The complete mitochondrial genome of the Chinese Sika deer (Cervus nippon Temminck, 1838), and phylogenetic analysis among Cervidae,Moschidae and Bovidae

The complete mitochondrial genomes of the Sichuan Sika deer (Cervus nippon sichuanicus) and the South China Sika deer (Cervus nippon kopschi) were determined. Their sizes were 16,429 and 16,428 base pairs, respectively. The similarity of the mitochondrial DNA genome among subspecies of the Chinese Sika deer was calculated, and the values estimated from complete nucleotide sequences and entire amino-acid sequences were 98.4–99.9% and 99.7–99.9%, respectively. Molecular phylogenetic analyses were conducted using maximum parsimony and Bayesian inference methods based on the sequences of 12 concatenated heavy-strand encoded protein-coding genes. The consensus of phylogenetic trees supported the monophyly of Moschidae, Cervidae and Bovidae, and placed Moschidae as a sister group to Cervidae/Bovidae. The relationships among Chinese Sika deer inferred from the phylogenetic analysis were inconsistent with subspecies designations and the present geographic distribution. Our complete mitochondrial genomes will be available as important and basic data for phylogenetics, breeding, genetics and conservation in Cervidae.