India's genetic mosaic is as intricate and diverse as its cultures and languages. A massive genetic study, encompassing 2,762 high-coverage genomes from individuals across various geographic regions, language speakers, and social strata, has shed light on the complex ancestral tapestry that weaves together the population of India. This extensive research published as a preprint on bioRxiv reveals that the genetic structure of the Indian population is predominantly shaped by three ancestral groups: ancient Iranian farmers, Eurasian Steppe pastoralists, and South Asian hunter-gatherers. Such a finding emphasises the pivotal role of migration and admixture events in the evolutionary history of India's people.
The 2,762 genomes, including 22 mother-father-child trios, collected from 18 different states in India are samples from a subset of the Longitudinal Aging Study in India (LASI), a joint effort by the Harvard TH Chan School of Public Health (HSPH), the University of Southern California (USC), and the International Institute for Population Sciences (IIPS) in India. The study had its principal investigator teams located at the USC and the All India Institute Of Medical Sciences (AIIMS), among others.
This study captures a broad spectrum of India's demographic diversity, something that had not been done before, with the researchers noting that India has so far been "underrepresented in whole genome sequencing studies". By delving deep into the genomic sequences of individuals from across the country, the study had tried to fill a significant gap in the understanding of global genetic diversity, particularly concerning underrepresented populations.
India, A Major Reservoir Of Genetic Diversity
The ancestral roots of the Indian population trace back to a significant migration event from Africa approximately 50,000 years ago, underlining a shared origin with other out-of-Africa populations. However, the Indian genetic landscape is distinct, marked by a unique blend of ancestry from ancient Iranian farmers, suggesting an early Neolithic gene flow into the subcontinent. This contribution is notably separate from the later influx of Steppe pastoralist-related ancestry, illustrating a complex pattern of migrations and interactions in the region's prehistory.
Moreover, the study highlights India's position as a major reservoir of genetic diversity, showcasing the largest variation in Neanderthal ancestry among worldwide populations and significant Denisovan gene flow. This archaic hominin ancestry adds another layer to the complexity of Indian genetics, with implications for understanding human evolution and adaptation. The presence of segments from Neanderthals and a mysterious Denisovan-related ancestry not only connects the Indian population to distant relatives but also suggests a deep and intertwined history of archaic and modern humans.
The findings also underline the significant impact of endogamy and founder events on the genetic structure of the Indian population. These social practices have led to a high degree of homozygosity and shared identity-by-descent among individuals, particularly pronounced in certain regions and social groups. Such patterns are reflective of historical population dynamics, including the establishment of the caste system and localized social practices.
The Surprise Find
One of the most surprising elements emerging from this study is the significant genetic contribution from Denisovans to the Indian gene pool, despite the absence of any Denisovan fossil discoveries in India to date.
Denisovans, an extinct group of archaic humans identified through their genetic legacy in modern humans and a scant fossil record ranging from Siberia to Southeast Asia, have long been a subject of mystery. According to Science journal, Denisovans may have been around until 30,000 years ago, going by their genetic legacy in persons living in Southeast Asia.
The detection of Denisovan ancestry in India's population, without corresponding archaeological evidence, points to a historical narrative much more complex than previously acknowledged. It suggests that Denisovans may have had a wider geographic spread across Asia than the fossil record currently indicates or that their genetic contributions to South Asia occurred through intermediary populations.
"...a majority of Neanderthal ancestry that exists today in present-day individuals is found in India, while other worldwide populations retain only a subset of this variation. Indians also harbor the most Denisovan ancestry among Eurasian populations," the authors noted.
They also said the findings raise questions about how humans dispersed and settled outside Africa. Asking if the range of Neanderthals and Denisovans extended to South Asia, or if modern humans encountered Neanderthals, and also Denisovans, further east in Eurasia and not the Middle East as is widely believed, the authors concluded: "These observations call for a re-evaluation of models of human origins, for both modern human and archaic hominins, in light of the complex diversity in India."