Holocene North Asian gene flow and cryptic substructure in the genome history of Nilgiri tribes

The Nilgiri Hills of the Western Ghats harbour several historically isolated tribal populations whose genomic history remains incompletely resolved. Here, we present a comprehensive analysis of whole genome and complete mitochondrial data from three major Nilgiri groups i.,e, Toda, Kota, and Kurumba, in the context of a broad Eurasian reference panel. Autosomal analyses reveal previously unrecognised fine scale substructure, with both Kota and Kurumba resolving into two genetically distinct clusters (Kota1/Kota2 and Kurumba1/Kurumba2). Principal component, ADMIXTURE, and fineSTRUCTURE analyses identify Toda as the most genetically drifted Nilgiri group, whereas Kota2 exhibits elevated Austroasiatic related ancestry. qpWave analysis indicates that the five genetic clusters require at least three independent ancestry streams, while qpAdm further differentiates the groups based on Onge, Indus Periphery, and Western SteppeMLBA related ancestry. Toda shows the highest Indus Periphery related and lowest Onge related ancestry among the Nilgiri groups. A distinctive ancestry component shared by Kurumba2, Kota1, Gaud and the Sri Lankan Vedda suggests deeper ancestral connections across the southern Indian Ocean region. Mitochondrial genomes reveal strong founder effects and lineage specific patterns, including R5a2b in Toda, M3a1 in Kota, and multiple M subclades together with the rare C4a2c1 lineage in Kurumba. Notably, C4a2c1, previously understudied in South India, shows phylogenetic and ancient DNA continuity with North Asian and Siberian lineages. Bayesian dating suggests its arrival in the Indian subcontinent during the early mid Holocene (~7 ka), followed by local diversification after ~5 ka. Together, these findings reveal a complex history of long range Holocene maternal gene flow and subsequent isolation driven differentiation, providing new insights into the genomic history of South Indian tribal populations.