BURIAL SITE: A team of scientists in Rakhigarhi working on one of the four human skeletons that were sampled for ancient DNA (Manoj Dhaka/AFP)

The 'petrous bone' is an inelegant but useful chunk of the human skull -- basically it protects your inner ear. But that's not all it protects. In recent years, genetic scientists working to extract DNA from ancient skeletons have discovered that, thanks to the extreme density of a particular region of the petrous bone (the bit shielding the cochlea, since you ask), they could sometimes harvest 100 times more DNA from it than from any other remaining tissue.

Now this somewhat macabre innovation may well resolve one of the most heated debates about the history of India.

As the dust of the petrous bones of a 4,500-year-old skeleton from Rakhigarhi, Haryana, settles, we may have the answer to a few questions that have vexed some of the best minds in history and science -- and a lot of politicians along the way:

Q: Were the people of the Harappan civilisation the original source of the Sanskritic language and culture of Vedic Hinduism? A: No.

Q: Do their genes survive as a significant component in India's current population? A: Most definitely.

Q: Were they closer to popular perceptions of 'Aryans' or of 'Dravidians'? A: Dravidians.

Q: Were they more akin to the South Indians or North Indians of today? A: South Indians.

All loaded questions, of course. A paper suggesting these conclusions is likely to be online in September and later published in the journal Science.

These revelations are part of the long-awaited and much-postponed results of an excavation conducted in 2015 by a team led by Dr Vasant Shinde, an archaeologist and vice chancellor of Pune's Deccan College.

Why did it take so long? One answer was on offer exactly a year ago when this writer spoke to Shinde who was then holding out the promise of publishing the findings in September 2017. "It's a very politically sensitive issue," he said.

NOT THE SAME: The Indus Valley people lacked the steppe and ancestry that marks many North Indian high castes today (Photograph by Bandeep Singh, for representational purpose only)

The archaeologist was referring to the fact that any research dealing with the Harappan civilisation would have to confront the Hindutva agenda of the government of India -- whose politics demands a genuflection to Vedic Hinduism as the origin of Indian civilisation.

For historians or anyone working on the Harappan or Indus Valley Civilisation, this is a complication. Indeed, when the Indus Valley Civilisation was first 'discovered' in the 1920s, colonial archaeologists quickly identified it as evidence of a pre-Vedic culture, which, they theorised, had been utterly destroyed by the advent of 'Aryan' invaders from the Northwest who represented the dawn of Hindu India.

In later years, most mainstream historians have discarded the 'Aryan invasion theory' or 'AIT' as an oversimplification -- while retaining a chronology that places the Vedic civilisation as a successor to the Indus Valley Civilisation.

And the Aryan invasion theory continues to rankle Hindutva nationalists even as it has taken root in South India as the core narrative of a popular politics which sees the Indus Valley Civilisation as a Dravidian culture that has survived 'Brahminical' invaders only south of the Vindhyas.

GREAT EXPECTATIONS

Meanwhile, the reality of who the Indus Valley Civilisation people were has remained a mystery. Shinde knows all too well the incongruous burden of expectations that has now settled on a 4,500-year-old resident (classified as 'I4411') of Rakhigarhi, a ramshackle village in the dusty khadar or floodplain of an almost extinguished river.

You may know of Rakhigarhi too: over the last decade-and-a-half, the name has become a staple of school textbooks, tourism pamphlets and journalism-invoked as the largest Harappan/Indus Valley site in India. In fact, since 2014, it has been regularly cited as 'even larger than Mohenjo-Daro' -- the archaeological site in Sindh, Pakistan, first excavated in the 1920s.

Despite the element of hyperbole, excavations here -- conducted intermittently since the late 1960s -- have established its significance as an extensive and enduring urban settlement with its beginnings arguably as early as the 7th millennium BCE.

Most importantly, the village with its seven teelas or mounds has produced enough evidence to identify it as the site of a 'mature' Harappan settlement of the 2nd and 3rd millennium BCE. In other words, a town that witnessed the rise and -- more than 4,000 years ago -- the mysterious fall, of India's first urban civilisation.

If the 'rewriting of Indian history' was lurching ahead on the Hindutva fringe of academia, science was steadily advancing in another direction

On the face of it, the single most startling revelation of the Rakhigarhi research may be what it doesn't talk about: the complete absence of any reference to the genetic marker R1a1 in the ancient DNA retrieved from the site.

This is significant because R1a1, often loosely called 'the 'Aryan gene', is now understood to have originated in a population of Bronze Age pastoralists who dispersed from a homeland in the Central Asian 'Pontic steppe' (the grasslands sprawling between the Black Sea and the Caspian) some 4,000 years ago. The genetic impact of their migrations has left a particularly strong and 'sex-biased', (i.e. male-driven) imprint on the populations of two geographically distant but linguistically related parts of the world: Northern India and Northern Europe.

READ | Why DNA findings from Rakhigarhi site are controversial

"We are not discussing R1a," says Niraj Rai, the lead genetic researcher on the Rakhigarhi DNA project. "R1a is not there." The admission came wrapped in some prevarication but was all the more telling given that the Rakhigarhi data presented in this paper are derived primarily from the genetic material of 'I4411', a male individual -- R1a is a mutation seen only in samples of the male Y chromosome.

The absence of this genetic imprint in the first genome sample of an individual from the Indus Valley culture will bolster what is already a consensus among genetic scientists, historians and philologists: that the Indus Valley culture preceded and was distinct from this population of cattle-herding, horse-rearing, chariot-driving, battle-axe-wielding, proto-Sanskrit-speaking migrants whose ancestry is most evident in high-caste North Indian communities today.

Rai points out that the fact that haplogroup R1a did not show up in the Rakhigarhi sample could be attributed to the limited amount of genetic data retrieved. Or it could be because it's just not there. "We do not have much coverage of the Y chromosome regions [of the genome]," Rai says, revealing that they had retrieved more data from the mitochondrial and autosomal DNA in their sample (mitochondrial DNA reflects maternal descent and autosomal tests reveal genetic information inherited from both parents).

However, he was emphatic in acknowledging that while "a mass movement of Central Asians happened and significantly changed the South Asian genetic make-up", the inhabitants of ancient Rakhigarhi "do not have any affinity with the Central Asians". In other words, while the citizens of the Indus Valley Civilisation had none of this ancestry, you, dear average Indian reader, owe 17.5 per cent of your male lineage to people from the Steppe.

It's worth noting that this genetic footprint is of an entirely more impressive order than the relatively inconsequential biological legacy of Islamic or European colonial invasions that often preoccupy the political imagination in India.

So much for what we have now learned about who our 4,500-year-old ancestor 'I4411' was not. What about who he was? The short answer, says Rai, is that I4411 "has more affinity with South Indian tribal populations". Notably, the Irula in the Nilgiri highlands.

A draft of the paper argues that this individual could be modelled as part of a clade [a group sharing descent from a common ancestor] with the Irula but not with groups with higher proportions of West Eurasian related ancestry such as Punjabis, and goes on to suggest that the inhabitants of Rakhigarhi probably spoke an early Dravidian language.

Most mainstream historians have discarded the 'Aryan invasion theory' or 'AIT' as an oversimplification

However, the results also show clear evidence of mixing with another population from outside the subcontinent, labelled 'Iranian agriculturalist'. This is a population that had been identified in earlier studies of ancient DNA and is consistent with the hypothesis that some agricultural technologies were introduced to the subcontinent through contact with the 'fertile crescent' in West Asia, widely regarded as one of the birthplaces of Eurasian agriculture in the 5th-8th millennium BC.

For an older generation of Indians, the Rakhigarhi results may sound like a reboot of half-remembered schoolbooks: 'Dravidian' Harappans followed by Vedic horsemen from the Steppe. And for anyone who has been following more recent developments in population genetics too, the latest findings will sound familiar.

Meanwhile, in the popular press, coverage of recent discoveries in the archaeology or genetics of Harappan India has been obsessively and distractingly focused on the 'Aryan invasion theory'. What gives? And why does it matter? The answer has to do with the fact that recent years have been a very busy time in ancient Indian history. And modern Indian politics.

SKULDUGGERY

In the months preceding the news of the Rakhigarhi findings, anticipation was high, and fuelled by a series of related research papers and their journalistic glosses, an amusing if acrimonious debate erupted in the social media and the blogosphere. Shinde for his part was given to dropping broad hints that the Rakhigarhi results would point to a 'continuity' between the population of the ancient town and its present-day inhabitants (predominantly Jats, a population marked by pronounced R1a Steppe ancestry).

Perhaps it should be no surprise, in these fractious times, that fake news would be deployed as a weapon in the civil war that has consumed ancient Indian history. In January this year, a Hindi newspaper carried an article purportedly based on an interview with Rai, asserting that the Rakhigarhi DNA was, in fact, a close match for North Indian Brahmins and that the findings would establish that India was the 'native place' of the Indo-European language family.

"Utter crud!" was the reaction of David Wesolowski, host of the Eurogenes blog-well regarded by some of the world's leading geneticists as a go-to site for the latest debate. Wesolowski's site witnessed frequent arguments over the likelihood that Rakhigarhi DNA would turn up the R1a1 marker.

Here, extended and nuanced discussions of the finer points of molecular evidence would often conclude with kiss-offs along the lines of "you're an idiot" or "you're going to need psychiatric help when the results are out". In the event, Wesolowski's own prediction, "Expect no R1a in Harappa but a lot of ASI [Ancestral South Indian]", would prove to be spot on.

The single most startling revelation of the Rakhigarhi research may be the complete absence of any reference to the genetic marker R1a1, often loosely called 'the 'Aryan gene'

Behind the surly invective and the journalistic misdirection were rumours and whispers of a face-off between a rising tide of scientific evidence and the political pressures of nativist, Hindutva sentiments.

The saga of 'Hindutvist history' is by now another familiar tale, with its origins in early Hindu nationalist reaction to colonial archaeology and linguistics, a monomaniacal obsession with refuting the 'Aryan invasion theory'.

It is perhaps most clearly expressed in an irate passage from former RSS sarsanghchalak M.S. Golwalkar's screed Bunch of Thoughts (1966): "It was the wily foreigner, the Britisher, who carried on the insidious propaganda that we were never one nation, that we were never the children of the soil but mere upstarts having no better claim than the foreign hordes of Muslims or the British over this country."

In recent years, this resentful impulse has focused particularly intently on asserting the wishful conclusion that the Indus Valley Civilisation itself must be 'Vedic'. This has understandably gained traction in the popular imagination in tandem with the political rise of Hindutva. In 2013, Amish Tripathi, a bestselling author of 'Hinduistical fantasy' novels, gave vent to the keening desire for a 'Vedic IVC' in a short fiction in which future archaeologists discover clinching evidence "that the Indus Valley Civilisation and the Vedic-erroneously called Aryan-civilisation were one and the same." The story is poignantly titled, 'Science Validates Vedic History'.

Inevitably, the advent of a BJP majority government in the general elections of 2014 has given new energy -- and funding-to the self-gratifying urges of Hindutvist history.

The Rakhigarhi findings build on earlier work by some of the same researchers revealing the story of population migrations from the Eurasian steppe at the close of the Indus Valley Civilisation. What emerges is a remarkable parallel in the prehistory of South Asia and Northern Europe as populations from the steppe advanced into both subcontinents. The migrations produce the population mixes that now inhabit both areas and help explain the linguistic connections between them.

The charge has been led by the Union minister for culture Mahesh Sharma, who has prioritised the project of 'rewriting Indian history', whether by appointing a pliant obscurantist as head of the Indian Council of Historical Research or promoting the 'research' of para-scientific outfits such as I-SERVE (Institute of Scientific Research on Vedas) and a former customs officer who uses hobby astronomy software to establish that "thus Shri Ram was born on 10th January in 5114 BC...around 12 to 1 noontime [in Ayodhya]".

In March this year a Reuters report revealed details of a meeting of a 'history committee' convened by Sharma at the office of the Director General of the Archaeological Survey of India in January 2017. Its task, according to the committee chairman K.N. Dixit, was "to present a report that will help the government rewrite certain aspects of ancient history".

The minutes of the meeting apparently "set out its aims: to use evidence such as archaeological finds and DNA to prove that today's Hindus are directly descended from the land's first inhabitants many thousands of years ago, and make the case that ancient Hindu scriptures are fact, not myth".

Yet, if the 'rewriting of Indian history' was lurching ahead on the Hindutva fringe of academia, mainstream science was steadily advancing in quite another direction.

In March this year, the Harvard population geneticist David Reich published an overview of the state of research in his field, the surprise bestseller Who We Are and How We Got Here, including an account of how the extreme sensitivity of leading Indian scientists about earlier evidence suggesting an ancient migration of Eurasian people from the Northwest into the subcontinent had nearly scuppered an important scientific collaboration in 2008.

The Indian scientists Lalji Singh and K. Thangaraj "implied that the suggestion of a migration would be politically explosive", Reich writes. The issue was ultimately resolved by means of a terminological sleight-of-hand -- using the nomenclature 'Ancestral South Indian' (ASI) and 'Ancestral North Indian' (ANI) to obscure the revelation that ANI represented a population with a significant genetic contribution from outside the subcontinent.

But the same dynamic appears to have emerged this year around a paper involving both Reich and his team at Harvard on the one hand and the scientists leading the Rakhigarhi project on the other. Entitled, rather flatly, The Genomic Formation of South and Central Asia, this paper (usually referred to by the shorthand 'M Narasimhan et al') -- made public as a 'pre print' in April -- would make headlines in the Indian press and social media and reveal some more of the political pressures that colour research on ancient Indian history today.

Shinde said that he had complained to Reich about an earlier draft of that paper, and insisted that any reference to 'migrations' into South Asia be avoided. Or else. He suggested the more ambivalent term 'interaction' be used instead.

As the results of the Rakhigarhi study leak steadily into the public domain, a political backlash seems inevitable

Given that Shinde controlled access to the Rakhigarhi samples which Reich was keen to work on, this would have been a potent threat, and indeed the paper manages to eschew the term 'migration' entirely while ultimately making more potent statements about the impact of post-Harappan 'Middle to Late Bronze Age' (MLBA) Steppe populations on the Indian gene pool.

However, the timing of the paper remains curious to say the least, given that it would have benefitted from the Rakhigarhi data which it seemed to pre-empt -- despite the fact that several of its co-authors, including Rai, Shinde, Thangaraj, Narasimhan and Reich now share credit for the mysteriously delayed paper.

The official word on this was that the Rakhigarhi research was behind schedule due to the 'contamination of one sample', but at the time the geneticist community was abuzz with rumours that the slowdown was because of the Indian team's discomfort with politically inconvenient results.

According to one US-based researcher, who prefers to remain anonymous, "It was common knowledge through the grapevine that the Harvard team became impatient and eventually pushed to release their preprint before Indian colleagues were totally comfortable. Some samples [read 'Rakhigarhi'] were removed because of disagreements between collaborators."

In more recent conversations with this writer, Shinde seemed intent on dissembling the results of his team's paper, offering that the results showed that Rakhigarhi's inhabitants were "just like the locals with some contact with South Indian tribals". Peculiarly, in a recent magazine interview, Shinde is convinced that the ancient people of Rakhigarhi were "tall and sharp-featured like the modern Haryanvis", leading his interviewer to label Wazir Chand Saroae, a prominent local historian of Rakhigarhi and a self-identified Dalit, as a 'Sirohi Jat'.

However, Shinde is no geneticist, and from what we now know, the Rakhigarhi study endorses the findings of the Narasimhan paper -- indeed, it can be seen as a companion piece to that earlier work of the common authors.

Significantly, while Narasimhan and others predicted a model of the Harappan genome using samples of DNA from ancient skeletons of apparent Indus Valley 'visitors' found in sites that were in trading contact with the Harappans, as well as remains of post-Harappan (1200-BC-1 CE) individuals from Swat, the Rakhigarhi paper suggests that this model was accurate. It recommends that the Narasimhan paper's tentative label of 'Indus Valley periphery' for this model is a significant match for I4411 of Rakhigarhi and this genetic cluster should now be recognised as the 'Harappan cline'.

IT'S STILL COMPLICATED

As the results of the Rakhigarhi study leak steadily into the public domain, a political backlash seems inevitable -- and largely predictable: some exultation from Dravidianists and the legion of anti-Hindutva Indians for many of whom the fall of Delhi in the 2014 election is seen as a calamitous replay of that fabled 'Vedic Aryan invasion'.

And we can expect sullen scepticism from the saffron right. Intriguingly, some of the strongest reservations about the Rakhigarhi project have already been expressed from an unexpected quarter: established historians.

Romila Thapar, always a name to reckon with in ancient Indian history and a perennial target of Hindutva polemic, has followed the genetics story keenly, but expressed her reservations about this new science.

As it turns out, the Rakhigarhi research was not without glitches -- apparently, a misleading 'East Asian' signal in the early data is the reason why the Korean scientists who first worked on the samples may not be credited in the final paper.

Meanwhile, another respected historian, Nayanjot Lahiri, declared complete disinterest in the work on 'Harappan DNA', voicing impatience at the obsession with the 'Aryan' question and scepticism about the narrow sampling of ancient genetic material. "As far as the whole question of Aryans and the Vedic component in the Indus Valley Civilisation goes, until the Harappan script is deciphered, it's not decided," she says.

While such responses may be unduly harsh -- even small genetic samples can reveal considerable demographic depth and geneticists are in any case expanding the range of samples at an impressive rate -- some cold water is not amiss.

Certainly any triumphalism or despair on the basis of the emerging genetic profile of the 'Harappan Indians' would be misplaced.

While the evidence does point convincingly to the Indus Valley Civilisation being a distinct population from the 'post-Vedic' population infused with MLBA Steppe genes that stamp India's population to this day, it's also the case that the Indus Valley Civilisation's population represents "the single most important source of ancestry in South Asia" today (as the Narasimhan paper puts it).

Similarly, any impulse to equate the apparent Dravidian affinities of ancient Indus Valley people with the culture and people of South India today or to cast the latter as the 'original inhabitants' of the subcontinent would be an exaggeration.

India is composed of a large number of small populations - Geneticist David Reich

Quite apart from the fact that the people and cultures across the subcontinent today display evidence of having mixed with each other (and populations beyond the borders of present day India) over millennia, there is also no population in the region that can claim to represent a 'pure' lineage of ancient Indians.

Not even the Irula or any other South Indian or 'Adivasi' group. Nor should the evidence of the deeply intertwined genetic history of Indian communities lull anyone into a cosy fable of Indic cosmopolitanism.

What our DNA tells us instead is that while India witnessed phases of extensive genetic mixing for a millennium after the collapse of the Indus Valley Civilisation, this was followed by a long period of deep endogamy -- which has been a uniquely unhealthy stamp of the subcontinent.

Reich summed it up in his recent book: "People tend to think of India, with its more than 1.3 billion people, as having a tremendously large population. But genetically, this is an incorrect way to view the situation. The Han Chinese are truly a large population. They have been mixing freely for thousands of years The truth is that India is composed of a large number of small populations."

UNEARTHING ANCIENT ORIGINS The researchers took extra care to reduce sample contamination to the minimum (Photo courtesy: 2018 Shinde et al)

If this sounds complicated, that's because it is. And the more we discover about India's past, the more complicated it is likely to become. One of the more intriguing asides in the Rakhigarhi study, is a suggestion that while the Indus Valley Civilisation population was evidently multi-ethnic, a persistent genetic 'substructure' also indicates that the Harappan civilisation may have been characterised by 'high within-group endogamy'.

Such teasers indicate that there is still much work to be done; they are reminders not to jump to conclusions or project modern fantasies onto an ancient civilisation we still know so little about. In truth, this has been a pathology of the 'liberal' imagination in India as much as it has been of the 'Hindutvist'.

In that foundational text of Indian nationalism, The Discovery of India, Jawaharlal Nehru could not resist a moment of secularist rapture when he first set eyes on Mohenjo-Daro. "What was the secret of this strength? Where did it come from?" he wondered. "It was, surprisingly enough, a predominantly secular civilisation, and the religious element, though present, did not dominate the scene."

At the end of the day, Nehru's vision too is a modern nationalist fantasy. In the years to come, we are certain to discover much more about the enduringly mysterious civilisation of the Harappans and what elements of culture and social behaviour they bequeathed us -- along with their genes. For now, miraculously, their ears are speaking. We would do well to listen for a while.

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