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Mitochondrial DNA
The Journal of DNA Mapping, Sequencing, and Analysis
Volume 26, 2015 - Issue 3
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Research Article

Classification and phylogeny of sika deer (Cervus nippon) subspecies based on the mitochondrial control region DNA sequence using an extended sample set

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Pages 373-379 | Received 05 May 2013, Accepted 16 Aug 2013, Published online: 25 Sep 2013

References

  • Akaike H. (1974). A new look at the statistical model identification. IEEE Trans Automat Cont 19:716–23
  • Barančekov M, Krojerov-Prokešov J, Voloshina IV, Myslenkov AI, Kawata Y, Oshida T, Lamka J, Koubek P. (2012). The origin and genetic variability of the Czech sika deer population. Ecol Res 27:991–1003
  • Bartoš L. (2009). Sika deer in continental Europe. In: McCullough D, Takatsuki S, Kaji K, editors. Sika deer. Japan: Springer. p 573--574
  • Beolens B, Watkins M, Grayson M, Ebrary I. (2009). The eponym dictionary of mammals. Baltimore: Johns Hopkins University Press
  • Brown WM, George Jr M, Wilson AC. (1979). Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci USA 76:1967–71
  • Cook CE, Wang Y, Sensabaugh G. (1999). A mitochondrial control region and cytochrome b phylogeny of sika deer (Cervus nippon) and report of tandem repeats in the control region. Mol Phylogenet Evol 12:47–56
  • Dueck GS. (1998). Genetic relations and phylogeography of wood-land and barren ground caribou. MSc Thesis. University of Alberta, Edmonton, AB
  • Felsenstein J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783–91
  • Groves C. (2006). The genus Cervus in eastern Eurasia. Eur J Wildlife Res 52:14–22
  • Guo YS, Zheng HZ. (2000). On the geological distribution, taxonomic status of species and evolutionary history of sike deer in China. Acta Theriologica Sinica 20:168–79 (in Chinese)
  • Hasegawa M, Kishino H, Yano T. (1985). Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22:160–74
  • Hewitt GM. (1999). Post-glacial re-colonization of European biota. Biol J Linnean Soc 68:87–112
  • Huelsenbeck JP, Ronquist F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–5
  • Krojerova-Prokesova J, Barancekova M, Voloshina I, Myslenkov A, Lamka J, Koubek P. (2013). Dybowskii’s sika deer (Cervus nippon hortulorum): Genetic divergence between natural primorian and Introduced Czech populations. J Hered 104:312--26
  • Kuwayama R, Ozawa T. (2000). Phylogenetic relationships among European red deer, wapiti, and sika deer inferred from mitochondrial DNA sequences. Mol Phylogenet Evol 15:115–23
  • Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, et al. (2007). Clustal W and clustal X version 2.0. Bioinformatics 23:2947–8
  • Larson A. (1995). Molecular markers, natural-history and evolution. Avise J Sci 267:115–16
  • Lu XP, Wei FW, Li M, Yang G, Liu H. (2006). Genetic diversity among Chinese sika deer (Cervus nippon) populations and relationships between Chinese and Japanese sika deer. Chin Sci Bull 51:433–40
  • Ma YQ. (1986). Mammalian of Helongjian province. Harbin, China: Heilongjiang Science and Technology (in Chinese)
  • Mahmut H, Masuda R, Onuma M, Takahashi M, Nagata J, Suzuki M, Ohtaishi N. (2002). Molecular phylogeography of the red deer (Cervus elaphus) populations in Xinjiang of China: Comparison with other Asian, European, and North American populations. Zoo Sci 19:485–95
  • Mikko S, Andersson L. (1995). Low major histocompatibility complex class-II diversity in European and North-American moose. Proc Natl Acad Sci USA 92:4259–63
  • Nagata J, Masuda R, Mc Y. (1995). Nucleotide sequences of the cytochrome b and 12S rRNA in the Japanese sika deer Cervus nippon. J Mamm Soc Jpn 20:1–8
  • Nagata J, Masuda R, Tamate HB, Hamasaki S, Ochiai K, Asada M, Tatsuzawa S, et al. (1999). Two genetically distinct lineages of the sika deer, Cervus nippon, in Japanese islands: Comparison of mitochondrial D-loop region sequences. Molec Phylogenet and Evolution 13:511–19
  • Nicholas KB, Nicholas HB, Deerfield DW. (1997). GeneDoc: Analysis and visualization of genetic variation. EMBNEW NEWS 4:14
  • Nylander JAA. (2004). MrModeltest v2. Program distributed by the author. Uppsala University: Evolutionary Biology Centre
  • Ohshima K. (1990). The history of straits around the Japanese islands in the Late-Quaternary [in Japanese with English abstract]. Quaternary Res 29:193–208
  • Polziehn RO, Strobeck C. (2002). A phylogenetic comparison of red deer and wapiti using mitochondrial DNA. Mol Phylogenet Evol 22:342–56
  • Qu YH, Ericson PGP, Lei FM, Li SH. (2005). Postglacial colonization of the Tibetan plateau inferred from the matrilineal genetic structure of the endemic red-necked snow finch, Pyrgilauda ruficollis. Mol Ecol 14:1767–81
  • Randi E, Mucci N, Claro-Hergueta F, Bonnet A, Douzery EJP. (2001). A mitochondrial DNA control region phylogeny of the Cervinae: Speciation in Cervus and implications for conservation. Animal Conserv 4:1–11
  • Sheng HL, Ohtaishi N. (1993). The status of deer in China. Deer of China, Biology and Management. Shanghai, China: Elsevier Science Publishers
  • Shimodaira H, Hasegawa M. (2001). CONSEL: For assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246–7
  • Swofford DL. (2002). PAUP*: Phylogenetic analysis using parsimony (* and other methods). version 4. Sunderland, MA: Sinauer
  • Tamate HB, Tatsuzawa S, Suda K, Izawa M, Doi T, Sunagawa K, Miyahira F, Tado H. (1998). Mitochondrial DNA variations in local populations of the Japanese sika deer, Cervus nippon. J Mammal 79:1396–403
  • Tamate HB, Tsuchiya T. (1995). Mitochondrial DNA polymorphism in subspecies of the Japanese Sika deer, Cervus nippon. J Hered 86:211–15
  • Tamura K, Nei M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–26
  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–9
  • Wada K, Nishibori M, Yokohama M. (2007). The complete nucleotide sequence of mitochondrial genome in the Japanese Sika deer (Cervus nippon), and a phylogenetic analysis between Cervidae and Bovidae. Small Rumin Res 69:46--54
  • Whitehead GK. (1993). The encyclopedia of deer. Shrewsbury, UK: Swan Hill
  • Yang CZ, Li P, Zhang XY, Guo YS, Gao YM, Xiong YQ, Wang LB, et al. (2012). The complete mitochondrial genome of the Chinese Sika deer (Cervus nippon Temminck, 1838), and phylogenetic analysis among Cervidae, Moschidae and Bovidae. J Natural Hist 46:1747--59
  • Zdansky O. (1925). Fossile Hirsche Chinas. Palaeontol Sin Ser C 2:1--94

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