Genetic variability and relationships in mitochondrial DNA CO II gene sequence of red common carps in China

Nucleotide sequence of Cytochrome coxidase subunit II (CO II) of mitochondrial DNA ( mtDNA) was analyzed from four populations of the red common carp (C. c. var. singuonensis, C. c. var. wananensis, C. c. var. wuyuanensis and C. c. var. color) as well as one population of wild common carp in China to detect their genetic variability and phylogenetic relationship. Nineteen nucleotide variable positions were detected in analyzed 607 bp length sequence and 15 haplotypes were defined among five populations,but only one shared haplotype was observed in C. c. var. singuonensis and C. c. var. color, respectively. The characteristic intrapopulation single nucleotide polymorphisms (SNP) were observed in 103th, 149th, 239th, 368th, 395th nucleotide position. The highest haplotypic diversity (h) and nucleotide diversity (pi) existed in C. c. var. wuyuanensis and the lowest exited in C. c. var. wananensis. The significant fixation indices (Fst) in most comparisons between populations were observed. The neighbor-joining trees from haplotypes and populations of red common carp indicated C. c. var singuonensis and C. c. var. color might have originated from one monophyletic group, while C. c. var. wananensis and C. c. var. wuyuanenesis might have originated from an independent evolutionary branch.