Genetics and the Origins of Ancient Indian Civilization

In addition to its vast patchwork of languages, cultures and religions, the Indian subcontinent also harbours a huge genetic diversity, second to Africa alone. The question of the origin of all this is an area of heated controversy, not only among scientists, but also among the peoples concerned.

Recently, a scientific paper published in the journal BMC Evolutionary Biology concluded that the genetic ancestry of all modern Indians displays evidence of significant mixing with populations that moved to the subcontinent from northern Iran and the Caspian region some 4,000-5,000 years ago. These findings have reignited the long-simmering and highly politicized debate about the origins of Vedic culure and the Indo-European language family, which includes almost all European languages as well as Persian, Sanskrit and Hindi. Indo-European languages are spoken across northern and central India, and also in Pakistan and Bangladesh. Southern India, on the other hand, is dominated by Dravidian languages.

Many Hindu nationalists are uncomfortable with the idea that the ancient roots of the Indian peoples, or even the origins of the "Vedic Aryans," may lie outside the sacred geography of the subcontinent. Meanwhile, there is often an element of liberal schadenfreude in embracing the narrative that suggests a parallel between the Vedic Aryans as conquering invaders, not unlike the later visitations of Islamic and European empires.

Using arguments that exist outside of politics and nationalism, most geneticists nowadays point to the Pontic steppe as the area of origin of the Indo-European languages. In this model, known as the Indo-Aryan migration theory, Indo-European speaking herdsmen from Central Eurasia and West Asia migrated into the Indian subcontinent and founded the Vedic civilization. Archaeological findings have shown that around 4500 BC, these tribes had domesticated the horse and were probably first to use the wheel. Wheels play an important role in ancient Hinduist texts such as the "Mahabharata" and even today, a chariot wheel symbolizing the "Wheel of Dharma" is printed on the flag of India.

In contrast, the Indigenous Aryans theory, better known as the Out of India model, proposes that the Indo-European languages originated within the Indian subcontinent and that the Indus Valley Civilization wás the Vedic civilization. Proponents of this theory cite archaeological evidence of civilizational and cultural continuity, and various Indian literary sources.

Ten years ago, one could reasonably support the Out of India model from a genetic perspective. The exploration of mitochondrial lineages, the direct maternal ancestry out of Africa, remained the dominant method of inference. That line of evidence strongly suggests that South Asian populations are deeply rooted in the subcontinent.

But other researchers were looking at the descent of males, the direct paternal lineage as recorded by mutations of the Y chromosome. The evidence from these results was more equivocal. One of the more common South Asian Y lineages, R1a1a, is also very common in Eastern Europe and Central Asia.

The discovery of this lineage in the 1990s, by the geneticist Spencer Wells, strongly supported a significant migration from the steppes of Eastern Europe and Central Asia into India in the past 5,000 years. Obviously, this is in conflict with the mitochondrial results. Because R1a1a is not very diverse, it was difficult to get a sense of where or when it may have originated. Many researchers contended that R1a1a may have been indigenous to South Asia.

Today, we know more about R1a1a than we did in the 2000s. Whereas then researchers looked at a few hundred markers on the Y chromosome, or perhaps some regions with very high diversity, today they can sequence most of the Y chromosome. In line with Wells' original suspicion, after looking at whole genomes, many scholars now surmise that R1a1a entered South Asia approximately 4,000-5,000 years ago. The reason R1a1a is not so diverse is that it underwent a massive, recent expansion: not much time has elapsed for mutations to accumulate.

A resolution to the paradox of mtDNA and Y chromosomal lineages pointing in different directions has now presented itself. The answer: migration into India was not sex balanced. This is a major point in the BMC paper. Martin Richards, co-author of the paper, explains: "There's a very marked sex bias in the arrival of new peoples from, ultimately, the steppe zone of Eastern Europe, in the Bronze Age." (This is the case in Europe too, with steppe migrants overwhelmingly male).

With whole genome analysis, one can see that European R1a1a is one lineage, while Central Asian and South Asian R1a1a strains form another. This high resolution allows for both very detailed genealogical information and quite precise genetic dating, so that it can be determined where and when lineages branched off into a new territory. It is notable that the R1a1a lineages of the Scythians, who dwelt north of the Caspian Sea some 4,000 years ago, are the same as Central Asians and South Asians, not Europeans.

The Sarasvati River

The Sarasvati River in North-Western India was once a mighty river along which Indian civilization’s earliest settlements were founded. Bhirrana, a site on the banks of the now-defunct Sarasvati, was a bustling metropolis as far back as 8,000 to 9,000 BC and continued to thrive.

Archaeologists have learned much about this civilization since it was discovered along the Indus river in present day Pakistan about a century ago. Excavations have uncovered huge carefully designed cities with massive grain stores, metal workshops, public baths, dockyards and household plumbing, as well as magnificent works of art.

But after 5000 BC, climate change gradually undermined the irrigation-based agriculture on which the urban society was ultimately dependent. In the same period, sudden and drastic climate change turned the Sahara in North Africa from lakes and grasslands with hippos and giraffes into a vast desert. The Indus Valley Civilization, which once was at least as advanced and powerful as its better known contemporary counterparts in Egypt and Mesopotamia, thus declined. Around 1500 BC the Sarasvati had largely dried out.

In the Vedas, however, the Sarasvati River is extensively mentioned as the “greatest of rivers,” the “mother of floods” and still "glorious" as ever. The Vedas are Hinduism's foundational literary texts, dating from thousands of years before Christ, and are written in a very old Indo-Aryan language called Sanskrit (literally: "holy script").

In ancient Hindu mythology a primordial river goddess, named Danu, is mentioned as the mother of the Danava clan. In Sanskrit, the root word “dānu” means “to flow, drop.” Linguistically, the names of European rivers like the Danube, Dnieper, and Don are also derived from this. These rivers flow across Eastern & Central Europe and seem to trace the gradual westward migration through Europe of ancient Indo-Aryans.

The Danavas revolted against the Devas, and were eventually defeated and banished. So did they end up in Europe? Interestingly, in Irish & Celtic mythology the ancient, supernatural people of Ireland are called the "Tuatha Dé Danann", which is interpreted by some as the "Peoples of Goddess Danu." This is a very speculative story, but there might be some genetic evidence to support it: the R1a1a haplogroup is rare in Ireland, at 2.5% of the population, but the fact that R1a1a is still present in Ireland indicates that people of Indo-Aryan origin settled there in the past.


Many perplexing questions remain unanswered. What is needed to settle the debate is ancient DNA, but unfortunately, there is currently no ancient DNA data from South Asia proper. Researchers are now trying to get genetic results from samples at Rakhigarhi, located near New Delhi. Rakhigarhi is a key site of the Indus Valley civilization, also known as the Harappan Civilisation, that flourished as long back as 5000 to 5500 BC.

The results are still to be made public, but a leak from the investigative team suggested that the genes of the 5,000 years old skeletons, excavated from 22 metres depth, live on in the current residents of Rakhigari. Apart from DNA samples, there is also a continuity in the traditions, food and art in Rakhigarhi. The residents there today use the same pottery designs as seen on the artifacts recovered during digging.

This is not unprecedented. The testing of samples from the Near East and Europe over the period between 5,000 and 10,000 years ago has shown that a few pulses of migration mixed together to create the predominant genetic patterns we see around us today. Should we expect India to be any different? In essence, in broadly the same time frame, we see Indo-European language speakers spreading out both to Europe and to South Asia, causing major population upheavals.

In the second millennium BC, a variety of economies and cultures where thriving and trading with each other in an area that stretched from Greece to Egypt and Mesopotamia. In the 12th century BC a number of them suddenly ceased to exist, along with writing systems, technology, and monumental architecture, due to the incursions of the Sea Peoples into the eastern Mediterranean.

Although not certain, it is likely that most of the Sea Peoples spoke different Indo-European languages, from Mycenaean Greek to the various languages of Italy and Sicily. Here again, droughts in the region have been partly blamed for these ancient, but disruptive migration patterns.

North and South

With whole genomes available for analysis, scientists have reshaped our understanding of the past of South Asia. In 2013, geneticist Priya Moorjani and colleagues published research concluding that two ancient, genetically divergent groups were mixing in the Indian subcontinent 2,000-4,000 years ago. Each contributed around 40-60% of their DNA to most present-day populations.

Moorjani says that: "There were unmixed ANI and ASI groups in the Indian subcontinent 4,000 years ago, but today all native South Asian groups display ancestry from both." ANI and ASI are acronyms for Ancestral North Indians and Ancestral South Indians.

The ANI lineage was genetically very similar to Middle Eastern, Central Asian and European populations. The further to the northwest of the subcontinent you go, the more ANI you will get. Upper class individuals and speakers of Indo-European languages such as Hindi also have more ANI ancestry, the researchers found. (Bengalis and Munda tribes have East Asian heritage that is neither ANI nor ASI).

The ASI lineage, on the other hand, was not close to any group outside of India, and was most common in people indigenous to the Andaman Islands, a remote archipelago in the Bay of Bengal. Those peoples, who still live there today even if their traditional way of life has come under pressure, have a very African appearance.

Social classes

Indian populations, although currently huge in number, were founded by relatively small bands of individuals and are much more highly subdivided than European populations. But whereas European ancestry is mostly carved up by geography, Indian segregation was driven largely by caste, with limited intermarriage.

Similar to the three-fold social structure described by Plato around 400 BC, the ancient Varna system of Hinduism arranges society in four classes: Brahmins (priests and teachers), Kshatriyas (rulers and warriors), Vaishyas (farmers and merchants) and Shudras (laborers). The Dalits (better known as "Untouchables") were called avarna and are not included in this system.

According to Moorjani, the ending of population mixing is correlated with the shifting attitudes towards mixing of the races in ancient texts: “The shift from widespread mixture to strict endogamy that we document is mirrored in ancient Indian texts.”

She estimates that Brahmins and Kshatriyas from the North are 60 per cent ANI, while Dalits from Southern India are 60 per cent ASI. This is exactly the pattern you would expect from Y chromosomal lineages such as R1a1a arriving from Central Asia in the last 4,000-5,000 years. Therefore, Moorjani thinks that "the direction of migration leading to ANI is probably into India."

Ideas and people can move in a bidirectional fashion. Indian religious and philosophical ideas did impact the West through Pythagoras, Plato and Christianity. Conversely, many Indian alphabets quite likely have their origins outside of India, just like lots of other cultural influences such as the creation of Buddha images, or the names of the days of the week.

So too with genes. South Asian genetic markers are found in Southeast Asia, from Thailand to Bali. Conversely, Bengalis, Assamese and Munda peoples show their Southeast Asian heritage on their faces, their genes, and in the case of the Munda, their languages. But this idea of ubiquitous gene flow has limitations.

The distinctive genetic heritage of India, the ASI component, deeply rooted in the subcontinent and not closely related to populations elsewhere, exists in low proportions in Iran and Afghanistan. But with the exception of the Roma people, ASI ancestry is notably absent throughout Western Eurasia aside from India's near neighbors. This suggests there has been very little westward movement out of India over the past few thousand years because, as Moorjani observed, all Indian populations have ASI ancestry within the past 4,000 years.

The migrations of Indo-European language speakers are among the most debated and politicized historical events. But one must not lose the bigger picture: R1a lineages form only about 17.5 % of Indian male lineage, and an even smaller percentage of the female lineage.

The vast majority of Indians owe their ancestry mostly to people from other migrations, starting with the original Out of Africa migrations of around 55,000 to 65,000 years ago, the crossbreeding with Neanderthals, the farming-related migrations from West Asia that probably occurred in multiple waves after 10,000 BC, or the migrations from East Asia the dating of which is yet to be determined.

What's abundantly clear is that India is a multi-source civilization, drawing its cultural impulses, its traditions and practices from a variety of lineages and migration histories. The Out of Africa immigrants, the pioneering explorers who discovered the subcontinent originally and whose lineages still form the bedrock of its population; those who built the Indus Valley civilization whose cultural ideas and practices shaped Indian society in fundamental ways; those who arrived from East Asia, bringing with them the practice of rice cultivation and all that goes with it; and those who came even later for trade or for conquest and chose to stay, all have mingled and contributed to everything that gave the people of India their greatness.

Sources: Razib Khan; A.L. Chavda; Tony Joseph