Classification and phylogeny of sika deer (Cervus nippon) subspecies based on the mitochondrial control region DNA sequence using an extended sample set

Abstract

To further refine the classification and phylogeny of sika deer subspecies, the well-annotated sequences of the complete mitochondrial DNA (mtDNA) control region of 13 sika deer subspecies from GenBank were downloaded, aligned and analyzed in this study. By reconstructing the phylogenetic tree with an extended sample set, the results revealed a split between Northern and Southern Mainland Asia/Taiwan lineages, and moreover, two subspecies, C.n.mantchuricus and C.n.hortulorum, were existed in Northern Mainland Asia. Unexpectedly, Dybowskii’s sika deer that was thought to originate from Northern Mainland Asia joins the Southern Mainland Asia/Taiwan lineage. The genetic divergences were ranged from 2.1% to 4.7% between Dybowskii’s sika deer and all the other established subspecies at the mtDNA sequence level, which suggests that the maternal lineage of uncertain sika subspecies in Europe had been maintained until today. This study also provides a better understanding for the classification, phylogeny and phylogeographic history of sika deer subspecies.

• Cervus nippon
• control region
• mitochondrial DNA
• phylogeny
• phylogeographic history
• sika deer

Acknowledgements

We wish to thank Dr Eric Lord for reading through the paper.

Declaration of interest

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.

We would also like to thank National 863 Program of China (No. 2011AA100603), National 973 Program of China (No. 2011CB111500) and Science and Technology Commission, Jilin (No. 201262514) for providing funds for this research.