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DNA found in ancient graveyard provides insight into Indus Valley Civilization

The first sequenced genome from an archaeological site associated with the ancient Indus Valley Civilization came from this woman buried at the city of Rakhigarhi. Credit: Vasant Shinde/Cell
The research is providing unprecedented detail about the relatively unknown 5,000-year-old civilization, including the ancestry of the people who lived there and the spread of agriculture and language in the region.
by Mahrukh Sarwar

At its peak, the Indus Valley Civilization (IVC) stretched from what is now Afghanistan and Pakistan all the way to the northwestern part of India. Even 5,000 years ago, they had urban centers and towns with baked brick houses and an elaborate underground drainage system. The use of standardized weights and measures was common for trade, and there existed a complex writing system for communication.

Then by 1800 BCE, the civilization began to decline.

Not much is known about the Indus people. Their language, consisting of symbols, drawings and other writings, continues to baffle scholars and has not yet been deciphered. It was only in 1921 when excavations took place at the ancient site of Harappa, then in British India, which uncovered a vast expanse of mounds covering the remains of once flourishing cities, that archeologists were able to understand the scale of the Bronze Age civilization that had existed there. Shortly afterwards, Mohenjo-daro, one of the world’s earliest major cities, was discovered west of the Indus River in what is today the Sindh province of Pakistan.

The first images of the announcement of the discovery of the ancient Indus Valley Civilization published in The Illustrated London News on September 20, 1924.

By studying antiquities, archeologists can find out how prehistoric societies lived and worked but the study of ancient human DNA can give us an insight into the shifting ancestry of these populations over time as well as the development of many cultural innovations such as agriculture and language.

For the first time, geneticists have been able to extract a small amount of preserved DNA from a skeletal remain in a 4,500-year-old graveyard at the site of one of the largest known towns of the IVC in the present-day state of Haryana in India. The research was published in the academic journal Cell on September 5 this year.

Talking to MIT Technology Review, co-author of the study and Harvard University geneticist Vagheesh Narasimhan said, “The biggest challenge was technical. The recovery of ancient DNA from hot and humid climates is extremely difficult due to degradation in such environments. Thus, only one of more than 60 skeletal samples screened for ancient DNA appeared to have any signature showing that it contained any authentic ancient DNA. We then made more than a 100 attempts on the sample, the largest number on any single sample in the field to recover data. By pooling information from all of these attempts, we managed to get enough data to do high-resolution population genetic analysis.”

Read more: She created a better way to sequence a genome

However, the genome from a single human sample is not representative of the entire IVC, also known as the Harappan Civilization, which at its peak had a population of over five million people. Fortunately, two authors of the Cell paper along with an international collaboration of geneticists, archaeologists and anthropologists from North America, Europe, Central Asia and South Asia, have published a related paper in the journal Science.

The study has analyzed the genome-wide data from 523 never before-studied ancient individuals spanning the last 8,000 years. These samples were mostly from Central Asia and northernmost South Asia, including regions such as the Iron Age Swat Valley in Pakistan and the Eurasian Steppe, a vast belt of grasslands stretching from northern China in the east to eastern Europe in the west.

The Science paper is the largest-ever study of ancient human DNA and it has increased the worldwide total of published ancient genomes by about 25 percent.

Digging into the past

Among the samples studied in the paper were 11 found in what is now Iran and Turkmenistan, and had a distinctive mix of ancestry different from the people around them. The skeletal samples had an Iranian-related ancestry specific to South Asia and were also related to Southeast Asian hunter-gatherers. Scientists propose that these were likely migrants from the IVC,  since they were found in sites known to have exchanged objects with the civilization.

Since the genome of the ancient human found in the Rakhigarhi graveyard in Haryana also matched those of these 11, scientists believe that these 12 samples together could be broadly representative of the ancestry that was present in the region during that time.

The researchers have analyzed these genomes by comparing them to one another as well as to previously sequenced genomes. They have compiled this information with other records and studied it from the lens of different scientific fields. Ron Pinhasi, co-senior author of the Science paper, said in a statement, “One of the most exciting aspects of this study is the way it integrates genetics with archaeology and linguistics. The new results emerged after combining data, methods and perspectives from diverse academic disciplines, an integrative approach that provides much more information about the past than any one of these disciplines could alone.”

By doing this, the researchers have been able to find out key details about various parts of the region from the Mesolithic Era (about 12,000 years ago) to the Iron Age (until around 2,000 years ago).

Read more: Study Finds 1,317 Knocked-out Genes in DNA Sample From Pakistan

“The introduction of new sampling methodologies has allowed us to minimize damage to skeletons, while maximizing the chance of obtaining genetic data from regions where DNA preservation is often poor,” said Pinhasi.

“We learned an incredible amount about samples that have extremely low levels of DNA preservation, and developed this procedure to extract DNA even in such conditions,” added Narasimhan. “We also learned a lot about how to perform sensitive analysis even when the coverage of data that we had was thin. Thus, our knowledge both on the molecular biology end of things as well as the informatics end of things have been enhanced by doing this study.”

The geographic location of the archaeological site of Rakhigarhi is labelled in blue and other significant Harappan sites are labelled in red to define the geographic range of the Indus Valley Civilization. The sites in the north and west which are labelled in black are those with which IVC people were in cultural contact. The areas specifically highlighted in yellow are the sites of Gonur and Shahr-i-Sokhta, which are the source of the 11 outlier individuals who were genetically similar to the Rakhigarhi individual. Credit: Vasant Shinde/Cell

Shifting ancestry over the ages

David Reich, professor of genetics at Harvard Medical School (HMS) and co-senior author of both papers, explained that with the help of technological advances and a larger number of samples, it was now possible to find subtle interactions between populations as well as outliers within populations.

The ancient IVC genome held some surprises for the researchers. The DNA did not contain any ancestry from steppe pastoralists, which is ubiquitous among modern South Asians. This is consistent with the model that that group hadn’t arrived in the region yet, and Steppe pastoralist ancestry only arrived after the decline of the civilization.

Earlier, scholars had hypothesized that there had been a large migration of farmers from Anatolia, now known as Turkey, into the region which led to the propagation of Indo-European languages and as well as farming. However, the wide scale study published in Science found that modern day South Asians have little ancestry from Anatolians so there was no wide-scale movement into the region. Instead, scholars believe that present-day people in the area have descended from a subgroup of herders from the Eurasian Steppe who moved into Central and South Asia thousands of years ago.

Moreover, the paper has shown that after the decline of the Harappan Civilization between 4,000 and 3,500 years ago, a portion of the group to which the 12 samples belonged mixed with people coming from the north who had steppe pastoralist ancestry, forming the Ancestral North Indians, one of the two primary ancestral populations of present-day people in the region. The other primary source population, the Ancestral South Indians, were formed when a portion of the original group mixed with people from peninsular India.

Another line of evidence showing a steppe origin is that researchers analyzed 140 modern South Asian groups, and out of them, a handful showed significant amount of ancestry from the steppe. Most of these populations were historical priestly groups, including Brahmins.

“Mixtures of the Ancestral North Indians and Ancestral South Indians—both of whom owe their primary ancestry to people like that of the IVC individual we sequenced—form the primary ancestry of South Asians today,” said co-author Nick Patterson, research fellow in genetics at HMS and a staff scientist at the Broad Institute of MIT and Harvard. So this study directly ties present-day South Asians to the ancient people of South Asia’s first civilization.

Spread of Indo-European languages and agriculture

 The genetic evidence found through this study also posits a new argument in favor of a steppe origin Indo-European languages spoken in South Asia. Indo-European languages including Urdu, Punjabi, Persian, Hindi, Russian, Spanish and English are the largest language family on Earth. The source and spread of these languages has been a source of debate among the scientific community for years.

The study also found genetic patterns connecting speakers of the Indo-Iranian and Balto-Slavic branches of Indo-European. Researchers discovered that modern-day speakers of both branches descend from a subgroup of steppe pastoralists who moved towards Europe almost 5,000 years ago and then spread back eastward into Central and South Asia in the next 1,500 years. This ancient migration helps explain why there are shared linguistic features between the two branches of Indo-European languages, which are separated by large distances.

These objects were recovered from north of the head of the buried individual. Certain aspects of the ceramics are characteristically Harappan.

 Additionally, the study helps explain cultural transformation of agriculture spread in the region. Due to shared ancestry between modern South Asians and early Iranian farmers, scholars had earlier thought that agriculture arrived in the Indo-Pakistani region via migration from the Fertile Crescent of the Middle East, a boomerang-shaped region that includes parts of  modern-day Iraq, Israel, Palestine, Syria, Lebanon, Egypt, Turkey, Jordan and Iran.

 However, the Iranian-related ancestry in the IVC comes from early Iranian farmers, herders, and hunter-gatherers before their ancestors separated. This contradicts the hypothesis that the shared ancestry between early Iranians and South Asians reflects a large-scale spread of western Iranian farmers east. Instead, sampled ancient genomes from the Iranian plateau and the Harappan Civilization descend from different groups of hunter-gatherers who began farming without being connected by substantial movement of people. This suggests that farming could have spread through an exchange of ideas rather than a mass migration, or perhaps even arose independently in South Asia.

Looking forward

Speaking to MIT Technology Review, Asko Parpola, professor emeritus of Indology and South Asian Studies at the University of Helsinki, recognized as the leading  expert on the Indus script, said, “The possibility of analyzing ancient DNA from human bodies belonging to specific cultures has revolutionized archaeology. The analysis confirms the detailed reconstruction based on historical linguistics and archaeology (without DNA) that I have been developing for decades, summarized in my book The Roots of Hinduism: The Early Aryans and the Indus Civilization.”

However, he also cautioned that analyzing the genome of only a few skeletal samples limits the conclusions that can be drawn about the entire population of the Harappan Civilization.  “To confirm the results of the Science article beyond any reasonable doubt, more bodies of Indus people should be analyzed,” advised Parpola, who was not involved with the study.

Narasimhan, one of the researchers who led the research, confirmed that the team is expanding the scope of research. “We are in the process of screening samples from other IVC sites. One of the hypotheses that this paper has thrown up is that the IVC was a heterogenous civilization given its large geographic range,” he said. “We want to directly test this hypothesis as well as sample other sites from India and Pakistan both before and after the IVC to understand longer term population dynamics.”

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