The formation of human populations in South and Central Asia

Abstract

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.

Fig. 1. Overview of ancient DNA data.

(A) Distribution of sites and associated archeological or radiocarbon dates along with the number of individuals meeting our analysis thresholds from each site. (B) Locations of ancient individuals for whom we generated ancient DNA that passed our analysis thresholds along with the locations of individuals from 140 groups from present-day South Asia that we analyzed as forming the Modern Indian Cline. Shapes distinguish the individuals from different sites. Data from 106 South Asian groups that do not fit along the Modern Indian Cline as well as AHG are not shown. (C) PCA analysis of ancient and modern individuals projected onto a basis formed by 1,340 present day Eurasians reflects clustering of individuals that mirrors their geographical relationships. An interactive version of this figure is presented in the Online Data Visualizer.

Fig. 2.. Outlier analysis reveals ancient contacts between sites.

We plot the average of Principal Component 1 (x-axis) and Principal Component 2 (y-axis) for the West Eurasian and All Eurasian PCA plots, as we found that this aids visual separation of the ancestry profiles. (A) In the Middle to Late Bronze Age Steppe, we observe in addition to the Western_Steppe_MLBA and Central_Steppe_MLBA clusters (indistinguishable in this projection), outliers admixed with other ancestries. The BMAC-related admixture in Kazakhstan documents northward gene flow onto the Steppe and confirms the Inner Asian Mountain Corridor as a conduit for movement of people. (B) At Shahr-i-Sokhta in eastern Iran, there are two primary groupings: one with ~20% Anatolian farmer-related ancestry and no detectable AHG-related ancestry, and the other with ~0% Anatolian farmer-related ancestry and substantial AHG-related ancestry (Indus Periphery Cline). (C) In individuals of the BMAC and successor sites, we observe a main cluster as well as numerous outliers: outliers >2000 BCE with admixture related to WSHG, outliers >2000 BCE on the Indus Periphery Cline (with an ancestral similar similar to the outliers at Shahr-i-Sokhta), and outliers after 2000 BCE that reveal how Central_Steppe_MLBA ancestry had arrived. (D) In the Late Bronze Age and Iron Age of northernmost South Asia, we observe a main cluster consistent with admixture between peoples of the Indus Periphery Cline and Central_Steppe_MLBA, and variable Steppe pastoralist-related admixture.

Fig. 3.. Ancestry Transformations in Holocene Eurasia.

(A) Ancestry clines before and after the advent of farming. We document a South Eurasian Early Holocene Cline of increasing Iranian farmer- and West Siberian hunter-gatherer related ancestry moving west-to-east from Anatolia to Iran, and a North Eurasian Early Holocene Cline of increasing relatedness to East Asians moving west-to-east from Europe to Siberia. Mixtures of peoples along these two clines following the spread of farming formed five later gradients (shaded): moving west-to-east: the European Cline, the Caucasus Cline from which the Yamnaya formed, the Central Asian Cline which characterized much of Central Asia in the Copper and Bronze Ages, the Southwest Asian Cline established by spreads of farmers in multiple directions from several loci of domestication, and the Indus Periphery Cline. (B) Following the appearance of the Yamnaya Steppe pastoralists, Western_Steppe_EMBA (Yamnaya-like) ancestry then spread across this vast region. We use arrows to show plausible directions of spread of increasingly diluted ancestry (the arrows are not meant as exact routes which we do not have enough sampling to determine at present). Rough estimates of the timing of the arrival of this ancestry and estimated ancestry proportions are shown.

Fig. 4.. The Genomic Formation of South Asia.

(A) The degree of allele sharing with southern Asian hunter-gatherers (AASI) measured by f₄(Ethiopia_4500BP, X; Ganj_Dareh_N, AHG) and with Steppe pastoralists measured by f₄(Ethiopia_4500BP, X; Central_Steppe_MLBA, Ganj_Dareh_N) reveals three ancestry clines that succeeded each other in time: the Indus Periphery Cline prior to ~2000 BCE, the Steppe Cline represented by northern South Asian individuals after ~2000 BCE, and the Modern Indian Cline. (B) Modeling South Asians as a mixture of Central_Steppe_MLBA, AHG (as a proxy for AASI), and Indus_Periphery_West (the individual from the Indus Periphery Cline with the least AASI ancestry). Groups along the edges of the triangle fit a two-way model, and in the interior only fit a three-way model. The 140 present-day South Asian groups on the Modern Indian Cline are shown as small dots. (C) Groups that traditionally view themselves as being of priestly status in this and the preceding panel are shown in red (“Brahmin,” “Pandit,” and “Bhumihar” but excluding “Catholic Brahmins”), and tend to have a significantly higher ratio of Central_Steppe_MLBA to Indus_Periphery_Cline ancestry than other groups. (D) Plot of the proportion of Central_Steppe_MLBA ancestry on the autosomes (x-axis) and the Y chromosome (y-axis) shows that the source of this ancestry is primarily from females in Late Bronze Age and Iron Age individuals from the Swat District of northernmost South Asia, and primarily from males in most present-day South Asians.

Fig. 5.. Admixture Graph Model.

The largest deviation between empirical and theoretical f-statistics is |Z|=2.9, indicating a good fit considering the large number of f-statistics analyzed. Admixture events are shown as dotted lines labeled by proportions, with the minor ancestry in gray. The present-day groups are shown in orange ovals, the ancient ones in blue, and unsampled groups in white. (The ovals and admixture events are positioned according to guesses about their relative dates to help in visualization, although the dates are in no way meant to be exact.) In this graph we do not attempt to model the contribution of WSHG and Anatolian farmer-related ancestry, and thus cannot model Central_Steppe_EMBA, the proximal source of Steppe ancestry in South Asia (instead we model the Steppe ancestry in South Asia through the more distally related Yamnaya). However, the admixture graph does highlight several key findings of the study, including the deep separation of the AASI from other Eurasian lineages, and the fact that some Austroasiatic-speaking groups in South Asia (e.g. Juang) harbor ancestry from a South Asian group with a higher ratio of AASI-related to Iranian farmer-related ancestry than any groups on the Modern Indian Cline, thus revealing that groups with substantial Iranian farmer-related ancestry were not ubiquitous in peninsular South Asia in the 3^rd millennium BCE when Austroasiatic languages likely spread across the subcontinent.