Comprehensive phylogeny of the family Sparidae (Perciformes: Teleostei) inferred from mitochondrial gene analyses

Genes and Genetic Systems

Volumn 84, Issue 2, 2009, Pages 153-170

  Chiba, Satoru N ^a   Iwatsuki, Yukio ^b   Yoshino, Tetsuo ^c   Hanzawa, Naoto ^a  

^a YAMAGATA UNIVERSITY   (Japan)

^b UNIVERSITY OF MIYAZAKI   (Japan)

^c UNIVERSITY OF THE RYUKYUS   (Japan)

Author keywords

Bayes; Character state reconstruction; Convergent evolution; ML; Sequence variation

Indexed keywords

CYTOCHROME B;

ACANTHOPAGRUS; ARTICLE; BAYES THEOREM; CHARACTER STATE; CHEIMERIUS; CLADISTICS; CLASSIFICATION; CODON; DENTEX; DIPLODUS; DNA EXTRACTION; FISH; GENE SEQUENCE; GENETIC ANALYSIS; MAXIMUM LIKELIHOOD METHOD; MITOCHONDRIAL GENE; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PAGELLUS; PAGRUS; PERCIFORMES; PHYLOGENETIC TREE; PHYLOGENY; SPECIES DISTRIBUTION; SPICARA; TAXON;

ANIMALS; CYTOCHROMES B; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENETIC VARIATION; LIKELIHOOD FUNCTIONS; MOLECULAR SEQUENCE DATA; PERCIFORMES; PHYLOGENY; SEQUENCE ANALYSIS, DNA; TIME FACTORS;

ACANTHOPAGRUS; CENTRACANTHIDAE; CHEIMERIUS; DENTEX; DIPLODUS; PAGELLUS; PAGRUS; PERCIFORMES; PISCES; SPARIDAE; SPICARA; TELEOSTEI;

EID: 67650085264     PISSN: 13417568     EISSN: None     Source Type: Journal    
DOI: 10.1266/ggs.84.153     Document Type: Article

References (84)

1. Akazaki, M. (1962) Studies on the perciform fishes: anatomy, phylogeny, ecology, and taxonomy (in Japanese with English summary). Misaki Mar. Biol. Inst. Kyoto Univ. Spec. Rep. 1, Kosugi Ltd., Osaka.
2. Akazaki, M. (1970) Specific divergence of spariform fishes when considered from their geographical distribution. Honyuruikagaku 20-21, 131-146.
3. Akazaki, M. (1984) Sparidae. In: The fishes of the Japanese archipelago (eds.: H. Masuda, K. Amaoka, C. Araga, T. Uyeno and T. Yoshino), pp. 170-173. pls 166-167. Tokai University Press, Tokyo.
4. Akaike, H. (1973) Information theory as an extension of the maximum likelihood principle. In: Second international symposium on information theory (eds.: B. N. Petrov and F. Caski), pp. 267-281. Akademia Kiado, Budapest.
5. Akihito, Iwata, A., Kobayashi, T., Ikeo, K., Imanishi, T., Ono, H., Umehara, Y., Hamamatsu, C., Sugiyama, K., Ikeda, Y., et al. (2000) Evolutionary aspects of gobioid fishes based upon a phylogenetic analysis of mitochondrial cytochrome B genes. Gene 259, 5-15. (Pubitemid 32119231)
6. Allegrucci, G., Caccone, A., and Sbordoni, V. (1999) Cytochrome b sequence divergence in the European sea bass (Dicentrarchus labrax) and phylogenetic relationships among some Perciformes species. J. Zoolog. Syst. Evol. Res. 37, 149-156.
7. Azuma, Y., Kumazawa, Y., Miya, M., Mabuchi, K., and Nishida, N. (2008) Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences. BMC Evol. Biol. 8, 215.
8. Basagila, F. (1991) Interspecific gene differences and phylogeny of the Sparidae family (Perciformes, Teleostei), estimated from electrophoretic data on enzymatic tissue-expression. Comp. Biochem. Physiol., B 99, 495-508.
9. Bauchot, M. L., and Hureau, J. C. (1986) Sparidae. In: Fishes of the Northern-Eastern Atlantic and the Mediterranean, Vol.2. (eds.: P. J. P. Whitehead, M. L. Bauchot, J. C. Hureau, J. Nielsen and E. Tortonese), pp. 883-907, United Nations Educational Scientific and Cultural Organization, Paris.
10. Bauchot, M.-L., and Skelton, P. H. (1986) Sparidae. In: Check-list of the freshwater fishes of Africa (CLOFFA) vol.2 (eds.: J. Daget, J.-P. Gosse and D.F.E. Thys van den Audenaerde), pp. 331-332. Tervuren; and ORSTOM, Paris.
11. Benton, M. J., and Donoghue, P. C. (2007) Paleontological evidence to date the tree of life. Mol. Biol. Evol. 24, 26-53.
12. Cantatore, P., Roberti, M., Pesole, G., Ludovico, A., Milella, F., Gadaleta, M. N., and Saccone, C. (1994) Evolutionary analysis of cytochrome b sequences in some Perciformes: evidence for a slower rate of evolution than in mammals. J. Mol. Evol. 39, 589-597.
13. Carpenter, K. E. (2001) Family Sparidae. In: The living marine resources of the western central Pacific, FAO species identification guide for fishery purposes. vol.5, part 3 (eds.: K. E. Carpenter and V. H. Niem), pp. 2990-3003. FAO, Rome.
14. Carpenter, K. E., and Johnson, G. D. (2002) A phylogeny of sparoid fishes (Perciformes, Percoidei) based on morphology. Ichthyol. Res. 49, 114-127.
15. Cuvier, G. (1817) Le Règne Animal distribué d'après son organisation pour servir de base à l'histoire naturelle des animaux et d'introduction à l'anatomie comparée. Les reptiles, les poissons, les mollusques et les annélides. Edition 1. Règne Animal (ed. 1) 2, Deterville, Paris.
16. Cuvier, G. (1829) Le Règne Animal, distribué d'après son organisation, pour servir de base à l'histoire naturelle des animaux et d'introduction à l'anatomie comparée. Edition 2. Règne Animal (ed. 2) 2, Deterville, Paris.
17. Day, J. D. (2002) Phylogenetic relationships of the Sparidae (Teleostei: Percoidei) and implications for convergent trophic evolution. Biological Journal of the Linnean Society 76, 269-301. (Pubitemid 35045078)
18. Day, J. D. (2003) Evolutionary relationships of the Sparidae (Teleostei: Percoidei): integrating fossil and Recent data. Transactions of the Royal Society of Edinburgh. Earth Sciences 93, 333-353. (Pubitemid 38306024)
19. de la Herrán, R., Rejón, C. R., Rejón, M. R., and Garrido-Ramos, M. A. (2001) The molecular phylogeny of the Sparidae (Pisces, Perciformes) based on two satellite DNA families. Heredity 87, 691-697. (Pubitemid 34119511)
20. Dor, M. (1984) Checklist of the fishes of the Red Sea (CLOFRES). pp. 437. The Israel Academy of Sciences and Humanities, Jerusalem.
21. Duftner, N., Sefc, K. M., Koblmuller, S., Salzburger, W., and Taborsky, M. (2007) Parallel evolution of facial stripe patterns in the Neolamprologus brichardi/pulcher species complex endemic to Lake Tanganyika. Mol. Phylogenet. Evol. 45, 706-715.
22. Eschmeyer, W. N. (2008) Catalog of Fishes electronic version (updated 23 April 2008): http://www.calacademy.org/research/ichthyology/catalog/ fishcatsearch.html
23. Felsenstein, J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
24. Fiedler, K. (1991) Family Sparidae. In: Lehrbuch der speziellen zoologie, Teil2: Fische, (ed.: D. Starck), pp. 354-355, Gustav Fischer Verlag, Jena.
25. Froese, R., and Pauly, D. (2008) FishBase. World Wide Web electronic publication. www.fishbase.org, version (06/2008).
26. Garrido-Ramos, M. A., Jamilena, M., Lozano, R., Cardenas, S., Rejon, C. R., and Rejon, M. R. (1995) Phylogenetic relationships of the Sparidae family (Pisces, Perciformes) inferred from satellite-DNA. Hereditas 122, 1-6.
27. Garrido-Ramos, M. A., de la Herrán, R., Rejón, C. R., and Rejón, M. R. (1998) A satellite DNA of the Sparidae family (Pisces, Perciformes) associated with telomeric sequences. Cytogenet. Cell Genet. 83, 3-9.
28. Garrido-Ramos, M. A., de la Herrán, R., Jamilena, M., Lozano, R., Rejón, C. R., and Rejón, M. R. (1999) Evolution of centromeric satellite DNA and its use in phylogenetic studies of the Sparidae family (Pisces, Perciformes). Mol. Phylogenet. Evol. 12, 200-204.
29. Graybeal, A. (1998) Is it better to add taxa or characters to a diffcult phylogenetic problem? Syst. Biol. 47, 9-17. (Pubitemid 128449782)
30. Hanel, R., and Sturmbauer, C. (2000) Multiple recurrent evolution of trophic types in northeastern Atlantic and Mediterranean seabreams (Sparidae, Percoidei). J. Mol. Evol. 50, 276-283. (Pubitemid 30429982)
31. Harrison, G. L., McLenachan, P. A., Phillips, M. J., Slack, K. E., Cooper, A., and Penny, D. (2004) Four new avian mitochondrial genomes help get to basic evolutionary questions in the late Cretaceous. Mol. Biol. Evol. 21, 974-983.
32. Hayashi, M. (2002) Sparidae. In: Fishes of Japan with pictorial keys to species, English edition (ed: T. Nakabo), pp. 856-859. Tokai University Press, Tokyo.
33. Hillis, D. M. (1996) Inferring complex phylogenies. Nature 383, 130-131.
34. Hillis, D. M. (1998) Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47, 3-8.
35. Hillis, D. M., Pollock, D. D., McGuire, J. A., and Zwick, D. J. (2003) Is sparse taxon sampling a problem for phylogenetic inference? Syst. Biol. 52, 124-126. (Pubitemid 36300065)
36. Inoue, J. G., Miya, M., Tsukamoto, K., and Nishida, M. (2000) Complete mitochondrial DNA sequence of the Japanese sardine Sardinops melanostictus. Fisheries science 66, 924-932.
37. Iwatsuki, Y., and Carpenter, K. E. (2006) Acanthopagrus taiwanensis, a new sparid fish (Perciformes), with comparisons to Acanthopagrus berda (Forsskal, 1775) and other nominal species of Acanthopagrus. Zootaxa 1202, 1-19. (Pubitemid 43943519)
38. Iwatsuki, Y., Akazaki, M., and Taniguchi, N. (2007) Review of the species of the genus Dentex (Perciformes: Sparidae) in the western Pacific defined as the D. hypselosomus complex with the description of a new species, Dentex abei and a redescription of Evynnis tumifrons. Bull. Natl. Mus. Nat. Sci., Ser. A, Suppl. 1, 29-49.
39. Jean, C. T., Hui, C. F., Lee, S. L., and Chen, C. T. (1995) Variation in mitochondrial DNA and phylogenetic relationships of fishes of subfamily Sparinae (Perciformes: Sparidae) in the Coastal waters of Taiwan. Zoological Studies 34, 270-280. (Pubitemid 3004677)
40. Johnson, G. D. (1980) The limits and relationships of the Lutjanidae and associated families. Bull. Scripps Inst. Oceanography, University of California press, Ltd., London.
41. Kume, M., and Yoshino, T. (2008) Acanthopagrus chinshira, a new sparid fish (Perciformes: Sparidae) from the East Asia. Bull. Natl. Mus. Nat. Sci., Ser. A, Suppl. 2, 47-57.
42. Kuriiwa, K., Hanzawa, N., Yoshino, T., Kimura, S., and Nishida, M. (2007) Phylogenetic relationships and natural hybridization in rabbitfishes (Teleostei: Siganidae) inferred from mitochondrial and nuclear DNA analyses. Mol. Phylogenet. Evol. 45, 69-80.
43. Lo Galbo, A. M., Carpenter, K. E., and Reed, D. L. (2002) Evolution of trophic types in emperor fishes (Lethrinus, Lethrinidae, Percoidei) based on cytochrome B gene sequence variation. J. Mol. Evol. 54, 754-762.
44. Mabuchi, K., Miya, M., Azuma, Y., and Nishida, M. (2007) Independent evolution of the specialized pharyngeal jaw apparatus in cichlid and labrid fishes. BMC Evol. Biol. 7, 10.
45. Maddison, W. P., and Maddison, D. R. (2007) Mesquite: A modular system for evolutionary analysis. version 2.0. http://mesquiteproject.org.
46. Miller, J. A., and Hormiga, G. (2004) Clade stability and the addition of data: a case study from erigonine spiders (Araneae: Linyphiidae, Erigoninae). Cladistics 20, 385-442. (Pubitemid 40047705)
47. Minegishi, Y., Aoyama, J., Inoue, J. G., Miya, M., Nishida, M., and Tsukamoto, K. (2005) Molecular phylogeny and evolution of the freshwater eels genus Anguilla based on the whole mitochondrial genome sequences. Mol. Phylogenet. Evol. 34, 134-146.
48. 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. Mol. Biol. Evol. 18, 1993-2009.
49. Miya, M., and 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.
50. Miya, M., Takeshima, H., Endo, H., Ishiguro, N. B., Inoue, J. G., Mukai, T., Satoh, T. P., Yamaguchi, M., Kawaguchi, A., Mabuchi, K., et al. (2003) Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol. Phylogenet. Evol. 26, 121-138.
51. Munro, I. S. R. (1948) Sparidentex hasta (Valenciennes), a new name for Chrysophrys cuvieri Day. Copeia, 275-280.
52. Munro, I. S. R. (1949) Revision of australian silver breams Mylioand Rhabdosargus. Mem. Qld. Mus. 12, pls. xvi-xxiii, pp. 182-223.
53. Nelson, J. S. (1994) Fishes of the world, 3rd ed., John Wiley & Sons, Inc., New York.
54. Nelson, J. S. (2006) Fishes of the world, 4th ed., John Wiley & Sons, Inc., Hoboken, New Jersey.
55. Nishida, M., Ohkawa, T., and Iwata, H. (1998) Methods of analysis of genetic population structure with mitochondrial DNA markers. Suisanikusyu 26, 36-55.
56. Orrell, T. M., Carpenter, K. E., Musick, J. A., and Graves, J. E. (2002) Phylogenetic and biogeographic analysis of the Sparidae (Perciformes: Percoidei) from cytochrome b sequences. Copeia, 618-631. (Pubitemid 34929593)
57. Orrell, T. M., and Carpenter, K. E. (2004) A phylogeny of the fish family Sparidae (porgies) inferred from mitochondrial sequence data. Mol. Phylogenet. Evol. 32, 425-434.
58. Patterson, C. (1993) Osteichthyes: Teleostei. In: The fossil record 2 (ed.: M. J. Benton), pp. 621-665 Chapman & Hall, London.
59. Pérez, G. A. C., ŘÍčan, O., Ortí, G., Bermingham, E., Doadrio, I., and Zardoya, R. (2007) Phylogeny and biogeography of 91 species of heroine cichlids (Teleostei: Cichlidae) based on sequences of the cytochrome b gene. Mol. Phylogenet. Evol. 43, 91-110.
60. Phillips, M. J., and Penny, D. (2003) The root of the mammalian tree inferred from whole mitochondrial genomes. Mol. Phylogenet. Evol. 28, 171-185.
61. Pollock, D. D., Zwichkl, D. J., McGuire, J. A., and Hillis, D. M. (2002) Increased taxon sampling is advantageous for phylogenetic inference. Syst. Biol. 51, 664-671.
62. Ponce, M., Infante, C., Jimenez-Cantizano, R. M., Perez, L., and Manchado, M. (2008) Complete mitochondrial genome of the blackspot seabream, Pagellus bogaraveo (Perciformes: Sparidae), with high levels of length heteroplasmy in the WANCY region. Gene 409, 44-52.
63. Posada, D., and Crandall, K. A. (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14, 817-818. (Pubitemid 28552116)
64. Rokas, A., and Caroll, S. B. (2005) More Genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol. Biol. Evol. 22, 1337-1344.
65. Ronquist, F., and Huelsenbeck, J. P. (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574. (Pubitemid 37038874)
66. Rosenberg, M. S., and Kumar, S. (2001) Incomplete taxon sampling is not a problem for phylogenetic inference. Proc. Natl. Acad. Sci. USA 98, 10751-10756.
67. Rosenberg, M. S., and Kumar, S. (2003) Taxon sampling, bioinformatics, and phylogenomics. Syst. Biol. 52, 119-124.
68. Saitoh, K., Sado, T., Mayden, R. L., Hanzawa, N., Nakamura, K., Nishida, M., and Miya, M. (2006) 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, 826-841.
69. Sasaki, T., Kartavtsev, Y. P., Chiba, S. N., Uematsu, T., Sviridov, V. V., and Hanzawa, N. (2006) Genetic divergence and phylogenetic independence of Far Eastern species in subfamily Leuciscinae (Pisces: Cyprinidae) inferred from mitochondrial DNA analyses. Genes Genet. Syst. 82, 329-340.
70. Smith, J. L. B. (1938) The south African fishes of the families Sparidae and Denticidae. Transactions of the Royal society of south Africa 26, pls. xviii-xxix, pp. 225-305.
71. Smith, J. L. B., and Smith, M. M. (1986) Sparidae. In: Smiths' sea fishes, (eds.: M. M. Smith and P. C. Heemstra), pls. lviii-lxii, pp. 580-594, Springer-Verlag, Berlin.
72. Springer, V. G., and Johnson, G. D. (2004) Study of the dorsal gill-arch musculature of teleostome fishes, with special reference to the Actinopterygii. Bull. Bio. Soc. Wash. 11, 1-260.
73. Stamatakis, A., Hoover, P., and Rougemont, J. (2008) A Rapid Bootstrap Algorithm for the RaxML Web-Servers. Syst. Biol. 57, 758-771.
74. Summerer, M., Hanel, R., and Sturmbauer, C. (2001) Mitochondrial phylogeny and biogeographic affinities of sea breams of the genus Diplodus (Sparidae). J. Fish Biol. 59, 1638-1652.
75. Swofford, D. L. (2002) PAUP*: Phylogenetic analysis using parsimony. (* and other methods), Ver. 4.0b10. Sinauer Associates, Sunderland, MA.
76. Taniguchi, N., Fujita, M., and Akazaki, M. (1986) Genetic divergence and systematics in Sparid fish from Japan. In: Proc. 2nd. Int'l Conf. Indo-Pacific Fishes, (eds.: T. Uyeno, R. Arai, T. Taniuchi and K. Matsuura), pp. 849-858, Ichthyological Society of Japan, Tokyo.
77. Thompson, J. D., Gibson, T. G., Plewniak, F., Jeanmougin, F., and Higgins, D. G. (1997) The clustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucletic Acids Res. 24, 4876-4882. (Pubitemid 28022245)
78. Timm, J., Figiel, M., and Kochzius, M. (2008) Contrasting patterns in species boundaries and evolution of anemonefishes (Amphiprioninae, Pomacentridae) in the centre of marine biodiversity. Mol. Phylogenet. Evol. 49, 268-276.
79. Westneat, M. W., Alfaro, M. E., Wainwright, P. C., Bellwood, D. R., Grubich, J. R., Fessler, J. L., Clements, K. D., and Smith, L. L. (2005) Local phylogenetic divergence and global evolutionary convergence of skull function in reef fishes of the family Labridae. Proc. R. Soc. B 272, 993-1000.
80. Xia, J., Xia, K., Gong, J., and Jiang, S. (2007) Complete mitochondrial DNA sequence, gene organization and genetic variation of control regions in Parargyrops edita. Fisheries science 73, 1042-1049. (Pubitemid 47547477)
81. Yamanoue, Y., Miya, M., Matsuura, K., Yagishita, N., Mabuchi, K., Sakai, H., Katoh, M., and Nishida, M. (2007) Phylogenetic position of tetraodontiform fishes within the higher teleosts: Bayesian inferences based on 44 whole mitochondrial genome sequences. Mol. Phylogenet. Evol. 45, 89-101.
82. Yamanoue, Y., Miya, M., Inoue, J. G., Matsuura, K., and Nishida, M. (2006) The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes. Genes Genet. Syst. 81, 29-39.
83. Yang, Z. H. (2007) PAML: aprogram package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555-556.
84. Zwickl, D. J., and Hillis, D. M. (2002) Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 51, 588-598.