PMC

Neighbor-joining (bootstrap repeat is 10,000) and maximum-likelihood (bootstrap repeat is 1,000) phylogenetic trees of 30 complete mitogenomes: Cervus canadensis nannodes (MT430939 used in this study), Cervus elaphus alxaicus (KU942399), Cervus elaphus (NC_007704 and KP172593), Cervus elaphus kansuensis (NC_039923), Cervus elaphus songaricus (NC_014703), Cervus elaphus yarkandensis (NC_013840), Cervus elaphus hippelaphus (KT290948), Cervus elaphus macneilli (KX449334), Cervus elaphus (MF872248 and MF872247), Cervus nippon yesoensis (NC_006973), Cervus nippon centralis (NC_006993), Cervus nippon yakushimae (NC_007179), Cervus nippon hortulorum (NC_013834), Cervus nippon hortulorum (HQ191428), Cervus nippon hortulorum (KR868807), Cervus nippon taiouanus (NC_008462), Cervus nippon taiouanus (EF058308), Cervus nippon sichuanicus (NC_018595), Cervus nippon kopschi (NC_016178), Cervus nippon kopschi (JN389444), and Muntiacus vuquangensis (NC_016920) as an outgroup. Phylogenetic tree was drawn based on the maximum-likelihood tree. The numbers above branches indicate bootstrap support values of maximum-likelihood and neighbor-joining phylogenetic trees, respectively.

Correspondence analysis plots obtained for the nucleotide composition of 13 protein-coding genes (PCG), RNA genes and control region (CR) as well as selected PCG from various Cervus taxa: a—C. albirostris; c—C. canadensis; c_ala—C. canadensis alashanicus; c_kan—C. canadensis kansuensis; c_sib—C. canadensis sibiricus; c_son—C. canadensis songaricus; c_xan—C. canadensis xanthopygus; e_A—C. elaphus haplogroup A; e_B—C. elaphus haplogroup B; e_C—C. elaphus haplogroup C; e_D—C. elaphus haplogroup D; e_E—C. elaphus haplogroup E; e_mac—C. elaphus macneilli (probably mislabelled, see caption to Fig. ); h—C. hanglu yarkandensis; n_cen—C. nippon centralis; n_hor—C. nippon hortulorum; n_kop—C. nippon kopschi; n_sic—C. nippon sichuanicus; n_tai—C. nippon taiouanus; n_yak—C. nippon yakushimae; n_yes—C. nippon yesoensis. The plots for other genes and control region are shown in Fig. .

Phylogenetic ML tree of all Cervus species based on the individual SNP matrices. Phylogenetic analyses were conducted using maximum likelihood (ML) on individual SNP matrix. One colour for each group: R. tarandus, OrangeRed; C. eldii, LightSlateGray; C. unicolor, Green; C. albirostris, HotPink; C. elaphus (New Zealand), DarkMagenta; C. e. yarkandensis, Yellow; C. c. songaricus, LightCoral; C. c. sibiricus, LightPink; C. c. xanthopygus, Indigo; C. c. macneilli, DodgerBlue; C. c. kansuensis, RoyalBlue; C. c. alashanicus, Crimson; C. c. canadensis, Orchid; C. nippon (shuangyang), SpringGreen; C. nippon (tonghua), Olive; C. nippon (dongda), Blue; C. nippon (dongfeng), MidnightBlue; C. nippon (siping), GreenYellow; C. nippon (aodong), PaleVioletRed; C. nippon (ussuri), Goldenrod; C. nippon (xingkaihu), DarkSlateGray; C. n. aplodontus, CadetBlue. Phylogenetic ML tree of all Cervus species based on the individual SNP matrices was basically the same as inter-population combined analysis, but some of the samples fell within their respective groups as anticipated, such as C. c. songaricus and C. c. sibiricus, C. c. macneilli and C. c. kansuensis (these populations do have overlapping ranges), C. c. xanthopygus was split to 2 populations, one of which has close relationships with C. c. sibiricus and C. c. songaricus, and the other was grouped with C. c. alashanicus. Similarly, the C. nippon populations except C. n. aplodontus could not be well-separated. The phylogenetic ML tree of all C. elaphus and C. canadensis based on the individual SNP matrices, together with geographic distribution, have showed that, there were three major subclades in China, namely C. e. yarkandensis (distributed in Tarim Basin, with 92% bootstrap support), C. c. macneilli/C. c. kansuensis/C. c. alashanicus (distributed in middle west of China, with 89% bootstrap support), and C. c. songaricus/C. c. sibiricus (distributed in northwest and northeast of China, with 89% bootstrap support)