Analysis of the genetic diversity of Tahe red deer and population structure of Cervus elaphu/hanglu/canadensis.

The Tahe red deer is currently the largest breeding population of antlered Cervus elaphus in China. It has unique characteristics such as drought and roughage tolerance, high antler yield and early sexual maturity. It is a high-quality provenance for cultivating high-yield Cervus elaphus breeds and is also the subject of study on the origin, evolution, and classification of Cervus elaphus. The breeding quantity of Tahe red deer has decreased significantly in recent years due to the influence of feeding conditions and consumer market. This has resulted in a serious threat to its genetic resources. To provide a scientific theoretical basis for the protection of the Tahe red deer population, we performed PCR amplification and direct sequencing of the AMELY2, DBY and SRY genes of the Y chromosome, and the ND1, COX1, ATP6, ND5, Cyt b and D-loop regions of the mtDNA, and analysed their genetic diversity and population genetic structure. The results showed high haplotype diversity and low nucleotide diversity in both the Y chromosome and mtDNA genes. The phylogenetic tree and haplotype network diagram, constructed using white-lipped deer as the outgroup, indicate that Tahe red deer has two distinct ancestral types. The phylogenetic tree, based on the Cyt b gene and D-loop region, reveals that the Cervus elaphus/hanglu/canadensis is divided into three clades: western, central, and eastern. Tahe red deer, C.h.bactrianus, and C.h.hanglu are clustered in the central clade. The study results indicate that Tahe red deer has low genetic diversity and two distinct ancestor types. It is speculated that the central clade is either the earliest differentiation from the ancestor species or the closest to it.