Mitochondrial DNA (mtDNA) control region (5′ hypervariable region, 554 bp) sequences from 71 samples of blue sheep ( Pseudois nayaur Hodgson, 1833) collected from six study localities throughout Helan Mountain Nature Reserve in Ningxia province of China were investigated to analyse distribution patterns of genetic variability, elucidate matrilineal structure, and investigate population history. Haplotype diversity (h) among the 71 samples was estimated to be 0.792 ± 0.037, and nucleotide diversity (Π) was relatively low (0.00392 ± 0.00046). A χ2 contingency analysis of all mtDNA haplotype frequencies revealed that these haplotypes were distributed in a nonrandom fashion among study localities (χ2 = 86.205, P = 0.092). Additional evidence of matrilineal structure was provided by the finding that a significant amount (9.02%; P < 0.01) of mtDNA variation was partitioned among different localities in the study area. We conclude that blue sheep of Helan Mountain Nature Reserve are structured spatially along matrilines. Pairwise computations of Φst and an AMOVA indicated that some sampling localities are differentiated relative to a random collection of genotypes and reflected differences in the spatial distribution of genetic variation. Isolation-by-distance (IBD) models (Mantel tests) revealed no obvious association between genetic differentiation and geographical distance. These results could be a basis for the development of suitable management strategies for conservation purposes. This work represents the first analysis of blue sheep mitochondrial control region DNA to be performed from a population genetics perspective.
