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

Vasant Shinde; Vagheesh M Narasimhan; Nadin Rohland; Swapan Mallick; Matthew Mah; Mark Lipson; Nathan Nakatsuka; Nicole Adamski; Nasreen Broomandkhoshbacht; Matthew Ferry; Ann Marie Lawson; Megan Michel; Jonas Oppenheimer; Kristin Stewardson; Nilesh Jadhav; Yong Jun Kim; Malavika Chatterjee; Avradeep Munshi; Amrithavalli Panyam; Pranjali Waghmare; Yogesh Yadav; Himani Patel; Amit Kaushik; Kumarasamy Thangaraj; Matthias Meyer; Nick Patterson; Niraj Rai; David Reich

doi:10.1016/j.cell.2019.08.048

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

Cell. 2019 Oct 17;179(3):729-735.e10. doi: 10.1016/j.cell.2019.08.048. Epub 2019 Sep 5.

Authors

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.

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Asian People / genetics
DNA, Ancient / chemistry*
Evolution, Molecular
Genome, Human*
Human Migration*
Humans
Iran
Pakistan
Pedigree*
Population / genetics*

Substances

DNA, Ancient

Abstract

Publication types

MeSH terms

Substances

Grants and funding