Divergent Eurasian ancestry and local adaptation shape the genetic landscapes of the Yugur and Uyghur

Abstract The Yugur and Uyghur people of northwestern China share documented Early Medieval origins, yet the evolutionary processes that shaped their present-day genomes remain unresolved. Here, we generate high-coverage whole-genome sequences for the Yugurs and compare them with Uyghur genomes to reconstruct their demographic histories, ancestry profiles, and adaptive trajectories. Both groups derive from mixtures of East Eurasian ancestry (EEA) and West Eurasian ancestry (WEA) but in sharply contrasting proportions: the Yugur retain predominantly EEA (~90%), whereas the Uyghur harbor a near-equal balance. Modeling reveals distinct episodes of admixture in Gansu and Xinjiang, with identity-by-descent patterns indicating persistent but substantially reduced genetic continuity (FST = 0.021). Strikingly, despite their EEA-rich background, the Yugur show WEA-shifted allele frequencies at craniofacial loci, including EDAR and LIMS1, suggesting subtle trait convergence. Signals of recent positive selection further differentiate the two populations: the Yugur display strong selection on the FADS locus linked to lipid metabolism, whereas both groups exhibit selection at PPARA but with greater intensity in the Uyghur, consistent with their higher WEA. Functional enrichment analyses highlight overlapping immune and metabolic pathways, consistent with shared biological patterns shaped by demographic history and long-term residence in Northwestern China. Together, these findings show how divergent admixture proportions and region-specific natural selection have produced distinct genomic architectures in two historically related populations along the Silk Road.