Complex maternal genetic landscape in the Koṅkaṇī population of India

The Koṅkaṇ region on the west coast of India is a hotspot of culture, folklore and ethnolinguistic diversity, yet its maternal genetic landscape remains largely unresolved. The present study captures the genetic affinities of the Koṅkaṇī population, residing along the Koṅkaṇ Malabar coast by analysing complete mitochondrial genomes (n = 85) and control region hypervariable sequences (n = 210). Our results reveal divergent maternal histories between the Sārasvata and the non-Sārasvata groups. Comparative analysis against over 5000 mitochondrial genomes from Eurasia demonstrates that the Koṅkaṇī maternal gene pool is shaped by both deep-rooted South Asian (macro-haplogroup M) and West Eurasian lineages. Demographic modelling identifies a pre-Last Glacial Maximum (LGM) expansion and a post-LGM recovery, with macro-haplogroup N lineages serving as the primary drivers of internal genetic structuring. At the subpopulation level, occupational groups such as the Khārvi and Kuḍubi exhibit genetic signatures that are consistent with historic founder events followed by increased genetic drift relative to Gauḍa Sārasvata Brahmins and Roman Catholics, where populations display higher haplotype diversity. Social practices, including endogamy, may contribute to the differences observed between these populations. While the non-Sārasvata group clusters with autochthonous tribes, the Sārasvata groups share genetic affinities with West Eurasian and Steppe-linked lineages, suggesting that the Bronze Age migrations into South Asia were not exclusively male-mediated. Overall, this study highlights the Koṅkaṇ coast as a genetic confluence, where Late Pleistocene migrations, LGM refugia, and Holocene admixture collectively shaped its maternal ancestry. It also illustrates how climate and social shifts moulded the extant genetic diversity along western India.