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Friday, October 3, 2025

Neanderthals and Denisovans in India?


Although Levallois stone tool technology (marker of Neanderthal presence) has been found in India, there are no bones or remains of these people, or of the elusive Denisovans in the large Indian subcontinent.


However, genetic studies have shown that modern Indians have a high level of Neanderthal and Denisovan admixture, at least that is what is reported in a paper published in Feb. 2024 (Elise Kerdoncuff, Laurits Skov, Nick Patterson, et. al., 50,000 years of Evolutionary History of India: Insights from ∼2,700 Whole Genome Sequences. bioRxiv 2024.02.15.580575; doi: https://doi.org/10.1101/2024.02.15.580575).


The authors state that: "Indians derive around 1-2% of their ancestry from gene flow from archaic hominins, Neanderthals and Denisovans. By assembling the surviving fragments of archaic ancestry in modern Indians, we recover ∼1.5 Gb (or 50%) of the introgressing Neanderthal and ∼0.6 Gb (or 20%) of the introgressing Denisovan genomes, more than any other previous archaic ancestry study. Moreover, Indians have the largest variation in Neanderthal ancestry, as well as the highest amount of population-specific Neanderthal segments among worldwide groups."


The paper notes that the Neanderthal genes in India are similar to those found in America or Europe (1.4% and 1.3% respectively) but lower to those found in East Asians (around 1.8%).


When it comes to Denisovans the values are similar to globale levels of 0.1%, well below the 1.8% found in Oceanians.


However they detected Neanderthal sequences that are unique to India ("11.7% of uniquely India-specific Neanderthal sequences. Strikingly, ∼90.7% of worldwide Neanderthal sequences are seen in "). The same applies to Denisovan sequences: "Around 51% of Denisovan sequence is unique to India... we find significant enrichment for unique Denisovan sequences in Indians"


These Denisovan genes are from a group that is not the Altai Denisovan, it is only "distantly related" to it.


They also found an archaic inflow of genes: "Beyond Neanderthal and Denisovan ancestry, we inferred 0.42% (0.37–0.48%) of archaic ancestry from an unknown source in Indians." But the authors attribute it to methodology and sequencing artifacts ("this suggests that there is no clear evidence for additional contribution from other unknown archaic hominins to Indians (more than other worldwide populations), contrary to previous claims."


neaderthal and denisovan share in populations chart
Denisovan and Neanderthal share in different populations. Source

The authors find evidence of an early Out-Of-Africa (OOA) event that took place some 74,000 years ago which provided between 0 and 3% of the ancestry to modern Indians, the second OOA migration took place around 50,000 years ago and provides most of the genetic makeup of modern Indians.


The archaic ancesty differs across India, the Andamese hunter-gatherers (AHG) which are indigenous people that live in the Andaman Islands, and are a "Negrito" group are closely linked to a higher Denisovan and Neanderthal genetic makeup: "we find the AHG-related ancestry is positively correlated with both Denisovan and Neanderthal ancestries... This suggests that a large amount of the archaic ancestry seen in present-day Indians is inherited through AHG-related ancestry and in turn, groups with higher AHG-related ancestry in the South have higher archaic ancestry."


The AHG people have lived in the Andaman Islands in isolation since sea levels rose after the end of the last Ice Age some 12,000 years ago, they survive with their unique dialects and cultures as Onge, Jarawa, Sentinelese and Andamanese tribes. The picture below shows a group of northern Andamanese using bows and arrows for fishing (photograph: Radcliffe-Broewn ca.1906):

Andamanese people 1906
Andamanese people in 1906

The authors point out that the unique Neanderhtal and Denisovan ancestry, plus the deep mtDNA and Y-chromosome haplogroups found in Andamanese people, coupled with the ancient Acheulean and the Mid-Pleistocene Levallois stone tool industries point at complex story regarding human migrations into the subcontinent. They ask: "Did the range of Neanderthals and Denisovans extend to South Asia? Did modern humans encounter Neanderthals, and to some extent Denisovans, further east in Eurasia rather than the Middle East as widely believed?"


Further discoveries may reveal the true complexity of how modern humans originated and spread across the globe and the underlying archaic populations, often ignored by those who support the OOA theory.



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