Molecular phylogeny and stripe pattern evolution in the cardinalfish genus Apogon

Molecular Phylogenetics and Evolution - Tập 38 - Trang 90-99 - 2006
Kohji Mabuchi1, Noboru Okuda2, Mutsumi Nishida1
1Ocean Research Institute, The University of Tokyo, 1-15-1 Minamidai, Nakano-ku, Tokyo 164-8639, Japan
2Center for Marine Environmental Studies, Ehime University, 2-5 Bunkyo-cho, Matsuyama 790-8577, Japan

Tài liệu tham khảo

Albertson, 1999, Phylogeny of a rapidly evolving clade: the cichlid fishes of lake Malawi, East Africa, Proc. Natl. Acad. Sci. USA, 96, 5107, 10.1073/pnas.96.9.5107 Allender, 2003, Divergent selection during speciation of Lake Malawi cichlid fishes inferred from parallel radiations in nuptial coloration, Proc. Natl. Acad. Sci. USA, 100, 14074, 10.1073/pnas.2332665100 Barlow, 1972, The attitude of fish eye-lines in relation to body shape and to stripes and bars, Copeia, 1972, 4, 10.2307/1442777 Bellwood, 1996, The Eocene fishes of Monte Bolca: the earliest coral reef fish assemblage, Coral Reefs, 15, 11, 10.1007/BF01626074 Bremer, 1988, The limits of amino acid sequence data in angiosperm phylogenetic reconstruction, Evolution, 42, 795, 10.1111/j.1558-5646.1988.tb02497.x Bremer, 1994, Branch support and tree stability, Cladistics, 10, 295, 10.1111/j.1096-0031.1994.tb00179.x Brooks, 1994, Historical ecology as a research programme: scope, limitations and the future, 1 Endler, 1978, A predator’s view of animal color patterns, Evol. Biol., 11, 319 Endler, 1980, Natural selection on color patterns in Poecilia reticulata, Evolution, 34, 76, 10.1111/j.1558-5646.1980.tb04790.x Endler, 1983, Natural and sexual selection on color patterns in poeciliid fishes, Environ. Biol. Fish., 9, 173, 10.1007/BF00690861 Endler, 1986 Endler, 1991, Variation in the appearance of guppy color patterns to guppies and their predators under different visual conditions, Vision Res., 31, 587, 10.1016/0042-6989(91)90109-I Felsenstein, 1985, Confidence limits on phylogenetics: an approach using the bootstrap, Evolution, 39, 783, 10.1111/j.1558-5646.1985.tb00420.x Fraser, 1972, Comparative osteology of the shallow water cardinal fishes (Perciformes: Apogonidae) with reference to the systematics and evolution of the family, Ichthyol. Bull., 34, 1 Fraser, 1998, 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, 986 Fraser, 1985, A revision of the cardinalfish subgenera Pristiapogon and Zoramia of the Indo-Pacific region (Teleostei: Apogonidae), Smith Contr. Zool., 412, 1, 10.5479/si.00810282.412 Galis, 1998, Why are there so many cichlid species?, Trends Ecol. Evol., 13, 1, 10.1016/S0169-5347(97)01239-1 Gon, 1986, Family Apogonidae, 546 Gon, 1987, Redescription of Apogon (Ostorhinchus) fleurieu (Lacepède, 1802) with notes on its synonymy, Jpn. J. Ichthyol., 34, 138, 10.1007/BF02912408 Gon, 1995, Revision of the cardinalfish subgenus Lepidamia (Perciformes, Apogonidae, Apogon), Israel J. Zool., 41, 1 Haffter, 1996, Mutations affecting pigmentation and shape of the adult zebrafish, Dev. Genes Evol., 206, 260, 10.1007/s004270050051 Hanel, 2002, Phylogenetic relationships, evolution of broodcare behaviour, and geographic speciation in the wrasse tribe Labrini, J. Mol. Evol., 55, 776, 10.1007/s00239-002-2373-6 Harvey, 1991 Hayashi, 2002, Apogonidae, 750 Huelsenbeck, 1997, Phylogeny estimation and hypothesis testing using maximum likelihood, Annu. Rev. Ecol. Syst., 28, 437, 10.1146/annurev.ecolsys.28.1.437 Huelsenbeck, 2001, MRBAYES: bayesian inference of phylogenetic trees, Bioinformatics, 17, 754, 10.1093/bioinformatics/17.8.754 Johnson, 1995, Genetic control of adult pigment stripe development in zebrafish, Dev. Biol., 167, 27, 10.1006/dbio.1995.1004 Kawakami, 2000, Proviral insertion in the zebrafish hagoromo gene, encoding an F-box/WD40-repeat protein, cause stripe pattern anomalies, Curr. Biol., 10, 463, 10.1016/S0960-9822(00)00444-9 Kimura, 1980, A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences, J. Mol. Evol., 16, 111, 10.1007/BF01731581 Kjer, 1994, Mosquito large subunit ribosomal RNA: simultaneous alignment of primary and secondary structure, Biochem. Biophys. Acta, 1217, 147 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. Kumazawa, 1993, Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics, J. Mol. Evol., 37, 380, 10.1007/BF00178868 Lord, 1995, Seed size and phylogeny in six temperate floras: constrains, niche conservatism, and adaptation, Am. Nat., 146, 349, 10.1086/285804 Mabuchi, 2003, Genetic comparison of two color-morphs of Apogon properuptus from Southern Japan, Ichthyol. Res., 50, 293, 10.1007/s10228-003-0171-9 Mabuchi, 2004, Genetic differentiation between two color-morphs of Apogon taeniophorus from Southern Japan, Ichthyol. Res., 51, 180, 10.1007/s10228-003-0201-7 Meyer, 1990, Monophyletic origin of Lake Victoria cichlid fishes suggested by mitochondrial DNA sequences, Nature, 347, 550, 10.1038/347550a0 Milinski, 1993, Predation risk and feeding behaviour, 285 Miya, 2000, Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion, Mol. Phylogenet. Evol., 17, 437, 10.1006/mpev.2000.0839 Myers, 1999 Nishida, 1991, Lake Tanganyika as an evolutionary reservoir of old lineages of East African cichlid fishes: inference from allozyme data, Experientia, 47, 974, 10.1007/BF01929896 Peterson, 1999, Conservatism of ecological niches in evolutionary time, Science, 285, 1265, 10.1126/science.285.5431.1265 Posada, 1998, Modeltest: testing the model of DNA substitution, Bioinformatics, 14, 817, 10.1093/bioinformatics/14.9.817 Rambaut, A., Charleston, M., 2001. TreeEdit. Ver. 1.0. University of Oxford, Oxford. Ricklefs, 1992, Intercontinental correlation of geographical ranges suggests stasis in ecological traits of relict genera of temperate perennial herbs, Am. Nat., 139, 1305, 10.1086/285388 Ritchie, 1996, Mitochondrial phylogeny of Trematomid fishes (Nototheniidae, Perciformes) and the evolution of antarctic fish, Mol. Phylogenet. Evol., 5, 383, 10.1006/mpev.1996.0033 Sanderson, 1997, A nonparametric approach to estimate divergence times in the absence of rate constancy, Mol. Biol. Evol., 14, 1218, 10.1093/oxfordjournals.molbev.a025731 Seehausen, 1999, Evolution of colour patterns in East African cichlid fish, J. Evol. Biol., 12, 514, 10.1046/j.1420-9101.1999.00055.x Schluter, 2000 Shimodaira, 1999, Multiple comparisons of log-likelihoods with applications to phylogenetic inference, Mol. Biol. Evol., 16, 1114, 10.1093/oxfordjournals.molbev.a026201 Snoeks, 2000, How well known is the ichthyodiversity of the large East African lakes?, vol. 31, 17 Streelman, 2002, Evolutionary history of the parrotfishes: biogeography, ecomorphology, and comparative diversity, Evolution, 56, 961, 10.1111/j.0014-3820.2002.tb01408.x Sugie, 2004, The evolution of genes for pigmentation in African cichlid fishes, Gene, 343, 337, 10.1016/j.gene.2004.09.019 Swofford, 2001, Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods, Syst. Biol., 50, 525, 10.1080/106351501750435086 Terai, 2002, 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, 574, 10.1093/oxfordjournals.molbev.a004114 Terai, 2003, 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, 12798, 10.1073/pnas.2132833100 Thompson, 1997, The ClustalX-Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucleic Acids Res., 25, 4876, 10.1093/nar/25.24.4876 Verheyen, 2003, Origin of the superflock of cichlid fishes from Lake Victoria, East Africa, Science, 300, 325, 10.1126/science.1080699 Webb, 2002, Phylogenies and community ecology, Annu. Rev. Ecol. Syst., 33, 475, 10.1146/annurev.ecolsys.33.010802.150448 Westoby, 1995, On misinterpreting the “phylogenetic correction”, J. Ecol., 83, 531, 10.2307/2261605 Westoby, 1995, Further remarks on phylogenetic correction, J. Ecol., 83, 727, 10.2307/2261640