Molecular characteristics of mitochondrial DNA and phylogenetic analysis of the loach (Misgurnus anguillicaudatus) from the Poyang Lake

References

• Abbas K, Li MY, Wang WM, Zhou XY. 2009. First record of the natural occurrence of hexaploid loach Misgurnus anguillicaudatus in Hubei Province, China. J Fish Biol. 75 2: 435–441.
   Google Scholar
• Arai K. 2003. Genetics of the loach, Misgurnus anguillicaudatus: Recent progress and perspective. Folia Biol (Krakow). 51S:107–117.
   Google Scholar
• Brown KH, Drew RE, Weber LA, Thorgaard GH. 2006. Intraspecific variation in the rainbow trout mitochondrial DNA genome. Comp Biochem Phys D: Genomics and Proteomics. 1 2: 219–226.
   Google Scholar
• Brown WG, George MJ, Wilson AC. 1979. Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci. 76:1967–1971.
   PubMed Web of Science ®Google Scholar
• Casati S, Bernasconi MV, Gern L, Piffaretti JC. 2008. Assessment of intraspecific mtDNA variability of European Ixodes ricinus sensu stricto (Acari: Ixodidae). Infect Gent Evol. 8:152–158.
   Web of Science ®Google Scholar
• Douglas MR, Brunner PC, Bernatchez L. 1999. Do assemblages of Coregonus (Teleostei: Salmoniformes) in the Central Alpine region of Europe represent species flocks. Mol Ecol. 8:589–603.
   Web of Science ®Google Scholar
• Foitzik S, Sturm H, Pusch KD, Ettorre P, Heinze J. 2007. Nestmate recognition and intraspecific chemical and genetic variation in Temnothorax ants. Anim Behav. 73:999–1007.
   Google Scholar
• Garant D, Dodson JJ, Bernatchez L. 2000. Ecological determinants and temporal stability of the within-river population structure in Atlantic salmon (Salmo salar L.). Mol Ecol. 9:615–628.
   PubMed Web of Science ®Google Scholar
• Gerlach G, Schardt U, Eckmann R, Meyer A. 2001. Kin-structured subpopulations in Eurasian perch (Perca fluviatilis L.). Heredity. 86:213–221.
   PubMed Web of Science ®Google Scholar
• Gutell R, Gray M, Schnare M. 1993. A compilation of large subunit (23S and 23S-like) ribosomal RNA structures. Nucleic Acids Res. 21:3055–3074.
   PubMed Web of Science ®Google Scholar
• He SP, Gu X, Mayden RL, Chen WJ, Conway KW, Chen Y. 2008. Phylogenetic position of the enigmatic genus Psilorhynchus (Ostariophysi: Cypriniformes): Evidence from the mitochondrial genome. Mol Phylogenet. 47 1: 419–425.
   PubMed Web of Science ®Google Scholar
• Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W. 2004. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. PNAS. 101 41: 14812–14817.
   PubMed Web of Science ®Google Scholar
• Hurst CD, Bartlett SE, Davidson WS, Bruce IJ. 1999. The complete mitochondrial DNA sequence of the Atlantic salmon. Salmo salar. Gene. 239:237–242.
   Google Scholar
• Inoue JG, Miya M, Aoyama J, Ishikawa S, Tsukamoto K, Nishida M. 2001. Complete mitochondrial DNA sequence of the Japanese eel Anguilla japonica. Fish Sci. 67:118–125.
   Web of Science ®Google Scholar
• Irwin DM, Kocher TD, Wilson AC. 1991. Evolution of the cytochrome b gene of mammals. J Mol Evol. 32:128–144.
   PubMed Web of Science ®Google Scholar
• Johns GC, Avise JC. 1998. Tests for ancient species flocks based on molecular phylogenetic appraisals of Sebastes rockfishes and other marine fishes. Evolution. 52:1135–1146.
   PubMed Web of Science ®Google Scholar
• Johnson ML, Gaines MS. 1990. Evolution of dispersal: Theoretical models and empirical tests using birds and mammals. Ann Rev Ecolog Syst. 21:449–480.
   Google Scholar
• Kartavtsev YP, Lee J. 2006. Analysis of nucleotide diversity at the cytochrome b and cytochrome oxidase 1 genes at the population, species, and genus levels. Russ J Genet. 42:341–362.
   Web of Science ®Google Scholar
• Kartavtsev YP, Jung SO, Lee YM, Byeon HK, Lee JS. 2007. Complete mitochondrial genome in the bullhead torrent catfish, Liobagrus obesus (Siluriformes, Amblycipididae): Genome description and phylogenetic considerations inferred from the Cyt b and 16S rRNA genes. Gene. 396:13–27.
   PubMed Web of Science ®Google Scholar
• Khan MMR, Arai K. 2000. Allozyme variation and genetic differentiation in the loach Misgurnus anguillicaudatus. Fish Sci. 66:211–222.
   Google Scholar
• Khan MMR, Arai K, Kuroda K, Umino T, Nakagawa H. 2005. Genetic variation of Japanese loach inferred from restriction fragment length polymorphism analysis of mitochondrial DNA. Afr J Biotechnol. 4:318–325.
   Google Scholar
• Kim IC, Kweon HS, Kim YJ, Kim CB, Gye MC, Lee WO, Lee YS, Lee JS. The complete mitochondrial genome of the javeline goby Acanthogobius hasta (Perciformes, Gobiidae) and phylogenetic considerations. Gene. 2004a; 336:147–153.
   PubMed Web of Science ®Google Scholar
• Kim YJ, Kweon HS, Kim IC, Lee YM, Kim JM, Lee JS. The complete mitochondrial genome of the floating gobby, Gymnogobius petschiliensis (Perciformes, Gobiidae). Mol Cells. 2004b; 17:446–453.
   PubMed Web of Science ®Google Scholar
• Kimura M. 1978. Protein polymorphism and geographic variation in the loach Misgurnus anguillicandatus. Anim Blood Graps Biochem Genet. 9:13–20.
   Google Scholar
• Kumar S, Tamura K, Nei M. 2004. MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform. 5 2: 150–163.
   PubMed Web of Science ®Google Scholar
• Kumazawa Y, Nishida M. 1993. Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. J Mol Evol. 37:380–398.
   PubMed Web of Science ®Google Scholar
• Kumazawa Y, Nishida M. 1995. Variations in mitochondrial tRNA gene organization of reptiles as phylogenetic markers. Mol Biol Evol. 12:759–772.
   Google Scholar
• Lewis RL, Beckenbach AT, Mooers Aø. 2005. The phylogeny of the subgroups within the melanogaster species group: Likelihood tests on COI and COII sequences and a Bayesian estimate of phylogeny. Mol Phylogenet Evol. 37:15–24.
   Google Scholar
• Li WH. 1997. Molecular evolution. Sunderland, MA: Sinauer Associates.
   Google Scholar
• Mabuchi K, Miya M, Senou H, Suzuki T, Nishida M. 2006. Complete mitochondrial DNA sequence of the Lake Biwa wild strain of common carp (Cyprinus carpio L.): Further evidence for an ancient origin. Aquaculture. 257:68–77.
   Web of Science ®Google Scholar
• Man SH, Hodgkiss IJ. 1981. Hong Kong freshwater fishes. Hong Kong: Urban Council.
   Google Scholar
• Mettke-Hofmann C, Gwinner E. 2004. Differential assessment of environmental information in a migratory and a nonmigratory passerine. Anim Behav. 68:1079–1086.
   Google Scholar
• Meyer A. 1993. Evolution of mitochondrial DNA in fishes. In: Hochachka P.W., Mommsen T.P.. editors. Biochemistry and molecular biology of fishes1–38 Elsevier Science Publishers, New York.
   Google Scholar
• Miya M, Nishida M. 1999. Organization of the mitochondrial genome of a deep-sea fish, Gonostoma gracile (Teleostei: Stomiiformes): First example of transfer RNA gene rearrangements in bony fishes. Mar Biotechnol. 1:416–426.
   PubMed Web of Science ®Google Scholar
• Miya M, Nishida M. 2000. Use of mitogenomic information in teleostean molecular phylogenetics: A tree-based exploration under the maximum-parsimony optimality criterion. Mol Phylogenet Evol. 17:437–455.
   PubMed Web of Science ®Google Scholar
• Miya M, Takeshima H, Endo H, Ishiguro NB, Inoue JG, Mukai T, Satoh TP, Yamaguchi M, Kawaguchi A, Mabuchi K. 2003. Major patterns of higher teleostean phylogenies: A new perspective based on 100 complete mitochondrial DNA sequences. Mol Phylogenet Evol. 26:121–138.
   PubMed Web of Science ®Google Scholar
• Morishima K, Nakamura-Shiokawa Y, Bando E, Li YJ, Boron A, Khan MM, Arai K. 2008. Cryptic clonal lineages and genetic diversity in the loach Misgurnus anguillicaudatus (Teleostei: Cobitidae) inferred from nuclear and mitochondrial DNA analyses. Genetica. 132:159–171.
   PubMed Web of Science ®Google Scholar
• Nachman MW, Brown WM, Stoneking M, Aquadro CF. 1996. Nonneutral mitochondrial DNA variation in humans and chimpanzees. Genetics. 142:953–963.
   Google Scholar
• Nagase M, Aimi T, Suginaka K, Kitamoto Y, Morinaga T. 2005. Complete mitochondrial DNA sequence of the Japanese flying fish Cypselurus hiraii. Fish Sci. 71:914–923.
   Web of Science ®Google Scholar
• Nei M. 1987. Molecular evolutionary genetics. New York: Columbia University Press.
   Google Scholar
• Nei M, Kumar S. 2000. Molecular evolution and phylogenetics. New York: Oxford University Press.
   Google Scholar
• Nelson JS. 1994. Fishes of the World. New York: Wiley.
   Google Scholar
• Papetti C, LiÒ P, RÜber L, Patarnello T, Zardoya R. 2007. Antarctic fish mitochondrial genomes lack ND6 gene. J Mol Evol. 65:519–528.
   PubMed Web of Science ®Google Scholar
• Peng QL, Nie LW, Pu YG. 2006. Complete mitochondrial genome of Chinese big headed turtle, Platysrernon megacephalm, with a novel gene organization in Vertebrate mtDNA. Gene. 380:14–20.
   PubMed Web of Science ®Google Scholar
• Posada D, Crandall KA. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics. 14:817–818.
   PubMed Web of Science ®Google Scholar
• Rand DM, Kann LM. 1998. Mutation and selection at silent and replacement sites in the evolution of animal mitochondrial DNA. Genetica. 102 103: 393–407.
   Google Scholar
• Reuter JS, Mathews DH. 2010. RNA structure: Software for RNA secondary structure prediction and analysis. BMC Bioinform. 11:129.
   PubMed Web of Science ®Google Scholar
• Ruiz-García M, Castillo MI, Vásquez C, Rodriguez K, Pinedo-Castro M, Shostell J, Leguizamonc N. 2010. Molecular phylogenetics and phylogeography of the white-fronted capuchin (Cebus albifrons; Cebidae, Primates) by means of mtCOII gene sequences. Mol Phylogenet Evol. 57:1049–1061.
   PubMed Web of Science ®Google Scholar
• Saccone S, Federico C, Solovei I, Croquette MF, Della VG, Bernardi G. 1999. Identification of the gene-richest bands in human prometaphase chromosomes. Chromosome Res. 7:379–386.
   PubMedGoogle Scholar
• Safi K, Kerth G. 2003. Secretions of the interaural gland contain information about individuality and colony membership in Bechstein's bat. Anim Behav. 65:363–369.
   Google Scholar
• Saitoh K, Kim I-S, Lee E-H. 2004. Mitochondrial gene introgression between spined loaches via hybridogenesis. Zool Sci. 21:795–798.
   PubMed Web of Science ®Google Scholar
• Saitoh K, Chen WJ, Mayden RL. 2010. Extensive hybridization and tetrapolyploidy in spined loach fish. Mol Phylogenet Evol. 56 3: 1001–1010.
   Google Scholar
• Schattner P, Brooks AN, Lowe TM. 2005. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 33 2: 686–689.
   Google Scholar
• Slechtova V, Bohlen J, Perdices A. 2008. Molecular phylogeny of the freshwater fish family Cobitidae (Cypriniformes: Teleostei): Delimitation of genera, mitochondrial introgression and evolution of sexual dimorphism. Mol Phylogenet Evol. 47:812–831.
   PubMed Web of Science ®Google Scholar
• Su X, Wu XB, Yan P, Cao SY, Hu YL. 2007. Rearrangement of a mitochondrial tRNA gene of the concave-eared torrent frog, Amolops tormotus. Gene. 394 1-2: 25–34.
   PubMed Web of Science ®Google Scholar
• Swofford DL. 2002. PAUP. Phylogenetic analysis using parsimony (and other methods). Sunderland, MA: Sinauer Associates.
   Google Scholar
• Tang QY, Xiong BX, Yang XP, Liu HZ. 2005. Phylogeny of the East Asian botiine loaches (Cypriniformes, Cobitidae) inferred from mitochondrial cytochrome b gene sequences. Hydrobiologia. 544:249–258.
   Web of Science ®Google Scholar
• Tang QY, Liu HZ, Mayden R, Xiong BX. 2006. Comparison of evolutionary rates in the mitochondrial DNA cytochrome b gene and control region and their implications for phylogeny of the Cobitoidea (Teleostei: Cypriniformes). Mol Phylogenet Evol. 39:347–357.
   PubMed Web of Science ®Google Scholar
• Tzeng CS, Hui CF, Shen SC, Huang PC. 1992. The complete nucleotide sequence of the Crossostoma lacustre mitochondrial genome: Conservation and variations among vertebrates. Nucleic Acids Res. 20 18: 4853–4858.
   PubMed Web of Science ®Google Scholar
• Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higguns DG. 1997. The clustal-X windows interface: Flexible strategies for multiple sequene alignment aided by quality analysis tools. Nucleic Acids Res. 24:4876–4882.
   Web of Science ®Google Scholar
• Wang ZW, Wu QJ, Zhou JF, Ye YZ, Tong JG. 2003. Silver carp, Hypophthalmichthys molitrix, in the Poyang Lake belong to the Ganjiang River population rather than the Changjiang River population. Environ Biol Fish. 68:261–267.
   Google Scholar
• Yang CT, Cao L, Wang WM, Yang Y, Abbas K, Yan BL, Wang HP, Su L, Sun YH, Wang HL. 2009. Comparative and evolutionary analysis in natural diploid and tetraploid weather loach Misgurnus anguillicaudatus based on cytochrome b sequence data in central China. Environ Biol Fish. 86:145–153.
   Google Scholar
• Yin J, Zhao ZS, Chen XQ, Li YQ, Zhu LY. 2005. Karyotype comparison of diploid and tetraploid loach. Acta Hydrobiol Sin. 29 4: 469–472 (in Chinese with English abstract).
   Google Scholar
• You CH, Yu XM, Tong JG. 2009. Detection of hybridization between two loach species (Paramisgurnus dabryanus and Misgurnus anguillicaudatus) in wild populations. Environ Biol Fish. 86:65–71.
   Web of Science ®Google Scholar
• Zeng LG, Zhang W, Gan YF, Wang JH, Hong YJ. 2010. The Genetic Diversity of loach Misgurnus angullicaudatus From the Poyang Lake. Acta Hydrobiol Sin. 34 5: 966–972 (in Chinese with English abstract).
   Google Scholar