Molecular phylogeny and stripe pattern evolution in the cardinalfish genus Apogon

Molecular Phylogenetics and Evolution

Volumn 38, Issue 1, 2006, Pages 90-99

  Mabuchi, Kohji ^a   Okuda, Noboru ^b,c   Nishida, Mutsumi ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b EHIME UNIVERSITY   (Japan)

^c KYOTO UNIVERSITY   (Japan)

Author keywords

Apogon; Mitochondrial DNA; Phylogenetic niche conservatism; Stripe pattern

Indexed keywords

MITOCHONDRIAL DNA; RIBOSOME RNA; RNA 16S; RNA, RIBOSOMAL, 12S; VALINE TRANSFER RNA;

ANIMAL; ARTICLE; CLASSIFICATION; GENETICS; MOLECULAR EVOLUTION; MORPHOGENESIS; PERCIFORMES; PHYLOGENY;

ANIMALS; BODY PATTERNING; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; PERCIFORMES; PHYLOGENY; RNA, RIBOSOMAL; RNA, RIBOSOMAL, 16S; RNA, TRANSFER, VAL;

ANTHOZOA; APOGON; APOGONIDAE; FOWLERIA; PISCES;

EID: 28844478564     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2005.05.003     Document Type: Article

References (60)

1. R.C. Albertson, J.A. Markert, P.D. Danley, and T.D. Kocher Phylogeny of a rapidly evolving clade: the cichlid fishes of lake Malawi, East Africa Proc. Natl. Acad. Sci. USA 96 1999 5107 5110
2. C.J. Allender, O. Seehausen, M.E. Knight, G.F. Turner, and N. Maclean Divergent selection during speciation of Lake Malawi cichlid fishes inferred from parallel radiations in nuptial coloration Proc. Natl. Acad. Sci. USA 100 2003 14074 14079
3. G.W. Barlow The attitude of fish eye-lines in relation to body shape and to stripes and bars Copeia 1972 1972 4 12
4. D.R. Bellwood The Eocene fishes of Monte Bolca: the earliest coral reef fish assemblage Coral Reefs 15 1996 11 19
5. K. Bremer The limits of amino acid sequence data in angiosperm phylogenetic reconstruction Evolution 42 1988 795 803
6. K. Bremer Branch support and tree stability Cladistics 10 1994 295 304
7. D.R. Brooks, and D.A. McLennan Historical ecology as a research programme: scope, limitations and the future P. Eggleton R.I. Vane-Wright Phylogenetics and Ecology 1994 Academic Press London 1 27
8. J.A. Endler A predator's view of animal color patterns Evol. Biol. 11 1978 319 364
9. J.A. Endler Natural selection on color patterns in Poecilia reticulata Evolution 34 1980 76 91
10. J.A. Endler Natural and sexual selection on color patterns in poeciliid fishes Environ. Biol. Fish. 9 1983 173 190
11. J.A. Endler Natural Selection in the Wild 1986 Princeton University Press Princeton
12. J.A. Endler Variation in the appearance of guppy color patterns to guppies and their predators under different visual conditions Vision Res. 31 1991 587 608
13. J. Felsenstein Confidence limits on phylogenetics: an approach using the bootstrap Evolution 39 1985 783 791
14. T.H. Fraser Comparative osteology of the shallow water cardinal fishes (Perciformes: Apogonidae) with reference to the systematics and evolution of the family Ichthyol. Bull. 34 1972 1 105
15. T.H. Fraser A new species of cardinalfish (Apogonidae) from the Philippines, with comments on species of Apogon with six first dorsal spines Proc. Biol. Soc. Wash. 111 1998 986 991
16. T.H. Fraser, and E.A. Lachner A revision of the cardinalfish subgenera Pristiapogon and Zoramia of the Indo-Pacific region (Teleostei: Apogonidae) Smith Contr. Zool. 412 1985 1 47
17. F. Galis, and J.A.J. Metz Why are there so many cichlid species? Trends Ecol. Evol. 13 1998 1 2
18. O. Gon Family Apogonidae M.M. Smith M.M. Heemstra Smiths' Sea Fishes 1986 Macmillan Johannesburg 546 561
19. O. Gon Redescription of Apogon (Ostorhinchus) fleurieu (Lacepède, 1802) with notes on its synonymy Jpn. J. Ichthyol. 34 1987 138 145
20. O. Gon Revision of the cardinalfish subgenus Lepidamia (Perciformes, Apogonidae, Apogon) Israel J. Zool. 41 1995 1 22
21. P. Haffter, J. Odenthal, M.C. Mullins, S. Lin, M.J. Farrell, E. Vogelsang, F. Haas, M. Brand, F.J.M. van Eeden, M. Furutani-Seiki, M. Granato, M. Hammerschmidt, C.-P. Heisenberg, Y.-J. Jiang, D.A. Kane, R.N. Kelsh, N. Hopkins, and C. Nüsslein-Volhard Mutations affecting pigmentation and shape of the adult zebrafish Dev. Genes Evol. 206 1996 260 276
22. R. Hanel, M.W. Westneat, and C. Sturmbauer Phylogenetic relationships, evolution of broodcare behaviour, and geographic speciation in the wrasse tribe Labrini J. Mol. Evol. 55 2002 776 789
23. P.H. Harvey, and M.D. Pagel The Comparative Method in Evolutionary Biology 1991 Oxford University Press Oxford
24. M. Hayashi Apogonidae T. Nakabo Fishes of Japan with Pictorial Keys to the Species English ed. 2002 Tokai University Press Tokyo 750 779 1544-1545
25. J.P. Huelsenbeck, and K.A. Crandall Phylogeny estimation and hypothesis testing using maximum likelihood Annu. Rev. Ecol. Syst. 28 1997 437 466
26. J.P. Huelsenbeck, and F.R. Ronquist MRBAYES: bayesian inference of phylogenetic trees Bioinformatics 17 2001 754 755
27. S.L. Johnson, D. Africa, C. Walker, and J.A. Weston Genetic control of adult pigment stripe development in zebrafish Dev. Biol. 167 1995 27 33
28. K. Kawakami, A. Amsterdam, N. Shimoda, T. Becker, J. Mugg, A. Shima, and N. Hopkins Proviral insertion in the zebrafish hagoromo gene, encoding an F-box/WD40-repeat protein, cause stripe pattern anomalies Curr. Biol. 10 2000 463 466
29. M. Kimura A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences J. Mol. Evol. 16 1980 111 120
30. K.M. Kjer, G.D. Baldridge, and A.M. Fallon Mosquito large subunit ribosomal RNA: simultaneous alignment of primary and secondary structure Biochem. Biophys. Acta 1217 1994 147 155
31. Kuiter, R.H., Kozawa, T., 1999. Pictorial guide to fishes of the Indo-West Pacific Apogonidae, ver. 2.0a. Aquatic Photographics and Anthis, Seaford and Okazaki.
32. Y. Kumazawa, and M. Nishida Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics J. Mol. Evol. 37 1993 380 398
33. J. Lord, M. Westoby, and M. Leishman Seed size and phylogeny in six temperate floras: constrains, niche conservatism, and adaptation Am. Nat. 146 1995 349 364
34. K. Mabuchi, N. Okuda, T. Kokita, and M. Nishida Genetic comparison of two color-morphs of Apogon properuptus from Southern Japan Ichthyol. Res. 50 2003 293 296
35. K. Mabuchi, N. Okuda, and M. Nishida Genetic differentiation between two color-morphs of Apogon taeniophorus from Southern Japan Ichthyol. Res. 51 2004 180 183
36. A. Meyer, T.D. Kocher, P. Basasibwaki, and A.C. Wilson Monophyletic origin of Lake Victoria cichlid fishes suggested by mitochondrial DNA sequences Nature 347 1990 550 553
37. M. Milinski Predation risk and feeding behaviour T.J. Pitcher Behaviour of Teleost Fishes second ed. 1993 Chapman and Hall London 285 305
38. M. Miya, and M. Nishida 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
39. R.F. Myers Micronesian Reef Fishes, a comparative guide to the coral reef fishes of Micronesia third ed. 1999 Coral Graphics Territory of Guam, USA
40. M. Nishida Lake Tanganyika as an evolutionary reservoir of old lineages of East African cichlid fishes: inference from allozyme data Experientia 47 1991 974 979
41. A.T. Peterson, J. Soberón, and V. Sanchez-Cordero Conservatism of ecological niches in evolutionary time Science 285 1999 1265 1267
42. D. Posada, and K.A. Crandall Modeltest: testing the model of DNA substitution Bioinformatics 14 1998 817 818
43. Rambaut, A., Charleston, M., 2001. TreeEdit. Ver. 1.0. University of Oxford, Oxford.
44. R.E. Ricklefs, and R.E. Latham Intercontinental correlation of geographical ranges suggests stasis in ecological traits of relict genera of temperate perennial herbs Am. Nat. 139 1992 1305 1321
45. P.A. Ritchie, L. Bargelloni, A. Meyer, J.A. Taylor, J.A. MacDonald, and D.M. Lambert Mitochondrial phylogeny of Trematomid fishes (Nototheniidae, Perciformes) and the evolution of antarctic fish Mol. Phylogenet. Evol. 5 1996 383 390
46. M. Sanderson A nonparametric approach to estimate divergence times in the absence of rate constancy Mol. Biol. Evol. 14 1997 1218 1231
47. O. Seehausen, P.J. Mayhew, and J.J.M. Van Alphen Evolution of colour patterns in East African cichlid fish J. Evol. Biol. 12 1999 514 534
48. D. Schluter The Ecology of Adaptive Radiation 2000 Oxford University Press Oxford
49. H. Shimodaira, and H. Hasegawa Multiple comparisons of log-likelihoods with applications to phylogenetic inference Mol. Biol. Evol. 16 1999 1114 1116
50. J. Snoeks How well known is the ichthyodiversity of the large East African lakes? A. Rossiter H. Kawanabe Ancient Lakes: Biodiversity, Ecology and Evolution (Advances in Ecological Research) vol. 31 2000 Academic Press London 17 38
51. J.T. Streelman, M. Alfaro, M.W. Westneat, D.R. Bellwood, and S.A. Karl Evolutionary history of the parrotfishes: biogeography, ecomorphology, and comparative diversity Evolution 56 2002 961 971
52. A. Sugie, Y. Terai, R. Ota, and N. Okada The evolution of genes for pigmentation in African cichlid fishes Gene 343 2004 337 346
53. D.L. Swofford, P.J. Waddell, J.P. Huelsenbeck, P.G. Foster, P.O. Lewis, and J.S. Rogers Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods Syst. Biol. 50 2001 525 539
54. Y. Terai, N. Morikawa, K. Kawakami, and N. Okada Accelerated evolution of the surface amino acids in the WD-repeat domain encoded by the hagoromo gene in an explosively speciated lineage of East African cichlid fishes Mol. Biol. Evol. 19 2002 574 578
55. Y. Terai, N. Morikawa, K. Kawakami, and N. Okada The complexity of alternative splicing of hagoromo mRNAs is increased in an explosively speciated lineage in East African cichlids Proc. Natl. Acad. Sci. USA 100 2003 12798 12803
56. J.D. Thompson, T.J. Gibson, E. Plewniak, F. Jeanmougin, and D.G. Higgins The ClustalX-Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res. 25 1997 4876 4882
57. E. Verheyen, W. Salzburger, J. Snoeks, and A. Meyer Origin of the superflock of cichlid fishes from Lake Victoria, East Africa Science 300 2003 325 329
58. C.O. Webb, D.D. Ackerly, M.A. McPeek, and M.J. Donoghue Phylogenies and community ecology Annu. Rev. Ecol. Syst. 33 2002 475 505
59. M. Westoby, M. Leishman, and J. Lord On misinterpreting the "phylogenetic correction" J. Ecol. 83 1995 531 534
60. M. Westoby, M. Leishman, and J. Lord Further remarks on phylogenetic correction J. Ecol. 83 1995 727 729