Major issues in the origins of ray-finned fish (Actinopterygii) biodiversity

Biological Reviews

Volumn 89, Issue 4, 2014, Pages 950-971

  Sallan, Lauren C ^a,b  

^a UNIVERSITY OF CHICAGO   (United States)

^b UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Diversification; Fossils; Ichthyology; Molecular clocks; Palaeontology; Palaeozoic; Systematics; Teleost

Indexed keywords

ACTINOPTERYGII; AMIIDAE; CHONDROSTEI; HOLOSTEI; POLYODONTIDAE (FISH); POLYPTERIDAE; POLYPTERIFORMES; TELEOSTEI;

ANIMAL; BIODIVERSITY; CLASSIFICATION; EVOLUTION; FISH; GENETICS;

ANIMALS; BIODIVERSITY; BIOLOGICAL EVOLUTION; FISHES;

EID: 84925282659     PISSN: 14647931     EISSN: 1469185X     Source Type: Journal    
DOI: 10.1111/brv.12086     Document Type: Article

References (204)

1. Abouheif, E. (2008). Parallelism as the pattern and process of mesoevolution. Evolution and Development 10, 3-5.
2. Agassiz, J. L. R. (1833-1844). Recherches sur les Poissons Fossiles. Text (Volume V) and Atlas (Volume II). Petitpierre, Neuchatel.
3. Albert, J. S., Johnson, D. M. & Knouft, J. H. (2009). Fossils provide better estimates of ancestral body size than do extant taxa in fishes. Acta Zoologica 90, 357-384.
4. Alfaro, M. E., Santini, F., Brock, C., Alamillo, H., Dornberg, A., Rabosky, D. L., Carnevale, G. & Harmon, L. J. (2009). Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proceedings of the National Academy of Sciences of the United States of America 106, 13410-13414.
5. Allis, E. P. (1922). The cranial anatomy of Polypterus, with special reference to Polypterus bichir. Journal of Anatomy 56, 189-294.
6. Amores, A., Force, A., Yan, Y.-L., Joly, L., Amemiya, C., Fritz, A., Ho, R. K., Langeland, J., Prince, V., Wang, Y.-L., Westerfield, M., Ekker, M. & Postlethwait, J. H. (1998). Zebrafish hox clusters and vertebrate genome evolution. Science 282, 1711-1714.
7. Arnason, U., Gullberg, A. & Janke, A. (2001). Molecular phylogenetics of gnathostome (jawed) fishes: old bones, new cartilage. Zoologica Scripta 30, 249-255.
8. Arnason, U., Gullberg, A., Janke, A., Joss, J. & Elmerot, C. (2004). Mitogenomic analyses of deep gnathostome divergences: a fish is a fish. Gene 333, 61-70.
9. Arratia, G. (1999). The monophyly of Teleostei and stem-group teleosts. Consensus and disagreements. In Mesozoic Fishes 2 - Systematics and Fossil Record (eds G. Arratia and H.-P. Schultze ), p. 265. Verlag Dr. Friedrich Pfiel, München.
10. Arratia, G. (2000). Remarkable teleostean fishes from the Late Jurassic of southern Germany and their phylogenetic relationships. Fossil Record 3, 137-179.
11. Arratia, G. (2001). The sister-group of Teleostei: consensus and disagreements. Journal of Vertebrate Paleontology 21, 767-773.
12. Arratia, G. & Cloutier, R. (1996). Reassessment of the morphology of Cheirolepis canadensis (Actinopterygii). In Devonian Fishes and Plants of Miguasha, Quebec, Canada (eds H.-P. Schultze and R. Cloutier ), p. 165. Verlag Dr. Friedrich Pfiel, Munich.
13. Azuma, Y., Kumazawa, Y., Miya, M., Mabuchi, K. & Nishida, M. (2008). Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences. BMC Evolutionary Biology 8, 215.
14. Bambach, R. K. (2006). Phanerozoic biodiversity mass extinctions. Annual Review of Earth and Planetary Sciences 34, 127-155.
15. Basden, A. M., Young, G. C., Coates, M. I. & Ritchie, A. (2000). The most primitive osteichthyan braincase? Nature 403, 185-188.
16. Bell, M. A. (1994). Evolutionary Biology of the Threespine Stickleback. Oxford University, Oxford.
17. Bellwood, D. R. (2003). Origins and escalation of herbivory in fishes: a functional perspective. Paleobiology 29, 71-83.
18. Bemis, W. E., Findeis, E. K. & Grande, L. (1997). An overview of Acipenseriformes. Environmental Biology of Fishes 48, 25-71.
19. Benton, M. J. (2005). Vertebrate Paleontology. Blackwell, Malden.
20. Berg, L. S. (1940). Classification of fishes both recent and fossil. Travaux de l'Institut Zoologique de l'Academie des Sciences de l'URSS 5, 85-517.
21. Berg, L. S., Kazantseva, A. A. & Obruchev, D. V. (1967). Superorder Palaeonisci. In Fundamentals of Paleontology: Agantha, Pisces (Volume XI), (ed. Y. A. Orlov ), p. 528 Israel Program for Scientific Translations, Jerusalem.
22. Betancur-R, R., Broughton, R. E., Wiley, E. O., Carpenter, K., Lopez, J. A., LI, C., Holcroft, N. I., Arcila, D., Sanciango, M., Cureton, J. C., Zhang, F., Buser, T., Campbell, M. A., Ballesteros, J. A., Roa-Varon, A., Willia, S., Borden, W. C., Rowley, R., Reneau, P. C., Hough, D. J., Lu, G., Grande, T., Arratia, G. & Orti, G. (2013). The tree of life and a new classification of bony fishes. PLoS Currents Tree of Life [last modified: 2013 Jun 3]. Edition 1 (doi: 10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288).
23. Bjerring, H. C. (1985). Facts and thoughts on piscine phylogeny. In Evolutionary Biology of Primitive Fishes (eds R. E. Foreman, A. Gorbman, J. Dood and R. Olsson ), p. 31. Plenum, New York.
24. Botella, H., Blom, H., Dorka, M., Ahlberg, P. E. & Janvier, P. (2007). Jaws and teeth of the earliest bony fishes. Nature 448, 583-586.
25. Bradley Dyne, M. (1939). The skull of Amphicentrum granulosum. Proceedings of the Zoological Society, London B 109, 195-210.
26. Brett, C. E. & Walker, S. E. (2002). Predators and predation in Paleozoic marine environments. Paleontological Society Papers 8, 93-118.
27. Brezinski, D. K., Cecil, C. B. & Skema, V. W. (2010). Late Devonian glacigenic and associated facies from the central Appalachian Basin, eastern United States. The Geological Society of America Bulletin 122, 265-281.
28. Broughton, R. E., Betancur-R, R., Li, C., Arratia, G. & Orti, G. (2013). Multi-locus phylogenetic analyses reveals the pattern and tempo of bony fish evolution. PLoS Currents Tree of Life [last modified: 2013 May 9]. Edition 1 (doi: 10.1371/currents.tol.2ca8041495ffafd0c92756e75247483e).
29. Calliet, G., Love, M. & Ebeling, A. (1996). Fishes: A Field and Laboratory Manual on Their Structure, Identification and Natural History. Waveland, Long Grove.
30. Caplan, M. L. & Bustin, R. M. (1999). Devonian-Carboniferous Hangenberg mass extinction event, widespread organic-rich mudrock and anoxia: causes and consequences. Palaeogeography, Palaeoclimatology, Palaeoecology 148, 187-207.
31. Carrete Vega, G. & Wiens, J. J. (2012). Why are there so few fish in the sea? Proceedings of the Royal Society of London B 279, 2323-2329.
32. Carroll, R. L. (1988). Vertebrate Paleontology and Evolution. W.H. Freeman and Company, New York.
33. Cavin, L. & Suteethorn, V. (2006). A new semionotiform (Actinopterygii, Neopterygii) from Upper Jurassic - Lower Cretaceous deposits of north-east Thailand, with comments on the relationships of the semionotiforms. Palaeontology 49, 339-353.
34. Chakrabarty, P. (2010). The transitioning state of systematic ichthyology. Copeia 2010, 513-515.
35. Chen, D., Janvier, P., Ahlberg, P. E. & Blom, H. (2012a). Scale morphology and squamation in the osteichthyan Andreolepis from Gotland, Sweden. Historical Biology 24, 411-423.
36. Chen, M., Zou, M., Yang, L. & He, S. (2012b). Basal jawed vertebrate phylogenomics using transcriptomic data from Solexa sequencing. PLoS One 7, e36256.
37. Choo, B. (2011). Revision of the actinopterygian genus Mimipiscis (=Mimia) from the Upper Devonian Gogo Formation of Western Australia and the interrelationships of the early Actinopterygii. Earth and Environmental Science Transactions of the Royal Society of Edinburgh 102, 77-104.
38. Claeson, K., Bemis, W. E. & Hagadorn, J. W. (2007). New interpretations of the skull of a primitive bony fish Erpetoichthys calabaricus (Actinopterygii: Cladistia). Journal of Morphology 268, 1021-1039.
39. Cloutier, R. & Arratia, G. (2004). Early diversification of actinopterygian fishes. In Recent Advances in the Origin and Early Radiation of Vertebrates (eds G. Arratia, M. H. V. Wilson and R. Cloutier ), p. 217. Verlag Dr. Friedrich Pfiel, München.
40. Coates, M. I. (1988). A new fauna of Namurian (Carboniferous) fish from Beardsden, Glasgow. PhD Thesis: University of Newcastle-upon-Tyne.
41. Coates, M. I. (1993). New actinopterygian fish from the Namurian Manse Burn Formation of Beardsden, Scotland. Palaeontology 36, 123-146.
42. Coates, M. I. (1996). The Devonian tetrapod Acanthostega gunnari Jarvik: postcranial anatomy, basal tetrapod interrelationships and patterns of skeletal evolution. Transactions of the Royal Society of Edinburgh, Earth Science 87, 363-421.
43. Coates, M. I. (1998). Actinopterygians from the Namurian of Bearsden, Scotland, with comments on early actinopterygian neurocrania. Zoological Journal of the Linnean Society 122, 27-59.
44. Coates, M. I. (1999). Endocranial preservation of a Carboniferous actinopterygian from Lancashire, UK, and the interrelationships of primitive actinopterygians. Philosophical Transactions of the Royal Society of London B 354, 453-462.
45. Coates, M. I. & Clack, J. A. (1995). Romer's gap: tetrapod origins and terrestriality. Bulletin du Museum National d'Histoire Naturelle, Paris 17, 373-388.
46. Cope, E. D. (1887). Geology and Paleontology. American Naturalist 21, 1014-1019.
47. Crow, K. D., Stadler, P. F., Lynch, V. J., Amemiya, C. & Wagner, G. P. (2006). The "fish specific" Hox cluster duplication is coincident with the origin of teleosts. Molecular Biology and Evolution 23, 126-131.
48. Crow, K. D., Smith, C. D., Cheng, J.-F., Wagner, G. P. & Amemiya, C. T. (2012). An independent genome duplication inferred from Hox paralogs in the American paddlefish - a representative ray-finned basal fish and important comparative reference. Genome Biology and Evolution 4, 825-841.
49. Davis, S. P., Finarelli, J. A. & Coates, M. I. (2012). Acanthodes and shark-like conditions in the last common ancestor of modern gnathostomes. Nature 486, 247-250.
50. Dietze, K. (1999). Paramblypterus duvernoyi (Actinopterygii): skull morphology and intra-specific variation, and its implications for the systematics of paramblypterid fishes. Journal of Vertebrate Paleontology 19, 247-262.
51. Dietze, K. (2000). A revision of the paramblypterid and amblypterid actinopterygians from Upper Carboniferous-Lower Permian lacustrine deposits of central Europe. Palaeontology 2000, 927-966.
52. Dineley, D. L. & Metcalfe, S. J. (1999). Fossil Fishes of Great Britain. Joint Nature Conservation Conservancy, Peterborough.
53. Diogo, R., Doadrio, I. & Vandewalle, P. (2008). Teleostean phylogeny based on osteological and morphological characters. International Journal of Morphology 26, 463-522.
54. Duthiel, D. B. (1999). The first articulated fossil cladistian: Serenoichthys kemkemensis, gen. et sp. nov., from the Cretaceous of Morocco. Journal of Vertebrate Paleontology 19, 243-246.
55. Faircloth, B. C., Sorensen, L., Santini, F. & 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.
56. Felsenstein, J. (2004). Inferring Phylogenies. Sinauer, Sunderland.
57. Frey, E. & Tischlinger, H. (2012). The Late Jurassic pterosaur Rhamphorhynchus, a frequent victim of the fish Aspidorhynchus? PloS One 7, e31945.
58. Friedman, M. & Blom, H. (2006). A new actinopterygian from the Famennian of East Greenland and the interrelationships of Devonian ray-finned fishes. Journal of Paleontology 80, 1186-1204.
59. Friedman, M. & Brazeau, M. D. (2010). A reappraisal of the origin and basal radiation of the Osteichthyes. Journal of Vertebrate Paleontology 30, 36-56.
60. Friedman, M. & Sallan, L. C. (2012). Five hundred million years of extinction and recovery: a Phanerozoic survey of large-scale diversity patterns in fishes. Palaeontology 55, 707-742.
61. Gardiner, B. G. (1967a). Further notes on paleoniscoids with a classification of the Chondrostei. Bulletin of the British Museum of Natural History, Geological Series 8, 225-325.
62. Gardiner, B. G. (1967b). The significance of the preoperculum in actinopterygian evolution. Journal of the Linnean Society (Zoology) 47, 197-209.
63. Gardiner, B. G. (1984). The relationships of the palaeoniscid fishes, a review based on new specimens of Mimia and Moythomasia from the Late Devonian of West Australia. Bulletin of the British Museum of Natural History 34, 173-440.
64. Gardiner, B. G. (1985). Actinopterygian fish from the Dinantian of Foulden, Berwickshire, Scotland. Transactions of the Royal Society of Edinburgh, Earth Sciences 76, 61-66.
65. Gardiner, B. G. (1993). Osteichthyes: basal actinopterygians. In The Fossil Record 2 (ed. M. J. Benton ), p. 611. Chapman and Hall, London.
66. Gardiner, B. G. & Schaeffer, B. (1989). The interrelationships of lower actinopterygian fishes. Zoological Journal of the Linnean Society 97, 135-187.
67. Gardiner, B. G., Schaeffer, B. & Masserie, J. A. (2005). A review of lower actinopterygian phylogeny. Zoological Journal of the Linnean Society 144, 511-525.
68. Goatley, C. H. R., Bellwood, D. R. & Bellwood, O. (2010). Fishes on coral reefs: changing roles over the past 240 million years. Paleobiology 36, 415-427.
69. Goodrich, E. S. (1928). Polypterus, a palaeoniscid? Palaeobiologica 1, 87-91
70. Gradstein, F. M., Ogg, J. G., Schmitz, M. & Ogg, G. (2012). A Geologic Timescale 2012 2-Volume Set. Elsevier Science Press, Oxford.
71. Gosline, W. A. (1971). Functional morphology and classification of fishes. University Press Hawaii, Hawaii.
72. Grande, L. (2010). An empirical synthetic pattern study of gars (Lepisosteiformes) and closely related species, based mostly on skeletal anatomy. The resurrection of Holostei. American Society of Ichthyologists and Herpetologists, Special Publication 6, 1-871.
73. Grande, L. & Bemis, W. E. (1991). Osteology and phylogenetic relationships of fossil and recent paddlefishes (Polyodontidae) and the interrelationships of Acipenseriformes. Journal of Vertebrate Paleontology Special Memoir 1, 1-121.
74. Grande, L. & Bemis, W. E. (1998). A comprehensive phylogenetic study of amiid fishes (Amiidae) based on comparative skeletal anatomy. An empirical search for interconnected patterns of natural history. Memoir (Society of Vertebrate Paleontology) 4, 1-690.
75. Grandstaff, B. S., Smith, J. B., Lamanna, M. C., Lacovara, K. J. & Abdel-Ghani, M. S. (2012). Bawitius, gen. nov., a giant polypterid (Osteichthyes, Actinopterygii) from the Upper Cretaceous Bahariya Formation of Egypt. Journal of Vertebrate Paleontology 32, 17-26.
76. Greenwood, P. H., Rosen, D. E., Weitzman, S. H. & Myers, G. S. (1966). Phyletic studies of teleostean fishes, with a provisional classification of living forms. Bulletin of the American Museum of Natural History 131, 339-456.
77. Greenwood, P. H., Miles, R. S. & Patterson, C. (1973). Interrelationships of Fishes. Academic Press, New York.
78. Gregory, W. K. (1933). Fish skulls: a study of the evolution of natural mechanisms. Transactions of the American Philosophical Society 23, 75-481.
79. Gross, W. (1968). Fragliche Actinopterygier-Schuppen aud den Silur Gotlands. Lethaia 1, 184-218.
80. Hallam, A. & Wignall, P. B. (1999). Mass extinctions and sea level changes. Earth Science Reviews 48, 217-250.
81. Hilton, E. J. & Forey, P. L. (2011). Redescription of Chondrosteus acipenseroides Egerton, 1858 (Acipenseriformes, Chondrosteidae) from the Lower Lias of Lyme Regis (Dorset, England), with comments on the evolution of sturgeon and paddlefishes. Journal of Systematic Palaeontology 7, 427-453.
82. Hilton, E. J., Grande, L. & Bemis, W. E. (2011). Skeletal anatomy of the shortnose sturgeon, Acipenser brevirorostrum Lesueur 1818, and the systematics of sturgeons (Acipenseriformes, Acipenseridae). Fieldiana (Life and Earth Sciences) 3, 1-168.
83. Hoegg, S., Brinkman, H., Taylor, J. S. & Meyer, A. (2004). Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish. Journal of Molecular Evolution 59, 190-203.
84. Hou, L.-H., Martin, L. D., Zhou, Z. & Feduccia, A. (1996). Early adaptive radiation of birds: evidence from fossils from northeastern China. Science 274, 1164-1167.
85. Huxley, T. H. (1861). Preliminary essay upon the systematic arrangment of the fishes of the Devonian Epoch. Memoirs of the Geological Survey of Great Britain, decade 10 23, 1-40.
86. Hurley, I. A., Mueller, R. L., Dunn, K., Schmidt, E., Friedman, M., Ho, R. K., Prince, V. E., Yang, Z., Thomas, M. G. & Coates, M. I. (2007). A new timescale for ray-finned fish evolution. Proceedings of the Royal Society B 274, 489-498.
87. Inoue, J. G., Miya, M., Tsukamoto, K. & Nishida, M. (2001). A mitogenomic perspective on the basal teleostean phylogeny: resolving higher-level relationships with longer DNA sequences. Molecular Phylogenetics and Evolution 20, 275-285.
88. Inoue, J. G., Miya, M., Tsukamoto, K. & Nishida, M. (2003). Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of "ancient fish". Molecular Phylogenetics and Evolution 26, 110-120.
89. Inoue, J. G., Miya, M., Venkatesh, B. & Nishida, M. (2005). The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between two coelacanths. Gene 349, 227-335.
90. Inoue, J. G., Kumazawa, Y., Masaki, M. & Nishida, M. (2009). The historical biogeography of the freshwater knifefishes using mitogenomic approaches: a Mesozoic origin of the Asian notopterids (Actinopterygii: Osteoglossomorpha). Molecular Phylogenetics and Evolution 51, 486-499.
91. Inoue, J. G., Donoghue, P. C. J. & Yang, Z. (2010). Impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Systematic Biology 59, 74-89.
92. Janvier, P. (1996). Early Vertebrates. Clarendon, Oxford.
93. Jessen, H. L. (1973). Interrelationships of actinopterygians and branchiopterygians: evidence from pectoral anatomy. In Interrelationships of Fishes (eds P. H. Greenwood, R. S. Miles and C. Patterson ), p. 227. Academic Press, New York.
94. Kikugawa, K., Katoh, S., Kuraku, S., Sakurai, H., Ishida, O., Iwabe, N. & Miyata, T. (2004). Basal jawed vertebrate phylogeny inferred from multiple nuclear DNA-coded genes. BMC Biology 2, 3 (doi:10.1186/1741-7007-2-3).
95. Korn, D. & Klug, C. (2012). Palaeozoic ammonoids - diversity and development of conch morphology. In Earth and Life (ed. J. A. Talent ), p. 491. Springer, Heidelberg.
96. Kornfield, I. & Smith, P. F. (2000). African cichlid fishes: model systems for evolutionary biology. Annual Reviews of Ecology and Systematics 31, 163-196.
97. Lamsdell, J. C. & Braddy, S. J. (2010). Cope's rule and Romer's theory: patterns of diversity and gigantism in eurypterids and Palaeozoic vertebrates. Biology Letters 6, 265-269.
98. Langler, K. F., Bardach, J. E. & Miller, R. F. (1962). Ichthyology. University of Michigan, Ann Arbor.
99. Lauder, G. V. (1982). Patterns of evolution in the feeding mechanism of actinopterygian fishes. American Zoologist 22, 275-285.
100. Lauder, G. V. & Liem, K. F. (1983). The evolution and interrelationships of actinopterygian fishes. Bulletin of the Museum of Comparative Zoology 150, 95-197.
101. Lecointre, G., Philippe, H., Le, H. L. V. & Le Guyader, H. (1994). How many nucleotides are required to resolve a genetic problem? The use of a new statistical method applicable to available sequences. Molecular Phylogenetics and Evolution 3, 292-309.
102. Lerosey-Aubril, R. & Feist, R. (2012). Quantitative approach to diversity and decline in Late Palaeozoic trilobites. In Earth and Life (ed. J. A. Talent ), p. 535. Springer, Heidelberg.
103. Li, C., Lu, G. & Orti, G. (2008). Optimal data partitioning and a test case for ray-finned fishes (Actinopterygii) based on ten nuclear loci. Systematic Biology 57, 519-539.
104. Linnaeus, C. (1758). Systema naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis (in Latin) (10th ed.). Laurentius Salvius, Stockholm.
105. Long, J. A. (1988). New palaeoniscoid fishes from the Late Devonian and Early Carboniferous of Victoria. Memoirs of the Association of Australasian Palaeontologists 7, 1-64.
106. Long, J. A. (1995). The Rise of Fishes: 500 Million Years of Evolution. Johns Hopkins University, Baltimore.
107. Long, J. A. (2011). The Rise of Fishes: 500 Million Years of Evolution. Second Edition. Johns Hopkins University, Baltimore.
108. Long, J. A., Choo, B. & Young, G. C. (2008). A new basal actinopterygian fish from the Middle Devonian Aztec Siltstone of Antarctica. Antarctic Science 20, 1-20.
109. Lopez-Arbarello, A. (2012). Phylogenetic interrelationships of ginglymodian fishes (Actinopterygii: Neopterygii). PLoS One 7, e39370.
110. Lund, R. (2000). The new actinopterygian order Guildayichthyiformes from the Lower Carboniferous of Montana. Geodiversitas 22, 171-206.
111. Lund, R. & Poplin, C. (2002). Cladistic analysis of the relationships of the tarrasiids (Lower Carboniferous actinopterygians). Journal of Vertebrate Paleontology 22, 480-486.
112. Maisey, J. G. (1996). Discovering Fossil Fishes. Henry Holt, New York.
113. Mallatt, J. & Winchell, C. J. (2007). Ribosomal RNA genes and deuterostome phylogeny revisited: more cyclostomes, elasmobranchs, reptiles, and a brittle star. Molecular Phylogenetics and Evolution 43, 1005-1022.
114. Markey, M. J. & Marshall, C. (2007). Linking form and function of the fibrous joints in the skull: a new quantification scheme for cranial sutures using the extant fish Polypterus endlicherii. Journal of Morphology 268, 89-102.
115. Marss, T. (2001). Andreolepis (Actinopterygii) in the Upper Silurian of northern Eurasia. Proceedings of the Estonian Academy of Sciences and Geology 50, 174-189.
116. McGhee, G. R. (1996). The Late Devonian Mass Extinction: The Frasnian/Famennian Crisis. Columbia University, New York.
117. Meyer, A. & Zardoya, R. (2003). Recent advances in the (molecular) phylogeny of vertebrates. Annual Review of Ecology, Evolution and Systematics 34, 311-338.
118. Mickle, K. E. (2011). The early actinopterygian fauna of the Manning Canyon Shale Formation (upper Mississippian, lower Pennsylvanian) of Utah, USA. Journal of Vertebrate Paleontology 31, 962-980.
119. Mickle, K. E. & Bader, K. (2009). A new platysomid from the Upper Carboniferous of Kansas (USA) and remarks on the systematics of deep-bodied lower actinoperygians. Acta Zoologica 90, 211-219.
120. Mickle, K. E., Lund, R. & Grogan, E. D. (2009). Three new palaeoniscoid fishes from the Bear Gulch Limestone (Serpukhovian, Mississippian) of Montana (USA) and the relationships of lower actinopterygians. Geodiversitas 31, 623-668.
121. Moy-Thomas, J. A. & Bradley Dyne, M. (1938). Actinopterygian fishes from the Lower Carboniferous of Glencartholm, Eskdale, Dumfriesshire. Transactions of the Royal Society of Edinburgh 59, 437-480.
122. Moy-Thomas, J. A. & Miles, R. S. (1971). Palaeozoic Fishes. Chapman and Hall, London.
123. Müller, J. (1844). Über den Bau and die Grenzen der Ganoiden und über das natürliche System der Fische. Physikalisch-Mathematische Abhandlungen der Koniglichen Akademie dei Wissenschaften zu Berlin 1845, 117-216.
124. Müller, J. (1846). Über den Bau und die Grenzen der Ganoiden und über das natürliche System der Fische. Abhandlungen der Deutschen Akademie der Wissenschaften zu Berlin 1844, 119-216.
125. Near, T. & Miya, M. (2009). Ray-finned fishes (Actinopterygii). In The Timetree of Life (eds S. B. Hedges and S. Kumar ), p. 328. Oxford University, Oxford.
126. Near, T. J., Eytan, R. I., Dornberg, A., Kuhn, K. L., Moore, J. A., Davis, M. P., Wainwright, P. C., Friedman, M. & Smith, W. L. (2012). Resolution of ray-finned fish phylogeny and timing of diversification. Proceedings of the National Academy of Sciences of the United States of America 109, 13698-13703.
127. Near, T. J., Eytan, R. I., Keck, B. P., Smith, W. L., Kuhn, K. L., Moore, J. A., Price, S. A., Burbrink, F. T., Friedman, M. & Wainwright, P. C. (2013). Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes. Proceedings of the National Academy of Sciences of the United States of America 110, 12738-12743.
128. Nelson, G. J. (1969a). Gill arches and the phylogeny of fishes: with notes on the classification of vertebrates. Bulletin of the American Museum of Natural History 141, 475-552.
129. Nelson, G. J. (1969b). Origin and diversification of teleostean fishes. Annals of the New York Academy of Sciences 167, 18-30.
130. Nelson, J. S. (1994). Fishes of the World. John Wiley, New York.
131. Nelson, J. S. (2006). Fishes of the World. John Wiley, New York.
132. Nielsen, E. (1942). Studies on Triassic fishes from East Greenland I. Glaucolepis and Boreosomus. Meddelelser om Gronland 138, 1-403.
133. Noack, K., Zardoya, R. & Meyer, A. (1996). The complete mitochondrial DNA sequence of the bichir (Polypterus ornatipinnis), a basal ray-finned fish: ancient establishment of the consensus vertebrate gene order. Genetics 144, 1165-1180.
134. Normark, B. B., McCune, A. R. & Harrison, R. G. (1991). Phylogenetic relationships of neopterygian fishes, inferred from mitochondrial DNA sequences. Molecular Biology and Evolution 8, 819-834.
135. Olsen, P. E. (1984). The skull and pectoral girdle of the parasemionotid fish Watsonulus eugnathoides from the early Triassic Sakamena Group of Madagascar, with comments on the relationships of the holostean fishes. Journal of Vertebrate Paleontology 4, 481-499.
136. Olsen, P. E. & McCune, A. R. (1991). Morphology of the Semionotus elegans species group from the Early Jurassic part of the Newark Supergroup of Eastern North America with comments on the family Semiotidae (Neopterygii). Journal of Vertebrate Paleontology 11, 269-292.
137. Patterson, C. (1973). Interrelationships of holosteans. In Interrelationships of Fishes (eds P. H. Greenwood, R. S. Miles and C. Patterson ), p. 233. Academic Press, New York.
138. Patterson, C. (1977). The contribution of paleontology to teleostean phylogeny. In Major Patterns in Vertebrate Evolution (eds M. K. Hecht, P. C. Goody and B. M. Hecht ), p. 579. Plenum, New York.
139. Patterson, C. (1982). Morphology and interrelationships of primitive actinopterygian fishes. American Zoologist 22, 241-295.
140. Patterson, C. (1993). Osteichthyes: Teleostei. In The Fossil Record 2 (ed. M. J. Benton ), p. 621. Chapman and Hall, London.
141. Pearson, D. M. (1982). Primitive bony fishes, with special reference to Cheirolepis and paleonisciform actinopterygians. Zoological Journal of the Linnean Society 74, 35-67.
142. Pearson, D. M. & Westoll, T. S. (1979). The Devonian actinopterygian Cheirolepis trailli Agassiz. Transactions of the Royal Society of Edinburgh 70, 337-399.
143. Poplin, C. & Lund, R. (2000). Two new deep-bodied palaeoniscoid actinopterygians from Bear Gulch (Montana, USA, Lower Carboniferous). Journal of Vertebrate Paleontology 20, 428-449.
144. Poplin, C. & Lund, R. (2002). Two Carboniferous fine-eyed palaeoniscoids (Pisces, Actinopterygii) from Bear Gulch (USA). Journal of Palaeontology 76, 1014-1028.
145. Rabosky, D. L., Santini, F., Eastman, J., Smith, S. A., Sidlauskas, B., Chang, J. & Alfaro, M. E. (2013). Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nature Communications 4, 1958.
146. Racki, G. (2005). Toward understanding Late Devonian global events: few answers, many questions. In Understanding Late Devonian and Permian-Triassic Biotic and Climatic Events: Towards an Integrated Approach (eds D. J. Over, J. R. Morrow and P. B. Wignall ), p. 5. Elsevier, Amsterdam.
147. Raincrow, J. D., Dewar, K., Stocsits, C., Prohaska, S. J., Amemiya, C. T., Stadler, P. F. & Chiu, C.-H. (2011). Hox clusters of the bichir (Actinopterygii, Polypterus senegalus) highlight unique patterns of sequence evolution in gnathostome phylogeny. Journal of Experimental Zoology (Molecular and Developmental Biology) 316, 451-464.
148. Rasmussen, A.-S. & Arnason, U. (1999). Phylogenetic studies of complete mitochondrial DNA molecules place cartilaginous fishes with the tree of bony fishes. Journal of Molecular Evolution 48, 118-123.
149. Rasmussen, A.-S., Janke, A. & Arnason, U. (1998). The mitochondrial DNA molecule of the hagfish (Myxine glutinosa) and vertebrate phylogeny. Journal of Molecular Evolution 46, 382-388.
150. Rocco, L., Costagliola, D., Morescalchi, M. A. & Stingo, V. (2004). A molecular approach to the systematics of Polypteriformes among Osteichthyes. Italian Journal of Zoology 71, 347-351.
151. Romer, A. S. (1945). Vertebrate Paleontology, Second Edition. University of Chicago Press, Chicago.
152. Saitoh, K., Sado, T., Doosey, M. H., Bart, H. L., Inoue, J. G., Nishida, M., Mayden, R. L. & Miya, M. (2011). Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi). Zoological Journal of the Linnean Society 161, 633-662.
153. Sallan, L. C. (2012). Tetrapod-like axial regionalization in an early ray-finned fish. Proceedings of the Royal Society B 279, 3264-3271.
154. Sallan, L. C. & Coates, M. I. (2010). End-Devonian extinction and a bottleneck in the early evolution of modern jawed vertebrates. Proceedings of the National Academy of Sciences of the United States of America 107, 10131-10135.
155. Sallan, L. C. & Coates, M. I. (2013). Styracopterid (Actinopterygii) ontogeny and the multiple origins of post-Hangenberg deep-bodied fishes. Zoological Journal of the Linnean Society 169, 156-199.
156. Sallan, L. C. & Friedman, M. (2012). Heads or tails: staged diversification in vertebrate evolutionary radiations. Proceedings of the Royal Society B 279, 2025-2032.
157. Sallan, L. C., Kammer, T. W., Ausich, W. I. & Cook, L. A. (2011). Persistent predator-prey dynamics revealed by mass extinction. Proceedings of the National academy of Sciences of the United States of America 108, 8335-8338.
158. Santini, F., Harmon, L. J., Carnevale, G. & Alfaro, M. E. (2009). Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes. BMC Evolutionary Biology 9, 194.
159. Schaeffer, B. (1955). Evolution in subholostean fishes. Evolution 10, 201-212.
160. Schaeffer, B. (1973). Interrelationships of chondrosteans. In Interrelationships of Fishes (eds P. H. Greenwood, R. S. Miles and C. Patterson ), p. 207. Academic Press, New York.
161. Schaeffer, B. & Rosen, D. E. (1961). Major adaptive levels in the evolution of the actinopterygian feeding mechanism. American Zoologist 1, 187-204.
162. Schultze, H.-P. (1968). Palaeoniscoidea-Schuppen aus dem Unterdevon Australiens und Kanadas und aus dem Mitteldevon Spitzbergens. Bulletin of the British Museum (Natural History): Geology 16, 342-368.
163. Schultze, H. P. & Cumbaa, S. L. (2001). Dialipina and the characters of basal actinopterygians. In Major Events in Early Vertebrate Evolution: Palaeontology, Phylogeny, Genetics and Development (ed. P. E. Ahlberg ), p. 316. Taylor & Francis, London.
164. Sepkoski, J. J. (2002). A compendium of fossil marine animal genera. Bulletin of American Paleontology 363, 1-560.
165. Setiamarga, D. H. E., Miya, M., Inoue, J. G., Ishiguro, N. B., Mabuchi, K. & Nishida, M. (2009). Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates. Biology Letters 5, 812-816.
166. Shima, A. & Mitani, H. (2004). Medaka as a research organism: past, present and future. Mechanisms of Development 121, 599-604.
167. Smith, J. L. B. (1939). The living coelacanthid fish from South Africa. Nature 143, 748-750.
168. Stanley, S. M. (2007). An analysis of the history of marine animal diversity. Paleobiology 33, 1-55.
169. Stanley, S. M. (2008). Predation beats competition on the seafloor. Paleobiology 34, 1-21.
170. Steinke, D., Salzburger, W. & Meyer, A. (2006). Novel relationships among ten fish model species revealed based on phylogenomic analysis using ESTs. Journal of Molecular Evolution 62, 772-784.
171. Streelman, J. T. & Danley, P. D. (2003). The stages of vertebrate evolutionary radiation. Trends in Ecology & Evolution 18, 126-131.
172. Stuart, G. W., Moffett, K. & Leader, J. J. (2002). A comprehensive vertebrate phylogeny using vector representations of protein sequences from whole genomes. Molecular Biology and Evolution 19, 554-562.
173. Suzuki, D., Brandley, M. C. & Tokita, M. (2010). The mitochondrial phylogeny of an ancient lineage of ray-finned fishes (Polypteridae) with implications for the evolution of body elongation, pelvic fin loss, and craniofacial morphology in Osteichthyes. BMC Evolutionary Biology 10, 21.
174. Swartz, B. A. (2009). Devonian actinopterygian phylogeny and evolution based on a redescription of Stegotrachelus finlayi. Zoological Journal of the Linnean Society 56, 750-784.
175. Taverne, L. H. (1996). Osteologie et position systematique des Tarrasiiformes, Actinopterygiens (Pisces) du Carbonifere de l'Ecosse et des Etats-Unis. Biologisch Jaarboek Dodonea 64, 138-159.
176. Taverne, L. H. (1997). Osorioichthyes marginis, 'Paleonisciform' du famennien de Belgique, et la phylogenie de Actinopterygiens devonians (Pisces). Bulletin de l'Institute Royal es Sciences Naturelles des Belgique, Sciences de la Terre 67, 57-78.
177. Taylor, J. S., Van de Peer, Y., Braasch, I. & Meyer, A. (2001). Comparative genomics provides evidence for an ancient genome duplication event in fish. Philosophical Transactions of the Royal Society of London, Series B 356, 1661-1679.
178. Traquair, R. H. (1877-1914). The Ganoid Fishes of the British Carboniferous Formations, Palaeontographical Society Monograph, 1877-1914., Palaeontographical Society, London.
179. Traquair, R. H. (1879). On the structure and affinities of the Platysomidae. Transactions of the Royal Society of Edinburgh 29, 314-391.
180. Traquair, R. H. (1881). Report on the fossil fishes collected by the Geological Survey of Scotland in Eskdale and Liddesdale. Part 1. Ganoidei. Transactions of the Royal Society of Edinburgh 30, 15-71.
181. Traquair, R. H. (1887). Notes on Chondrosteus acipenseroides. Geological Magazine 4, 248-257.
182. Venkatesh, B., Erdmann, M. V. & Brenner, S. (2001). Molecular synapomorphies resolve evolutionary relationships of extant jawed vertebrates. Proceedings of the National Academy of Sciences of the United States of America 98, 11382-11387.
183. Vermeij, G. J. (1977). The Mesozoic marine revolution: evidence from snails, predators, and grazers. Paleobiology 3, 245-258.
184. Walbaum, J. J. (ed.) (1792). Petri Artedi sueci genera piscium in quibus systema totum ichthyologiae proponitur cum classibus, ordinibus, generum characteribus, specierum differentiis, observationibus plurimis: redactis speciebus 242 ad genera 52: Ichthyologiae pars 3. Ant. Ferdin. Röse: Grypeswaldiae. 3 plates, pp. 723.
185. Wang, N. Z. & Dong, Z. Z. (1989). Discovery of Late Silurian microfossils of Agnatha and fishes from Yunnan, China. Acta Palaeontologica Sinica 28, 192-206.
186. Ward, A. B. & Brainerd, E. L. (2007). Evolution of axial patterning in elongate fishes. Biological Journal of the Linnean Society 90, 97-116.
187. Watson, D. M. S. (1925). The structure of certain palaeonicids and the relationships of that group with other bony fishes. Proceedings of the Zoological Society of London 54, 815-870.
188. Watson, D. M. S. (1928). On some points of the structure of palaeoniscid and allied fishes. Proceedings of the Zoological Society of London 1928, 49-70.
189. Webb, P. W. (1982). The evolution of locomotor patterns in the evolution of actinopterygian fishes. American Zoologist 22, 329-342.
190. Westneat, M. W. (2004). The evolution of levers and linkages in the feeding mechanisms of fishes. Integrative and Comparative Biology 44, 378-389.
191. White, E. I. (1927). The fish-fauna of the Cementstones of Foulden, Berwickshire. Transactions of the Royal Society of Edinburgh 55, 255-287.
192. White, E. I. (1939). A new kind of paleoniscid fish: with remarks on the evolution of the actinopterygian pectoral fin. Proceedings of the Zoological Society of London, B 109, 41-61.
193. Wiley, E. O., Chakrabarty, P., Craig, M. T., Davis, M. P., Holcroft, N. I., Mayden, R. L. & Smith, W. L. (2011). Will the real phylogeneticists please stand up? Zootaxa 2947, 7-16.
194. Willughby, F. & Ray, J. (1686). De Historia Piscium. Oxford University, Oxford.
195. Wilson, G. P., Evans, A. R., Corfe, I. J., Smits, P. D., Fortelius, M. & Jernvall, J. (2012). Adaptive radiation of multituberculate mammals before the extinction of dinosaurs. Nature 483, 457-460.
196. Wright, J. J., David, S. R. & Near, T. J. (2012). Gene trees, species trees, and morphology converge on a similar phylogeny of living gars (Actinopterygii: Holostei: Lepisosteidae), an ancient clade of ray-finned fishes. Molecular Phylogenetics and Evolution 63, 848-856.
197. Xu, G.-H. & Gao, K.-Q. (2011). A new scanilepiform from the Lower Triassic of northern Gansu Province, China, and the phylogenetic relationships of non-teleostean Actinopterygii. Zoological Journal of the Linnean Society 161, 595-612.
198. Xu, G.-H. & Wu, F.-X. (2011). A deep-bodied ginglymodian fish from the Middle Triassic of eastern Yunnan Province, China and the phylogeny of lower neopterygians. Chinese Science Bulletin 56, 1-8.
199. Yamanoue, Y., Miya, M., Inoue, J. G., Matsuura, K. & Nishida, M. (2006). The mitochondrial genomes of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetrapodontiformes) and divergence time estimation among model organisms in fishes. Gene and Genetic Systems 81, 29-39.
200. Yu, Z., Zhou, L.-Q., Anh, V. V., Chu, K. H. & Li, C. P. (2007). Distance-based analysis to reveal vertebrate phylogeny without sequence alignment using complete mitochondrial genomes. In Proceedings of the 11th World Multi-Conference on Systemics, Cybernetics and Informatics: WMSCI 2007, pp. 206-211. Orlando, Florida.
201. Zardoya, R. & Meyer, A. (2001). Vertebrate phylogeny: limits of inference of mitochondrial genome and nuclear rDNA sequence data due to an adverse phylogenetic signal/noise ratio. In Major Events in Early Vertebrate Evolution: Paleontology, Phylogeny, Genetics, and Development (ed. P. E. Ahlberg ), p. 106. Taylor & Francis, London.
202. Zhao, G. Z., Gui, L., Li, Z. Q., Yuan, X. P. & Zhang, Q. Y. (2008). Establishment of a Chinese sturgeon Acipenser sinensis tail-fin cell line and its susceptibility to frog iridovirus. Journal of Fish Biology 73, 2058-2067.
203. Zhu, M., Yu, X. & Janvier, P. (1999). A primitive fossil fish sheds light on the origin of bony fishes. Nature 397, 607-610.
204. Zhu, M., Zhao, W., Jia, L., Lu, J., Qiao, T. & Qu, Q. (2009). The oldest articulated osteichthyan reveals mosaic gnathostome characters. Nature 458, 469-474.