were in fact primarily developed to study Indian population history.

  We first tested the hypothesis that Europeans and Indians descend from a common ancestral population that split at an earlier time from the ancestors of East Asians such as Han Chinese. We identified DNA letters where European and Indian genomes differed, and then measured how often Chinese samples had the genetic types seen in Europeans or Indians. We found that Chinese clearly share more DNA letters with Indians than they do with Europeans. That ruled out the possibility that Europeans and Indians descended from a common homogeneous ancestral population since their separation from the ancestors of Chinese.

  We then tested the alternative hypothesis that Chinese and Indians descend from a common ancestral population since their separation from the ancestors of Europeans. However, this scenario did not hold up either: European groups are more closely related to all Indians than to all Chinese.

  We found that the frequencies of the genetic mutations seen in all Indians are, on average, intermediate between those in Europeans and East Asians. The only way that this pattern could arise was through mixture of ancient populations—one related to Europeans, central Asians, and Near Easterners, and another related distantly to East Asians.

  We initially called the first population “West Eurasians,” as a way of referring to the large set of populations in Europe, the Near East, and central Asia, among which there are only modest differences in the frequencies of genetic mutations from one group to another. These differences are typically about ten times smaller than the differences between Europeans and the people of East Asia. It was striking to find that one of the two populations contributing to the ancestry of Indians today grouped with West Eurasians. This looked to us like the easternmost edge of the ancient distribution of West Eurasian ancestry, where it had mixed with other very different people. We could see that the other population was more closely related to present-day East Asians such as Chinese, but was also clearly tens of thousands of years separated from them. So it represented an early-diverging lineage that contributed to people living today in South Asia but not much to people living anywhere else.

  Having identified the mixture, we searched for present-day Indian populations that might have escaped it. All the populations on the mainland had some West Eurasian–related ancestry. However, the people of Little Andaman Island had none. The Andamanese were consistent with being isolated descendants of an ancient East Asian–related population that contributed to South Asians. The indigenous people of Little Andaman Island, despite a census size of fewer than one hundred, turned out to be key to understanding the population history of India.

  The Mixing of East and West

  The tensest twenty-four hours of my scientific career came in October 2008, when my collaborator Nick Patterson and I traveled 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.” Singh and Thangaraj objected to this formulation because, they argued, it implied that West Eura
sian 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 East and Europe. Based on their own mitochondrial DNA studies, it was clear to them that the great majority of mitochondrial DNA lineages present in India today had resided in the subcontinent for many tens of thousands of years.21 They did not want to be part of a study that suggested a major West Eurasian incursion into India without being absolutely certain as to how the whole-genome data could be reconciled with their mitochondrial DNA findings. They also implied that the suggestion of a migration from West Eurasia would be politically explosive. They did not explicitly say this, but it had obvious overtones of the idea that migration from outside India had a transformative effect on the subcontinent.

  Singh and Thangaraj suggested the term “genetic sharing” to describe the relationship between West Eurasians and Indians, a formulation that could imply common descent from an ancestral population. However, we knew from our genetic studies that a real and profound mixture between two different populations had occurred and made a contribution to the ancestry of almost every Indian living today, while their suggestion left open the possibility that no mixture had happened. We came to a standstill. At the time I felt that we were being prevented by political considerations from revealing what we had found.

  That evening, as the fireworks of Diwali, one of the most important holidays of the Hindu year, crackled, and as young boys threw sparklers beneath the wheels of moving trucks outside our compound, Patterson and I holed up in his guest room at Singh and Thangaraj’s scientific institute and tried to understand what was going on. 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 issues.