The formation of human populations in South and Central Asia

By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization’s decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages

The genomic formation of South and Central Asia

The genetic formation of Central and South Asian populations has been unclear because of an absence of ancient DNA. To address this gap, we generated genome-wide data from 362 ancient individuals, including the first from eastern Iran, Turan (Uzbekistan, Turkmenistan, and Tajikistan), Bronze Age Kazakhstan, and South Asia. Our data reveal a complex set of genetic sources that ultimately combined to form the ancestry of South Asians today. We document a southward spread of genetic ancestry from the Eurasian Steppe, correlating with the archaeologically known expansion of pastoralist sites from the Steppe to Turan in the Middle Bronze Age (2300-1500 BCE). These Steppe communities mixed genetically with peoples of the Bactria Margiana Archaeological Complex (BMAC) whom they encountered in Turan (primarily descendants of earlier agriculturalists of Iran), but there is no evidence that the main BMAC population contributed genetically to later South Asians. Instead, Steppe communities integrated farther south throughout the 2nd millennium BCE, and we show that they mixed with a more southern population that we document at multiple sites as outlier individuals exhibiting a distinctive mixture of ancestry related to Iranian agriculturalists and South Asian hunter-gathers. We call this group Indus Periphery because they were found at sites in cultural contact with the Indus Valley Civilization (IVC) and along its northern fringe, and also because they were genetically similar to post-IVC groups in the Swat Valley of Pakistan. By co-analyzing ancient DNA and genomic data from diverse present-day South Asians, we show that Indus Periphery-related people are the single most important source of ancestry in South Asia —} consistent with the idea that the Indus Periphery individuals are providing us with the first direct look at the ancestry of peoples of the IVC {— and we develop a model for the formation of present-day South Asians in terms of the temporally and geographically proximate sources of Indus Periphery-related, Steppe, and local South Asian hunter-gatherer-related ancestry. Our results show how ancestry from the Steppe genetically linked Europe and South Asia in the Bronze Age, and identifies the populations that almost certainly were responsible for spreading Indo-European languages across much of Eurasia

The formation of human populations in South and Central Asia

Ancient DNA has allowed us to begin tracing the history of human movements across the globe. Narasimhan et al. identify a complex pattern of human migrations and admixture events in South and Central Asia by performing genetic analysis of more than 500 people who lived over the past 8000 years (see the Perspective by Schaefer and Shapiro). They establish key phases in the population prehistory of Eurasia, including the spread of farming peoples from the Near East, with movements both westward and eastward. The people known as the Yamnaya in the Bronze Age also moved both westward and eastward from a focal area located north of the Black Sea. The overall patterns of genetic clines reflect similar and parallel patterns in South Asia and Europe.Science, this issue p. eaat7487; see also p. 981RATIONALETo elucidate the extent to which the major cultural transformations of farming, pastoralism, and shifts in the distribution of languages in Eurasia were accompanied by movement of people, we report genome-wide ancient DNA data from 523 individuals spanning the last 8000 years, mostly from Central Asia and northernmost South Asia.RESULTSThe movement of people following the advent of farming resulted in genetic gradients across Eurasia that can be modeled as mixtures of seven deeply divergent populations. A key gradient formed in southwestern Asia beginning in the Neolithic and continuing into the Bronze Age, with more Anatolian farmer–related ancestry in the west and more Iranian farmer–related ancestry in the east. This cline extended to the desert oases of Central Asia and was the primary source of ancestry in peoples of the Bronze Age Bactria Margiana Archaeological Complex (BMAC). This supports the idea that the archaeologically documented dispersal of domesticates was accompanied by the spread of people from multiple centers of domestication.The main population of the BMAC carried no ancestry from Steppe pastoralists and did not contribute substantially to later South Asians. However, Steppe pastoralist ancestry appeared in outlier individuals at BMAC sites by the turn of the second millennium BCE around the same time as it appeared on the southern Steppe. Using data from ancient individuals from the Swat Valley of northernmost South Asia, we show that Steppe ancestry then integrated further south in the first half of the second millennium BCE, contributing up to 30% of the ancestry of modern groups in South Asia. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the unique features shared between Indo-Iranian and Balto-Slavic languages.The primary ancestral population of modern South Asians is a mixture of people related to early Holocene populations of Iran and South Asia that we detect in outlier individuals from two sites in cultural contact with the Indus Valley Civilization (IVC), making it plausible that it was characteristic of the IVC. After the IVC’s decline, this population mixed with northwestern groups with Steppe ancestry to form the “Ancestral North Indians” (ANI) and also mixed with southeastern groups to form the “Ancestral South Indians” (ASI), whose direct descendants today live in tribal groups in southern India. Mixtures of these two post-IVC groups—the ANI and ASI—drive the main gradient of genetic variation in South Asia today.CONCLUSIONEarlier work recorded massive population movement from the Eurasian Steppe into Europe early in the third millennium BCE, likely spreading Indo-European languages. We reveal a parallel series of events leading to the spread of Steppe ancestry to South Asia, thereby documenting movements of people that were likely conduits for the spread of Indo-European languages.The Bronze Age spread of Yamnaya Steppe pastoralist ancestry into two subcontinents—Europe and South Asia.Pie charts reflect the proportion of Yamnaya ancestry, and dates reflect the earliest available ancient DNA with Yamnaya ancestry in each region. Ancient DNA has not yet been found for the ANI and ASI, so for these the range is inferred statistically.By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization’s decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages