The largest-ever study of ancient human DNA and the first genome of an individual from the ancient Indus Valley Civilization reveal in unprecedented detail the shifting ancestry of Central and South Asian populations over time.
The research, published online Sept. 5 in a pair of papers in Science and Cell, also answers longstanding questions about the origins of farming and the source of Indo-European languages in South and Central Asia.
Geneticists, archaeologists and anthropologists from North America, Europe, Central Asia and South Asia analyzed the genomes of 524 never before-studied ancient individuals. The work increased the worldwide total of published ancient genomes by about 25 percent.
By comparing these genomes to one another and to previously sequenced genomes, and by putting the information into context alongside archaeological, linguistic and other records, the researchers filled in many of the key details about who lived in various parts of this region from the Mesolithic Era (about 12,000 years ago) to the Iron Age (until around 2,000 years ago) and how they relate to the people who live there today.
“With this many samples, we can detect subtle interactions between populations as well as outliers within populations, something that has only become possible in the last couple of years through technological advances,” said David Reich, co-senior author of both papers and professor of genetics in the Blavatnik Institute at Harvard Medical School.
“These studies speak to two of the most profound cultural transformations in ancient Eurasia—the transition from hunting and gathering to farming and the spread of Indo-European languages, which are spoken today from the British Isles to South Asia—along with the movement of people,” said Vagheesh Narasimhan, co-first author of both papers and a postdoctoral fellow in the Reich lab. “The studies are particularly significant because Central and South Asia are such understudied parts of the world.”
“One of the most exciting aspects of this study is the way it integrates genetics with archaeology and linguistics,” said Ron Pinhasi of the University of Vienna, co-senior author of the Science paper. “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.”
“In addition, the introduction of new sampling methodologies allowed us to minimize damage to skeletons while maximizing the chance of obtaining genetic data from regions where DNA preservation is often poor,” Pinhasi added.
One of the most exciting aspects of this study is the way it integrates genetics with archaeology and linguistics.
Ron Pinhasi
University of Vienna
This problem has been in the air for 200 years or more and it’s now rapidly being sorted out.
Nick Patterson
Research fellow in genetics, HMS
First glimpse of the ancestry of the Indus Valley Civilization
Running from the Himalayas to the Arabian Sea, the Indus River Valley was the site of one of the first civilizations of the ancient world, flourishing between 4,000 and 5,000 years ago. People built towns with populations in the tens of thousands. They used standardized weights and measures and exchanged goods with places as far-flung as East Africa.
But who were they?
Before now, geneticists were unable to extract viable data from skeletons buried at Indus Valley Civilization archaeological sites because the heat and volatile climate of lowland South Asia have degraded most DNA beyond scientists’ ability to analyze it.
The Cell paper changes this.
After screening more than 60 skeletal samples from the largest known town of the Indus Valley Civilization, called Rakhigarhi, the authors found one with a hint of ancient DNA. After more than 100 sequencing attempts, they generated enough data to reach meaningful conclusions.
The ancient woman’s genome matched those of 11 other ancient people reported in the Science paper who lived in what is now Iran and Turkmenistan at sites known to have exchanged objects with the Indus Valley Civilization. All 12 had a distinctive mix of ancestry, including a lineage related to Southeast Asian hunter-gatherers and an Iranian-related lineage specific to South Asia. Because this mix was different from the majority of people living in Iran and Turkmenistan at that time, the authors propose that the 11 individuals reported in the Science paper were migrants, likely from the Indus Valley Civilization.
None of the 12 had evidence of ancestry from steppe pastoralists, consistent with the model that that group hadn’t arrived yet in South Asia.
The Science paper further showed that after the decline of the Indus Valley Civilization between 4,000 and 3,500 years ago, a portion of the group to which these 12 individuals 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 India. A portion of the original group also mixed with people from peninsular India to form the other primary source population, the Ancestral South Indians.
“Mixtures of the Ancestral North Indians and Ancestral South Indians—both of whom owe their primary ancestry to people like that of the Indus Valley Civilization individual we sequenced—form the primary ancestry of South Asians today,” said Patterson.
“The study directly ties present-day South Asians to the ancient peoples of South Asia’s first civilization,” added Narasimhan.
The authors caution that analyzing the genome of only one individual limits the conclusions that can be drawn about the entire population of the Indus Valley Civilization.“My best guess is that the Indus Valley Civilization itself was genetically extremely diverse,” said Patterson. “Additional genomes will surely enrich the picture.”
The study directly ties present-day South Asians to the ancient peoples of South Asia’s first civilization.
Vagheesh Narasimhan
Postdoctoral fellow, HMS
