An Ancient Harappan Genome

Lacks Ancestry from Steppe Pastoralists or Iranian Farmers

by 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, Cell, September 5, 2019


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  • The individual was from a population that is the largest source of ancestry for South Asians
  • Iranian-related ancestry in South Asia split from Iranian plateau lineages >12,000 years ago
  • First farmers of the Fertile Crescent contributed little to no ancestry to later South Asians


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.

Graphical Abstract

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