Historical factors that have shaped the evolution of tropical reef fishes: A review of phylogenies, biogeography, and remaining questions

Frontiers in Genetics

Volumn 5, Issue NOV, 2014, Pages

  Cowman, Peter F ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

Ancestral biogeography; Coral reef fishes; Diversification; Marine tropics; Phylogeny

Indexed keywords

BIODIVERSITY; BIOGEOGRAPHY; CONSERVATION GENETICS; CORAL REEF; GEOGRAPHIC DISTRIBUTION; MICROBIAL COLONIZATION; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; PHYLOGENETIC TREE; REVIEW;

ANTHOZOA; PISCES;

EID: 84917727720     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2014.00394     Document Type: Review

References (153)

1. Ackerman, J., and Bellwood, D. (2000). Reef fish assemblages: a re-evaluation using enclosed rotenone stations. Mar. Ecol. Ser. 206, 227-237. doi: 10.3354/meps206227
2. Alfaro, M. E., Brock, C. D., Banbury, B. L., and Wainwright, P. C. (2009). Does evolutionary innovation in pharyngeal jaws lead to rapid lineage diversification in labrid fishes? BMC Evol. Biol. 14:1-14. doi: 10.1186/1471-2148-9-255
3. Alfaro, M. E., Santini, F., and Brock, C. D. (2007). Do reefs drive diversification in marine teleosts? Evidence from the pufferfish and their allies (order Tetraodontiformes). Evolution 61, 2104-2126. doi: 10.1111/j.1558-5646.2007.00182.x
4. Allen, G. R. (2014). Review of Indo-Pacific coral reef fish systematics: 1980 to 2014. Ichthyol. Res. 1-7. doi: 10.1007/s10228-014-0411-1
5. Bannikov, A. F. (2010). Bellwoodilabrus landinii n. gen., n. sp., a new genus and species of labrid fish (Teleostei, Perciformes) from the Eocene of Monte Bolca. Geodiversitas 32, 201-220. doi: 10.5252/g2010n2a2
6. Barber, P. H., and Bellwood, D. R. (2005). Biodiversity hotspots: evolutionary origins of biodiversity in wrasses (Halichoeres: Labridae) in the Indo-Pacific and new world tropics. Mol. Phylogenet. Evol. 35, 235-253. doi: 10.1016/j.ympev.2004.10.004
7. Barraclough, T. G., and Savolainen, V. (2001). Evolutionary rates and species diversity in flowering plants. Evolution 55, 677-683. doi: 10.1554/0014-3820 (2001)055[0677:ERASDI]2.0.CO;2
8. Bellwood, D. R. (1996). The Eocene fishes of Monte Bolca: the earliest coral reef fish assemblage. Coral Reefs 15, 11-19. doi: 10.1007/BF01626074
9. Bellwood, D. R. (1998). What are reef fishes? - Comment on the report by D. R. Robertson: do coral-reef fish faunas have a distinctive taxonomic structure? Coral Reefs 17, 187-189. doi: 10.1007/s003380050114
10. Bellwood, D. R., Goatley, C. H. R., Brandl, S. J., and Bellwood, O. (2014a). Fifty million years of herbivory on coral reefs: fossils, fish and functional innovations. Proc. Biol. Sci. 281, 20133046. doi: 10.1098/rspb.2013.3046
11. Bellwood, D. R., Hoey, A. S., Bellwood, O., and Goatley, C. H. R. (2014b). Evolution of long-toothed fishes and the changing nature of fish-benthos interactions on coral reefs. Nat. Commun. 5, 3144. doi: 10.1038/ncomms4144
12. Bellwood, D. R., Goatley, C. H. R., Cowman, P. F., and Bellwood, O. (in press). "The evolution of fishes on coral reefs: fossils, phylogenies and functions," in Ecology of Fishes on Coral Reefs, ed. C. Mora (Cambridge: Cambridge University Press).
13. Bellwood, D. R., and Hughes, T. P. (2001). Regional-scale assembly rules and biodiversity of coral reefs. Science 292, 1532-1535. doi: 10.1126/science.1058635
14. Bellwood, D. R., Klanten, S., Cowman, P. F., Pratchett, M. S., Konow, N., and van Herwerden, L. (2010). Evolutionary history of the butterflyfishes (f: Chaetodontidae) and the rise of coral feeding fishes. J. Evol. Biol. 23, 335-349. doi: 10.1111/j.1420-9101.2009.01904.x
15. Bellwood, D. R., and Meyer, C. P. (2009a). Endemism and evolution in the Coral Triangle: a call for clarity. J. Biogeogr. 36, 2010-2012. doi: 10.1111/j.1365-2699.2009.02167.x
16. Bellwood, D. R., and Meyer, C. P. (2009b). Searching for heat in a marine biodiversity hotspot. J. Biogeogr. 36, 569-576. doi: 10.1111/j.1365-2699.2008.02029.x
17. Bellwood, D. R., Renema, W., and Rosen, B. R. (2012). "Biodiversity hotspots, evolution and coral reef biogeography," in Biotic Evolution and Environmental Change in Southeast Asia, eds D. Gower, K. Johnson, J. Richardson, B. Rosen, L. Rüber, and S. Williams (Cambridge: Cambridge University Press), 2-32.
18. Bellwood, D. R., van Herwerden, L., and Konow, N. (2004). Evolution and biogeography of marine angelfishes (Pisces: Pomacanthidae). Mol. Phylogenet. Evol. 33, 140-155. doi: 10.1016/j.ympev.2004.04.015
19. Bellwood, D. R., and Wainwright, P. C. (2002). "The history and biogeography of fishes on coral reefs," in Coral Reef Fishes: Dynamics and Diversity in a Complex Ecosystem, ed. P. Sale (London: Academic Press), 5-32.
20. Bernardi, G., Bucciarelli, G., Costagliola, D., Robertson, D. R., and Heiser, J. B. (2004). Evolution of coral reef fish Thalassoma spp. (Labridae). 1. Molecular phylogeny and biogeography. Mar. Biol. 144, 369-375. doi: 10.1007/s00227-003-1199-0
21. Bernardi, G., Holbrook, S. J., and Schmitt, R. J. (2001). Gene flow at three spatial scales in a coral reef fish, the three-spot dascyllus, Dascyllus trimaculatus. Mar. Biol. 138, 457-465. doi: 10.1007/s002270000484
22. Betancur-R, R., Broughton, R. E., Wiley, E. O., Carpenter, K., López, J. A., Li, C.,et al. (2013). The tree of life and a new classification of bony fishes. PLoS Curr. 5:1-41 doi: 10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288
23. Bowen, B. W., Muss, A., Rocha, L. A., and Grant, W. S. (2006). Shallow mtDNA coalescence in Atlantic pygmy angelfishes (genus Centropyge) indicates a recent invasion from the Indian Ocean. J. Hered. 97, 1-12. doi: 10.1093/jhered/esj006
24. Bowen, B. W., Rocha, L. A., Toonen, R. J., and Karl, S. A. (2013). The origins of tropical marine biodiversity. Trends Ecol. Evol. 28, 359-366. doi: 10.1016/j.tree.2013.01.018
25. Brawand, D., Wagner, C. E., Li, Y. I., Malinsky, M., Keller, I., Fan, S.,et al. (2014). The genomic substrate for adaptive radiation in African cichlid fish. Nature 513, 375-381. doi: 10.1038/nature13726
26. Briggs, J. C. (1999). Coincident biogeographic patterns: Indo-West Pacific Ocean. Evolution 53, 326-335. doi: 10.2307/2640770
27. Briggs, J. C. (2009). Diversity, endemism and evolution in the Coral Triangle. J. Biogeogr. 36, 2008-2010. doi: 10.1111/j.1365-2699.2009.02146.x
28. Briggs, J. C. (2003). Marine centres of origin as evolutionary engines. J. Biogeogr. 30, 1-18. doi: 10.1046/j.1365-2699.2003.00810.x
29. Briggs, J. C., and Bowen, B. W. (2012). A realignment of marine biogeographic provinces with particular reference to fish distributions. J. Biogeogr. 39, 12-30. doi: 10.1111/j.1365-2699.2011.02613.x
30. Bromham, L. (2011). The genome as a life-history character: why rate of molecular evolution varies between mammal species. Philos. Trans. R. Soc. Lond. B Biol. Sci. 366, 2503-2513. doi: 10.1098/rstb.2011.0014
31. Budd, A. F. (2000). Diversity and extinction in the Cenozoic history of Caribbean reefs. Coral Reefs 19, 25-35. doi: 10.1007/s003380050222
32. Carnevale, G. (2006). Morphology and biology of the Miocene butterflyfish Chaetodon ficheuri (Teleostei: Chaetodontidae). Zool. J. Linn. Soc. 146, 251-267. doi: 10.1111/j.1096-3642.2006.00203.x
33. Carpenter, K. E., Barber, P. H., Crandall, E. D., Ablan-lagman, M. C. A., Mahardika, G. N., Manjaji-Matsumoto, B. M.,et al. (2011). Comparative phylogeography of the coral triangle and implications for marine management. J. Mar. Biol. 2011, 1-14. doi: 10.1155/2011/396982
34. Choat, J. H., Klanten, O. Y. A. S., Van Herwerden, L., Robertson, D. R., Clements, K. D., and van Herwerden, L. (2012). Patterns and processes in the evolutionary history of parrotfishes (Family Labridae). Biol. J. Linn. Soc. 107, 529-557. doi: 10.1111/j.1095-8312.2012.01959.x
35. Coates, A. G., and Obando, J. A. (1996) "The geologic evolution of the Central American Isthmus," in Evolution and Environment in Tropical America, eds J. B. C. Jackson, A. F. Budd, and A. G. Coates (Chicago, IL: University of Chicago Press), 21-56.
36. Connolly, S. R., Bellwood, D. R., and Hughes, T. P. (2003). Indo-Pacific biodiversity of coral reefs: deviations from a mid-domain model. Ecology 84, 2178-2190. doi: 10.1890/02-0254
37. Cooper, W. J., Smith, L. L., and Westneat, M. W. (2009). Exploring the radiation of a diverse reef fish family: phylogenetics of the damselfishes (Pomacentridae), with new classifications based on molecular analyses of all genera. Mol. Phylogenet. Evol. 52, 1-16. doi: 10.1016/j.ympev.2008.12.010
38. Cowman, P. F., and Bellwood, D. R. (2011). Coral reefs as drivers of cladogenesis: expanding coral reefs, cryptic extinction events, and the development of biodiversity hotspots. J. Evol. Biol. 24, 2543-2562. doi: 10.1111/j.1420-9101.2011.02391.x
39. Cowman, P. F., and Bellwood, D. R. (2013a). The historical biogeography of coral reef fishes: global patterns of origination and dispersal. J. Biogeogr. 40, 209-224. doi: 10.1111/jbi.12003
40. Cowman, P. F., and Bellwood, D. R. (2013b). Vicariance across major marine biogeographic barriers: temporal concordance and the relative intensity of hard versus soft barriers. Proc. Biol. Sci. 280, 20131541. doi: 10.1098/rspb.2013.1541
41. Cowman, P. F., Bellwood, D. R., and van Herwerden, L. (2009). Dating the evolutionary origins of wrasse lineages (Labridae) and the rise of trophic novelty on coral reefs. Mol. Phylogenet. Evol. 52, 621-31. doi: 10.1016/j.ympev.2009.05.015
42. D'agata, S., Mouillot, D., Kulbicki, M., Andréfouët, S., Bellwood, D. R., Cinner, J. E.,et al. (2014). Human-mediated loss of phylogenetic and functional diversity in coral reef fishes. Curr. Biol. 24, 555-560. doi: 10.1016/j.cub.2014.01.049
43. Dornburg, A., Moore, J., Beaulieu, M., Eytan, R., and Near, T. J. (in press). The impact of shifts in marine biodiversity hotspots on patterns of range evolution: evidence from the Holocentridae (squirrelfishes and soldierfishes). Evolution doi: 10.1016/j.cub.2014.01.049
44. Dowle, E. J.,Morgan-Richards, M., and Trewick, S. A. (2013). Molecular evolution and the latitudinal biodiversity gradient. Heredity (Edinb.) 110, 501-510. doi: 10.1038/hdy.2013.4
45. Duchene, D., and Bromham, L. (2013). Rates of molecular evolution and diversification in plants: chloroplast substitution rates correlate with species-richness in the Proteaceae. BMC Evol. Biol. 13:65. doi: 10.1186/1471-2148-13-65
46. Duchene, D., Klanten, S. O., Munday, P. L., Herler, J., and Van Herwerden, L. H. (2013). Phylogenetic evidence for recent diversification of obligate coral-dwelling gobies compared with their host corals. Mol. Phylogenet. Evol. 69, 123-132. doi: 10.1016/j.ympev.2013.04.033
47. Ekman, S. (1953). Zoogeography of the Sea. London: Sigwick and Jackson. doi: 10.1186/1471-2148-13-65
48. Faircloth, B. C., Sorenson, L., Santini, F., and Alfaro, M. E. (2013). A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs). PLoS ONE 8:e65923. doi: 10.1371/journal.pone.0065923
49. Fessler, J. L., and Westneat, M. W. (2007). Molecular phylogenetics of the butterflyfishes (Chaetodontidae): taxonomy and biogeography of a global coral reef fish family. Mol. Phylogenet. Evol. 45, 50-68. doi: 10.1016/j.ympev.2007.05.018
50. Floeter, S. R., Guimaraes, R. Z. P., Rocha, L. A., Ferreira, C. E. L., Rangel, C. A., and Gasparini, J. L. (2001). Geographic variation in reef-fish assemblages along the Brazilian coast. Glob. Ecol. Biogeogr. 10, 423-431. doi: 10.1046/j.1466-822X.2001.00245.x
51. Floeter, S. R., Rocha, L. A., Robertson, D. R., Joyeux, J. C., Smith-Vaniz, W. F., Wirtz, P.,et al. (2008). Atlantic reef fish biogeography and evolution. J. Biogeogr. 35, 22-47. doi: 10.1111/j.1365-2699.2007.01790.x
52. Fontanillas, E., Welch, J. J., Thomas, J. A., and Bromham, L. (2007). The influence of body size and net diversification rate on molecular evolution during the radiation of animal phyla. BMC Evol. Biol. 7:95. doi: 10.1186/1471-2148-7-95
53. Frédérich, B., Sorenson, L., Santini, F., Slater, G. J., and Alfaro, M. E. (2013). Iterative ecological radiation and convergence during the evolutionary history of damselfishes (Pomacentridae). Am. Nat. 181, 94-113. doi: 10.1086/668599
54. Friedman, M. (2010). Explosive morphological diversification of spiny-finned teleost fishes in the aftermath of the end-Cretaceous extinction. Proc. Biol. Sci. 277, 1675-1683. doi: 10.1098/rspb.2009.2177
55. Gaither, M. R., and Rocha, L. A. (2013). Origins of species richness in the Indo-Malay-Philippine biodiversity hotspot: evidence for the centre of overlap hypothesis. J. Biogeogr. 40, 1638-1648. doi: 10.1111/jbi.12126
56. Goatley, C. H. R., Bellwood, D. R., and Bellwood, O. (2010). Fishes on coral reefs: changing roles over the past 240 million years. Paleobiology 36, 415-427. doi: 10.1666/09035.1
57. Goldie, X., Lanfear, R., and Bromham, L. (2011). Diversification and the rate of molecular evolution: no evidence of a link in mammals. BMC Evol. Biol. 11:286. doi: 10.1186/1471-2148-11-286
58. Halas, D., and Winterbottom, R. (2009). A phylogenetic test of multiple proposals for the origins of the East Indies coral reef biota. J. Biogeogr. 36, 1847-1860. doi: 10.1111/j.1365-2699.2009.02103.x
59. Hallam, A. (1994). An Outline of Phanerozoic Biogeography. Oxford: Oxford University Press. doi: 10.1111/j.1365-2699.2009.02103.x
60. Herler, J., Munday, P., and Hernaman, V. (2011). "Gobies on coral reefs," in The Biology of Gobies, eds R. A. Patzner,J. L. Van Tassell,M. Kovacic, and B. G. Kapoor (New Hampshire: Science Publishers),493-529.
61. Hillebrand, H. (2004). On the generality of the latitudinal diversity gradient. Am. Nat. 163, 192-211. doi: 10.1086/381004
62. Hobbs, J.-P., van Herwerden, L., Jerry, D., Jones, G., and Munday, P. (2013). High genetic diversity in geographically remote populations of endemic and widespread coral reef angelfishes (genus: Centropyge). Diversity 5, 39-50. doi: 10.3390/d5010039
63. Hodge, J. R., Read, C. I., Bellwood, D. R., and van Herwerden, L. (2013). Evolution of sympatric species: a case study of the coral reef fish genus Pomacanthus (Pomacanthidae). J. Biogeogr. 62, 653-663. doi: 10.1111/jbi.12124
64. Hodge, J. R., Read, C. I., van Herwerden, L., and Bellwood, D. R. (2012). The role of peripheral endemism in species diversification: evidence from the coral reef fish genus Anampses (Family: Labridae). Mol. Phylogenet. Evol. 62, 653-663. doi: 10.1016/j.ympev.2011.11.007
65. Hodge, J. R., van Herwerden, L., and Bellwood, D. R. (2014). Temporal evolution of coral reef fishes: global patterns and disparity in isolated locations. J. Biogeogr. 41, 2115-2127. doi: 10.1111/jbi.12356
66. Hoeksema, B. (2007). "Delineation of the Indo-Malayan centre of maximum marine biodiversity: the coral triangle," in Biogeography, Time, and Place: Distributions, Barriers, and Islands, ed. W. Renema (Dordrecht: Springer),117-178. doi: 10.1111/jbi.12356
67. Hoeksema, B. (2009). West-east variation in the Indonesian reef coral fauna: lines of division or zones of transition? in Proceedings of World Ocean Conference, Manado, 1-10.
68. Hubert, N.,Meyer, C. P., Bruggemann, H. J., Guérin, F., Komeno, R. J. L., Espiau, B.,et al. (2012). Cryptic diversity in Indo-Pacific coral-reef fishes revealed by DNA-barcoding provides new support to the centre-of-overlap hypothesis. PLoS ONE 7:e28987. doi: 10.1371/journal.pone.0028987
69. Hughes, T. P., Baird, A. H., Bellwood, D. R., Card, M., Connolly, S. R., Folke, C.,et al. (2003). Climate change,human impacts,and the resilience of coral reefs. Science 301, 929-933. doi: 10.1126/science.1085046
70. Hughes, T. P., Bellwood, D. R., Baird, A. H., Brodie, J., Bruno, J. F., and Pandolfi, J. M.et al. (2011). Shifting base-lines,declining coral cover,and the erosion of reef resilience: comment on Sweatman et al (2011). Coral Reefs 30, 653-660. doi: 10.1007/s00338-011-0787-6
71. Hughes, T. P., Bellwood, D. R., and Connolly, S. R. (2002). Biodiversity hotspots, centres of endemicity, and the conservation of coral reefs. Ecol. Lett. 5, 775-784. doi: 10.1046/j.1461-0248.2002.00383.x
72. Hundt, P. J., Iglésias, S. P., Hoey, A. S., and Simons, A. M. (2014). A multilocus molecular phylogeny of combtooth blennies (Percomorpha: Blennioidei: Blenniidae): multiple invasions of intertidal habitats. Mol. Phylogenet. Evol. 70, 47-56. doi: 10.1016/j.ympev.2013.09.001
73. Jetz, W., Thomas, G. H., Joy, J. B., Hartmann, K., and Mooers, A. O. (2012). The global diversity of birds in space and time. Nature 491, 444-448. doi: 10.1038/nature11631
74. Joyeux, J.-C., Floeter, S. R., Ferreira, C. E. L., and Gasparini, J. L. (2001). Biogeography of tropical reef fishes: the South Atlantic puzzle. J. Biogeogr. 28, 831-841. doi: 10.1046/j.1365-2699.2001.00602.x
75. Kazancioglu, E., Near, T. J., Hanel, R., and Wainwright, P. C. (2009). Influence of sexual selection and feeding functional morphology on diversification rate of parrotfishes (Scaridae). Proc. Biol. Sci. 276, 3439-3446. doi: 10.1098/rspb.2009.0876
76. Klanten, S. O., van Herwerden, L., Choat, J. H., and Blair, D. (2004). Patterns of lineage diversification in the genus Naso (Acanthuridae). Mol. Phylogenet. Evol. 32, 221-235. doi: 10.1016/j.ympev.2003.11.008
77. Kool, J. T., Paris, C. B., Barber, P. H., and Cowen, R. K. (2011). Connectivity and the development of population genetic structure in Indo-West Pacific coral reef communities. Glob. Ecol. Biogeogr. 20, 695-706. doi: 10.1111/j.1466-8238.2010.00637.x
78. Kulbicki, M., Parravicini, V., Bellwood, D. R., Arias-Gonzàlez, E., Chabanet, P., Floeter, S. R.,et al. (2013). Global biogeography of reef fishes: a hierarchical quantitative delineation of regions. PLoS ONE 8:e81847. doi: 10.1371/journal.pone.0081847
79. Lacson, J., and Nelson, S. (1993). Genetic distances among fishes of the genus Siganus (Siganidae) from the Western Pacific Ocean. Mar. Biol. 116, 187-192.
80. Lancaster, L. T. (2010). Molecular evolutionary rates predict both extinction and speciation in temperate angiosperm lineages. BMC Evol. Biol. 10:162. doi: 10.1186/1471-2148-10-162
81. Lanfear, R., Welch, J. J., and Bromham, L. (2010a). Watching the clock: studying variation in rates of molecular evolution between species. Trends Ecol. Evol. 25, 495-503. doi: 10.1016/j.tree.2010.06.007
82. Lanfear, R., Ho, S. Y. W., Love, D., and Bromham, L. (2010b). Mutation rate is linked to diversification in birds. Proc. Natl. Acad. Sci. U.S.A. 107, 20423-20428. doi: 10.1073/pnas.1007888107
83. Leprieur, F., Albouy, C., De Bortoli, J., Cowman, P. F., Bellwood, D. R., and Mouillot, D. (2012). Quantifying phylogenetic beta diversity: distinguishing between "True" turnover of lineages and phylogenetic diversity gradients. PLoS ONE 7:e42760. doi: 10.1371/journal.pone.0042760
84. Lessios, H. A., and Robertson, D. R. (2006). Crossing the impassable: genetic connections in 20 reef fishes across the eastern Pacific barrier. Proc. Biol. Sci. 273, 2201-2208. doi: 10.1098/rspb.2006.3543
85. Litsios, G., Pearman, P. B., Lanterbecq, D., Tolou, N., and Salamin, N. (2014). The radiation of the clownfishes has two geographical replicates. J. Biogeogr. 41, 2140-2149. doi: 10.1111/jbi.12370
86. Litsios, G., Sims, C. A., Wüest, R. O., Pearman, P. B., Zimmermann, N. E., and Salamin, N. (2012). Mutualism with sea anemones triggered the adaptive radiation of clownfishes. BMC Evol. Biol. 12:212. doi: 10.1186/1471-2148-12-212
87. Lobato, F. L., Barneche, D. R., Siqueira, A. C., Liedke, A. M. R., Lindner, A., Pie, M. R.,et al. (2014). Diet and diversification in the evolution of coral reef fishes. PLoS ONE 9:e102094. doi: 10.1371/journal.pone.0102094
88. McCoy, E. D., and Heck, K. L. (1976). Biogeography of corals, seagrasses, and mangroves: an alternative to the center of origin concept. Syst. Zool. 25, 201. doi: 10.2307/2412488
89. McMillan, W. O., and Palumbi, S. R. (1995). Pacific butterflyfishes concordant evolutionary patterns among Indo-West. Proc. R. Soc. London 260, 229-236. doi: 10.2307/2412488
90. McMillan, W. O., Weigt, L. A., and Palumbi, S. R. (1999). Color pattern evolution, assortative mating, and genetic differentiation in brightly colored butterflyfishes. Evolution 53, 247-260. doi: 10.1098/rspb.1995.0085
91. Micklich, N. R., Tyler, J. C., Johnson, G. D., Swidnicka, E., and Bannikov, A. F. (2009). First fossil records of the tholichthys larval stage of butterfly fishes (Perciformes, Chaetodontidae), from the Oligocene of Europe. Paläontol. Z. 83, 479-497. doi: 10.1007/s12542-009-0031-7
92. Montes, C., Cardona, A., McFadden, R., Moron, S. E., Silva, C. A., Restrepo-Moreno, S.,et al. (2012). Evidence for middle Eocene and younger land emergence in central Panama: implications for Isthmus closure. Geol. Soc. Am. Bull. 124, 780-799. doi: 10.1130/B30528.1
93. Mora, C., Chittaro, P. M., Sale, P. F., Kritzer, J. P., and Ludsin, S. A. (2003). Patterns and processes in reef fish diversity. Nature 421, 933-936. doi: 10.1038/nature01421.1
94. Mora, C., Tittensor, D. P., and Myers, R. A. (2008). The completeness of taxonomic inventories for describing the global diversity and distribution of marine fishes. Proc. Biol. Sci. 275, 149-55. doi: 10.1098/rspb.2007.1315
95. Morlon, H. (2014). Phylogenetic approaches for studying diversification. Ecol. Lett. 17, 508-25. doi: 10.1111/ele.12251
96. Morlon, H., Potts, M. D., and Plotkin, J. B. (2010). Inferring the dynamics of diversification: a coalescent approach. PLoS Biol. 8:e1000493. doi: 10.1371/journal.pbio.1000493
97. Mouillot, D., De Bortoli, J., Leprieur, F., Parravicini, V., Kulbicki, M., and Bellwood, D. R. (2013). The challenge of delineating biogeographical regions: nestedness matters for Indo-Pacific coral reef fishes. J. Biogeogr. 40, 2228-2237. doi: 10.1111/jbi.12194
98. Myers, N. (1988). Threatened biotas: "hot spots" in tropical forests. Environmentalist 8, 187-208. doi: 10.1111/jbi.12194
99. Myers, N., Mittermeier, R. A., Mittermeier, C. G., da Fonseca, G. A., and Kent, J. (2000). Biodiversity hotspots for conservation priorities. Nature 403, 853-858. doi: 10.1038/35002501
100. Near, T. J., Dornburg, A., Eytan, R. I., Keck, B. P., Smith, W. L., Kuhn, K. L.,et al. (2013). Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes. Proc. Natl. Acad. Sci. U.S.A. 110, 12738-1243. doi: 10.1073/pnas.1304661110
101. Near, T. J., Eytan, R. I., Dornburg, A., Kuhn, K. L., Moore, J. A, Davis, M. P.,et al. (2012). Resolution of ray-finned fish phylogeny and timing of diversification. Proc. Natl. Acad. Sci. U.S.A. 109, 13698-13703. doi: 10.1073/pnas.1206625109
102. Nelson, G. (1989). "Phylogeny of major fish groups," in The Hierarchy of Life, eds B. Fernholm, K. Bremer, and H. Jörnvall (Amsterdam: Excerpta Medica), 325-336.
103. O'Dea, A., Jackson, J. B. C., Fortunato, H., Smith, J. T., D'Croz, L., Johnson, K. G.,et al. (2007). Environmental change preceded Caribbean extinction by 2 million years. Proc. Natl. Acad. Sci. U.S.A. 104, 5501-5506. doi: 10.1073/pnas.0610947104
104. Olson, D. M., Dinerstein, E., Wikramanayake, E. D., Burgess, N. D., Powell, G. V. N., Underwood, E. C.,et al. (2001). Terrestrial ecoregions of the world: a new map of life on earth. Bioscience 51, 933-938. doi: 10.1073/pnas.0610947104
105. Palumbi, S. R. (1997). Molecular biogeography of the Pacific. Coral Reefs 16, S47-S52. doi: 10.1007/s003380050241
106. Parravicini, V., Kulbicki, M., Bellwood, D. R., Friedlander, A. M., Arias-Gonzalez, J. E., Chabanet, P.,et al. (2013). Global patterns and predictors of tropical reef fish species richness. Ecography (Cop.) 36, 1254-1262. doi: 10.1111/j.1600-0587.2013.00291.x
107. Pellissier, L., Leprieur, F., Parravicini, V., Cowman, P. F., Kulbicki, M., Litsios, G.,et al. (2014). Quaternary coral reef refugia preserved fish diversity. Science 344, 1016-1019. doi: 10.1126/science.1249853
108. Potts, D. C. (1985). "Sea level fluctuations and speciation in Scleractina," in Proceedings of the Fifth International Coral Reef Congress, Tahiti.
109. Price, S. A., Holzman, R., Near, T. J., and Wainwright, P. C. (2011). Coral reefs promote the evolution of morphological diversity and ecological novelty in labrid fishes. Ecol. Lett. 14, 462-469. doi: 10.1111/j.1461-0248.2011.01607.x
110. Price, S. A., Schmitz, L., Oufiero, C. E., Eytan, R. I., Dornburg, A., Smith, W. L.,et al. (2014). Two waves of colonization straddling the K-Pg boundary formed the modern reef fish fauna. Proc. Biol. Sci. 281, 20140321. doi: 10.1098/rspb.2014.0321
111. Price, S. A., Tavera, J. J., Near, T. J., and Wainwright, P. C. (2013). Elevated rates of morphological and functional diversification in reef-dwelling haemulid fishes. Evolution 67, 417-428. doi: 10.1111/j.1558-5646.2012.01773.x
112. Quenouille, B., Hubert, N., Bermingham, E., and Planes, S. (2011). Speciation in tropical seas: allopatry followed by range change. Mol. Phylogenet. Evol. 58, 546-552. doi: 10.1016/j.ympev.2010.12.009
113. Quental, T. B., and Marshall, C. R. (2009). Extinction during evolutionary radiations: reconciling the fossil record with molecular phylogenies. Evolution 63, 3158-3167. doi: 10.1111/j.1558-5646.2009.00794.x
114. Quental, T. B., and Marshall, C. R. (2010). Diversity dynamics: molecular phylogenies need the fossil record. Trends Ecol. Evol. 25, 434-441. doi: 10.1016/j.tree.2010.05.002
115. Rabosky, D. L. (2009a). Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions. Ecol. Lett. 12, 735-743. doi: 10.1111/j.1461-0248.2009.01333.x
116. Rabosky, D. L. (2009b). Extinction rates should not be estimated from molecular phylogenies. Evolution 4, 1816-1824. doi: 10.1111/j.1558-5646.2009.00926.x
117. Rabosky, D. L., Santini, F., Eastman, J., Smith, S. A., Sidlauskas, B., Chang, J.,et al. (2013). Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nat. Commun. 4, 1-8. doi: 10.1038/ncomms2958
118. Read, C. I., Bellwood, D. R., and van Herwerden, L. (2006). Ancient origins of Indo-Pacific coral reef fish biodiversity: a case study of the leopard wrasses (Labridae: Macropharyngodon). Mol. Phylogenet. Evol. 38, 808-819. doi: 10.1016/j.ympev.2005.08.001
119. Ree, R. H., and Sanmartín, I. (2009). Prospects and challenges for parametric models in historical biogeographical inference. J. Biogeogr. 36, 1211-1220. doi: 10.1111/j.1365-2699.2008.02068.x
120. Reed, D. L., Carpenter, K. E., and deGravelle, M. J. (2002). Molecular systematics of the Jacks (Perciformes: Carangidae) based on mitochondrial cytochrome b sequences using parsimony, likelihood, and Bayesian approaches. Mol. Phylogenet. Evol. 23, 513-524.
121. Renema, W., Bellwood, D. R., Braga, J. C., Bromfield, K., Hall, R., Johnson, K. G.,et al. (2008). Hopping hotspots: global shifts in marine biodiversity. Science 321, 654-657. doi: 10.1126/science.1155674
122. Roberts, C. M., McClean, C. J., Veron, J. E. N., Hawkins, J. P., Allen, G. R., McAllister, D. E.,et al. (2008). Marine biodiversity hotspots and conservation priorities for tropical reefs. Science 295, 1280-1284. doi: 10.1126/science.1067728
123. Robertson, D. R. (1998). Do coral-reef fish faunas have a distinctive taxonomic structure? Coral Reefs 17, 179-186. doi: 10.1007/s003380050113
124. Rocha, L. A., Robertson, D. R., Rocha, C. R., Van Tassell, J. L., Craig, M. T., Bowen, B. W.,et al. (2005a). Recent invasion of the tropical Atlantic by an Indo-Pacific coral reef fish. Mol. Ecol. 14, 3921-3928. doi: 10.1111/j.1365-294X.2005.02698.x
125. Rocha, L. A., Robertson, D. R., Roman, J., and Bowen, B. W. (2005b). Ecological speciation in tropical reef fishes. Proc. Biol. Sci. 272, 573-579. doi: 10.1098/2004.3005
126. Rocha, L. A., and Bowen, B. W. (2008). Speciation in coral-reef fishes. J. Fish. Biol. 72, 1101-1121. doi: 10.1111/j.1095-8649.2007.01770.x
127. Rolland, J., Condamine, F. L., Jiguet, F., and Morlon, H. (2014). Faster speciation and reduced extinction in the tropics contribute to the mammalian latitudinal diversity gradient. PLoS Biol. 12:e1001775. doi: 10.1371/journal.pbio.1001775
128. Rosen, B. R. (1984). "Reef coral biogeography and climate through the late Cainozoic: just islands in the sun or a critical pattern of islands?" in Fossil and Climate, ed. P. Brenchley (Chichester: John Wiley and Sons), 201-262.
129. Rüber, L., Tassell, J., and Zardoya, R. (2003). Rapid speciation and ecological divergence in the American seven-spined gobies (Gobiidae, Gobiosomatini) inferred from a molecular phylogeny. Evolution 57, 1584-1598. doi: 10.1111/j.0014-3820.2003.tb00366.x
130. Rüber, L., and Zardoya, R. (2005). Rapid cladogenesis in marine fishes revisited. Evolution 59, 1119-1127. doi: 10.1111/j.0014-3820.2005.tb01048.x
131. Sanderson, M. (2003). r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19, 301-302.
132. Schluter, D., and Conte, G. L. (2009). Genetics and ecological speciation. Proc. Natl. Acad. Sci. U.S.A. 9955-9962. doi: 10.1073/pnas.0901264106
133. Smith, L. L., Fessler, J. L., Alfaro, M. E., Streelman, J. T., and Westneat, M. W. (2008). Phylogenetic relationships and the evolution of regulatory gene sequences in the parrotfishes. Mol. Phylogenet. Evol. 49, 136-152. doi: 10.1016/j.ympev.2008.06.008
134. Sorenson, L., Santini, F., and Alfaro, M. E. (2014). The effect of habitat on modern shark diversification. J. Evol. Biol. 27, 1536-1548. doi: 10.1111/jeb.12405
135. Sorenson, L., Santini, F., Carnevale, G., and Alfaro, M. E. (2013). A multi-locus timetree of surgeonfishes (Acanthuridae, Percomorpha), with revised family taxonomy. Mol. Phylogenet. Evol. 68, 150-160. doi: 10.1016/j.ympev.2013.03.014
136. Spalding, M. D., Fox, H. E., Allen, G. R., Davidson, N., Ferdaña, Z. A., Finlayson, M.,et al. (2007). Marine ecoregions of the world: a bioregionalization of coastal and shelf areas. Bioscience 57, 573. doi: 10.1641/B570707
137. Steininger, F. F., and Rögl, F. (1979). The paratethys history. A contribution towards the Neogene geodynamics of the alpine orogene. Ann. Geol. Pays Hell. 3, 1153-1165. doi: 10.1641/B570707
138. Taylor, M. S., and Hellberg, M. E. (2005). Marine radiations at small geographic scales: speciation in neotropical reef gobies (Elacatinus). Evolution 59, 374-385. doi: 10.1554/04-590
139. Thacker, C. E., and Roje, D. M. (2009). Phylogeny of cardinalfishes (Teleostei: Gobiiformes: Apogonidae) and the evolution of visceral bioluminescence. Mol. Phylogenet. Evol. 52, 735-745. doi: 10.1016/j.ympev.2009.05.017
140. Thomson, R. C., and Shaffer, H. B. (2010a). Rapid progress on the vertebrate tree of life. BMC Biol. 8:19. doi: 10.1186/1741-7007-8-19
141. Thomson, R. C., and Shaffer, H. B. (2010b). Sparse supermatrices for phylogenetic inference: taxonomy, alignment, rogue taxa, and the phylogeny of living turtles. Syst. Biol. 59, 42-58. doi: 10.1093/sysbio/syp075
142. Timm, J., and Kochzius, M. (2008). Geological history and oceanography of the Indo-Malay Archipelago shape the genetic population structure in the false clown anemonefish (Amphiprion ocellaris). Mol. Ecol. 17, 3999-4014. doi: 10.1111/j.1365-294X.2008.03881.x
143. Tittensor, D. P., Mora, C., Jetz, W., Lotze, H. K., Ricard, D., Berghe, E. V.et al. (2010). Global patterns and predictors of marine biodiversity across taxa. Nature 466, 1098-1101. doi: 10.1038/nature09329
144. Venditti, C., and Pagel, M. (2010). Speciation as an active force in promoting genetic evolution. Trends Ecol. Evol. 25, 14-20. doi: 10.1016/j.tree.2009.06.010
145. Wainwright, P. C., Smith, W. L., Price, S. A., Tang, K. L., Sparks, J. S., Ferry, L. A.,et al. (2012). The evolution of pharyngognathy: a phylogenetic and functional appraisal of the pharyngeal jaw key innovation in labroid fishes and beyond. Syst. Biol. 61, 1001-1027. doi: 10.1093/sysbio/sys060
146. Wallace, C. C., and Rosen, B. R. (2006). Diverse staghorn corals (Acropora) in high-latitude Eocene assemblages: implications for the evolution of modern diversity patterns of reef corals. Proc. Biol. Sci. 273, 975-982. doi:10.1098/rspb.2005.3307
147. Westneat, M. W., and Alfaro, M. E. (2005). Phylogenetic relationships and evolutionary history of the reef fish family Labridae. Mol. Phylogenet. Evol. 36, 370-390. doi: 10.1016/j.ympev.2005.02.001
148. Whiting, A. S., Lawler, S. H., Horwitz, P., and Crandall, K. A. (2000). Biogeographic regionalization of Australia: assigning conservation priorities based on endemic freshwater crayfish phylogenetics. Anim. Conserv. 3, 155-163. doi: 10.1016/j.ympev.2005.02.001
149. Whittaker, R. J., Araujo, M. B., Paul, J., Ladle, R. J., Watson, J. E. M., and Willis, K. J. (2005). Conservation biogeography: assessment and prospect. Divers. Distrib. 11, 3-23. doi: 10.1111/j.1366-9516.2005.00143.x
150. Williams, S. T., and Duda, T. F. (2008). Did tectonic activity stimulate oligomiocene speciation in the Indo-West Pacific. Evolution 62, 1618-1634. doi: 10.1111/j.1558-5646.2008.00399.x
151. Willig, M. R., Kaufman, D. M., and Stevens, R. D. (2003). Latitudinal gradients of biodiversity: pattern, process, scale, and synthesis. Annu. Rev. Ecol. Evol. 34, 273-309. doi: 10.1146/annurev.ecolsys.34.012103.44032
152. Wilson, M. E. J. and Rosen, B. R. (1998). "Implications of paucity of corals in the Paleogene of SE Asia: plate tectonics or centre of origin?," in Biogeography and Geological Evolution of SE Asia, eds R. Hall and J. D. Holloway (Leiden: Backhuys Publishers), 165-195.
153. Zapata, F. A., and Robertson, D. R. (2006). How many species of shore fishes are there in the Tropical Eastern Pacific? J. Biogeogr. 34, 38-51. doi: 10.1111/j.1365-2699.2006.01586.x