Mitogenomic evaluation of the unique facial nerve pattern as a phylogenetic marker within the percifom fishes (Teleostei: Percomorpha)

Molecular Phylogenetics and Evolution

Volumn 53, Issue 1, 2009, Pages 258-266

  Yagishita, Naoki ^a   Miya, Masaki ^b   Yamanoue, Yusuke ^c   Shirai, Shigeru M ^d   Nakayama, Kouji ^e   Suzuki, Nobuaki ^f   Satoh, Takashi P ^g   Mabuchi, Kohji ^g   Nishida, Mutsumi ^g   Nakabo, Tetsuji ^a  

^a KYOTO UNIVERSITY   (Japan)

^b NATURAL HISTORY MUSEUM AND INSTITUTE   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

^d FISHERIES RESEARCH AGENCY   (Japan)

^e KYOTO UNIVERSITY   (Japan)

^f FISHERIES RESEARCH AGENCY   (Japan)

^g UNIVERSITY OF TOKYO   (Japan)

Author keywords

Facial nerve; Mitochondrial genome; Percomorpha; RLA pattern 10

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BAYES THEOREM; CLASSIFICATION; DNA SEQUENCE; FISH; GENETICS; HISTOLOGY; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; PHYLOGENY; STATISTICAL MODEL;

ANIMALS; BAYES THEOREM; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; FISHES; GENOME, MITOCHONDRIAL; LIKELIHOOD FUNCTIONS; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

ARRIPIDAE; BRAMIDAE; CHIASMODONTIDAE; DICHISTIIDAE; KUHLIIDAE; KYPHOSIDAE; OPLEGNATHIDAE; PERCIFORMES; PERCOIDEI; PERCOMORPHA; PISCES; SCOMBRIDAE; SCOMBROIDEI; STROMATEOIDEI; TELEOSTEI; TERAPONTIDAE; TRACHINOIDEI;

EID: 67949114078     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2009.06.009     Document Type: Article

References (58)

1. Ayvazian S.G., Bastow T.P., Edmonds J.S., How J., and Nowara G.B. Stock structure of Australian herring (Arripis georgiana) in southwestern Australia. Fish. Res. 67 (2004) 39-53
2. Broughton R., and Reneau P. Spatial covariation of mutation and nonsynonymous substitution rates in vertebrate mitochondrial genomes. Mol. Biol. Evol. 23 (2006) 1516-1524
3. Chen W.J., Bonillo C., and Lecointre G. Repeatability of clades as a criterion of reliability: a case study for molecular phylogeny of Acanthomorpha (Teleostei) with larger number of taxa. Mol. Phylogenet. Evol. 26 (2003) 262-288
4. Cheng S., Higuchi R., and Stoneking M. Complete mitochondrial genome amplification. Nat. Genet. 7 (1994) 350-351
5. Collette, B.B., 2001. Scombridae. In: Carpenter, K.E., Niem, V.H. (Eds.), The Living Marine Resources of the Western Central Pacific. Bony Fishes pt. 4 (Labridae to Latimeriidae), vol. 6. FAO Species Identification Guide for Fishery Purposes. FAO, Rome, Italy, pp. 3721-3756.
6. Dettai A., and Lecointre G. Further support for the clades obtained by multiple molecular phylogenies in the acanthomorph bush. C. R. Biol. 328 (2005) 674-689
7. Dettai A., and Lecointre G. New insights into the organization and evolution of vertebrate IRBP genes and utility of IRBP gene sequences for the phylogenetic study of the Acanthomorpha (Actinopterygii: Teleostei). Mol. Phylogenet. Evol. 48 (2008) 258-269
8. Freihofer W.C. Patterns of the ramus lateralis accessorius and their systematic significance in teleostean fishes. Stanford Ichthyol. Bull. 8 (1963) 80-189
9. Gosline W.A. Relationships among some relatively deep-bodied percoid fish groups. Jpn. J. Ichthyol. 31 (1985) 351-357
10. Helfman G.S., Collette B.B., and Facey D.E. The Diversity of Fishes (1997), Blackwell Science, Cambridge, MA
11. Holcroft N. A molecular analysis of the interrelationships of tetraodontiform fishes (Acanthomorpha: Tetraodontiformes). Mol. Phylogenet. Evol. 34 (2005) 525-544
12. Inoue J.G., Miya M., Tsukamoto K., and Nishida M. Complete mitochondrial DNA sequence of the Japanese sardine Sardinops melanostictus. Fish. Sci. 66 (2000) 924-932
13. Inoue J.G., Miya M., Tsukamoto K., and Nishida M. Complete mitochondrial DNA sequence of the Japanese anchovy Engraulis japonicus. Fish. Sci. 67 (2001) 828-835
14. Ishiguro N.B., Miya M., and Nishida M. Complete mitochondrial DNA sequence of ayu, Plecoglossus altivelis. Fish. Sci. 67 (2001) 474-481
15. Johnson D.G. Percomorph phylogeny: progress and problems. Bull. Mar. Sci. 52 (1993) 3-28
16. Johnson D.G., and Fritzsche R.A. Graus nigra, an omnivorous girellid, with a comparative osteology and comments on relationships of the Girellidae (Pisces: Perciformes). Proc. Acad. Nat. Sci. Phila. 141 (1989) 1-27
17. Johnson D.G., and Patterson C. Percomorph phylogeny: a survey of acanthomorph characters and a new proposal. Bull. Mar. Sci. 52 (1993) 554-626
18. Kawaguchi A., Miya M., and Nishida M. Complete mitochondrial DNA sequence of Aulopus japonicus (Teleostei: Aulopiformes), a basal Eurypterygii: longer DNA sequences and higher-level relationships. Ichthyol. Res. 48 (2001) 213-223
19. Kawahara R., Miya M., Mabuchi K., Lavoué S., Inoue J.G., Satoh T.P., Kawaguchi A., and Nishida M. Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): a new perspective based on whole mitogenome sequences from 75 higher teleosts. Mol. Phylogenet. Evol. 46 (2008) 224-236
20. Kim I.C., and Lee J.S. The complete mitochondrial genome of the rockfish Sebastes schlegeli (Scorpaeniformes, Scorpaenidae). Mol. Cells 17 (2004) 322-328
21. Kim I.C., Kweon H.S., Kim Y.J., Kim C.B., Gye M.C., Lee W.O., Lee Y.S., and Lee J.S. The complete mitochondrial genome of the javeline goby Acanthogobius hasta (Perciformes, Gobiidae) and phylogenetic considerations. Gene 336 (2004) 147-153
22. Kuiter R.H. Coastal Fishes of South-Eastern Australia (1993), University of Hawaii Press, Honolulu, Hawaii
23. Leis J.M., and van der Lingen C.D. Larval development and relationships of the perciform family Dichistiidae (= Coracinidae), the galjoen fishes. Bull. Mar. Sci. 60 (1997) 100-116
24. Li B., Dettai A., Cruaud C., Couloux A., Desoutter-Meniger M., and Lecointre G. RNF213, a new nuclear marker for acanthomorph phylogeny. Mol. Phylogenet. Evol. 50 (2009) 345-363
25. Lötynoja A., and Milinkovitch M.C. A hidden Markov model for progressive multiple alignment. Bioimformatics 19 (2003) 1505-1513
26. Mabuchi M., Miya M., Azuma Y., and Nishida M. Independent evolution of the specialized pharyngeal jaw apparatus in cichlid and labrid fishes. BMC Evol. Biol. 7 (2007) 10
27. Maddison W.P., and Maddison D.R. MacClade Version 4 (2000), Sinauer Associates, Sunderland, MA
28. McDowall, R.M., 2001. Centrolophidae. In: Carpenter, K.E., Niem, V.H. (Eds.), The Living Marine Resources of the Western Central Pacific. Bony Fishes pt. 4 (Labridae to Latimeriidae), vol. 6. FAO Species Identification Guide for Fishery Purposes. FAO, Rome, Italy, pp. 3767-3770.
29. Miya M., Kawaguchi A., and Nishida M. 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 (2001) 1993-2009
30. Miya M., and Nishida M. 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 (1999) 416-426
31. Miya M., and Nishida M. Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion. Mol. Phylogenet. Evol. 17 (2000) 437-455
32. Miya M., Satoh T.P., and Nishida M. The phylogenetic position of toadfishes (order Batrachoidiformes) in the higher ray-finned fish as inferred from partitioned Bayesian analysis of 102 whole mitochondrial genome sequences. Biol. J. Linn. Soc. Lond. 85 (2005) 289-306
33. Miya M., Takeshima H., Endo H., Ishiguro N.B., Inoue J.G., Mukai T., Satoh T.P., Yamaguchi M., Kawaguchi A., Mabuchi K., Shirai S.M., and Nishida M. Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol. Phylogenet. Evol. 26 (2003) 121-138
34. Mok H.K., and Shen S.C. Osteology and phylogeny of Squamipinnes. Taiwan Mus. Spec. Publ. Ser. Zool. 1 (1983) 1-87
35. Mooi, R.D., Paxton, J.R., 2001. Chiasmodontidae. In: Carpenter, K.E., Niem, V.H. (Eds.), The Living Marine Resources of the Western Central Pacific. Bony Fishes pt. 4 (Labridae to Latimeriidae), vol. 6. FAO Species Identification Guide for Fishery Purposes. FAO, Rome, Italy, pp. 3495-3496.
36. Nelson J.S. Fishes of the World. third ed. (1994), Wiley, New York
37. Nelson J.S. Fishes of the World. fourth ed. (2006), Wiley, New York
38. Phillips M.J., Delsuc F., and Penny D. Genome-scale phylogeny and the detection of systematic biases. Mol. Biol. Evol. 21 (2004) 1455-1458
39. Phillips M.J., and Penny D. The root of the mammalian tree inferred from whole mitochondrial genomes. Mol. Phylogenet. Evol. 28 (2003) 171-185
40. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
41. Rosen D.E. Interrelationships of higher teleostean fishes. In: Greenwood P.H., Miles R.S., and Patterson C. (Eds). Interrelationships of Fishes (1973), Academic Press, London 397-513
42. Saitoh K., Hayashizaki K., Yokoyama Y., Asahida T., Toyohara H., and Yamashita Y. Complete nucleotide sequence of Japanese flounder (Paralichthys olivaceus) mitochondrial genome: structural properties and cue for resolving teleostean relationships. J. Hered. 91 (2000) 271-278
43. Saitoh K., Sado T., Mayden R.L., Hanzawa N., Nakamura K., and Nishida M. Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): the first evidence toward resolution of higher-level relationships of the world's largest freshwater fish clade based on 59 whole mitogenome sequences. J. Mol. Evol. 63 (2006) 826-841
44. Setiamarga D.H.E., Miya M., Yamanoue Y., Mabuchi K., Satoh T.P., Inoue J.G., and Nishida M. Interrelationships of Atherinomorpha (medakas, flyingfishes, killifishes, silversides, and their relatives): the first evidence based on whole mitogenome sequences. Mol. Phylogenet. Evol. 49 (2008) 598-605
45. Shimodaira H., and Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16 (1999) 1114-1116
46. Shimodaira H., and Hasegawa M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17 (2001) 1246-1247
47. Smith M.M. Bramidae. In: Smith M.M., and Heemstra P.C. (Eds). Smith's Sea Fishes (1986), Southern Book Publishers, Johannesburg 633-636 pl. 78
48. Smith W.L., and Craig M.T. Casting the percomorph net widely: the importance of broad taxonomic sampling in the search for the placement of serranid and percoid fishes. Copeia 1 (2007) 35-55
49. Smith W.L., and Wheeler W.C. Polyphyly of the mail-cheeked fishes (Teleostei: Scorpaeniformes): evidence from mitochondrial and nuclear sequence data. Mol. Phylogenet. Evol. 32 (2004) 627-646
50. Springer V.G., and Johnson G.D. Study of the dorsal gill-arch musculature of teleostome fishes, with special reference to the Actinopterygii. Bull. Biol. Soc. Wash. 11 (2004) 1-263 1-205 pls
51. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analysis with thousands of taxa and mixed models. Bioinformatics 22 (2006) 2688-2690
52. Stiassny M.L.J., Wiley E.O., Johnson G.D., and de Carvalho M.R. Gnathostome fishes. In: Donaghue M.J., and Cracraft J. (Eds). Assembling the Tree of Life (2004), Oxford University Press, New York 410-429
53. Takeshima Y., Morita T., and Yamashita M. Complete mitochondrial DNA sequences of Atlantic horse mackerel Trachurus trachurus and molecular identification of two commercially important species T. trachurus and T. japonicus using PCR-RFLP. Fish. Sci. 72 (2006) 1054-1065
54. Wiley E.O., Johnson G.D., and Dimmick W.W. The interrelationships of Acanthomorph fishes: a total evidence approach using molecular and morphological data. Biochem. Syst. Ecol. 28 (2000) 319-350
55. Yagishita N., Kobayashi T., and Nakabo T. Review of monophyly of the Kyphosidae (sensu Nelson, 1994), inferred from the mitochondrial ND2 gene. Ichthyol. Res. 49 (2002) 103-108
56. Yamanoue Y., Miya M., Matsuura K., Katoh M., Sakai H., and Nishida M. Mitochondrial genomes and phylogeny of the ocean sunfishes (Tetraodontiformes: Molidae). Ichthyol. Res. 51 (2004) 269-273
57. Yamanoue Y., Miya M., Matsuura K., Yagishita N., Mabuchi K., Sakai H., Katoh M., and Nishida M. Phylogenetic position of tetraodontiform fishes within the higher teleosts: Bayesian inferences based on 44 whole mitochondrial genome sequences. Mol. Phylogenet. Evol. 45 (2007) 89-101
58. Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39 (1994) 306-314