Genetic evidence of shared ancestry among diverse ethno-linguistic human populations of Himachal Pradesh

•We genotyped a large dataset, belonging to 594 individuals from 12 districts of Himachal Pradesh using PowerPlex® 21 System (Promega, USA).•These individuals were genetically unrelated and belonged to eight different populations following different ethnicity, language, geography and social organization.•This study documents the first-ever report on the population genetic structure of Himachal Pradesh and the phylogenetic analysis grouped the populations of Brahmins, Rajputs, and Scheduled castes into one cluster which indicated a long genetic admixture in the ancestral populations. In Indian montane system, human populations often exhibit an unparallel social organization where inter-caste marriages are still not common. This attribute affects the demography and population genetic structure of the resident populations. Further, human populations residing in the mountains in India are poorly studied for their genetic make-up and allele distribution patterns. In the present study, we genotyped 594 unrelated individuals using PowerPlex® 21 System (Promega, USA) from eight different populations belonging to 12 districts of Himachal Pradesh which differed in ethnicity, language, geography and social organization. Altogether, we obtained 1415 alleles with a mean of 8.84 ± 0.26 alleles per locus and 0.80 mean observed heterozygosity. Locus Penta E showed the highest combined power of discrimination and was found most informative for forensic purposes. Interestingly, phylogenetic analysis grouped the populations of Rajputs, Scheduled castes and Brahmins into one cluster, which indicated a deep genetic admixture in the ancestral populations. This study documents the first-ever report on the population genetic assignment of various castes in Himachal Pradesh and unveils the facts of cryptic gene flow among the diverse castes in the northern hilly state of India. Our results showed a genetic relationship among the various ethno-linguistically diverse populations of India.