Indigenous and foreign Y-chromosomes characterize the Lingayat and Vokkaliga populations of Southwest India

Abstract

Previous studies have shown that India's vast coastal rim played an important role in the dispersal of modern humans out of Africa but the Karnataka state, which is located on the southwest coast of India, remains poorly characterized genetically. In the present study, two Dravidian populations, namely Lingayat (N=101) and Vokkaliga (N=102), who represent the two major communities of the Karnataka state, were examined using high-resolution analyses of Y-chromosome single nucleotide polymorphisms (Y-SNPs) and seventeen short tandem repeat (Y-STR) loci. Our results revealed that the majority of the Lingayat and Vokkaliga paternal gene pools are composed of four Y-chromosomal haplogroups (H, L, F* and R2) that are frequent in the Indian subcontinent. The high level of L1-M76 chromosomes in the Vokkaligas suggests an agricultural expansion in the region, while the predominance of R1a1a1b2-Z93 and J2a-M410 lineages in the Lingayat indicates gene flow from neighboring south Indian populations and West Asia, respectively. Lingayat (0.9981) also exhibits a relatively high haplotype diversity compared to Vokkaliga (0.9901), supporting the historical record that the Lingayat originated from multiple source populations. In addition, we detected ancient lineages such as F*-M213, H*-M69 and C*-M216 that may be indicative of genetic signatures of the earliest settlers who reached India after their migration out of Africa.

Keywords: AMGX; AMGY; AMOVA; Analysis of molecular variance; CA; Correspondence analysis; DC; Discriminatory capacity; Dravidian population; Haplogroup; Haplotype; ISOGG; International Society of Genetic Genealogy; MDS; MJ; ML; Maximum likelihood; Median-joining; Mitochondrial DNA; Multidimensional scaling; N; NRY; Non-recombining region of the Y-chromosome; Phylogenetic analyses; SNP; STR; Sample size; Short tandem repeat; Single nucleotide polymorphism; X-homolog of the amelogenin locus; Y-SNP; Y-STR; Y-chromosomal single nucleotide polymorphism; Y-chromosome short tandem repeat; Y-homolog of the amelogenin locus; mtDNA.