Molecular phylogenetics of pricklebacks and other percoid fishes from the sea of Japan

Aquatic Biology

Volumn 8, Issue 1, 2009, Pages 95-103

  Kartavtsev, Yuri P ^a,b   Sharina, Svetlana N ^a   Goto, Tadasuke ^c   Rutenko, Olesya A ^b   Zemnukhov, Vladimir V ^a   Semenchenko, Alexander A ^b   Pitruk, Dmitri L ^a   Hanzawa, Naoto ^c  

^a INSTITUTE OF MARINE BIOLOGY   (Russian Federation)

^b FAR EASTERN FEDERAL UNIVERSITY   (Russian Federation)

^c YAMAGATA UNIVERSITY   (Japan)

Author keywords

Co 1; Cytochrome c oxidase 1; Identification; Mitochondrial DNA; Percoid

Indexed keywords

ACTINOPTERYGII; CYPRINIFORMES; PERCIFORMES; PERCOIDEI; PISCES; STICHAEIDAE;

EID: 74349113504     PISSN: 18647782     EISSN: 18647790     Source Type: Journal    
DOI: 10.3354/ab00205     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, Richmond RC (1974) Genetic differentiation during the speciation process in Drosophila. Evolution 28:576-592
3. Bush GL (1975) Modes of animal speciation. Annu Rev Ecol Syst 6:339-364
4. Craig MT, Hastings PA (2007) A molecular phylogeny of the groupers of the subfamily Epinephelinae (Serranidae) with a revised classification of the Epinephelini. Ichthyol Res 54:1-17
5. Dobzhansky T (1955) Evolution, genetics and man. John Wiley & Sons, New York
6. Felsenstein J (2004) Inferring phylogenies. Sinauer Associates, Sunderland, MA
7. Finnerty JR, Block BA (1995) Evolution of cytochrome-b in the Scombroidei (Teleostei)-molecular insights into Billfish (Istiophoridae and Xiphiidae) relationships. Fish Bull 93(1): 78-96
8. Froese R, Pauly D (eds) (2004) FishBase. www.fishbase.org
9. Froese R, Pauly D (eds) (2009) World Wide Web electronic publication. www.fishbase.org, version (10/2009)
10. Hall B (2001) Phylogenetic trees made easy. A how-to manual for molecular biologists. Sinauer Associates, Sunderland, MA
11. Harrison RG (1998) Linking evolutionary pattern and process: the relevance of species concepts for the study of speciation. In: Howard DJ, Berlocher SH (eds) Endless forms: species and speciation. Oxford University Press, Oxford, p 19-31
12. Hebert PD, Stoeckle MY, Zemlak TS, Francis CM (2004) Identification of birds through DNA barcodes. PLoS Biol 2:e312 doi: 10.1371/journal.pbio.0020312
13. Hillis DM (1998) Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst Biol 47:3-8
14. Hillis DM, Moritz C, Mable B (eds) (1996) Molecular systematics. Sinauer Associates, Sunderland, MA
15. Hubert N, Hanner R, Holm E, Mandrak NE and others (2008) Identifying Canadian freshwater fishes through DNA barcodes. PLoS ONE 3:e2490.doi:10.1371/journal.pone. 0002490
16. Huelsenbeck JP, Ronquist F (2001) Mr. BAYES: Bayesian inference of phylogeny. Bioinformatics 17:754-755
17. Johns GC, Avise JC (1998) A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene. Mol Biol Evol 15:1481-1490
18. Johnson GD, Paterson C (1993) Percomorph phylogeny: a survey of acanthomorphs and new proposal. Bull Mar Sci 52:554-626
19. Kartavtsev YP (2005) Molecular evolution and population genetics. Far Eastern State University Press, Vladivostok
20. Kartavtsev YP, Lee JS (2006) Analysis of nucleotide diversity at genes Cyt-b and Co-1 on population, species, and genera levels. Applicability of DNA and allozyme data in the genetics of speciation. Genetika 42:437-461
21. Kartavtsev YP, Sviridov VV, Sasaki T, Hanzawa N (2002) Genetic divergence of far eastern dace belonging to the genus Tribolodon (Pisces, Cyprinidae) and closely related taxa: some insights in taxonomy and speciation. Genetika 38:1518-1531 (In Russian)
22. Kartavtsev YP, Park TJ, Vinnikov KA, Ivankov VN, Sharina SN, Lee JS (2007a) Cytochrome b (Cyt-b) gene sequences analysis in six flatfish species (Pisces, Pleuronectidae) with phylogenetic and taxonomic insights. Mar Biol 152: 757-773
23. Kartavtsev YP, Jung SO, Lee YM, Byeon HK, Lee JS (2007b) 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
24. Kartavtsev YP, Park TJ, Lee JS, Vinnikov KA, Ivankov VN, Sharina SN, Ponomarev AS (2008) Phylogenetic inferences introduced on cytochrome b (Cyt-b) gene sequences data for six flatfish species (Teleostei, Pleuronectidae) and species synonymy between representatives of genera Pseudopleuronectes and Hippoglossoides from far eastern seas. Russ J Genet 44:451-458
25. Kim IC, Kweon HS, Kim YJ, Kim CB and others (2004) The complete mitochondrial 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 University Press, Cambridge
27. Kumar S, Tamura K, Nei M (1993) Manual for MEGA: molecular evolutionary genetics analysis software. Pennsylvania State University, University Park, PA
28. Lee JS (2000) The internally self-fertilized hermaphroditic teleost Rivulus marmoratus (Cyprinodontiformes, Rivulidae) β-actin gene: amplification and sequence analysis with conserved primers. Mar Biotechnol 2:161-166
29. Lindberg GU, Krasyukova ZV (1969) Fishes of the Sea of Japan and the adjacent areas of the Sea of Okhotsk and Yellow Sea, Part 3. Nauka, Leningrad
30. Lindberg GU, Krasyukova ZV (1975) Fishes of the Sea of Japan and the adjacent areas of the Sea of Okhotsk and Yellow Sea, i. Nauka, Leningrad
31. Lydeard C, Roe KJ (1997) The phylogenetic utility of themitochondrial cytochrome b gene for inferring relationships among Actinopterygian fishes. In: Kocher TD, Stepien CA (eds) Molecular systematics of fishes. Academic Press, San Diego, CA, p 285-303
32. Makushok VM (1986a) Stichaeidae. In: Whitehead PJP, Bauchot ML, Hureau JC, Nielsen J, Tortonese E (eds) Fishes of the North-eastern Atlantic and the Mediterranean, Vol. 3. UNESCO, Paris, p 1122-1123
33. Makushok VM (1986b) Lumpenidae (subfamily of Stichaeidae). In: Whitehead PJP, Bauchot ML, Hureau JC, Nielsen J, Tortonese E (eds) Fishes of the North-eastern Atlantic and the Mediterranean, Vol. 3. UNESCO, Paris, p 1126-1129
34. Mayr E (1982) Process of speciation in animals. In: Barigozzi C (ed) Mechanisms of speciation. Alan R. Liss, New York, p 1-20
35. Miya M, Kawaguchi A, 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. Mol Biol Evol 18:1993-2009
36. Miya M, Takeshima H, Endo H, Ishiguro NB and others (2003) Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol Phylogenet Evol 26:121-138
37. Naylor GJ, Collins TM, Brown WM (1995) Hydrophobicity and phylogeny. Nature 373:565-566
38. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
39. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New York
40. Nelson JS (2006) Fishes of the world, 4th edn. John Wiley and Sons, New York
41. Nohara M, Nishida M, Miya M, Nishikawa T (2005) Evolution of the mitochondrial genome in Cephalochordata as inferred from complete nucleotide sequences from two Epigonichthys species. J Mol Evol 60:526-537
42. Orrell TM, Carpenter KE (2004) A phylogeny of the fish family Sparidae (porgies) inferred from mitochondrial sequence data. Mol Phylogenet Evol 32:425-434
43. Page RDM (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357-358
44. Posada D, Crandall KA (1998) MODELTEST: testing the model DNA substitution. Bioinformatics 14:817-818 Radchenko OA, Chereshnev IA, Petrovskaya AV, Balanov AA (2009) Molecular systematics and phylogeny of the suborder Zoarcoidei. Vestn DVO 3:40-47 (In Russian)
45. Reed DL, Carpenter KE, deGravelle MJ (2002) Molecular systematics of the Jacks (Perciformes: Carangidae) based on mitochondrial cytochrome b sequences using parsimony, likelihood, and Bayesian approaches. Mol Phylogenet Evol 23(3):513-524
46. Rock J, Costa FO, Walker DI, North AW, Hutchinson WF, Carvalho GR (2007) DNA barcodes of fish of the Scotia Sea, Antarctica, indicate priority groups for taxonomic and systematics focus. Antarct Sci 20:253-262
47. Ronquist F, Huelsenbeck JP (2003) Mr.BAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574
48. Saitoh K, Hayashizaki K, Yokoyama Y, Asahida T, Toyohara H, Yamashita Y (2000) Complete nucleotide sequence of Japanese flounder (Paralichthys olivaceus) mitochondrial genome: structural properties and cues for resolving teleostean relationships. J Hered 91:271-278
49. Shiogaki M (1984) A review of the genera Pholidapus and Opisthocentrus (Stichaeidae). Jpn J Ichthyol 31:213-224
50. Simpson GG (1961) Principles of animal taxonomy. The species and lower categories. Columbia University Press, New York
51. Smith WL, Craig MT (2007) Casting the percomorph net widely: the importance of broad taxonomic sampling in the search for the placement of serranid and percid fishes. Copeia 2007:35-55
52. Song CB, Near TJ, Page LM (1998) Phylogenetic relations among percid fishes as inferred from mitochondrial cytochrome b DNA sequence data. Mol Phylogenet Evol 10: 343-353
53. Stepien CA, Dillon AK, Brooks MJ, Chase K, Hubers A (1997) The evolution of blennoid fishes based on an analysis of mitochondrial 12S rDNA. In: Cocher TD, Stepien CA (eds) Molecular systematics of fishes. Academic Press, San Diego, CA, p 245-270
54. Swofford DL (2002) PAUP*: phylogenetic analysis using parsimony, version 4.10. Sinauer Associates, Sunderland, MA Templeton AR (1981) Mechanisms of speciation-population genetic approach. Annu Rev Ecol Syst 12:23-48
55. Thompson JD, Higgins DG, 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 Res 22:4673-4680
56. Wallace DC (1992) Diseases of the mitochondrial DNA. Annu Rev Biochem 61:1175-1212
57. Ward RD, Holmes BH (2007) An analysis of nucleotide and amino acid variability in the barcode region of cytochrome c oxidase I (cox1) in fishes. Mol Ecol Notes 7:899-907
58. Ward RD, Zemlak TS, Innes BH, Last PA, Hebert PDN (2005) DNA barcoding Australia's fish species. Philos Trans R Soc Lond B Biol Sci 360:1847-1857
59. Wilcox TP, Garcia de Leon FJ, Hendrickson DA, Hillis DM (2004) Convergence among cave catfishes: long-branch attraction and a Bayesian relative rates test. Mol Phylogenet Evol 31:1101-1113