Comparison of evolutionary rates in the mitochondrial DNA cytochrome b gene and control region and their implications for phylogeny of the Cobitoidea (Teleostei: Cypriniformes)

Molecular Phylogenetics and Evolution

Volumn 39, Issue 2, 2006, Pages 347-357

  Tang, Qiongying ^a,b   Liu, Huanzhang ^a   Mayden, Richard ^c   Xiong, Bangxi ^b  

^a INSTITUTE OF HYDROBIOLOGY   (China)

^b HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^c SAINT LOUIS UNIVERSITY   (United States)

Author keywords

Cobitoidea; Control region; Cytochrome b; Phylogenetic analysis; Sequence divergence

Indexed keywords

CYTOCHROME B; MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BAYES THEOREM; CHEMISTRY; CLASSIFICATION; COMPARATIVE STUDY; CYPRINIFORMES; DNA BASE COMPOSITION; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; TIME;

ANIMALS; BASE COMPOSITION; BAYES THEOREM; CYPRINIFORMES; CYTOCHROMES B; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; TIME FACTORS;

BALITORIDAE; BALITORINAE; BOTIINAE; CATOSTOMIDAE; COBITIDAE; COBITINAE; COBITOIDEA; CYPRINIFORMES; CYPRINUS CARPIO; DANIO RERIO; GYRINOCHEILIDAE; NEMACHEILINAE; TELEOSTEI;

EID: 30844448458     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2005.08.007     Document Type: Article

References (51)

1. Bǎnǎrescu P.M., and Nalbant T.T. A generical classification of Nemacheilinae with description of two new genera (Teleostei: Cypriniformes: Cobitidae). Trav. Mus. Hist. Nat. "Grigore Antipa" 35 (1995) 429-496
2. Berg L.S. Classification of fishes, both recent and fossil. Trav. Inst. Zool. Acad. Sci. USSR 5 (1940) 87-345
3. Bernatchez L., and Danzmann R.G. Congruence in control-region sequence and restriction-site variation in mitochondrial DNA of brook charr (Salvelinus fontinalis Mitchill). Mol. Biol. Evol. 10 (1993) 1002-1014
4. Brown W. The mitochondrial genome of animals. In: Macinttyre R. (Ed). Molecular Evolutionary Genetics (1985), Plenum Press, New York 95-130
5. Brown G.G., Gadaleta G., Pepe G., Saccone C., and Sbisa E. Structural conservation and variation in the D-loop-containing region of vertebrate mitochondrial DNA. J. Mol. Biol. 192 (1986) 503-511
6. Bull J.J., Huelsenbeck J.P., Cunning C.W., Swofford D.L., and Waddell P.J. Partitioning and combing data in phylogenetic analysis. Syst. Biol. 42 (1993) 384-397
7. Chen J., and Zhu S. Phylogenetic relationships of subfamilies in the loach family Cobitidae (Pisces). Acta Zootaxon. Sin. 9 (1984) 201-207
8. Crochet P.A., and Desmarais E. Slow rate of evolution in the mitochondiral control region of Gulls (Aves: Laridae). Mol. Biol. Evol. 17 (2000) 1797-1806
9. Cunningham C.W. Can three incongruence tests predict when data should be combined?. Mol. Biol. Evol. 14 (1997) 733-740
10. Doda J.N., Wright C.T., and Clayton D.A. Elongation of displacement-loop strands in human and mouse mitochondrial DNA is arrested near specific template sequences. Proc. Natl. Acad. Sci. USA 78 (1981) 6116-6120
11. Farris J.S., Källerjö M., Kluge A.G., and Butt C. Testing significance of incongruence. Cladistics 10 (1994) 315-319
12. Galtier N., Gouy M., and Gautier C. SEAVIEW and PHYLO-WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput. Appl. Biosci. 12 (1996) 543-548
13. He S.P., Yue P.Q., and Chen Y.Y. Comparative study in the morphology and development of the pharyngeal dentition in the families of Cypriniformes. Acta Zootaxon. Sin. 43 (1997) 255-262
14. Hora S.L. Classification, bionomics and evolution of Homalopteridae fishes. Mem. Indian Mus. 12 (1932) 263-330
15. Huelsenbeck J.P., and Ronquist F. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17 (2001) 754-755
16. Kocher T.D., Thomas W.K., Meyer A., Edwards S.V., Paabo S., Villablanca F.X., and Wilson A.C. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. USA 86 (1989) 6196-6200
17. Kottelat M. Indian and Indochinese species of Balitora (Osteichthyes: Cypriniformes) with description of two new species and comments on the family-group names Balitoridae and Homalopteridae. Rev. Suisse. Zool. 95 (1988) 487-504
18. Kottelat M. Fishes of Laos (2001), WHT, Colombo, Sri Lanka
19. Lee W., Conroy J., Howell W.H., and Kocher T.D. Structure and evolution of teleost mitochondrial control regions. J. Mol. Evol. 41 (1995) 54-66
20. Liu H., and Chen Y. Phylogeny of the east Asian cyprinids inferred from sequences of the mitochondrial DNA control region. Can. J. Zool. 81 (2003) 1938-1946
21. Liu H., Tzeng C.S., and Teng H.Y. Sequence variations in the mitochondrial DNA control region and their implications for the phylogeny of the Cypriniformes. Can. J. Zool. 80 (2002) 569-581
22. Meyer A. Evolution of mitochondrial DNA in fishes. In: Hochachka P.W., and Mommsen T.P. (Eds). Biochemistry and Molecular Biology of Fishes Vol. 2 (1993), Elsevier, Amsterdam 1-38
23. Mickevich M.F., and Farris J.S. The implications of congruence in menidia. Syst. Biol. 30 (1981) 351-370
24. Moum T., and Árnason E. Genetic diversity and population history of two related seabird species based on mitochondrial DNA control region sequences. Mol. Ecol. 10 (2001) 2463-2478
25. Nalbant T. A study of the genera of Botiinae and Cobitinae (Pisces, Ostariophysi, Cobitidae). Trav. Mus. Nat. "Grigore Antipa" 4 (1963) 343-375
26. Nalbant T. Sixty million years of evolution. Part one: family Botiidae (Pisces: Ostariophysi: Cobitidae). Trav. Mus. Nat. "Grigore Antipa" 44 (2002) 343-379
27. Nalbant T.T., and Bianco P.G. The loaches of Iran and adjacent region with description of six new species (Cobitoidea). Ital. J. Zool. 65 (1998) 109-123
28. Nelson J.S. Fishes of the World. third ed. (1994), Wiley, New York
29. Peng Z., He S., and Zhang Y. Phylogenetic relationships of glyptosternoid fishes (Siluriformes: Sisoridae) inferred from mitochondrial cytochrome b gene sequence. Mol. Phylogenet. Evol. 31 (2004) 979-987
30. Perdices A., Cunha C., and Coelho M.M. Phylogenetic structure of Zacco platypus (Teleostei, Cyprinidae) populations on the upper and middle Chang Jiang (=Yangtze) drainage inferred from cytochrome b sequences. Mol. Phylogenet. Evol. 31 (2004) 192-203
31. Posada D., and Crandall K.A. Model test: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
32. Ramaswami L.S. Skeleton of cyprinoid fishes in relation to phylogenetic studies. V. The skull and the gasbladder capsule of the Cobitidae. Proc. Natl. Inst. Sci. India 18 (1953) 519-538
33. Randi E., and Lucchini V. Organization and evolution of the mitochondrial DNA control region in the avian genus Alectoris. J. Mol. Evol. 47 (1998) 149-162
34. Regan C.T. The classification of the teleostean fishes of the order Ostariophysi I. Cyprinidae. Ann. Mag. Nat. Hist. Ser. 8 (1911) 13-32
35. Roukonen M., and Kvist L. Structure and evolution of the avian mitochondrial control region. Mol. Phylogenet. Evol. 23 (2002) 422-432
36. Rychel A.L., Reeder T.W., and Berta A. Phylogeny of mysticete whales based on mitochondrial and nuclear data. Mol. Phylogenet. Evol. 32 (2004) 892-901
37. Saccone C., Pesole G., and Sbisà E. The main regulatory region of mammalian mitochondrial DNA: structure-function model and evolutionary pattern. J. Mol. Evol. 33 (1991) 83-91
38. Saunders M.A., and Edwards S.V. Dynamics and phylogenetic implications of mtDNA control region sequences in New World Jays (Aves: Corvidae). J. Mol. Evol. 51 (2000) 97-109
39. Sawada, Y., 1982. Phylogeny and zoogeography of the superfamily Cobitoidea (Cyprinoidei, Cypriniformes). Memoirs of the Faculty of Fisheries, Hokkaido University 28, 65-223.
40. Sbisà E., Tanzariello F., Reyes A., Pesole G., and Sacone C. Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implifications. Gene 205 (1997) 125-140
41. Shedlock A.M., Parker J.D., Crispin D.A., Pietsch T.W., and Burmer G.C. Evolution of the salmonid mitochondrial control region. Mol. Phylogenet. Evol. 1 (1992) 179-192
42. Siebert, D.J., 1987. Interrelationships among families of the order Cypriniformes (Teleostei). Ph.D. Dissertation, City University of New York, New York.
43. Southern S.O., Southern P.J., and Dizon A.E. Molecular characterization of a cloned dolphin mitochondrial genome. J. Mol. Evol. 28 (1988) 32-42
44. *: Phylogenetic Analysis Using Parsimony (* and other Methods), Version 4. Sinauer, Sunderland, MA.
45. Tang Q., Xiong B., Yang X., and Liu H. Phylogeny of the East Asian botiine loaches (Cypriniformes, Botiidae) inferred from mitochondrial cytochrome b gene sequences. Hydrobiologia 544 (2005) 249-258
46. Taylor M.F., McKechnie S.W., Pierce N., and Kreitman M. The Lepidopteran mitochondrial control region: structure and evolution. Mol. Biol. Evol. 10 (1993) 1259-1272
47. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The Clustal X windows interface: flexible strategies for multiple sequences alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
48. Wiens J.J. Combing data sets with different phylogenetic histories. Syst. Biol. 47 (1998) 568-581
49. Wu X., Chen Y., Chen X., and Chen J. A taxonomical system and phylogenetic relationship of the families of the suborder Cyprinoidei (Pisces). Sci. Sin. 24 (1981) 563-572
50. Xiao W., Zhang Y., and Liu H. Molecular systematics of Xenocyprinae (Teleostei: Cyprinidae): taxonomy, biogeography, and coevolution of a special group restricted in east Asia. Mol. Phylogenet. Evol. 18 (2001) 163-173
51. Zhu D., Jamieson B.G., Hugall A., and Moritz C. Sequence evolution and phylogenetic signal in control-region and cytochrome b sequences of rainbow fishes (Melanotaeniidae). Mol. Biol. Evol. 11 (1994) 672-683