Unveiling the genetic tapestry of Kohistan: a population genetic analysis of autosomal STRs in a South Asian population

The Kohistani population of northern Pakistan, an understudied group with distinct geographic, ethnic, and cultural characteristics, presents a unique opportunity to explore genetic diversity in South Asia. We analyzed 21 autosomal STR loci in 200 unrelated Kohistani males using the GlobalFiler™ PCR Amplification Kit, identifying 329 distinct allele combinations with allele frequencies ranging from 0.0025 to 0.2975. Forensic parameters revealed high informativeness, with a combined power of discrimination (CPD) of 0.999999999999999999999999999999378 and a combined power of exclusion (CPE) of 0.9999336, though loci like TPOX showed reduced diversity (GD: 0.7389, Ho: 0.545) compared to Pashtuns (GD: 0.73–0.92) and Punjabis (GD: 0.75–0.95), reflecting endogamy. After sequential Bonferroni correction, no significant deviations from Hardy-Weinberg equilibrium were detected, but initial deviations and linkage disequilibrium in 16 locus pairs suggest genetic drift, similar to patterns in Baloch populations. Analyses of genetic distances, multi-dimensional scaling (MDS), principal component analysis (PCA), STRUCTURE, and phylogenetic trees showed a genetic affinity between the Kohistani population and neighboring South Asian populations. This genetic connection aligns with linguistic, ethnic, and geographical classifications, placing Kohistani in close proximity to populations like Punjabi, Pashtuns, and Bangladeshi, reflecting shared ancestry and regional gene flow. These findings highlight Kohistani’s genetic structure, shaped by isolation and endogamy, and contribute to understanding South Asian genetic diversity.