The story so far: Last Thursday, the journal Cell published a paper, An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists and Iranian Farmers, which claimed that the inhabitants of the Indus Valley Civilisation lacked the steppe-pastoralist ancestry which had brought Indo-European languages into South Asia. The findings of the paper, whose key authors are the archaeologist Vasant Shinde, and the geneticists Vagheesh M. Narasimhan and David Reich et al, are based on the DNA sequencing of the remains of a woman found at Rakhigarhi in present-day Haryana. Another paper, published in the journal Science by the same authors and others, established baselines for the DNA of South and Central Asian populations over the last 10,000 years.
What is ancient DNA (aDNA) and what has it been used to study?
Ancient DNA can be carefully extracted from archaeologically recovered bones, teeth or fossil plant remains. Small fragments are processed to sequence the genome of those ancient organisms. aDNA becomes degraded, on account of its age and the climatic and soil conditions it was buried in. Techniques developed over the past three decades have led to a revolution in how we understand the evolution and genetic history of a range of animals and plants, including species that are extinct today. Palaeogeneticists have been able to establish, for example, how genetic variation might relate to the independent evolution of species on different continents that were previously thought to be related, or how different subspecies of horses emerged after their domestication, or how populations that today appear distinct and in different geographical areas were once related and likely existed together in one region.
What can be done with aDNA from human samples?
Special challenges are attached to the study of ancient human DNA, especially as contamination from modern human DNA is a real hazard and requires special techniques at every stage of the recovery and extraction process.
Over the past decade, the DNA of archaeologically recovered individuals has been extracted from various sites across the world and for their interpretation modern DNA databases are crucial. Modern human DNA databases are built on samples from people like us, alive today. They have been used for several applications, prominently including attempts to understand the genetic predisposition towards certain diseases and responses to medicines in different social groups in South Asia.
The comparison of aDNA samples with other aDNA and modern DNA databases can reveal otherwise unsuspected genetic histories. Scientists can trace the deep ancestry of ancient individuals and assess how their genetic makeup is distinct on account of specific variant genes (alleles), mutations and other markers (99% of all human DNA is common) and see how this compares with that of modern groups. Thus, the most common way of understanding the relatedness of DNA between groups and individuals is by their admixture percentages.
Importantly, genes may co-vary with a group’s ethnicity — understood as the combination of language and material practices — but they also may not. There is no necessary correlation between the genes of the author of these words or the reader and what language their ancestors must have spoken, nor what their ‘identity’ was. The social processes of history are not the same as those which can be observed through population genetics. While populations display aggregate trends of admixture and patterns of deep shared ancestry, there are no ‘Aryan’ or ‘Harappan’ or ‘Dravidian’ genes.
What are the recent results? What do they establish?
The two recent papers, (in Science and Cell), have provided complementary levels of insights into South Asian population history. For a detailed account of their findings and misunderstandings of their conclusions please see Tony Joseph’s article in this newspaper (Magazine, “We are all migrants”, September 15, 2019; https://bit.ly/2kJdrss).
The first paper, ‘The Formation of Human Populations in South and Central Asia’, establishes baselines for the genetic history of populations in these two linked regions. Based on an unprecedented 523 aDNA samples ranging over 8,000 years across Eurasia, the authors demonstrate clearly what was known before but is now shown in greater detail with clear evidence, that over the last 10,000 years, the present-day distinctive mix of South Asian genetic variability was formed through the admixture of populations then resident in the region with successive groups who moved into the region. This is a process that happened not just once but several times.
What does the woman from Rakhigarhi teach us?
The second paper presents the results of the first successful aDNA extraction from prehistoric South Asia. Individual 6113 was an elite woman buried between 2300 and 2800 BCE (estimated) in a cemetery on the outskirts of the Harappan town of Rakhigarhi, located near the present day city of Hissar in Haryana. This is a scientific achievement, especially as efforts to extract archaeological DNA have hitherto been few in South Asia and several attempts resulted in DNA that was too degraded or was contaminated.