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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.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5785-z) contains supplementary material, which is available to authorized users.

Genome-wide study on genetic diversity and phylogeny of five species in the genus Cervus