An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers

Vasant Shinde¹, Vagheesh M Narasimhan², Nadin Rohland³, Swapan Mallick⁴, Matthew Mah⁴, Mark Lipson³, Nathan Nakatsuka³, Nicole Adamski⁵, Nasreen Broomandkhoshbacht⁵, Matthew Ferry⁵, Ann Marie Lawson⁵, Megan Michel⁵, Jonas Oppenheimer⁵, Kristin Stewardson⁵, Nilesh Jadhav⁶, Yong Jun Kim⁶, Malavika Chatterjee⁶, Avradeep Munshi⁶, Amrithavalli Panyam⁶, Pranjali Waghmare⁶, Yogesh Yadav⁶, Himani Patel⁷, Amit Kaushik⁸, Kumarasamy Thangaraj⁹, Matthias Meyer¹⁰, Nick Patterson¹¹, Niraj Rai¹², David Reich¹³

Affiliations

¹ Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India. Electronic address: vasant.shinde@dcpune.ac.in.
² Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address: vagheesh@mail.harvard.edu.
³ Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
⁴ Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
⁵ Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
⁶ Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India.
⁷ Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India.
⁸ Amity Institute of Biotechnology, Amity University, Noida 201313, India.
⁹ CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India.
¹⁰ Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.
¹¹ Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
¹² Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India; CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India. Electronic address: nirajrai@bsip.res.in.
¹³ Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address: reich@genetics.med.harvard.edu.

PMID: 31495572
PMCID: PMC6800651
DOI: 10.1016/j.cell.2019.08.048

An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers

Vasant Shinde et al. Cell. 2019.

. 2019 Oct 17;179(3):729-735.e10.

doi: 10.1016/j.cell.2019.08.048. Epub 2019 Sep 5.

Authors

Affiliations

¹ Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India. Electronic address: vasant.shinde@dcpune.ac.in.
² Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address: vagheesh@mail.harvard.edu.
³ Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
⁴ Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
⁵ Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
⁶ Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India.
⁷ Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India.
⁸ Amity Institute of Biotechnology, Amity University, Noida 201313, India.
⁹ CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India.
¹⁰ Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.
¹¹ Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
¹² Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India; CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India. Electronic address: nirajrai@bsip.res.in.
¹³ Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address: reich@genetics.med.harvard.edu.

PMID: 31495572
PMCID: PMC6800651
DOI: 10.1016/j.cell.2019.08.048

Abstract

We report an ancient genome from the Indus Valley Civilization (IVC). The individual we sequenced fits as a mixture of people related to ancient Iranians (the largest component) and Southeast Asian hunter-gatherers, a unique profile that matches ancient DNA from 11 genetic outliers from sites in Iran and Turkmenistan in cultural communication with the IVC. These individuals had little if any Steppe pastoralist-derived ancestry, showing that it was not ubiquitous in northwest South Asia during the IVC as it is today. The Iranian-related ancestry in the IVC derives from a lineage leading to early Iranian farmers, herders, and hunter-gatherers before their ancestors separated, contradicting the hypothesis that the shared ancestry between early Iranians and South Asians reflects a large-scale spread of western Iranian farmers east. Instead, sampled ancient genomes from the Iranian plateau and IVC descend from different groups of hunter-gatherers who began farming without being connected by substantial movement of people.

Keywords: Harappan Civilization; Indus Valley Civilization; South Asia; ancient DNA; anthropology; archaeology; population genetics.

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Conflict of interest statement

Declaration of Interests

The authors declare no competing interests.

Figures

**Figure 1.. Archeological context of the individual that yielded ancient DNA**
(A) We label the geographic location of the archaeological site of Rakhigarhi (blue) and other significant Harappan sites (red) to define the geographic range of the IVC. We label in black sites in the north and west with which IVC people were in cultural contact, and specifically highlight in yellow the sites of Gonur and Shahr-i-Sokhta, which are the source of the 11 outlier individuals who genetically form a cline of which the Rakhigarhi individual is a part. (B) Photograph of the I6113 burial (skeletal code RGR7.3, BR-01, HS-02) and associated typical IVC grave goods and illustrating typical North-South orientation of IVC burials. High resolution images of IVC-style ceramics associated with the grave are shown in Figure S1.

**Figure 2.. Population genetic analysis**
(A) PCA of ancient DNA from South and Central Asia projected onto a basis of whole genome sequencing data from present-day Eurasians. I6113 and I11042 (a non-outlier individual from the site of Gonur of similar data quality), are shown along with black error bars indicating 1 standard error as estimated using a chromosomal block jackknife. I6113’s position in the PCA is inconsistent with that of present-day South Asians and with Iranian groups, but is consistent with a set of 11 outliers who represent 25% of analyzed individuals at the sites of Gonur and Shahr-i-Sokhta and who with I6113 for the *IVC Cline*. (B) ADMIXTURE analysis of individuals from South and Central Asia shown with components in Green, Teal, Orange, Blue and Red maximized in Iranian farmers, Anatolian farmers, Eastern European Hunter-Gatherers, Western European Hunter-Gatherers, and Andamanese Hunter-Gatherers, respectively. (C) Estimated proportions of three ancestry profiles in ancient and present-day individuals. The three components are maximized in Middle to Late Bronze Age Steppe Pastoralists (*Central_Steppe_MLBA*), the reconstructed hunter-gatherer population of South Asia (represented by *Andamanese Hunter-Gatherers (AHG)* as proxy for with greatest relatedness to southeast Asian hunter-gatherers), and *Indus_Periphery_West*, an individual on the *IVC Cline* represented with the lowest proportion of *AHG*-related ancestry. Individuals that fit a two-way model of mixture between these three sources are shown on the triangle edges, whereas individuals that could only be fit with a three way model are shown in the interior. I6113 is shown on the *IVC Cline* as a red dot; the other IVC cline individuals are shown as orange dots; later individuals who formed as mixtures between people on the *IVC Cline* and people with Steppe ancestry are shown as green dots; and diverse modern South Asian groups who formed as a mixture of two later mixed groups are shown as blue dots

**Figure 3. Best-fitting admixture graph relating populations with Iranian-related ancestry.**
The Iranian-related subtree is shown in green, the Anatolian farmer-related subtree in blue, the southeast Asian-related subtree in red, and mixed populations as pie charts (other fitting topologies all share the feature that the *IVC Cline* descends from the first-splitting lineage in the subtree of Iranian-related ancestry). The dates of the analyzed populations are shown on the vertical axis and provide minima on the population split dates. The observation that the Iranian-related lineage contributing to the *IVC Cline* split earlier than Belt Cave at ~10000 BCE and Ganj Dareh at ~8000 BCE is incompatible with the hypothesis that the advent of farming in South Asia after ~7000–6000 BCE was associated with a large-scale eastward migration bringing ancestry from people related to western Zagros mountain farmers or herders across the Iranian plateau to South Asia.

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An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers

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An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers

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