Genome-wide study on genetic diversity and phylogeny of five species in the genus Cervus
Pengfei Hu,
Yuanchen Shao,
Jiaping Xu,
Tianjiao Wang,
Yiqing Li,
Huamiao Liu,
Min Rong,
Weilin Su,
Binxi Chen,
Songhuan Cui,
Xuezhe Cui,
Fuhe Yang,
Hidetoshi Tamate,
Xiumei Xing
Affiliations
Pengfei Hu
State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences
Yuanchen Shao
State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences
Jiaping Xu
State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences
Tianjiao Wang
State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences
Yiqing Li
State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences
Huamiao Liu
State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences
Min Rong
State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences
Weilin Su
State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences
Binxi Chen
Animal Health Supervision Institute of Hainan Province
Songhuan Cui
State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences
Xuezhe Cui
State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences
Fuhe Yang
State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences
Hidetoshi Tamate
Faculty of Science, Yamagata University
Xiumei Xing
State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences
Abstract Background Previous investigations of phylogeny in Cervus recovered many clades without whole genomic support. Methods In this study, the genetic diversity and phylogeny of 5 species (21 subspecies/populations from C. unicolor, C. albirostris, C. nippon, C. elaphus and C. eldii) in the genus Cervus were analyzed using reduced-representation genome sequencing. Results A total of 197,543 SNPs were identified with an average sequencing depth of 16 x. A total of 21 SNP matrices for each subspecies/population and 1 matrix for individual analysis were constructed, respectively. Nucleotide diversity and heterozygosity analysis showed that all 21 subspecies/populations had different degrees of genetic diversity. C. eldii, C. unicolor and C. albirostris showed relatively high expected and observed heterozygosity, while observed heterozygosity in C. nippon was the lowest, indicating there was a certain degree of inbreeding rate in these subspecies/populations. Phylogenetic ML tree of all Cervus based on the 21 SNP matrices showed 5 robustly supported clades that clearly separate C. eldii, C. unicolor, C. albirostris, C. elaphus and C. nippon. Within C. elaphus clade, 4 subclades were well differentiated and statistically highly supported: C. elaphus (New Zealand), C. e. yarkandensis, C. c. canadensis and the other grouping the rest of C. canadensis from China. In the C. nippon clade, 2 well-distinct subclades corresponding to C. n. aplodontus and other C. nippon populations were separated. Phylogenetic reconstruction indicated that the first evolutionary event of the genus Cervus occurred approximately 7.4 millions of years ago. The split between C. elaphus and C. nippon could be estimated at around 3.6 millions of years ago. Phylogenetic ML tree of all samples based on individual SNP matrices, together with geographic distribution, have shown that there were 3 major subclades of C. elaphus and C. canadensis in China, namely C. e. yarkandensis (distributed in Tarim Basin), C. c. macneilli/C. c. kansuensis/C. c. alashanicus (distributed in middle west of China), and C. c. songaricus/C. c. sibiricus (distributed in northwest of China). Among them, C. e. yarkandensis was molecularly the most primitive subclade, with a differentiation dating back to 0.8–2.2 Myr ago. D statistical analysis showed that there was high probability of interspecific gene exchange between C. albirostris and C. eldii, C. albirostris and C. unicolor, C. nippon and C. unicolor, and there might be 2 migration events among 5 species in the genus Cervus. Conclusions Our results provided new insight to the genetic diversity and phylogeny of Cervus deer. In view of the current status of these populations, their conservation category will need to be reassessed.
