Maternal genetic affinities of Koṅkaṇī population in the southwest coast of India

Abstract Koṅkaṇ region on the west coast of India is a hotspot of culture, folklore and ethnolinguistic diversity. The genetic landscape of this region remains understudied. The present study features Koṅkaṇī population residing along the Koṅkaṇ Malabar coast. We have sequenced complete mitogenomes of 85 and the hypervariable region of 210 Koṅkaṇī individuals to understand the maternal gene pool of this region. Comparative analysis of the over 5000 mitogenomes revealed that the Koṅkaṇī population clustered at a convergence point on the PCA plot, presumably due to a diverse maternal gene pool with both autochthonous and West Eurasian components. A distinct clustering pattern was observed within the subgroups of Sārasvata and non-Sārasvata Koṅkaṇī groups, indicating unique ancestral maternal lineages in them. This distinction is majorly due to the N macrohaplogroup lineages found in this population. We observe low haplotype and nucleotide diversity in Citrapur Sārasvata Brahmins (CSB), Rājāpur Sārasvata Brahmins (RSB), Khārvi and Kuḍubi compared to Gauḍa Sārasvata Brahmins (GSB) and Roman Catholics. The assimilation of both pre and post Last Glacial Maximum (LGM) haplogroups like M57, M36, M37, M3, M30, R8 and U2 in the Koṅkaṇī population suggests active movement and settlement along the Koṅkaṇ region on the west coast of India since the Late Pleistocene through the Holocene.