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Original

A comprehensive analysis of three Asiatic black bear mitochondrial genomes (subspecies ussuricus, formosanus and mupinensis), with emphasis on the complete mtDNA sequence of Ursus thibetanus ussuricus (Ursidae)

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Pages 418-429 | Received 04 Jun 2008, Accepted 05 Aug 2008, Published online: 11 Jul 2009

References

  • Anderson S, Bankier AT, Barrell BG, de Bruijin MHL, Coulson AR, Drouin J, et al. Sequence and organization of the human mitochondrial genome. Nature 1981; 290: 457–465
  • Arnason E, Rand DM. Heteroplasmy of short tandem repeats in mitochondrial DNA of Atlantic cod, Gadus morhua. Genetics 1992; 132: 211–220
  • Burke T, Rainey WE, White TJ. Molecular variation and ecological problems. Genes in ecology, RJ Berry, TJ Crawford, GM Hewitt. Blackwell Scientific Publications, Oxford 1992; 229–254
  • Cantatore P, Roberti M, Pesole G, Ludovico A, Milella F, Gadaleta MN, Saccone C. Evolutionary analysis of cytochrome b sequences in some Perciformes: Evidence for a slower rate of evolution than in mammals. J Mol Evol 1994; 39: 589–597
  • Chang Y-C, Hunag F-L, Lo T-B. The complete nucleotide sequence and gene organization of carp (Cyprinus carpio) mitochondrial genome. J Mol Evol 1994; 38: 138–155
  • Delisle I, Strobeck C. Conserved primers for rapid sequencing of the complete mitochondrial genome from carnivores, applied to three species of bears. Mol Biol Evol 2002; 19: 357–361
  • Doda JN, Wright CT, Clayton DA. Elongation of displacement-loop strands in human and mouse mitochondrial DNA is arrested near specific template sequences. Proc Natl Acad Sci USA 1981; 78: 6116–6120
  • Ellerman JR, Morrison-Scott TCS. Checklist of palaearctic and Indian mammals 175819462nd ed. The British Museum (Natural History), London 1966; 810
  • Gutell RR, Gray MW, Schnare MN. A compilation of large subunit (23S and 23S-like) ribosomal RNA structures. Nucl Acids Res 1993; 21: 3055–3074
  • Hou WR, Chen Y, Wu X, Hu JC, Peng ZS, Yang J, et al. A complete mitochondrial genome sequence of Asian black bear Sichuan subspecies (Ursus thibetanus mupinensis). Int J Biol Sci 2007; 3: 85–90
  • Huelsenbeck JP, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001; 17: 754–755
  • Ishibashi Y, Saitoh T. Phylogenetic relationships among fragmented Asian black bear (Ursus thibetanus) populations in western Japan. Conserv Genet 2004; 5: 311–323
  • Kinouchi M, Kanaya S, Ikemura T, Kudo Y. Detection of tRNA based on the cloverleaf secondary structure. Genome Inform 2000; 11: 301–302
  • Kumazawa Y, Ota H, Nishida M, Ozawa T. The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions. Genetics 1998; 150: 313–329
  • Lowe TM, Eddy SR. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucl Acids Res 1997; 25: 955–964
  • Lunt DH, Whipple LE, Hyman BC. Mitochondrial DNA variable number tandem repeats (VNTRs): Utility and problems in molecular ecology. Mol Ecol 1998; 7: 1441–1455
  • Matsuhashi T, Masuda R, Mano T, Yoshida MC. Microevolution of the mitochondrial DNA control region in the Japanese brown bear (Ursus arctos) population. Mol Biol Evol 1999; 16: 676–684
  • Ohnishi N, Saitoh T, Ishibashi Y. Phylogenetic relationships among fragmented Asian black bear (Ursus thibetanus) populations in western Japan. Conserv Genet 2007; 5: 311–323
  • Pagès M, Calvignac S, Klein C, Paris M, Hughes S, Hänni C. Combined analysis of fourteen nuclear genes refines the Ursidae phylogeny. Mol Phylogenet Evol 2008; 47: 73–83
  • Posada D, Crandall KA. MODELTEST: Testing the model of DNA substitution. Bioinformatics 1998; 14: 817–818
  • Saccone S, Giorgi CD, Gissi C. Evolutionary genomics in Metazoa: The mitochondrial DNA as a model system. Gene 1999; 238: 195–209
  • Sbisà E, Tanzariello F, Reyes A, Pesole G, Saccone C. Mammalian mitochondrial D-loop region structural analysis: Identification of new conserved sequences and their functional and evolutionary implications. Gene 1997; 205: 125–140
  • Servheen C. The status and conservation of the bears of the world. Int Conf Bear Res Manage Monogr Ser 1990; 2: 1–32
  • Shimodaira H, Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 1999; 16: 1114–1116
  • Swofford DL. PAUP* 4.0: Phylogenetic analysis using parsimony (* and other methods). Sinauer Associates, Sunderland, MA 2002
  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The Clustal X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 1997; 24: 4876–4882
  • Walberg MW, Clayton DA. Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA. Nucl Acids Res 1981; 9: 5411–5421
  • Wang S. China red data book of endangered animals: Mammalia. Science Press, Beijing 1998; 341–344
  • Wilkinson GS, Chapman AM. Length and sequence variation in evening bat D-loop mtDNA. Genetics 1991; 128: 607–617
  • Yu L, Li QW, Ryder OA, Zhang YP. Phylogeny of the bears (Ursidae) based on nuclear and mitochondrial genes. Mol Phylogenet Evol 2004; 32: 480–494
  • Yu L, Li YW, Ryder OA, Zhang YP. Analysis of complete mitochondrial genome sequences increases phylogenetic resolution of bears (Ursidae), a mammalian family that experienced rapid speciation. BMC Evol Biol. 2007; 7: 198
  • Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucl Acids Res 2003; 31: 3406–3415

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