Comparative Analysis of Y-Chromosome Data from Xinjiang and Ningxia Hui Populations with the Hui Population Nationwide

The Hui population, the third largest ethnic group in China, is dispersed throughout the country and has a history of assimilation with indigenous East Asians. Previous studies have primarily focused on Hui populations in specific regions, lacking comprehensive comparative analyses. This study analyzed 338 unrelated male individuals from Hui populations in Altay, Xinjiang Province, and Haiyuan or Tongxin, Ningxia Province, using 108 Y-chromosomal single-nucleotide polymorphisms and 24 Y-chromosomal short tandem repeats, comparing findings with data from 749 published individuals from Hui populations in 11 provinces and 997 published Eurasian populations. The analysis reveals that the national Hui population can be categorized into three groups: Hui_Northwestern, Hui_Northern, and Hui_Southern, supported by analysis of molecular variance and principal components analysis. In Xinjiang and Ningxia Provinces, the most prevalent Y-haplogroups in East Asian populations accounted for 53.8% and 59.1%, respectively, while common haplogroups in West Eurasian populations accounted for 46.2% and 40.9%, respectively. This suggests a mixed paternal origin from both East Asian and Eurasian populations in both study regions. High frequencies of haplogroups R1a1a1b2-Z93 and J-M304 were observed in the Hui populations studied, with the network of haplogroup J-M304 indicating a unique cluster within the western Asian subhaplogroup J2a-M410. The most recent common ancestor for this cluster was estimated to be approximately 1341.9 years ago. Additionally, the network of haplogroup R1a1a1b2-Z93 revealed similarities between northwestern Hui populations and Iranian/Turkic-speaking populations. Our study provides insights into the complexity of Hui populations on a national scale and sheds light on potential events and ancestral origins related to the formation of the Hui population.