Research Article

The formation of human populations in South and Central Asia

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Science  06 Sep 2019:
Vol. 365, Issue 6457, eaat7487
DOI: 10.1126/science.aat7487
  • 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.

  • Fig. 1
  • 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 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 ancestry similar to the outliers at Shahr-i-Sokhta), and outliers after 2000 BCE that reveal how Central_Steppe_MLBA ancestry had arrived. (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 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. (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, as well as 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 that 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; Ganj_Dareh_N, Central_Steppe_MLBA) reveals three ancestry clines that succeeded each other in time: the Indus Periphery Cline before ~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) 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. (D) Groups that traditionally view themselves as being of priestly status (Brahmin, Pandit, and Bhumihar, but excluding Catholic Brahmins) tend to have a significantly higher ratio of Central_Steppe_MLBA to Indus_Periphery_Cline ancestry than other groups and are labeled in red in this panel and in (B).

  • 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 third millennium BCE when Austroasiatic languages likely spread across the subcontinent.

Supplementary Materials

  • The formation of human populations in South and Central Asia

    Vagheesh M. Narasimhan, Nick Patterson, Priya Moorjani, Nadin Rohland, Rebecca Bernardos, Swapan Mallick, Iosif Lazaridis, Nathan Nakatsuka, I˜igo Olalde, Mark Lipson, Alexander M. Kim, Luca M. Olivieri, Alfredo Coppa, Massimo Vidale, James Mallory, Vyacheslav Moiseyev, Egor Kitov, Janet Monge, Nicole Adamski, Neel Alex, Nasreen Broomandkhoshbacht, Francesca Candilio, Kimberly Callan, Olivia Cheronet, Brendan J. Culleton, Matthew Ferry, Daniel Fernandes, Suzanne Freilich, Beatriz Gamarra, Daniel Gaudio, Mateja Hajdinjak, Éadaoin Harney, Thomas K. Harper, Denise Keating, Ann Marie Lawson, Matthew Mah, Kirsten Mandl, Megan Michel, Mario Novak, Jonas Oppenheimer, Niraj Rai, Kendra Sirak, Viviane Slon, Kristin Stewardson, Fatma Zalzala, Zhao Zhang, Gaziz Akhatov, Anatoly N. Bagashev, Alessandra Bagnera, Bauryzhan Baitanayev, Julio Bendezu- Sarmiento, Arman A. Bissembaev, Gian Luca Bonora, Temirlan T. Chargynov, Tatiana Chikisheva, Petr K. Dashkovskiy, Anatoly Derevianko, Miroslav Dobeš, Katerina Douka, Nadezhda Dubova, Meiram N. Duisengali, Dmitry Enshin, Andrey Epimakhov, Alexey V. Fribus, Dorian Fuller, Alexander Goryachev, Andrey Gromov, Sergey P. Grushin, Bryan Hanks, Margaret Judd, Erlan Kazizov, Aleksander Khokhlov, Aleksander P. Krygin, Elena Kupriyanova, Pavel Kuznetsov, Donata Luiselli, Farhod Maksudov, Aslan M. Mamedov, Talgat B. Mamirov, Christopher Meiklejohn, Deborah C. Merrett, Roberto Micheli, Oleg Mochalov, Samariddin Mustafokulov, Ayushi Nayak, Davide Pettener, Richard Potts, Dmitry Razhev, Marina Rykun, Stefania Sarno, Tatyana M. Savenkova, Kulyan Sikhymbaeva, Sergey M. Slepchenko, Oroz A. Soltobaev, Nadezhda Stepanova, Svetlana Svyatko, Kubatbek Tabaldiev, Maria Teschler-Nicola, Alexey A. Tishkin, Vitaly V. Tkachev, Sergey Vasilyev, Petr Velemínský, Dmitriy Voyakin, Antonina Yermolayeva, Muhammad Zahir, Valery S. Zubkov, Alisa Zubova, Vasant S. Shinde, Carles Lalueza-Fox, Matthias Meyer, David Anthony, Nicole Boivin‡, Kumarasamy Thangaraj‡, Douglas J. Kennett‡, Michael Frachetti†, Ron Pinhasi†, David Reich

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Figs. S1 to S61
    • Captions for Tables S1 to S5
    • Tables S6 to S93
    • Genotypes for Newly Reported Individuals
    • References
    Tables S1 to S5

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