Sequence analysis and phylogeny of deer (Cervidae) MtDNA control regions

The complete control regions of three Muntiacinae species of Cervidae (M. reevesi, M. muntjak and M. crinifrons) were located after their complete mtDNA genomes were sequenced. In addition the control region sequences of nine species of other three Cervidae subfamilies were obtained from the Genbank. Base compositions, genetic distances and percent similarities among these regions were calculated and the homologous sequences were compared. Based on their control region sequences, the molecular phylogenetic tree was constructed by Neighbor-Joining method and rooted using the mtDNA control region sequence of O. aries. Furthermore, the phylogenetic relationship among the twelve species was discussed. The lengths of their control regions ranged from 909 bp to 1 049 bp and A + T content is 62.06%. The sequence alignment revealed considerable variation in 363 nucleotide sites (about 34%). According to the phylogenetic tree, we suggest: (1) As a whole, the phylogenetic taxon of the twelve Cervidae species based on their control region sequences is consistent with that made by the NCBI; (2) A. alces, a species of Alces (subfamily: Odocoileinae) is most antique one among the twelve Cervidae species; (3) M. reevesi is more antique than M. muntjak and M. crinifrons; (4) H. inermis, belonging to the subfamily Hydropotinae, is merged into the branch which includes C. capreolus and C. pygargus, two species of Capreolus (subfamily: Odocoileinae).