Bengaluru: Scientists have sequenced and analysed the largest genome set yet from South Asia to trace the ancestry of Indians. According to their preprint study, ancestral populations of local hunter-gatherers, Middle Eastern farmers, and Central Asian herders have contributed much more to the genetic makeup of India than ancestral African populations. The study also traced the most significant contact between ancestral Indian and African populations to a single migration event out of Africa 50,000 years ago.
The scientists at the University of California, Berkeley, headed by population geneticist Priya Moorjani, studied 2,700 inclusive and whole genome sequences. The study has been uploaded online and submitted for peer review to the journal Nature.
The study also found that Neanderthals and Denisovans — archaic hominins, or past species that were cousins to Homo sapiens — account for nearly 2 percent of Indian ancestry. The finding raised the question of how that came to be because palaeontologists have, so far, not found fossil remains of either in India. The highest percentage of archaic ancestry is found among east and northeast Indians and the lowest among north Indians.
Largest genome sequencing in region
Large-scale genetic studies have traditionally excluded the diverse genetic population of the Indian subcontinent. The lack of inclusion in European and American studies has left plenty of open questions about the population history of India.
The new study attempted to account for the diversity of genetic groups in India. The scientists collected 2,672 high-quality genomes from 18 states. There were also volunteers from 23 states — 63 percent from rural areas, 4 percent from the Scheduled Tribes, 18 percent from the Scheduled Castes, and 44 percent from the Other Backward Classes.
The study found that the genetic makeup of India is mostly derived from South Asian hunter-gatherers who lived on the land for tens of thousands of years, farmers with an Iranian ancestry who arrived 6,700-5,000 years ago, and herders from the Central Eurasian steppe who swept the region still later.
The scientists compared various genetic sets to existing ancestral ones to establish the timeline and map of migration. For instance, they drew comparisons with the genomes of ancient Iranian-related groups. Of them, the genomes from the ancient farming hub of Sarazm, now in northwest Tajikistan, had the closest match.
Iranian individuals have already shown evidence of trading and cultural mixing with ancient India. One individual from Sarazm had traces of Indian ancestry, while a buried Iranian farmer had ceramic bracelets that appeared Indian.
Archaeological and anthropological evidence also suggested that Sarazm might have been a crucial trading and travel hub, allowing farming and cattle to spread towards north and northwest India.
So, the scientists concluded the Iranian gene flow occurred much before the steppe herders’ gene flow in the Bronze Age.
Ultimately, the gene flows from these groups contributed much more to Indian genomes than ancestral African populations.
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Ancient hominins in DNA
Archaic hominins play a key role in human DNA, giving us many of their genetic remnants and conferring protection against certain diseases.
Neanderthals or Homo neanderthalensis are an extinct species or subspecies of ancient humans who lived in Eurasia. They probably died out 40,000 years ago. The ancestors of modern humans, Homo sapiens, even mated with them. Neanderthal fossils have turned up in various parts of Europe and some parts of Asia, like Uzbekistan. The oldest bones date back to 4,30,000 years.
Denisovans are another extinct subspecies of humans, but too few of them have turned up to provide them a scientific name. Paleontologists discovered the first Denisovan fossil in 2010 in the Denisova Cave in the Altai Mountains of Siberia, and later, more such fossils in the Tibetan plateau and Laos.
Neanderthals and Denisovans also mated with each other, with new evidence from a 90,000-year-old fossil of a teenage girl born to a Neanderthal mother and a Denisovan father.
When the scientists compared the DNA sequences from India with sequenced Neanderthal and Denisovan genomes, they found that 1.48 percent of the DNA sequences are Neanderthal and 0.4 percent Denisovan. The scientists also found that the Neanderthal and Denisovan segments of the DNA sequences had more variation than in any other population group today.
Nearly 11.7 percent of the DNA sequences were uniquely India-specific Neanderthal sequences, and 90.7 percent were worldwide Neanderthal sequences, a majority European. Also, 50 percent of the Denisovan sequence is unique to India, different from the Denisovan sequence in Oceanian and South Asian groups that have the most Denisovan ancestry sequences in their DNA.
When modern humans arrived in India
When studying human migration waves out of Africa to various parts of the world tens of thousands of years ago, a common question is when modern humans or Homo sapiens first arrived in India.
Existing archaeological evidence has confirmed that people lived in northern India before and after the Toba volcano eruption 74,000 years ago. However, it is unclear if these people were ancestors to modern humans.
Through the current study, the scientists deduced that existing ancient populations in India first mixed with the African populations 53,932 years ago.
Most genetic variations in the Indian DNA came from a migration event out of Africa 50,000 years ago, with just 0-3 percent from the earlier migration 74,000 years ago.
The study put forth multiple questions, some of which the scientists have posed in their paper. For instance, whether Neanderthals and Denisovans lived as far down south as South Asia and whether modern humans encountered archaic humans more in east Asia than in the Arabian region.
The scientists said the study offered a big incentive to conduct more genome studies in the Indian subcontinent, saying that their findings “underscore the value of expanding genomic surveys to diverse groups outside Europe”.
(Edited by Madhurita Goswami)
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