Ecological speciation in marine v. freshwater fishes

Journal of Fish Biology

Volumn 75, Issue 5, 2009, Pages 960-996

  Puebla, O ^a,b  

^a MCGILL UNIVERSITY   (Canada)

^b SMITHSONIAN TROPICAL RESEARCH INSTITUTE   (Panama)

Author keywords

Adaptive radiation; Ecology; Molecular genetics; Natural selection; Reproductive isolation; Sexual selection

Indexed keywords

ANIMAL; AQUATIC SPECIES; CLASSIFICATION; ECOSYSTEM; FISH; LIMNOLOGY; MATE CHOICE; PHYLOGENY; PHYSIOLOGY; REVIEW; SPECIES DIFFERENTIATION;

ANIMALS; AQUATIC ORGANISMS; ECOSYSTEM; FISHES; FRESHWATER BIOLOGY; GENETIC SPECIATION; MATING PREFERENCE, ANIMAL; PHYLOGENY;

ANTHOZOA; PISCES; TELEOSTEI;

EID: 70449455430     PISSN: 00221112     EISSN: 10958649     Source Type: Journal    
DOI: 10.1111/j.1095-8649.2009.02358.x     Document Type: Review

References (236)

1. Abzhanov, A., Protas, M., Grant, B. R., Grant, P. R. & Tabin, C. J. (2004). Bmp4 and morphological variation of beaks in Darwin's finches. Science 305, 1462 1465.
2. Albert, A. Y. K., Sawaya, S., Vines, T. H., Knecht, A. K., Miller, C. T., Summers, B. R., Balabhadra, S., Kingsley, D. M. & Schluter, D. (2007). The genetics of adaptive shape shift in stickleback: pleiotropy and effect size. Evolution 62, 76 85.
3. Albertson, R. C. & Kocher, T. D. (2006). Genetic and developmental basis of cichlid trophic diversity. Heredity 97, 211 221.
4. Albertson, R. C., Streelman, J. T. & Kocher, T. D. (2003). Directional selection has shaped the oral jaws of Lake Malawi cichlid fishes. Proceedings of the National Academy of Sciences of the United States of America 100, 5252 5257.
5. Albertson, R. C., Streelman, J. T., Kocher, T. D. & Yelick, P. C. (2005). Integration and evolution of the cichlid mandible: the molecular basis of alternate feeding strategies. Proceedings of the National Academy of Sciences of the United States of America 102, 16287 16292.
6. Alesandrini, S. & Bernardi, G. (1999). Ancient species flocks and recent speciation events: what can rockfish teach us about cichlids (and vice versa)? Journal of Molecular Evolution 49, 814 818.
7. Alfaro, M. E., Santini, F. & Brock, C. D. (2007). Do reefs drive diversification in marine teleosts? Evidence from the pufferfish and their allies (Order Tetraodontiformes). Evolution 61, 2104 2126.
8. Almeida, C. R. & de Abreu, F. V. (2003). Dynamical instabilities lead to sympatric speciation. Evolutionary Ecology Research 5, 739 757.
9. Arnegard, M. E. & Kondrashov, A. S. (2004). Sympatric speciation by sexual selection alone is unlikely. Evolution 58, 222 237.
10. Baird, N. A., Etter, P. D., Atwood, T. S., Currey, M. C., Shiver, A. L., Lewis, Z. A., Selker, E. U., Cresko, W. A. & Johnson, E. A. (2008). Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3, e3376.
11. Barnett, A., Bellwood, D. R. & Hoey, A. S. (2006). Trophic ecomorphology of cardinalfishes. Marine Ecology Progress Series 322, 249 257.
12. Barreto, F. S. & McCartney, M. A. (2007). Extraordinary AFLP fingerprint similarity despite strong assortative mating between reef fish color morphospecies. Evolution 62, 226 233.
13. Bellwood, D. R., van Herwerden, L. & Konow, N. (2004). Evolution and biogeography of marine angelfishes (Pisces: Pomacanthidae). Molecular Phylogenetics and Evolution 33, 140 155.
14. Bellwood, D. R., Wainwright, P. C., Fulton, C. J. & Hoey, A. S. (2006). Functional diversity supports coral reef biodiversity. Proceedings of the Royal Society B 273, 101 107.
15. Bernardi, G. (2009). The name of the father: conflict between Louis and Alexander Agassiz and the Embiotoca surfperch radiation. Journal of Fish Biology 74, 1049 1055.
16. Bernatchez, L. (2004). Ecological theory of adaptive radiation: an empirical assessment from Coregonine fishes (Salmoniformes). In Evolution Illuminated: Salmon and Their Relatives (Hendry, A. P. & Stearns, S. C., eds), pp. 175 207. Oxford : Oxford University Press.
17. Böhlke, J. E. & Chaplin, C. C. G. (1993). Fishes of the Bahamas and Adjacent Tropical Waters. Austin, TX : University of Texas Press.
18. Böhlke, J. & Robins, C. (1968). Western Atlantic seven-spined gobies, with descriptions of 10 new species and a new genus, and comments on Pacific relatives. Proceedings of the Academy of Natural Sciences of Philadelphia 120, 45 174.
19. Bohonak, A. J. (1999). Dispersal, gene flow, and population structure. Quarterly Review of Biology 74, 21 45.
20. Bolnick, D. I. (2006). Multi-species outcomes in a common model of sympatric speciation. Journal of Theoretical Biology 241, 734 744.
21. Bolnick, D. I. & Fitzpatrick, B. M. (2007). Sympatric Speciation: models and empirical evidence. Annual Review of Ecology, Evolution, & Systematics 38, 459 487.
22. Boughman, J. W. (2001). Divergent sexual selection enhances reproductive isolation in sticklebacks. Nature 411, 944 947.
23. Boughman, J. W. (2002). How sensory drive can promote speciation. Trends in Ecology and Evolution 17, 571 577.
24. Borsa, P., Lemer, S. & Aurell, D. (2007). Pattern of lineage diversification in rabbitfishes. Molecular Phylogenetics and Evolution 44, 427 435.
25. Bouza, C., Hermida, M., Pardo, B. G., Fernández, C., Fortes, G. G., Castro, J., Sánchez, L., Presa, P., Pérez, M., Sanjuán, A., de Carlos, A., Álvarez-Dios, J. A., Ezcurra, S., Cal, R. M., Piferrer, F. & Martínez, P. (2007). A microsatellite genetic map of the turbot (Scophthalmus maximus). Genetics 177, 2457 2467.
26. Braasch, I., Volff, J.-N. & Schartl, M. (2008). The evolution of teleost pigmentation and the fish-specific genome duplication. Journal of Fish Biology 73, 1891 1918.
27. Briggs, J. C. (1999). Coincident biogeographic patterns: Indo-West Pacific Ocean. Evolution 53, 326 335.
28. Briggs, J. C. (2005). The marine East Indies: diversity and speciation. Journal of Biogeography 32, 1517 1522.
29. Briggs, J. C. (2006). Proximate sources of marine biodiversity. Journal of Biogeography 33, 1 10.
30. Buonaccorsi, V. P., Westerman, M., Stannard, J., Kimbrell, C., Lynn, E. & Vetter, R. D. (2004). Molecular genetic structure suggests limited larval dispersal within grass rockfish, Sebastes rastrelliger. Marine Biology 145, 779 788.
31. Buonaccorsi, V. P., Kimbrell, C.A., Lynn, E. A. & Vetter, R. D. (2005). Limited realized dispersal and introgressive hybridization influence genetic structure and conservation strategies for brown rockfish, Sebastes auriculatus. Conservation Genetics 6, 697 713.
32. Bürger, R. (2002). On a genetic model of intraspecific competition and stabilizing selection. American Naturalist 160, 661 682.
33. Bürger, R. (2005). A multilocus analysis of intraspecific competition and stabilizing selection on a quantitative trait. Journal of Mathematical Biology 50, 355 396.
34. Bürger, R., Schneider, K. A. & Willensdorfer, M. (2006). The conditions for speciation through intraspecific competition. Evolution 60, 2185 2206.
35. Caley, M. J. & Munday, P. L. (2003). Growth trades off with habitat specialization. Proceedings of the Royal Society 270, S175 S177.
36. Carleton, K. L. & Kocher, T. D. (2001). Cone opsin genes of African cichlid fishes: tuning spectral sensitivity by differential gene expression. Molecular Biology and Evolution 18, 1540 1550.
37. Carleton, K. L., Spady, T. C., Streelman, J. T., Kidd, M. R., McFarland, W. N. & Loew, E. R. (2008). Visual sensitivities tuned by heterochronic shifts in opsin gene expression. BMC Biology 6, 22.
38. Cheney, K. L. & Côté, I. M. (2005). Frequency-dependent success of aggressive mimics in a cleaning symbiosis. Proceedings of the Royal Society B 272, 2635 2639.
39. Cheney, K. L., Grutter, A. S. & Marshall, N. J. (2008). Facultative mimicry: cues for colour change and colour accuracy in a coral-reef fish. Proceedings of the Royal Society B 275, 117 122.
40. Chistiakov, D. A., Tsigenopoulos, C. S., Lagnel, J., Guo, Y.-M., Hellmans, B., Haley, C. S., Volckaert, F. A. M. & Kotoulas, G. (2008). A combined AFLP and microsatellite linkage map and pilot comparative genomic analysis of European sea bass Dicentrarchus labrax L. Animal Genetics 39, 623 634.
41. Christiansen, F. B. & Loeschcke, V. (1980). Evolution and intraspecific exploitative competition I. One-locus theory for small additive gene effects. Theoretical Population Biology 18, 297 313.
42. Clarke, A. & Johnston, I. A. (1996). Evolution and adaptive radiation in Antarctic fishes. Trends in Ecology and Evolution 11, 212 218.
43. Clements, K. D., Gray, R. D. & Choat, J. H. (2003). Rapid evolutionary divergence in reef fishes of the family Acanthuridae (Perciformes: Teleostei). Molecular Phylogenetics and Evolution 26, 190 201.
44. Collar, D. C., Wainwright, P. C. & Alfaro, M. E. (2008). Integrated diversification of locomotion and feeding in labrid fishes. Biology Letters 4, 84 86.
45. Coyne, J. A. & Orr, H. A. (2004). Speciation. Sunderland, MA : Sinauer Associates, Inc.
46. Cummings, M. E. (2007). Sensory trade-offs predict signal divergence in surfperch. Evolution 61, 530 545.
47. Darwin, C. (1859). On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. London : John Murray.
48. Day, J. J. (2002). Phylogenetic relationships of the Sparidae (Teleostei: Percoidei) and implications for convergent trophic evolution. Biological Journal of the Linnean Society 76, 269 301.
49. de Cara, M. A. R., Barton, N. H. & Kirkpatrick, M. (2008). A model for the evolution of assortative mating. The American Naturalist 171, 580 596.
50. Dieckmann, U. & Doebeli, M. (1999). On the origin of species by sympatric speciation. Nature 400, 354 357.
51. Diehl, S. R. & Bush, G. L. (1989). The role of habitat preference in adaptation and speciation. In Speciation and Its Consequences (Otte, D. & Endler, J. A., eds), pp. 345 365. Sunderland, MA : Sinauer Associates, Inc.
52. Dobzhansky, T. (1937). Genetics and the Origin of Species. New York, NY : Columbia University Press.
53. Doebeli, M. & Dieckmann, U. (2000). Evolutionary branching and sympatric speciation caused by different types of ecological interactions. American Naturalist 156, S77 S101.
54. Doebeli, M., Blok, H. J., Leimar, O. & Dieckmann, U. (2007). Multimodal pattern formation in phenotype distributions of sexual populations. Proceedings of the Royal Society B 274, 347 357.
55. Domeier, M. L. (1994). Speciation in the Serranid fish Hypoplectrus. Bulletin of Marine Science 54, 103 141.
56. Eagle, J. V. & Jones, G. P. (2004). Mimicry in coral-reef fishes: ecological and behavioural responses of a mimic to its model. Journal of Zoology 264, 33 43.
57. Eastman, J. T. (2005). The nature of the diversity of Antarctic fishes. Polar Biology 28, 93 107.
58. Eastman, J. T. & McCune, A. R. (2000). Fishes on the Antarctic continental shelf: evolution of a marine species flock? Journal of Fish Biology 57 (Suppl. A), 84 102.
59. Ellegren, H. (2008). Sequencing goes 454 and takes large-scale genomics into the wild. Molecular Ecology 17, 1629 1635.
60. Emerson, S. B. & Arnold, S. J. (1989). Intra- and interspecific relationships between morphology, performance, and fitness. In Complex Organismal Functions: Integration and Evolution in Vertebrates (Wake, D. B. & Roth, G., eds), pp. 295 314. Chichester : Wiley.
61. Endler, J. A. (1992). Signals, signal conditions, and the direction of evolution. American Naturalist 139, S125 S153.
62. Endler, J. A. & Basolo, A. L. (1998). Sensory ecology, receiver biases and sexual selection. Trends in Ecology and Evolution 13, 415 520.
63. Fischer, E. A. (1980a). Speciation in the hamlets (Hypoplectrus: Serranidae) - a continuing enigma. Copeia 298, 649 659.
64. Fischer, E. A. (1980b). The relationship between mating system and simultaneous hermaphro-ditism in the coral-reef fish, Hypoplectrus nigricans (Serranidae). Animal behaviour 28, 620 633.
65. Fischer, E. A. (1981). Sexual allocation in a simultaneously hermaphroditic coral-reef fish. American Naturalist 117, 64 82.
66. Fisher, R. A. (1930). The Genetical Theory of Natural Selection. Oxford : Clarendon Press.
67. Fitzpatrick, B. M., Fordyce, J. A. & Gavrilets, S. (2008). What, if anything, is sympatric speciation? Journal of Evolutionary Biology 21, 1452 1459.
68. Franch, R., Louro, B., Tsalavouta, M., Chatziplis, D., Tsigenopoulos, C. S., Sarropoulou, E., Antonello, J., Magoulas, A., Mylonas, C. C., Babbucci, M., Patarnello, T., Power, D. M., Kotoulas, G. & Bargelloni, L. (2006). A genetic linkage map of the hermaphrodite teleost fish Sparus aurata L. Genetics 174, 851 861.
69. Frisch, A. (2006). Are juvenile coral-trouts (Plectropomus) mimics of poisonous pufferfishes (Canthigaster) on coral reefs? Marine Ecology 27, 247 222.
70. Fry, J. D. (2003). Multilocus models of sympatric speciation: Bush versus Rice versus Felsenstein. Evolution 57, 1735 1746.
71. García-Machado, E., Chevalier Monteagudo, P. P. & Solignac, M. (2004). Lack of mtDNA differentiation among hamlets (Hypoplectrus, Serranidae). Marine Biology 144, 147 152.
72. Gavrilets, S. (2000). Rapid evolution of reproductive barriers driven by sexual conflict. Nature 403, 886 889.
73. Gavrilets, S. (2004). Fitness Landscapes and the Origin of Species. Princeton, NJ : Princeton University Press.
74. Gavrilets, S. & Vose, A. (2005). Dynamic patterns of adaptive radiation. Proceedings of the National Academy of Science of the United States of America 102, 18040 18045.
75. Gavrilets, S. & Waxman, D. (2002). Sympatric speciation by sexual conflict. Proceedings of the National Academy of Sciences of the United States of America 99, 10533 10538.
76. Gomez-Uchida, D. & Banks, M. A. (2005). Microsatellite analyses of spatial genetic structure in darkblotched rockfish (Sebastes crameri): is pooling samples safe? Canadian Journal of Fisheries and Aquatic Sciences 62, 1874 1886.
77. Gyllensten, U. (1985). The genetic structure of fish: differences in the intraspecific distribution of biochemical genetic variation between marine, anadromous, and freshwater species. Journal of Fish Biology 26, 691 699.
78. Hanel, R. & Sturmbauer, C. (2000). Multiple recurrent evolution of trophic types in Northeastern Atlantic and Mediterranean seabreams (Sparidae, Percoidei). Journal of Molecular Evolution 50, 276 283.
79. Hayashi, T. I., Vose, M. & Gavrilets, S. (2007). Genetic differentiation by sexual conflict. Evolution 61, 516 529.
80. Heemstra, P. C., Anderson, W.D. & Lobel, P. S. (2002). Groupers (seabasses, creolefish, coney, hinds, hamlets, anthiines, and soapfishes). In The Living Marine Resources of the Western Central Atlantic (Carpenter, K. E., ed.), pp. 1308 1369. Rome : FAO.
81. Helvik, J. V., Drivenes, O., Naess, T. H., Fjose, A. & Seo, H.-C. (2001). Molecular cloning and characterization of five opsin genes from the marine flatfish Atlantic halibut (Hippoglossus hippoglossus). Visual Neuroscience 18, 767 780.
82. Higashi, M., Takimoto, G. & Yamamura, N. (1999). Sympatric speciation by sexual selection. Nature 402, 523 526.
83. Holt, B. G., Emerson, B. C., Newton, J., Gage, M. J. G. & Côté, I. M. (2008). Stable isotope analysis of the Hypoplectrus species complex reveals no evidence for dietary niche divergence. Marine Ecology Progress Series 357, 283 289.
84. Hudson, R. R., Kreitman, M. & Aguadé, M. (1987). A test of neutral molecular evolution based on nucleotide data. Genetics 116, 153 159.
85. Hyde, J. R., Kimbrell, C. A., Budrick, J. E., Lynn, E. A. & Vetter, R. D. (2008). Cryptic speciation in the vermilion rockfish (Sebastes miniatus) and the role of bathymetry in the speciation process. Molecular Ecology 17, 1122 1136.
86. Ito, H. C. & Shimada, M. (2007). Niche expansion: coupled evolutionary branching of niche position and width. Evolutionary Ecology Research 9, 675 695.
87. Johns, G. C. & Avise, J. C. (1998). Tests for ancient species flocks based on molecular phylogenetic appraisals of Sebastes rockfishes and other marine fishes. Evolution 52, 1135 1146.
88. Johnson, P. A., Hoppensteadt, F. C., Smith, J. J. & Bush G. L. (1996). Conditions for sympatric speciation: a diploid model incorporating habitat fidelity and non-habitat assortative mating. Evolutionary Ecology 10, 187 205.
89. Jones, A. G., Moore, G. I., Kvarnemo, C., Walker D. & Avise, J. C. (2003). Sympatric speciation as a consequence of male pregnancy in seahorses. Proceedings of the National Academy of Sciences of the United States of America 100, 6598 6603.
90. Jordan, D. S. (1905). The origin of species through isolation. Science 22, 545 562.
91. Kawata, M., Shoji, A. Kawamura, S. & Seehausen, O. (2007). A genetically explicit model of speciation by sensory drive within a continuous population in aquatic environments. BMC Evolutionary Biology 7, 99.
92. Kawecki, T. J. (1996). Sympatric speciation driven by beneficial mutations. Proceedings of the Royal Society B 263, 1515 1520.
93. Kawecki, T. J. (1997). Sympatric speciation via habitat specialization driven by deleterious mutations. Evolution 51, 1751 1763.
94. Kijimoto, T., Watanabe, M., Fujimura, K., Nakazawa, M., Murakami, Y., Kuratani, S., Kohara, Y., Gojobori, T. & Okada, N. (2005). cimp1, a novel astacin family metalloproteinase gene from East African Cichlids, is differentially expressed between species during growth. Molecular Biology and Evolution 22, 1649 1660.
95. Kirkpatrick, M. & Nuismer, S. L. (2004). Sexual selection can constrain sympatric speciation. Proceedings of the Royal Society B 271, 687 693.
96. Klanten, S. O., van Herwerden, L., Choat, J. H. & Blair, D. (2004). Patterns of lineage diversification in the genus Naso (Acanthuridae). Molecular Phylogenetics and Evolution 32, 221 235.
97. Kobayashi, N., Wanatabe, M., Kijimoto, T., Fujimura, K., Nakazawa, M., Ikeo, K., Kohara, Y., Gojobori, T. & Okada, N. (2006). magp4 gene may contribute to the diversification of cichlid morphs ant their speciation. Gene 373, 126 133.
98. Kondrashov, A. S. (1986). Multilocus model of sympatric speciation. III. Computer simulations. Theoretical Population Biology 29, 1 15.
99. Kondrashov, A. S. & Kondrashov, F. A. (1999). Interactions among quantitative traits in the course of sympatric speciation. Nature 470, 351 354.
100. Kopp, M. & Hermisson, J. (2008). Competitive speciation and costs of assortative mating. Journal of Evolutionary Biology 21, 1005 1023.
101. Kuraku, S. & Meyer, A. (2008). Genomic analysis of cichlid fish 'natural mutants'. Current Opinion in Genetics & Development 18, 551 558.
102. Lamason, R. L., Mohideen, M. P. K., Mest, J. R., Wong, A. C., Norton, H. L., Aros, M. C., Jurynec, M. J., Mao, X., Humphreville, V. R., Humbert, J. E., Sinha, S., Moore, J. L., Jagadeeswaran, P., Zhao, S., Ning, G., Makalowska, I., McKeigue, P. M., O'Donnell, D., Kittles, R., Parra, E. J., Mangini, N. J., Grunwald, D. J., Shriver, M. D., Canfield, V. A. & Cheng, K. C. (2005). SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Science 310, 1782 1786.
103. Lande, R. (1981). Models of speciation by sexual selection on polygenic traits. Proceedings of the National Academy of Sciences of the United States of America 78, 3721 3725.
104. Lande, R. (1982). Rapid origin of sexual isolation and character divergence in a cline. Evolution 36, 213 223.
105. Lande, R. & Kirkpatrick, M. (1988). Ecological speciation by sexual selection. Journal of Theoretical Biology 133, 85 98.
106. Lande, R., Seehausen, O. & van Alphen, J. J. M. (2001). Mechanisms of rapid sympatric speciation by sex reversal and sexual selection in cichlid fish. Genetica 112, 435 443.
107. Lessios, H. A. & Robertson, D. R. (2006). Crossing the impassable: genetic connections in 20 reef fishes across the eastern Pacific barrier. Proceedings of the Royal Society B 273, 2201 2208.
108. Lewontin, R., Kirk, D. & Crow, J. (1968). Selective mating, assortative mating, and inbreeding: definitions and implications. Eugenetics Quarterly 15, 141 143.
109. Lo Galbo, A. M., Carpenter, K. E. & Reed, D. L. (2002) Evolution of trophic types in emperor fishes (Lethrinus, Lethrinidae, Percoidei) based on cytochrome b gene sequence variation. Journal of Molecular Evolution 54, 754 762.
110. Loh, Y.-W. E., Katz, L. S., Mims, M. C., Kocher, T. D., Yi, S. V. & Streelman, J. T. (2008). Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids. Genome Biology 9, R113.
111. Luikart, G., England, P. R., Tallmon, D., Jordan, S. & Taberlet, P. (2003). The power and promise of population genomics: from genotyping to genome typing. Nature Reviews Genetics 4, 981 994.
112. Lythgoe, J. N., Muntz, W. R. A., Partridge, J. C., Shand, J. & Williams, D. McB. (1994). The ecology of the visual pigments of snappers (Lutjanidae) on the Great Barrier Reef. Journal of Comparative Physiology A 174, 461 467.
113. Maan, M. E., Hofker, K. D., van Alphen, J. J. M. & Seehausen, O. (2006). Sensory drive in cichlid speciation. American Naturalist 167, 947 954.
114. Mank, J. E. (2007). Mating preferences, sexual selection and patterns of cladogenesis in ray-finned fishes. Journal of Evolutionary Biology 20, 597 602.
115. Matessi, C., Gimelfarb, A. & Gavrilets, S. (2001). Long-term buildup of reproductive isolation promoted by disruptive selection: how far does it go? Selection 2, 41 64.
116. Maynard Smith, J. (1966). Sympatric speciation. American Naturalist 100, 637 650.
117. Mayr, E. (1940). Speciation phenomena in birds. American Naturalist 74, 249 278.
118. Mayr, E. (1942). Systematics and the Origin of Species. New York, NY : Columbia University Press.
119. Mayr, E. (1947). Ecological factors in speciation. Evolution 1, 263 288.
120. Mayr, E. (1954). Geographic speciation in tropical echinoids. Evolution 8, 1 18.
121. McCartney, M. A., Acevedo, J., Heredia, C., Rico, C., Quenoville, B., Bermingham, E. & McMillan, W. O. (2003). Genetic mosaic in a marine species flock. Molecular Ecology 12, 2963 2973.
122. McDonald, J. H. (1998). Improved tests for heterogeneity across a region of DNA sequence in the ratio of polymorphism to divergence. Molecular Biology and Evolution 15, 377 384.
123. McMillan, W. O., Weigt, L. A. & Palumbi, S. R. (1999). Color pattern evolution, assortative mating, and genetic differentiation in brightly colored butterflyfishes (Chaetodontidae). Evolution 53, 247 260.
124. Miller, C. T., Beleza, S., Pollen, A. A., Schluter, D., Kittles, R. A., Shriver, M. D. & Kingsley, D. M. (2007). Expression and parallel evolution of pigmentation in sticklebacks and humans. Cell 131, 1179 1189.
125. Miya, M. & Nishida, M. (1996). Molecular phylogenetic perspective on the evolution of the deep-sea fish genus Cyclothone (Stomiiformes: Gonostomatidae). Ichthyological Research 43, 375 398.
126. Miyazaki, T., Kohbara, J. Takii, K., Ishibashi, Y. & Kumai, H. (2008). Three cone opsin genes and cone cell arrangement in retina of juvenile Pacific bluefin tuna Thunnus orientalis. Fisheries Science 74, 314 321.
127. Moland, E., Eagle, J. V. & Jones, G. P. (2005). Ecology and evolution of mimicry in coral-reef fishes. Oceanography and Marine Biology: An Annual Review 43, 455 482.
128. Moore, W. S. (1981) Assortative mating genes selected along a gradient. Heredity 46, 191 195.
129. Mora, C., Chittaro, P. M., Sale, P. F., Kritzer, J. P. & Ludsin, S. A. (2003). Patterns and processes in reef fish diversity. Nature 421, 933 936.
130. Motta, P. F. (1988). Functional morphology of the feeding apparatus of ten species of Pacific butterflyfishes (Perciformes, Chaetodontidae): an ecomorphological approach. Environmental Biology of Fishes 22, 39 67.
131. Munday, P. L. (2001). Fitness consequences of habitat use and competition among coral-dwelling fishes. Oecologia 128, 585 593.
132. Munday, P. L. (2004). Competitive coexistence of coral-dwelling fishes: the lottery hypothesis revisited. Ecology 85, 623 628.
133. Munday, P. L., Jones, G. P. & Caley, M. J. (1997). Habitat specialisation and the distribution and abundance of coral-dwelling gobies. Marine Ecology Progress Series 152, 227 239.
134. Munday, P. L., Jones, G. P. & Caley, M. J. (2001). Interspecific competition and coexistence in a guild of coral-dwelling fishes. Ecology 82, 2177 2189.
135. Munday, P. L., van Herwerden, L. & Dudgeon C. L. (2004). Evidence for sympatric speciation by host shift in the sea. Current Biology 14, 1498 1504.
136. Nagel, L. & Schluter, D. (1998). Body size, natural selection, and speciation in sticklebacks. Evolution 52, 209 218.
137. Nelson, J. S. (2006). Fishes of the World, 4th edn. Hoboken, NJ : John Wiley & Sons, Inc.
138. Nielsen, R. (2005). Molecular signatures of natural selection. Annual Review of Genetics 39, 197 218.
139. Norton, S. F. (1991). Capture success and diet of cottid fishes: the role of predator morphology and attack kinematics. Ecology 75, 1807 1819.
140. Norton, S. F. (1995). A functional approach to ecomorphological patterns of feeding in cottid fishes. Environmental Biology of Fishes 44, 61 78.
141. Orr, H. A. (1998). Testing natural selection vs genetic drift in phenotypic evolution using quantitative tait locus data. Genetics 149, 2099 2104.
142. Orr, M. R. & Smith, T. B. (1998). Ecology and speciation. Trends in Ecology and Evolution 13, 502 506.
143. Otto, S. P., Servedio, M. R. & Nuismer, S. L. (2008). Frequency-dependent selection and the evolution of assortative mating. Genetics 179, 2091 2112.
144. Palumbi, S. R. (1995). Using genetics as an indirect estimator of larval dispersal. In Ecology of Marine Invertebrate Larvae (McEdward, L. R., ed.), pp. 369 387. Boca Raton, FL : CRC Press.
145. Panhuis, T. M., Butlin, R., Zuk, M. & Tregenza, T. (2001). Sexual selection and speciation. Trends in Ecology and Evolution 16, 364 371.
146. Parry, J. W. L., Carleton, K. L., Spady, T., Carboo, A., Hunt, D. M. & Bowmaker, J. K. (2005). Mix and match color vision: tuning spectral sensitivity by differential opsin gene expression in Lake Malawi cichlids. Current Biology 15, 1734 1739.
147. Pennings, P. S., Kopp, M., Meszéna, G., Dieckmann, U. & Hermisson, J. (2008). An analytically tractable model for competitive speciation. American Naturalist 171, 44 71.
148. Pimm, S. L. (1979). Sympatric speciation: a simulation model. Biological Journal of the Linnean Society 11, 131 139.
149. Planes, S. & Doherty, P. J. (1997a). Genetic and color interactions at a contact zone of Acanthochromis polyacanthus: a marine fish lacking pelagic larvae. Evolution 51, 1232 1243.
150. Planes, S. & Doherty, P. J. (1997b). Genetic relationships of the colour morphs of Acanthochromis polyacanthus (Pomacentridae) on the northern Great Barrier Reef. Marine Biology 130, 109 117. (Pubitemid 28084508)
151. Puebla, O., Bermingham, E., Guichard, F. & Whiteman, E. (2007). Colour pattern as a single trait driving speciation in Hypoplectrus coral-reef fishes? Proceedings of the Royal Society B 274, 1265 1271.
152. Puebla, O., Bermingham, E. & Guichard, F. (2008). Population genetic analyses of Hypoplectrus coral-reef fishes provide evidence that local processes are operating during the early stages of marine adaptive radiations. Molecular Ecology 17, 1405 1415.
153. Puebla, O., Bermingham, E. & Guichard, F. (in press). Genetic signature of local dispersal in a coral-reef fish (Hypoplectrus puella): demography and scale matter. Ecology.
154. Ramon, M.L., Lobel, P.S. & Sorenson, M.D. (2003). Lack of mitochondrial genetic structure in hamlets (Hypoplectrus spp.): recent speciation or ongoing hybridization? Molecular Ecology 12, 2975 2980.
155. Randall, J. E. (1967). Food habits of reef fishes of the West Indies. Studies in Tropical Oceanography 5, 655 847.
156. Randall, J. E. (1996). Caribbean Reef Fishes. Neptune City, NJ : T.F.H. Publications.
157. Randall, J. E. (2005). A review of mimicry in marine fishes. Zoological Studies 44, 299 328.
158. Randall, J. E. & Randall, H. A. (1960). Examples of mimicry and protective resemblance in tropical marine fishes. Bulletin of Marine Science of the Gulf and Caribbean 10, 445 480.
159. Reed, D. L., Carpenter, K. E. & de Gravelle, M. J. (2002). Molecular systematics of the jacks (Perciformes: Carangidae) based on mitochondrial cytochrome b sequences using parsimony, likelihood, and Bayesian approaches. Molecular Phylogenetics and Evolution 23, 513 524.
160. Rice, W. R. (1984). Disruptive selection on habitat preference and the evolution of reproductive isolation: a simulation study. Evolution 38, 1251 1260.
161. Rice, W. R. (1985). Disruptive selection on habitat preference and the evolution of reproductive isolation: an exploratory experiment. Evolution 39, 646 656.
162. Rice, W. R. (1988). Speciation via disruptive selection on habitat preference: experimental evidence. American Naturalist 131, 911 917.
163. Rice, W. R. & Salt, G. W. (1990). The evolution of reproductive isolation as a correlated character under sympatric conditions: experimental evidence. Evolution 44, 1140 1152.
164. Ritchie, M. G. (2007). Sexual selection and speciation. Annual Review of Ecology, Evolution, & Systematics 38, 79 102.
165. Rocha, L. A. & Bowen, B. W. (2008). Speciation in coral-reef fishes. Journal of Fish Biology 72, 1101 1121.
166. Rocha, L. A., Robertson, D. R., Roman, J. & Bowen, B. W. (2005). Ecological speciation in tropical reef fishes. Proceedings of the Royal Society B 272, 573 579.
167. Rocha, L. A., Lindeman, K. C., Rocha, C. R. & Lessios, H. A. (2008). Historical biogeography and speciation in the reef fish genus Haemulon (Teleostei: Haemulidae). Molecular Phylogenetics and Evolution 48, 918 928.
168. Rogers, S. M. & Bernatchez, L. (2007). The genetic architecture of ecological speciation and the association with signatures of selection in natural lake whitefish (Coregonus sp. Salmonidae) species pairs. Molecular Biology and Evolution 24, 1423 1438.
169. Rosenblatt, R. H. & Waples, R. S. (1986). A genetic comparison of allopatric populations of shore fish species from the Eastern and Central Pacific Ocean: dispersal or vicariance? Copeia 1986, 275 284.
170. Rosenzweig, M. L. (1978). Competitive speciation. Biological Journal of the Linnean Society 10, 275 289.
171. Rousset, F. (1997). Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145, 1219 1228.
172. Rüber, L. & Zardoya, R. (2005). Rapid cladogenesis in marine fishes revisited. Evolution 59, 1119 1127.
173. Rüber, L., Van Tassell, J. L. & Zardoya, R. (2003). Rapid speciation and ecological divergence in the seven-spined gobies (Gobiidae, Gobiosomatini) inferred from a molecular phylogeny. Evolution 57, 1584 1598.
174. Rundle, H. D. & Nosil, P. (2005). Ecological speciation. Ecology Letters 8, 336 352.
175. Salzburger, W., Renn, S. C. P., Steinke, D., Braasch, I., Hofmann, H. A. & Meyer, A. (2008). Annotation of expressed sequence tags for the East African cichlid fish Astatotilapia burtoni and evolutionary analyses of cichlid ORFs. BMC Genomics 9, 96.
176. Schluter, D. (1996). Ecological speciation in postglacial fishes. Philosophical Transactions of the Royal Society B 351, 807 814.
177. Schluter, D. (2000). The Ecology of Adaptive Radiation. Oxford : Oxford University Press.
178. Schluter, D. (2001). Ecology and the origin of species. Trends in Ecology and Evolution 16, 372 412.
179. Schluter, D. & Price, T. (1993). Honesty, perception and population divergence in sexually selected traits. Proceedings of the Royal Society B 253, 117 122.
180. Schneider, K. A. & Bürger, R. (2006). Does competitive divergence occur if assortative mating is costly? Journal of Evolutionary Biology 19, 570 588.
181. Seehausen, O., Terai, Y., Magalhaes, I. S., Carleton, K. L., Mrosso, H. D. J., Miyagi, R., van der Sluijs, I., Schneider, M. V., Maan, M. A., Tachida, H., Imai, H. & Okada, N. (2008). Speciation through sensory drive in cichlid fish. Nature 455, 620 627.
182. Shulman, M. J. & Bermingham, E. (1995). Early life histories, ocean currents, and the population genetics of Caribbean reef fishes. Evolution 49, 897 910.
183. Simpson, G. G. (1953). The Major Features of Evolution. New York, NY : Columbia University Press.
184. Slatkin, M. (1982). Pleiotropy and parapatric speciation. Evolution 36, 263 270.
185. Smith, E. M. & Gregory, T. R. (2009). Patterns of genome size diversity in the ray-finned fishes. Hydrobiologia 625, 1 25.
186. Spady, T. C., Seehausen, O., Loew, E. R., Jordan, R. C., Kocher, T. D. & Carleton, K. L. (2005). Adaptive molecular evolution in the opsin genes of rapidly speciating cichlid species. Molecular Biology and Evolution 22, 1412 1422.
187. Spady, T. C., Parry, J. W. L., Robinson, P. R., Hunt, D. M., Bowmaker, J. K. & Carleton, K. L. (2006). Evolution of the cichlid visual palette through ontogenetic subfunctionalization of the opsin gene arrays. Molecular Biology and Evolution 23, 1538 1547.
188. Stauffer, J. R. & Gray, E. V. (2004). Phenotypic plasticity: its role in trophic radiation and explosive speciation in cichlids (Teleostei: Cichlidae). Animal Biology 54, 137 158.
189. St-Cyr, J., Derome N. & Bernatchez L. (2008). The transcriptomics of life-history trade-offs in whitefish species pairs (Coregonus sp). Molecular Ecology 17, 1850 1870.
190. Streelman, J. T. & Albertson, R. C. (2006). Evolution of novelty in the Cichlid dentition. Journal of Experimental Zoology B : 306, 216 226.
191. Streelman, J. T. & Danley, P. D. (2003). The stages of vertebrate evolutionary radiation. Trends in Ecology and Evolution 18, 126 131.
192. Streelman, J. T., Alfaro, M., Westneat, M. W., Bellwood, D. R. & Karl, S. A. (2002). Evolutionary history of the parrotfishes: biogeography, ecomorphology, and comparative diversity. Evolution 56, 961 971.
193. Streelman, J. T., Albertson, R. C. & Kocher, T. D. (2003). Genome mapping of the orange blotch colour pattern in cichlid fishes. Molecular Ecology 12, 2465 2471.
194. Streelman, J. T., Peichel, C. L. & Parichy, D. M. (2007). Developmental genetics of adaptation in fishes: the case for novelty. Annual Review of Ecology, Evolution, & Systematics 38, 655 681.
195. Sugie, A., Terai, Y., Ota, R. & Okada, N. (2004). The evolution of genes for pigmentation in African cichlid fishes. Gene 343, 337 346.
196. Takimoto, G., Higashi, M. & Yamamura, N. (2000). A deterministic model for sympatric speciation by sexual selection. Evolution 54, 1870 1881.
197. Taylor, M. S. & Hellberg, M. E. (2003). Genetic evidence for local retention of pelagic larvae in a Caribbean reef fish. Science 229, 107 109.
198. Taylor, M. S. & Hellberg, M. E. (2005). Marine radiations at small geographic scales: speciation in neotropical reef gobies (Elacatinus). Evolution 59, 374 385.
199. Terai, Y., Morikawa, N. & Okada, N. (2002a). The evolution of the pro-domain of bone morphogenetic protein 4 (Bmp4) in an explosively speciated lineage of East African cichlid Fishes. Molecular Biology and Evolution 19, 1628 1632.
200. Terai, Y., Morikawa, N., Kawakami, K. & Okada, N. (2002b). 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. Molecular Biology and Evolution 19, 574 578.
201. Terai, Y., Morikawa, N., Kawakami, K. & Okada, N. (2003). The complexity of alternative splicing of hagoromo mRNAs is increased in an explosively speciated lineage in East African cichlids. Proceedings of the National Academy of Sciences of the United States of America 100, 12798 12803.
202. Terai, Y., Seehausen, O., Sasaki, T., Takahashi, K., Mizoiri, S., Sugawara, T., Sato, T., Watanabe, M., Konijnendijk, N., Mrosso, H. D. J., Tachida, H., Imai, H., Shichida, Y. & Okada, N. (2006). Divergent selection on opsins drives incipient speciation in Lake Victoria Cichlids. PLoS Biology 4, 2244 2251.
203. Thibert-Plante, X. & Hendry, A. P. (2009). Five questions on ecological speciation addressed with individual-based simulations. Journal of Evolutionary Biology 22, 109 123.
204. Thresher, R. E. (1978). Polymorphism, mimicry, and the evolution of the hamlets (Hypoplectrus, serranidae). Bulletin of Marine Science 28, 345 353.
205. Tripathi, N., Hoffmann, M., Willing, E.-M., Lanz, C., Weigel, D. & Dreyer, C. (2009). Genetic linkage map of the guppy, Poecilia reticulata, and quantitative trait loci analysis of male size and colour variation. Proceedings of the Royal Society B 276, 2195 2208. doi: 10.1098/rspb.2008.1930
206. Turelli, M., Barton, N. H. & Coyne, J. A. (2001). Theory and speciation. Trends in Ecology and Evolution 16, 330 343.
207. Turner, G. F. & Burrows, M. T. (1995). A model of sympatric speciation by sexual selection. Proceedings of the Royal Society B 260, 287 292.
208. van Doorn, G. S., Noest, A. J. & Hogeweg, P. (1998). Speciation and extinction driven by environment dependent sexual selection. Proceedings of the Royal Society B 265, 1915 1919.
209. van Doorn, G. S., Dieckmann, U. & Weissing, F. J. (2004). Sympatric speciation by sexual selection: a critical reevaluation. American Naturalist 163, 709 725.
210. Van Herwerden, L. & Doherty, P. J. (2006). Contrasting genetic structures across two hybrid zones of a tropical reef fish, Acanthochromis polyacanthus (Bleeker 1855) Journal of Evolutionary Biology 19, 239 252.
211. Van Herwerden, L., Davies, C. R. & Choat, J. H. (2002). Phylogenetic and evolutionary perspectives of the Indo-Pacific grouper Plectropomus species on the Great Barrier Reef, Australia. Journal of Fish Biology 60, 1591 1596.
212. Via, S. (2001). Sympatric speciation in animals: the ugly duckling grows up. Trends in Ecology and Evolution 16, 381 389.
213. Victor, B. C. (1987). Growth, dispersal, and identification of planktonic labrid and pomacentrid reef-fish larvae in the eastern Pacific Ocean. Marine Biology 95, 145 152.
214. Wainwright, P. C. (1988). Morphology and ecology: functional basis of feeding constraints in Caribbean labrid fishes. Ecology 69, 635 345.
215. Wainwright, P. C., Bellwood, D. R., Westneat, M. W., Grubich, J. R. & Hoey, A. S. (2004). A functional morphospace for the skull of labrid fishes: patterns of diversity in a complex biomechanical system. Biological Journal of the Linnean Society 82, 1 125.
216. Ward, R. D., Woodwark, M. & Skibinski, D. O. F. (1994). A comparison of genetic diversity levels in marine, freshwater, and anadromous fishes. Journal of Fish Biology 44, 213 232.
217. Warner, R. R., Robertson, D. R. & Leigh, E. G. (1975). Sex change and sexual selection. Science 190, 633 638.
218. Watanabe, M., Hiraide, K. & Okada, N. (2007). Functional diversification of kir7.1 in cichlids accelerated by gene duplication. Gene 399, 46 52.
219. Wellenreuther, M. & Clements, K. D. (2007). Reproductive isolation in temperate reef fishes. Marine Biology 152, 619 630.
220. Wellenreuther, M., Barrett, P. T. & Clements, K. D. (2007). Ecological diversification in habitat use by subtidal triplefin fishes (Tripterygiidae). Marine Ecology Progress Series 330, 235 246.
221. Wellenreuther, M., Syms, C. & Clements, K. D. (2008). Body size and ecological diversification in a sister species pair of triplefin fishes. Evolutionary Ecology 22, 575 592.
222. West-Eberhard, M. J. (1983). Sexual selection, social competition, and speciation. The Quarterly Review of Biology 58, 155 183.
223. Westneat, M. W. (1994). Transmission of force and velocity in the feeding mechanisms of labrid fishes (Teleostei, Perciformes). Zoomorphology 114, 103 118.
224. Westneat, M. W. (2003). A biomechanical model for analysis of muscle force, power output and lower jaw motion in fishes. Journal of Theoretical Biology 223, 269 281.
225. Westneat, M. W. & Alfaro M. E. (2005). Phylogenetic relationships and evolutionary history of the reef fish family Labridae. Molecular Phylogenetics and Evolution 36, 370 390.
226. Westneat, M. W., Alfaro, M. E., Wainwright, P. C., Bellwood, D. R., Grubich, J. R., Fessler, J. L., Clements, K. D. & Smith, L. L. (2005). Local phylogenetic divergence and global evolutionary convergence of skull function in reef fishes of the family Labridae. Proceedings of the Royal Society B 272, 993 1000.
227. Whiteley, A. R., Derome, N., Rogers, S. M., St-Cyr, J., Laroche, J., Labbe, A., Nolte, A., Renault, S., Jeukens, J. & Bernatchez, L. (2008). The phenomics and expression quantitative trait locus mapping of brain transcriptomes regulating adaptive divergence in lake whitefish species pairs (Coregonus sp.). Genetics 180, 147 164.
228. Whiteman, E. A. & Gage, M. J. G. (2007). No barriers to fertilization between sympatric colour morphs in the marine species flock Hypoplectrus (Serranidae). Journal of Zoology 272, 305 310.
229. Whiteman, E. A., Côté, I. M. & Reynolds, J. D. (2007). Ecological differences between hamlet (Hypoplectrus: Serranidae) colour morphs: between-morph variation in diet. Journal of Fish Biology 71, 235 244.
230. Wilson, D. S. & Turelli, M. (1986). Stable underdominance and the evolutionary invasion of empty niches. American Naturalist 127, 835 850.
231. Wu, C. I. (1985). A stochastic simulation study on speciation by sexual selection. Evolution 39, 66 82.
232. Yagishita, N. & Nakabo, T. (2003). Evolutionary trends in feeding habits of Girella (Perciformes: Girellidae). Ichthyological Research 50, 358 366.
233. Yamanoue, Y., Miya, M., Matsuura, K., Katoh, M., Sakai, H. & Nishida, M. (2008). A new perspective on phylogeny and evolution of tetraodontiform fishes (Pisces: Acanthopterygii) based on whole mitochondrial genome sequences: basal ecological diversification? BMC Evolutionary Biology 8, 212.
234. Yamanoue, Y., Miya, M., Matsuura, K., Katoh, M., Sakai, H. & Nishida, M. (2009). Explosive speciation of Takifugu: another use of fugu as a model system for evolutionary biology. Molecular Biology and Evolution 26, 623 629.
235. Yang, Z. & Nielsen, R (2002). Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Molecular Biology and Evolution 19, 908 917.
236. Yang, Z., Nielsen, R., Goldman, N. & Pedersen, A. M. K. (2000). Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155, 431 449.