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A genome-based investigation of three endogamous Muslim populations,the Salar,Boan,and Dongxiang was conducted on 212 individuals (148 males,64 females),co-resident in Jishisan County,a minority autonomous region located in the province of Gansu,PR China.The Salar are believed to be of Turkic origin whereas the Boan and Dongxiang both speak Mongolian.Ten bi-parental dinucleotide markers on chromosomes 13 and 15 were analyzed to estimate genetic diversity and the effects of endogamy.Four tri-and tetranucleotide Y-chromosome markers and 15 Y-chromosome unique event polymorphisms (UEPs) were examined to determine male-mediated gene flow mtDNA (360 bp ofhypervariable region I) was sequenced for female lineage analysis.