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Largest DNA Study of Ancient Ancestry of Central and South Asia

December 2, 2019

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History of Medicine
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Mongol invasions and conquests seriously depopulated large areas of Muslim Central Asia. Graphics credit: by derivative work Bkkbrad / *File:Gengis Khan empire-fr.svg: historicair 17:01, 8 October 2007 (UTC) - File:Gengis Khan empire-fr.svg, CC BY-SA 3.0; Wikipedia Commons

Anatomically modern humans (Homo sapiens) reached Central Asia by 50,000 to 40,000 years ago. The Tibetan Plateau is thought to have been reached by 38,000 years ago. Populations who lived in Siberia during the Last Glacial Maximum have also contributed significantly to the populations of both Europe and the Americas. The history of Central Asia concerns the history of the various peoples that have inhabited Central Asia. The lifestyle of such people has been determined primarily by the area's climate and geography. The aridity of the region makes agriculture difficult and distance from the sea cut it off from much trade. Thus, few major cities developed in the region. Nomadic horse peoples of the steppe dominated the area for millennia. Relations between the steppe nomads and the settled people in and around Central Asia were marked by conflict. The nomadic lifestyle was well suited to warfare, and the steppe horse riders became some of the most militarily potent people in the world, due to the devastating techniques and ability of their horse archers. Periodically, tribal leaders or changing conditions would cause several tribes to organize themselves into a single military force, which would then often launch campaigns of conquest, especially into more ?civilized' areas. A few of these types of tribal coalitions included the Huns' invasion of Europe, various Turkic migrations into Transoxiana, the Wu Hu attacks on China and most notably the Mongol conquest of much of Eurasia.

The Mongol Empire existed during the 13th and 14th centuries, and was the largest contiguous land empire in all of history. Originating in Mongolia, the Mongol Empire eventually stretched from Eastern Europe and parts of Central Europe to the Pacific Ocean and the Sea of Japan, extending northwards into the Black Sea, parts of Siberia; eastwards and southwards into the Indian subcontinent, Mainland Southeast Asia and the Iranian Plateau; and westwards as far as Afghanistan, the Levant and the Carpathian Mountains. The Mongol Empire emerged from the unification of several nomadic tribes in the Mongol homeland under the leadership of Genghis Khan (c.? 1162-1227), whom a council proclaimed ruler of all the Mongols in 1206. The empire grew rapidly under his rule and that of his descendants, who sent out invading armies in every direction. The vast transcontinental empire connected the East with the West in an enforced Pax Mongolica, allowing the dissemination and exchange of trade (the silk route), technologies, commodities and ideologies across Eurasia.

The largest-ever study of ancient human DNA, along with 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 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. 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 study 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, subtle interactions between populations, can be detected, as well as outliers within populations, something that has only become possible, recently, through technological advances. 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 China to the British Isles to South Asia -- along with the movement of people. 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. 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 has minimized damage to skeletons while maximizing the chance of obtaining genetic data from regions where DNA preservation is often poor. For decades, specialists have debated how Indo-European languages made their way to distant parts of the world. Did they spread via herders from the Eurasian Steppe? Or did they travel with farmers moving west and east from Anatolia (present-day Turkey)? Studies indicate that Indo-European languages arrived in Europe via the steppe. The Science study now makes a similar case for South Asia by showing that present-day South Asians have little if any ancestry from farmers with Anatolian roots. Any large-scale spread of farmers with Anatolian roots into South Asia, can now be ruled out. This challenges the centerpiece of the ?Anatolian hypothesis' that such movement brought farming and Indo-European languages into the region. One new line of evidence in favor of a steppe origin for Indo-European languages is the detection of genetic patterns that connect speakers of the Indo-Iranian and Balto-Slavic branches of Indo-European. The study found that present-day speakers of both branches descend from a subgroup of steppe pastoralists who moved west toward Europe almost 5,000 years ago and then spread back eastward into Central and South Asia in the following 1,500 years. This provides a simple explanation in terms of ancient movements of people for the otherwise puzzling shared linguistic features of these two branches of Indo-European, which today are separated by vast geographic distances.

A second line of evidence in favor of a steppe origin is the researchers' discovery that of the 140 present-day South Asian populations analyzed in the study, a handful show a remarkable spike in ancestry from the steppe. All but one of these steppe-enriched populations are historically priestly groups, including Brahmins -- traditional custodians of texts written in the ancient Indo-European language Sanskrit. The finding that Brahmins often have more steppe ancestry than other groups in South Asia, controlling for other factors, provides a fascinating new argument in favor of a steppe origin for Indo-European languages in South Asia. The studies inform another longstanding debate, about whether the change from a hunting and gathering economy to one based on farming was driven more by movements of people, the copying of ideas or local invention.

In Europe, ancient-DNA studies have shown that agriculture arrived along with an influx of people with ancestry from Anatolia. The new study reveals a similar dynamic in Iran and Turan (southern Central Asia), where the researchers found that Anatolian-related ancestry and farming arrived around the same time. This confirms that the spread of agriculture entailed not only a westward route from Anatolia to Europe but also an eastward route from Anatolia into regions of Asia previously only inhabited by hunter-gatherer groups. Then, as farming spread northward through the mountains of Inner Asia thousands of years after taking hold in Iran and Turan, the links between ancestry and economy get more complex. By around 5,000 years ago, southwestern Asian ancestry flowed north along with farming technology, while Siberian or steppe ancestry flowed south onto the Iranian plateau. The two-way pattern of movement took place along the mountains, a corridor that previously showed was a “Bronze Age Silk Road“ along which people exchanged crops and ideas between East and West. In South Asia, however, the story appears quite different. Not only did the authors find no trace of the Anatolian-related ancestry that is a hallmark of the spread of farming to the west, but the Iranian-related ancestry they detected in South Asians comes from a lineage that separated from ancient Iranian farmers and hunter-gatherers before those groups split from each other. The authors concluded that farming in South Asia was not due to the movement of people from the earlier farming cultures of the west; instead, local foragers adopted it. Prior to the arrival of steppe pastoralists bringing their Indo-European languages about 4,000 years ago, no evidence was found, of large-scale movements of people into South Asia.

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. 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. After screening more than 60 skeletal samples from the largest known town of the Indus Valley Civilization, called Rakhigarhi, the study found one with a hint of ancient DNA. After more than 100 sequencing attempts, enough data was generated to reach meaningful conclusions. The ancient woman's genome matched those of 11 other ancient people 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 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 individuals that were sequenced -- form the primary ancestry of South Asians today. The study directly ties present-day South Asians to the ancient peoples of South Asia's first civilization. Analyzing the genome of only one individual limits the conclusions that can be drawn about the entire population of the Indus Valley Civilization. The Indus Valley Civilization itself was genetically extremely diverse, additional genomes will surely enrich the picture.

Sources: University of Washington; Harvard University; The Broad Institute; Harvard Medical School; The formation of human populations in South and Central Asia. Science, 2019; 365 (6457): eaat7487 DOI: 10.1126/science.aat7487; Harvard Medical School. “Largest-ever ancient-DNA study illuminates millennia of South and Central Asian prehistory.“ ScienceDaily; Wikipedia

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