Visitors at the archeological site of Mohenjo-daro in Sindh province, Pakistan, one of the main center of the Indus civilization. Waqar Hussain/EPA Wazir Chand is explaining life 4,000 years ago.

He points to the rocky mounds looming over a huddle of brick houses, a herd of black buffalo and a few stunted trees.

The rising sun burns off a chill mist over the north-west Indian plains.

A low rise was a fortification, Chand says, and a darker patch of red earth hides the site of an altar. Nimbly stepping around piles of buffalo dung, he points to a slight depression. This, apparently, was a pit that may have been a reservoir.

To the casual onlooker, Rakhigarhi is unimpressive. Yet the rubbish-strewn mounds and fields around and under this Indian village are set to deliver the answer to one of the deepest secrets of ancient times.

Rakhigarhi is a key site in the Indus Valley civilisation, which ruled a more than 1m sq km swath of the Asian subcontinent during the bronze age and was as advanced and powerful as its better known contemporary counterparts in Egypt and Mesopotamia.

Archaeologists have learned much about the civilisation since it was discovered along the Indus river in present day Pakistan about a century ago. Excavations have since uncovered huge carefully designed cities with massive grain stores, metal workshops, public baths, dockyards and household plumbing, as well as stunning distinctive seals. But many perplexing questions remain unanswered.

One has stood out: who exactly were the people of the Indus civilisation? A response may come within weeks.

“Our research will most definitely provide an answer. This will be a major breakthrough. I am very excited,” said Vasant Shinde, an Indian archaeologist leading current excavations at Rakhigarhi, which was discovered in 1965.

Shinde’s conclusions will be published in the new year. They are based on DNA sequences derived from four skeletons – of two men, a woman and a child – excavated eight months ago and checked against DNA data from tens of thousands of people from all across the subcontinent, central Asia and Iran.

“The DNA is likely to be incredibly interesting and it has the potential to address all sorts of challenging questions about the population history of the people of the Indus civilisation,” said Dr Cameron Petrie, an expert in south Asian and Iranian archaeology at the University of Cambridge.

The origins of the people of the Indus Valley civilisation has prompted a long-running argument that has lasted for more than five decades.

Some scholars have suggested that they were originally migrants from upland plateaux to the west. Others have maintained the civilisation was made up of indigenous local groups, while some have said it was a mixture of both, and part of a network of different communities in the region. Experts have also debated whether the civilisation succumbed to a traumatic invasion by so-called “Aryans” whose chariots they were unable to resist, or in fact peaceably assimilated a series of waves of migration over many decades or centuries.

The new data will provide definitive answers, at least for the population of Rakhigarhi.

“There is already evidence of intermarriage and mixing through trade and so forth for a long time and the DNA will tell us for sure,” Shinde said.

The conclusions from the new research on the skeletal DNA sample – though focused on the bronze age – are likely to be controversial in a region riven by religious, ethnic and nationalist tensions.

Hostile neighbours India and Pakistan have fought three wars since winning their independence from the British in 1947, and have long squabbled over the true centre of the Indus civilisation, which straddles the border between the countries.

Shinde said Rakhigarhi was a bigger city than either Mohenjo-daro or Harrapa, two sites in Pakistan previously considered the centre of the Indus civilisation.

Some in India will also be keen to claim any new research supports their belief that the Rig Veda, an ancient text sacred to Hindus compiled shortly after the demise of the Indus Valley civilisation, is reliable as an historical record.

The question of links between today’s inhabitants of the area and those who lived, farmed, and died here millennia ago has also prompted fierce argument.

There are other mysteries too. The Indus Valley civilisation flourished for three thousand years before disappearing suddenly around 1500 BC. Theories range from the drying up of local rivers to an epidemic. Recently, research has focused on climate change undermining the irrigation-based agriculture on which an advanced urban society was ultimately dependent.

Soil samples around the skeletons from which samples were sent for DNA analysis have also been despatched. Traces of parasites may tell archaeologists what the people of the Indus Valley civilisation ate. Three-dimensional modelling technology will also allow a reconstruction of the physical appearance of the dead.

“For the first time we will see the face of these people,” Shinde said.

In Rakhigarhi village, there are mixed emotions about the forthcoming revelations about the site.

Chand, the self-appointed guide and amateur expert, hopes the local government will finally fulfil longstanding promises to build a museum, an auditorium and hotel for tourists there.

“This is a neglected site and now that will change. This place should be as popular as the Taj Mahal. There should be hundreds, thousands of visitors coming,” Chand told the Guardian.

A brief glance at the rubbish strewn middens which the mounds of the ancient city have become, indicates the work to be done before Rakhigarhi becomes a major attraction. The inhabitants of today’s Rakhigarhi lack many of the facilities enjoyed by those who lived there in the bronze age. Raj Bhi Malik, the village head, sees an opportunity to develop more than the site’s ancient heritage.

“We want a museum and all that certainly … but also clean drinking water, proper sanitation, an animal hospital, a clinic too,” Malik said.