Sequence diversity at cytochrome oxidase 1 (co-1) gene among sculpins (scorpaenrformes, cottidae) and some other scorpionfish of russia far east with phylogenetic and taxonomic insights

Genes and Genomics

Volumn 31, Issue 2, 2009, Pages 183-197

  Kartavtsev, Yuri Ph ^a,c   Sharina, Svetlana N ^a   Goto, Tadasuke ^b   Balanov, Andrey A ^a   Hanzawa, Naoto ^b  

^a INSTITUTE OF MARINE BIOLOGY   (Russian Federation)

^b YAMAGATA UNIVERSITY   (Japan)

^c FAR EASTERN FEDERAL UNIVERSITY   (Russian Federation)

Author keywords

rdistance; Co 1; Molecular phylogeny; Scorpionfish; Sequence; Taxonomy

Indexed keywords

ACTINOPTERYGII; COTTIDAE; CYPRINIFORMES; PISCES; SCORPAENIFORMES; SCORPIONES;

EID: 67650101261     PISSN: 19769571     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF03191151     Document Type: Article

References (59)

1. Avise JC (2001) Phylogeography. The History and Formation of Species.Harvard University Press, Cambridge, MA.
2. Ayala FJ, Tracey ML, Hedgecock D and Richmond RC (1974) Genetic differentiation during the speciation process in Drosophila. Evolution. 28: 576-592.
3. Bolin RL (1944) A review of marine Cottid fishes of California.Natural history museum of Stanford University, Stanford University, California.
4. Bolin RL (1947) The evolution of marine Cottidae of California with a discussion of the genus as systematic category.Stanford University, California.
5. Bush GL (1975) Modes of animal speciation. Ann. Rev. Ecol. Syst. 6: 339-364.
6. Dobzhansky Th (1955) Evolution, Genetics And Man.John Wiley & Sons Inc. NY, Chapman & Hall, Limited-London, 398 p.
7. Fedorov vv (1986) Cottidae. In Fishes of the Northeastern Atlantic and the Mediterranean, PJP Whitehead, M-L Bavchot, J-C Hvreau, J Nislsen and E Tortonese, eds., Vol. 3, UNESCO, Paris, pp. 1243-1260.
8. Felsenstein J (2004) Inferring phylogenies.Sinauer Associates Inc. Sanderland, Massachusetts, 664 pp.
9. Hall B (2001) Phylogenetic trees made easy. A how- to manual for molecular biologists.Sinauer Assoc. Inc. Publishers, Sunderland, Massachusetts 01375.
10. Harrison RG (1998) linking evolutionary pattern and process: The relevance of species concepts for the study of speciation. In Endless Forms: Species and speciation, DJ Howard SH Berlocher, eds., Oxford Univ. Press, Oxford, NY, pp. 19-31.
11. Hebert FO, Stoeckle MY, Zemlak TS and Francis CM (2004) Identification of birds through DNA barcodes. PLoS Biology 2: e312.
12. Hillis DM (1998) Taxonomic sampling, phylogenetic accuracy, and investigator bias. Systematic Biology 47: 3-8.
13. Hillis DM, Moritz C and Mable B (1996) Molecular Systematics..Sinauer. Assoc. Inc., Sunderland, Massachusetts(01375- 0407, USA) pp. 407-514.
14. Hulsenbeck JP and Rondquist F (2001) Mr. BAYES: Bayesian inference of phylogeny. Bioinformatics. 17: 754-755.
15. Jackson KL (2003) Contributions to the systematics of Cottoid fishes (Teleostei: Scorpaeniformes).Department of Biological Sciences, University of Alberta, 13 pp. 181 leaves.
16. Johns GC and Avise JC (1998) A Comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene. Molecular Biology and Evolution 15: 1481-1490.
17. Kartavtsev YP (1975) A comparative electrophoretic analysis of haemoglobins, water soluble muscle and crystalline lens' proteins of five sculpin species of Cottidae family. Russian Journal of Marine Biology 2: 31-38.
18. Kartavtsev YP (2005) Molecular evolution and population genetics.Far Eastern State Univ. Press., Vladivostok, 234 p.
19. Kartavtsev YPh, Park T-J, Lee J-S, Vinnikov KA, Ivankov VN, Sharina SN and Ponomarev AS (2008) Phylogenetic inferences introduced on cytochrome b (Cyt-b)gene sequences data for six flatfish species (Pisces, Pleuronectidae) and species synonymy among representatives of genera Pseudopleuronectesand Hippoglossoidesfrom far eastern. RussiGenetics 44: 451-458.
20. Kartavtsev YP and Lee J"S (2006) Analysis of nucleotide diversity at genes Cyt-band Co-1on population, species, and genera levels. Applicability of DNA and allozyme data in the genetics of speciation. Russian J. Genetics 42: 437-461.
21. Kartavtsev YP, Lee YM. Jung S-O, Byeon HK and Lee J-S (2007a) Complete mitochondrial genome in the bullhead torrent catfish, Liobagrus obesus(Siluriformes, Amblycipididae) and phylogenetic considerations. Gene 396: 13-27.
22. Kartavtsev YP, Park TJ, Vlnnikov KA, Ivankov VN, Sharina SN and Lee J-S (2007b) Cytochrome b (Cyt-b)gene sequences analysis in six flatfish species (Pisces, Pleuronectidae) with phylogenetic and taxonomic insights. Journal Marine Biology 152: 757-773.
23. Kartavtsev YP, Sviridov vv. Sasaki T and Hanzawa N (2002) Genetic divergence of far eastern dace belonging to the genus Triholodon(Pisces, Cyprinidae) and closely related taxa: some insights in taxonomy and speciation. Genetica 38: 1518-1531 (In Russian, translated in English).
24. Kim l"Ch and Lee J"S (2004) The complete mitochondrial genome of the rockfish Srbastes schlegeli (Scorpaeniformes, Scorpaenidae). Mol. Cells 17: 322- 328.
25. Kim l-C, Kweon H-S, Kim Y\J, Kim C"B, Gye M"C, Lee W-O, Lee Y"S and Lee J"S (2004) The complete mitcchondrial genome of the javeline goby Acanthogobius hasta(Perciformes, Gobiidae) and phylogenetic considerations. Gene 336: 147-153.
26. King M (1993) Species Evolution: the role of chromosome change.Cambridge: Cambridge University Press, 336 pp.
27. Kontula T, Kirilchik SV and Vainola R (2003) Endemic diversification of the momophyletic cottoid fish species flock in Lake Baikal explored with mtDNA sequencing. Molecular Phylogenetics and Evolution 27: 143-155.
28. Kontula T and Vainola R (2003) Relationships of Palearctic and nearctic 'glacial relict' Myoxocephalussculpins from mitochondrial DNA data. Molecular Ecology 12: 3179-3184.
29. Kumar S, Tamura K and Nei M (1993) MEGA: Molecular evolutionary genetics analysis (with a 130-page printed manual). University Park: Pennsilvania State Univ. MEGA3. Web-base βversion , 2005 update.
30. Lee J-S (2000) The internally self-fertilized hermapriroditic teleost Rivulus marmoratus(Cyprincdontiformes, Rivulidae) (β-actin gene: Amplification and sequence analysis with conserved primers. Marine Biotechnology 2: 161-166.
31. Mayr E (1968) Zoological species and evolution.Mir Publishers, Moscow, 398 p. (Russian ed).
32. Mayr E (1982) Process of speciation in animals. In Mechanisms of speciation.Ed. C. Barigozzi. Alan R. Liss, NY pp. 1-20.
33. Miya M, Kawaguchi A and Nishida M (2001) Mitogenomic exploration of higher teleostean phylogenies: a case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences. Molecular Biology and Evolution 18: 1993- 2009.
34. Miya M, Takeshima H, Endo H, Ishiguro NB, Inoue JG, Mukai T, Satoh TP, Yamaguchi M, Kawaguchi A, Mabuchi K, Shirai SM and Nishida M (2003) Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Molecular Phylogenetics and Evolution l: 121-138.
35. Nailcf GJ, Collins TM and Brown WM (1996) Hydrophobicity and phylogeny. Nature 373: 565-566.
36. Nei M (1987) Molecular evolutionary genetics.Columbia Univ. Press, NY, 512 pp.
37. Nei M and Kumar S (2000) Molecular evolution and phylogenetics.Oxford Univ. Press, NY 333 pp.
38. Nelson JS (1994) Fishes of the world.John Wiley and Sons Inc., Third edition. New York, 600 p.
39. Nohara M, Nishida M, Miya M and Nishikawa T (2005) Evolution of the mitochondrial genome in cephalochordata as inferred from complete nucleotide sequences from two epigonichthys species. Journal of Molecular Evolution 60: 526-537.
40. Page RDM (1996) TREEVIEW An application to display phylogenetic trees on personal computers. Comparative and Applied Bioscience 12: 357-358.
41. Paxton JR, Hoese DF, Allen GR and Hanley JE (1989) Pisces. Petromyzontidae to Carangidae.Zoological Catalogue of Australia, Vol. 7, Australian Government Publishing Service, Canberra, 665 p.
42. Pietsch TW (1993) Systematics and distribution of cottid fishes of the genus Triglops Reinhardt(Teleostei: Scorpaeniformes). Zoological Journal of Linnean Society 109: 335-393.
43. Posada D and Grandal KA (1998) MODELTEST: testing the model DNA substitution. Bioinformatics 14: 817-818.
44. Radchenko OA, Chereshnev IA, Nazarkin MV, Petrovskaya AV and Chegodaeva EA (2008) Restriction variability of cytochrome b gene of mitochondrial DNA in some taxa of eel-pout of the family Zoarcidae (Pisces, Perciformes) in north part of the Sea of Okhotsk. Russian J. Genetics 44: 94-100.
45. Ramon ML and Knope ML (2008) Molecular support for marine sculpin (Cottidae; Oligocottinae) diversification during the transition from subtidal to intertidal habitat in the Northeastern Pacific Ocean. Molecular Phylogenetics and Evolution 46: 475-483.
46. Ronquist F and Huelsenbeck JP (2003) Mr.BAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
47. Ryazanova IN, Borisenko SA and Frolov SV (2008) Comparative analysis of the karyotype of the sculpin Myoxocephalus ochotensis(Pisces, Cottidae) from Odyan Bay, Sea of Okhotsk. Biologiya Morya, Vladivostok 33: 225-228.
48. Snedko SV and Miroshnichenko IL (2007) Phylogenetic relationships of sculpin Cottus volteTaranetz, 1993 Scorpaeniformes, Cottidae). Journal of Ichtiology 47: 21-25.
49. Simmons MP and Miya M (2004) Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches: a case study using mitogenomic data from 100 higher teleosts fishes. Molecular Phylogenetics and Evolution 31: 351-362.
50. Simpson GG (1961) Principles of Animal Taxonomy. The Species and Lower Categories.ColumbiaUniv. Press, NY.
51. Swofford DL (2002) PAUP&z.ast;: Phylogenetic analysis using parsimony, version 4.10. Sinauer Associates, Sunderland, MA.
52. Tamura K, Dudley J, Nei M and Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 10.1093/molbev/msm092.
53. Templeton AR (1981) Mechanisms of speciation- population genetic approach. Ann. Rev. Ecol. Syst. 12: 23-48.
54. Thompson JD. Higgins DG and Gibson TJ (1994) Clustal W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position, specific gap penalties, and weight matrix choice. Nucleic Acids Research 22: 4673-4680.
55. Wallace DC (1992) Diseases of the mitochondrial-DNA Annual Review of Biochemistry 61: 1175-1212.
56. Ward RD and Holmes BH (2007) An analysis of nucleotide and amino acid variability in the barcode region of cytochrome c oxidase I (coxl) in fishes. Mol. Ecol. Notes 7: 899-907.
57. Ward RD, Zemlak TS, Innes BH, Last PA and Hebert PDN (2005) DNA barcoding Australia fish species. Philosophical Transactions of the Royal Society of London B 360: 1847-1857.
58. Wilcox TP, Garcia de Leon FJ, Hendrickson DA and Hillis DM (2004) Convergence among cave catfishes: long-branch attraction and a Bayesian relative rates test. Molecular Phylogenetics and Evolution 31: 1101-1113.
59. Yabe M (1985) Comparative osteology and myology of superfamily Cottoidea (Pisces: Scorpaeniformes), and its phylogenetic classification. Faculty of Fishes, Hokkaido University, Hakodate, Japan.