Two genetically distinct lineages of the sika deer, Cervus nippon, in Japanese islands: comparison of mitochondrial D-loop region sequences.

To investigate genetic diversity among populations of the sika deer, Cervus nippon, nucleotide sequences (705-824 bases) of the mitochondrial D-loop regions were determined in animals from 13 localities in the Japanese islands. Phylogenetic trees constructed by the sequences indicated that the Japanese sika deer is separated into two distinct lineages: the northern Japan group (the Hokkaido island and most of the Honshu mainland) and the southern Japan group (a part of the southern Honshu mainland, the Kyushu island, and small islands around the Kyushu island). All sika deer examined in this study shared four to seven units of repetitive sequences (37 to 40 bases each) within the D-loop sequences. The number of tandem repeats was different among the populations, and it was specific to each population. Six or seven repeats occurred in populations of the northern Japan group, while four or five repeats occurred in populations of the southern Japan group. Each repeat unit included several nucleotide substitutions, compared with others, and 26 types were identified from 31 animals. Sequences of the first, second, and third units in arrays were clearly different between the northern and the southern groups. Based on these D-loop data, colonization and separation of the sika deer populations in the Japanese islands were estimated to have occurred less than 0.5 million years before present. Our results provide an invaluable insight into better understanding the evolutionary history, phylogeny, taxonomy, and population genetics of the sika deer.

Nagata J ，Masuda R ，Tamate HB ，Hamasaki Si ，Ochiai K ，Asada M ，Tatsuzawa S ，Suda K ，Tado H ，Yoshida MC ... -  《MOLECULAR PHYLOGENETICS AND EVOLUTION》

A mitochondrial control region and cytochrome b phylogeny of sika deer (Cervus nippon) and report of tandem repeats in the control region.

:Sika deer (Cervus nippon Temminck) are endemic to mainland and insular Asia. Numerous subspecies have been named, but they are not quantitatively well defined. Portions of the mitochondrial cytochrome b gene (450 bp) and control region (512 bp) were sequenced from 28 individuals belonging to five sika subspecies and two Cervus elaphus subspecies. Phylogenetic trees constructed using these sequences clearly demonstrated that sika are monophyletic with respect to C. elaphus. A survey of variation in the control region showed that approximately half the variation occurred in a 100-base segment between positions 150 and 250 in the left domain of the control region. Within this region there were three tandemly repeated copies of a 39-base motif. In addition, two of the samples (C. n. aplodontus and C. n. hortulorum) contained, respectively, two and four additional copies of the repeated motif.

Cook CE ，Wang Y ，Sensabaugh G 《MOLECULAR PHYLOGENETICS AND EVOLUTION》

Phylogenetic relationships among european red deer, wapiti, and sika deer inferred from mitochondrial DNA sequences.

We determined the mitochondrial cytochrome b gene sequences (1140 bp) of one subspecies of the European red deer (Cervus elaphus in Europe), three subspecies of the wapiti (C. elaphus in Asia and North America), and six subspecies of the sika deer (C. nippon in Japan). Our phylogenetic analysis revealed the monophyly of the European red deer, that of the wapiti, and that of the sika deer. The wapiti, however, was shown to be more closely related to the sika deer than to the European red deer. This is in conflict with traditional morphological results, which suggest a close sister group relationship between the wapiti and the European red deer. The divergence time between the European red deer and the wapiti plus the sika deer was estimated to be approximately 0.80 Ma, and that between the wapiti and the sika deer was estimated to be 0.57 Ma. The sika deer was subdivided into two subspecies groups, and the wapiti was also found to consist of an Asian group and a North American group.

Kuwayama R ，Ozawa T 《MOLECULAR PHYLOGENETICS AND EVOLUTION》

Bottleneck effects on the sika deer Cervus nippon population in Hokkaido, revealed by ancient DNA analysis.

Nabata D ，Masuda R ，Takahashi O ，Nagata J ... -  《ZOOLOGICAL SCIENCE》

A phylogenetic comparison of red deer and wapiti using mitochondrial DNA.

A phylogeny was constructed for red deer/wapiti (Cervus elaphus) subspecies using sequence data from the control region of mitochondrial DNA (mtDNA). The tree was rooted using Cervus nippon (sika deer), Cervus albirostris (Thorold's white-lipped deer), and several Odocoileinae species. A division between the mtDNA haplotypes of red deer (European) and wapiti (Asian/North American) corresponds to subspecies found on opposite sides of the Himalayan Mountains and Gobi, which suggests wapiti should be reconsidered for the status of C. canadensis. Using parsimony and distance analysis, red deer and wapiti are derived from a single recent common ancestor, which is consistent with current taxonomy that recognizes the subspecies of Cervus elaphus as monophyletic group. However, maximum-likelihood analysis using weighted transitional substitutions caused red deer to form a sister group to sika deer (Cervus nippon) and wapiti. A phenetic comparison revealed wapiti also share more nucleotide similarities with sika deer, although approximately 5% sequence divergence separates wapiti, sika, and red deer. Phylogenetic evidence from the cytochrome b sequences corroborated observations from the control region. Observations from this study suggest that the species status of wapiti should be reinstated.

Polziehn RO ，Strobeck C 《MOLECULAR PHYLOGENETICS AND EVOLUTION》