Abstract
Y-chromosomal reference data from Uyghur communities outside China remain limited, although these populations are central to understanding paternal genetic structure in Central Asia. We analysed 596 reportedly unrelated Uyghur males from four regions of southeastern Kazakhstan using 27 Y-STR loci and 20 core Y-SNP markers, and compared the resulting haplotypes with Uyghur and neighbouring Central Asian populations from the Y-Chromosome Haplotype Reference Database. The dataset yielded 515 distinct haplotypes, high overall haplotype diversity (0.9993), and a low observed haplotype match probability (0.0023), providing a robust baseline for forensic applications. The paternal pool was highly heterogeneous, with major contributions from R1a (19.97%), J2 (17.45%), C2 (12.25%) and O2 (10.74%) lineages, alongside additional minor western, eastern and northern Eurasian components. Median-joining networks displayed complex, multi-branched topologies, while an exploratory comparison with a separate, previously published NGS dataset (N = 19) confirmed that these broad haplogroups contain multiple phylogenetically distinct subclades. Pairwise RST and nonmetric multidimensional scaling (NMDS) analyses detected no statistically significant differentiation among Kazakhstani Uyghur regional groups and Xinjiang Uyghur populations after correction for multiple testing, whereas several Kazakh and Kyrgyz groups were more clearly differentiated. These results establish a highly discriminatory regional forensic reference dataset and position Kazakhstani Uyghurs within a cohesive Central Asian paternal continuum shaped by diverse multiple male-mediated inputs.