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Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation

Nakatani, Masanori, Miya, Masaki, Mabuchi, Kohji, Saitoh, Kenji, Nishida, Mutsumi·2011·BMC Evolutionary Biology
DOI 10.1186/1471-2148-11-177PMC PMC3141434
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Abstract

Background: Freshwater harbors approximately 12,000 fish species accounting for 43% of the diversity of all modern fish. A single ancestral lineage evolved into about two-thirds of this enormous biodiversity (≈ 7900 spp.) and is currently distributed throughout the world's continents except Antarctica. Despite such remarkable species diversity and ubiquity, the evolutionary history of this major freshwater fish clade, Otophysi, remains largely unexplored. To gain insight into the history of otophysan diversification, we constructed a timetree based on whole mitogenome sequences across 110 species representing 55 of the 64 families. Results: Partitioned maximum likelihood analysis based on unambiguously aligned sequences (9923 bp) confidently recovered the monophyly of Otophysi and the two constituent subgroups (Cypriniformes and Characiphysi). The latter clade comprised three orders (Gymnotiformes, Characiformes, Siluriformes), and Gymnotiformes was sister to the latter two groups. One of the two suborders in Characiformes (Characoidei) was more closely related to Siluriformes than to its own suborder (Citharinoidei), rendering the characiforms paraphyletic. Although this novel relationship did not receive strong statistical support, it was supported by analyzing independent nuclear markers. A relaxed molecular clock Bayesian analysis of the divergence times and reconstruction of ancestral habitats on the timetree suggest a Pangaean origin and Mesozoic radiation of otophysans. Conclusions: The present timetree demonstrates that survival of the ancestral lineages through the two consecutive mass extinctions on Pangaea, and subsequent radiations during the Jurassic through early Cretaceous shaped the modern familial diversity of otophysans. This evolutionary scenario is consistent with recent arguments based on biogeographic inferences and molecular divergence time estimates. No fossil otophysan, however, has been recorded before the Albian, the early Cretaceous 100-112 Ma, creating an over 100 million year time span without fossil evidence. This formidable ghost range partially reflects a genuine difference between the estimated ages of stem group origin (molecular divergence time) and crown group morphological diversification (fossil divergence time); the ghost range, however, would be filled with discoveries of older fossils that can be used as more reasonable time constraints as well as with developments of more realistic models that capture the rates of molecular sequences accurately.

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  • Although molecular phylogenetic studies have demonstrated frequent discordance between molecular data and morphological expectations, the monophyly of Siluriphysi has generally been maintained in traditional interpretations from early single-locus analyses to recent multiple genomic-scale loci, primarily to conform to morphological predictions.

    “Although numerous molecular phylogenetic studies have demonstrated frequent discordance between molecular data and morphological expectations, the monophyly of Siluriphysi has generally been maintained in traditional interpretations, from early single-locus analyses48 to recent multiple genomic-scale loci,49,50,51,52,53,54,55,56 primarily to conform to morphological predictions.”

    From A genomic compendium of hundreds of teleost fishes reveals their evolutionary landscape (2026) · cites this paper as [53]

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Research works printed but not linked: 124

  1. Dudgeon D, Arthington AH, Gessner MO, Kawabata ZI, Knowler DJ, Lévéque C, Naiman RJ, Prieur-Richard AH, Soto D, Stiassny MLJ: Freshwater biodiversity: importance, threats, status and conservation challenges. Biol Rev. 2005, 81 (02): 163-182. · DOI · Paper page
  2. Schindler DE: Fish extinctions and ecosystem functioning in tropical ecosystems. Proc Natl Acad Sci USA. 2007, 104 (14): 5707-5708. 10.1073/pnas.0700426104. · DOI
  3. Nelson JS: Fishes of the world. 2006, Hoboken, NJ: John Wiley & Sons, 4
  4. Saitoh K, Miya M, Inoue JG, Ishiguro NB, Nishida M: Mitochondrial genomics of ostariophysan fishes: Perspectives on phylogeny and biogeography. J Mol Evol. 2003, 56 (4): 464-472. 10.1007/s00239-002-2417-y. · DOI
  5. Poulsen JY, Møller PDR, Lavoué S, Knudsen SW, Nishida M, Miya M: Higher and lower-level relationships of the deep-sea fish order Alepocephaliformes (Teleostei: Otocephala) inferred from whole mitogenome sequences. Biol J Linn Soc. 2009, 98 (4): 923-936. 10.1111/j.1095-8312.2009.01323.x. · DOI
  6. Lavoué S, Miya M, Inoue JG, Saitoh K, Ishiguro NB, Nishida M: Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: Implications for higher-level relationships within the Otocephala. Mol Phylogenet Evol. 2005, 37 (1): 165-177. 10.1016/j.ympev.2005.03.024. · DOI
  7. Lavoué S, Miya M, Poulsen JY, Møller PR, Nishida M: Monophyly, phylogenetic position and inter-familial relationships of the Alepocephaliformes (Teleostei) based on whole mitogenome sequences. Mol Phylogenet Evol. 2008, 47 (3): 1111-1121. 10.1016/j.ympev.2007.12.002. · DOI
  8. Lecointre G: Gonorynchiformes in the teleostean phylogeny: molecules and morphology used to investigate interrelationships of the Ostariophysi. Gonorynchiformes and ostariophysan relationships: a comprehensive review. Edited by: Grande T, Poyato-Ariza FJ, Diogo R. 2010, Enfield, NH: Science Publishers
  9. Miya M, Satoh TP, Nishida M: The phylogenetic position of toadfishes (order Batrachoidiformes) in the higher ray-finned fish as inferred from partitioned Bayesian analysis of 102 whole mitochondrial genome sequences. Biol J Linn Soc. 2005, 85 (3): 289-306. 10.1111/j.1095-8312.2005.00483.x. · DOI
  10. Miya M, Takeshima H, Endo H, Ishiguro NB, Inoue JG, Mukai T, Satoh TP, Yamaguchi M, Kawaguchi A, Mabuchi K, et al: Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol Phylogenet Evol. 2003, 26 (1): 121-138. 10.1016/S1055-7903(02)00332-9. · DOI
  11. Saitoh K, Sado T, Mayden RL, Hanzawa N, Nakamura K, Nishida M, Miya M: Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): The first evidence toward resolution of higher-level relationships of the World's largest freshwater fish clade based on 59 whole mitogenome sequences. J Mol Evol. 2006, 63 (6): 826-841. 10.1007/s00239-005-0293-y. · DOI
  12. Saitoh K, Sado T, Doosey MH, Bart HLJ, Inoue JG, Nishida M, Mayden RL, Nishida M, Miya M: Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi). Zool J Linn Soc. 2011, 161: 633-662. 10.1111/j.1096-3642.2010.00651.x. · DOI
  13. Mayden RL, Tang KL, Wood RM, Chen W-J, Agnew MK, Conway KW, Yang L, Simons AM, Bart HL, Harris PM, et al: Inferring the Tree of Life of the order Cypriniformes, the earth's most diverse clade of freshwater fishes: implications of varied taxon and character sampling. J Systemat Evol. 2008, 46 (3): 424-438.
  14. Chen WJ, Miya M, Saitoh K, Mayden RL: Phylogenetic utility of two existing and four novel nuclear gene loci in reconstructing Tree of Life of ray-finned fishes: The order Cypriniformes (Ostariophysi) as a case study. Gene. 2008, 423 (2): 125-134. 10.1016/j.gene.2008.07.016. · DOI
  15. He S, Gu X, Mayden RL, Chen W-J, Conway KW, Chen Y: Phylogenetic position of the enigmatic genus Psilorhynchus (Ostariophysi: Cypriniformes): Evidence from the mitochondrial genome. Mol Phylogenet Evol. 2008, 47 (1): 419-425. 10.1016/j.ympev.2007.10.012. · DOI
  16. Mayden RL, Chen WJ, Bart HL, Doosey MH, Simons AM, Tang KL, Wood RM, Agnew MK, Yang L, Hirt MV, et al: Reconstructing the phylogenetic relationships of the earth's most diverse clade of freshwater fishes --order Cypriniformes (Actinopterygii: Ostariophysi): A case study using multiple nuclear loci and the mitochondrial genome. Mol Phylogenet Evol. 2009, 51 (3): 500-514. 10.1016/j.ympev.2008.12.015. · DOI
  17. Mayden RL, Chen WJ: The world's smallest vertebrate species of the Genus Paedocypris: A new family of freshwater fishes and the sister group to the world's most diverse clade of freshwater fishes (Teleostei: Cypriniformes). Mol Phylogenet Evol. 2010, 57 (1): 152-175. 10.1016/j.ympev.2010.04.008. · DOI
  18. Chen W-J, Mayden RL: Molecular systematics of the Cyprinoidea (Teleostei: Cypriniformes), the World's largest clade of freshwater fishes: further evidence from six nuclear genes. Mol Phylogenet Evol. 2009, 52: 544-549. 10.1016/j.ympev.2009.01.006. · DOI
  19. Ortí G, Meyer A: The radiation of characiform fishes and the limits of resolution of mitochondrial ribosomal DNA sequences. Syst Biol. 1997, 46 (1): 75-100. 10.1093/sysbio/46.1.75. · DOI
  20. Calcagnotto D, Schaefer SA, Desalle R: Relationships among characiform fishes inferred from analysis of nuclear and mitochondrial gene sequences. Mol Phylogenet Evol. 2005, 36 (1): 135-153. 10.1016/j.ympev.2005.01.004. · DOI
  21. Sullivan J, Lundberg J, Hardman M: A phylogenetic analysis of the major groups of catfishes (Teleostei: Siluriformes) using rag1 and rag2 nuclear gene sequences. Mol Phylogenet Evol. 2006, 41 (3): 636-662. 10.1016/j.ympev.2006.05.044. · DOI
  22. Hardman M: The phylogenetic relationships among non-diplomystid catfishes as inferred from mitochondrial cytochrome b sequences; the search for the ictalurid sister taxon (Otophysi: Siluriformes). Mol Phylogenet Evol. 2005, 37 (3): 700-720. 10.1016/j.ympev.2005.04.029. · DOI
  23. Alves-Gomes JA, Orti G, Haygood M, Heiligenberg W, Meyer A: Phylogenetic analysis of the South American electric fishes (order Gymnotiformes) and the evolution of their electrogenic system: a synthesis based on morphology, electrophysiology, and mitochondrial sequence data. Mol Biol Evol. 1995, 12: 298-318.
  24. Alves-Gomes JA: The mitochondrial phylogeny of the South American electric fish (Gymnotiformes) and an alternative hypothesis for the otophysan historical biogeography. Gonorynchiformes and ostriophysan relationships: A comprehensive review. Edited by: Grande T, Poyato-Ariza FJ, Diogo R. 2010, Enfield, NH: Science Publishers, 517-565. · DOI
  25. Hennig W: Phylogenetic systematics. 1996, Urbana, IL: University of Illinois Press
  26. Wiley EO: Phylogenetics: the theory and practice of phylogenetic systematics. 1981, New York: Wiley & Sons
  27. Fink SV, Fink WL: Interrelationships of the ostariophysan fishes (Teleostei). Zool J Linn Soc. 1981, 72 (4): 297-353. 10.1111/j.1096-3642.1981.tb01575.x. · DOI · Paper page
  28. Dimmick WW, Larson A: A molecular and morphological perspective on the phylogenetic relationships of the otophysan fishes. Mol Phylogenet Evol. 1996, 6 (1): 120-133. 10.1006/mpev.1996.0064. · DOI
  29. Ortí G, Meyer A: Molecular evolution of ependymin and the phylogenetic resolution of early divergences among euteleost fishes. Mol Biol Evol. 1996, 13 (4): 556-573. · DOI · Paper page
  30. Peng Z, He S, Wang J, Wang W, Diogo R: Mitochondrial molecular clocks and the origin of the major otocephalan clades (Pisces: Teleostei): a new insight. Gene. 2006, 370: 113-124. · DOI
  31. Li C, Lu G, Orti G: Optimal data partitioning and a test case for ray-finned fishes (Actinopterygii) based on ten nuclear loci. Syst Biol. 2008, 57 (4): 519-539. 10.1080/10635150802206883. · DOI
  32. Novacek MJ, Marshall LG: Early biogeographic history of ostariophysan fishes. Copeia. 1976, 1976 (1): 1-12. 10.2307/1443767. · DOI
  33. Briggs JC: The biogeography of otophysan fishes (Ostariophysi: Otophysi): a new appraisal. J Biogeogr. 2005, 32 (2): 287-294. 10.1111/j.1365-2699.2004.01170.x. · DOI
  34. Briggs JC: Ostariophysan zoogeography: an alternative hypothesis. Copeia. 1979, 1979: 111-118. 10.2307/1443735. · DOI
  35. Gayet M: Consideration sur la phylogenie et la paleobiographie des Ostariophysaries. Geobios. 1982, 6: 39-52. · DOI
  36. Banarescu P: Zoogeography of fresh waters. 1990, Wiesbaden, Germany: AULA-Verlag, 1:
  37. Lundberg JG: African-South American freshwater clades and continental drift: problems with a paradigm. Biological relationships between Africa and South America. Edited by: Goldblatt P. 1993, New Haven: Yale University Press, 156-199. · DOI
  38. Fara E, Gayet M, Taverne L: The Fossil record of Gonorynchiformes. Gonorynchiformes and ostariophysan relationships: A comprehensive review. Edited by: Grande T, Poyato-Ariza FJ, Diogo R. 2010, Enfield, NH: Science Publishers, 173-226. · DOI
  39. Malabarba MC, Malabarba LR: Biogeography of Characiformes: an evaluation of the available information of fossil and extant taxa. Origin and Phylogenetic Interrelationships of Teleosts. Edited by: Nelson JS, Schultze H-P, Wilson MVH. 2010, München: Verlag Dr. Friedrich Pfeil
  40. Conway KW, Hirt MV, Yang L, Mayden RL, Simons AM: Cypriniformes: systematics and paleontology. Origin and phylogenetic interrelationships of teleosts. Edited by: Nelson JS, Schultze H-P, Wilson MVH. 2010, München: Verlag Dr. Friedrich Pfeil
  41. Diogo R: Phylogeny, origin and biogeography of catfishes: support for a Pangean origin of 'modern teleosts' and reexamination of some Mesozoic Pangean connections between the Gondwanan and Laurasian supercontinents. Anim Biol. 2004, 54 (4): 331-351. 10.1163/1570756042729546. · DOI
  42. Arratia G: Mesozoic halecostomes and the early radiation of teleosts. Mesozoic fishes 3. Edited by: Arratia G, Tintori A. 2004, München, Germany: Verlag Dr. Friedrich Pfeil, 279-315.
  43. Azuma Y, Kumazawa Y, Miya M, Mabuchi K, Nishida M: Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences. BMC Evol Biol. 2008, 8 (1): 215-10.1186/1471-2148-8-215. · DOI
  44. Asahida T, Kobayashi T, Saitoh K, Nakayama I: Tissue preservation and total DNA extraction from fish stored at ambient temperature using buffers containing high concentration of urea. Fish Sci. 1996, 62: 727-730. · DOI
  45. Miya M, Nishida M: Organization of the mitochondrial genome of a deep-sea fish, Gonostoma gracile (Teleostei: Stomiiformes): first example of transfer RNA gene rearrangements in bony fishes. Mar Biotechnol. 1999, 1 (5): 416-426. 10.1007/PL00011798. · DOI
  46. Cheng S, Chang SY, Gravitt P, Respess R: Long PCR. Nature. 1994, 369 (6482): 684-645. 10.1038/369684a0. · DOI
  47. Katoh K, Toh H: Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinformatics. 2008, 9 (4): 286-298. 10.1093/bib/bbn013. · DOI
  48. Maddison WP, Maddison DR: MacClade Version 3. 2000, Sunderland: Sinauer Associates
  49. Miya M, Nishida M: Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion. Mol Phylogenet Evol. 2000, 17 (3): 437-455. 10.1006/mpev.2000.0839. · DOI
  50. Broughton RE: Phylogeny of teleosts based on mitochondrial genome sequences. Origin and phylogenetic interrelationships of teleosts. Edited by: Nelson JS, Shultze H-S, Wilson MVH. 2010, München, Germany: Verlag Dr. Friedrich Pfeil, 61-76.
  51. Brandley MC, Wang Y, Guo X, de Oca ANM, Fería-Ortíz M, Hikida T, Ota H: Accommodating high rates of evolution in molecular dating methods: an example using inter-continental dispersal of Plestiodon (Eumeces) lizards. Syst Biol. 2011, 60 (1): 3-15. 10.1093/sysbio/syq045. · DOI
  52. Posada D, Crandall KA: MODELTEST: testing the model of DNA substitution. Bioinformatics. 1998, 14 (9): 817-818. 10.1093/bioinformatics/14.9.817. · DOI · Paper page
  53. Adachi J, Hasegawa M: Model of amino acid substitution in proteins encoded by mitochondrial DNA. J Mol Evol. 1996, 42 (4): 459-468. 10.1007/BF02498640. · DOI
  54. Shimodaira H, Hasegawa M: CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics. 2001, 17 (12): 1246-1247. 10.1093/bioinformatics/17.12.1246. · DOI
  55. Shimodaira H: An approximately unbiased test of phylogenetic tree selection. Syst Biol. 2002, 51 (3): 492-508. 10.1080/10635150290069913. · DOI · Paper page
  56. Felsenstein J: Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985, 39 (4): 783-791. 10.2307/2408678. · DOI
  57. Kishino H, Hasegawa M: Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J Mol Evol. 1989, 29 (2): 170-179. 10.1007/BF02100115. · DOI
  58. Kawahara R, Miya M, Mabuchi K, Near T, Nishida M: Stickleback phylogenies resolved: Evidence from mitochondrial genomes and 11 nuclear genes. Mol Phylogenet Evol. 2009, 50 (1): 401-404. · DOI
  59. Yang Z: PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007, 24 (8): 1586-1591. 10.1093/molbev/msm088. · DOI · Paper page
  60. Drummond AJ, Rambaut A: BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 2007, 7: 214-10.1186/1471-2148-7-214. · DOI
  61. Zhong B, Yonezawa T, Zhong Y, Hasegawa M: Episodic evolution and adaptation of chloroplast genomes in ancestral grasses. PLoS ONE. 2009, 4 (4): e5297-10.1371/journal.pone.0005297. · DOI
  62. Yang Z, Rannala B: Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Mol Biol Evol. 1997, 14 (7): 717-724. · DOI · Paper page
  63. Setiamarga DHE, Miya M, Inoue JG, Ishiguro NB, Mabuchi K, Nishida M: Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates. Biol Lett. 2009, 5 (5): 81-86.
  64. Yang Z, Rannala B: Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol Biol Evol. 2006, 23 (1): 212-226. · DOI
  65. Page M: The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Syst Biol. 1999, 48 (3): 612-622. 10.1080/106351599260184. · DOI
  66. Schluter D, Price T, Mooers A, Ludwig D: Likelihood of ancestor states in adaptive radiation. Evolution. 1997, 51 (6): 1699-1711. 10.2307/2410994. · DOI
  67. Lewis PO: A likelihood approach to estimating phylogeny from discrete morphological character data. Syst Biol. 2001, 50 (6): 913-925. 10.1080/106351501753462876. · DOI · Paper page
  68. Lartillot N, Philippe H: A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol. 2004, 21 (6): 1095-1109. 10.1093/molbev/msh112. · DOI · Paper page
  69. Lartillot N, Lepage T, Blanquart S: PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics. 2009, 25 (17): 2286-2288. 10.1093/bioinformatics/btp368. · DOI · Paper page
  70. Buckup PA: Relationships of the Characidiinae and phylogeny of characiform fishes (Teleostei: Ostariophysi). Phylogeny and classification of neotropical fishes. Edited by: Malabarba LR, Reis RE, Vari RP, Lucena ZMS, Lucena CAS. 1998, Porto Alegre, Brasil: Edipucrs, 123-144.
  71. Fink SV, Fink WL: Interrelationships of ostariophysan fishes (Teleostei). Interrelationships of fishes. Edited by: Stiassny MLJ, Parenti LR, Johnson GD. 1996, San Diego: Academic Press, 209-249. · DOI
  72. Dahdul WM: Review of the phylogenetic relationships and fossil record of Characiformes. Gonorynchiformes and ostriophysan relationships: A comprehensive review. Edited by: Grande T, Poyato-Ariza FJ, Diogo R. 2010, Enfield, New Hampshire: Science Publishers, 441-464. · DOI
  73. Vari RP: Anatomy, relationships and classification of the families Citharinidae and Distichodontidae (Pisces, Characoidea). Bull Brit Mus (Nat Hist) Zool Ser. 1979, 36: 261-344. · DOI
  74. Ortí G, Petry P, Porto JIR, Jégu M, Meyer A: Patterns of nucleotide change in mitochondrial ribosomal RNA genes and the phylogeny of piranhas. J Mol Evol. 1996, 42 (2): 169-182. 10.1007/BF02198843. · DOI
  75. Grande L: Redescription of Hypsidoris farsonensis (Teleostei: Siluriformes), with a reassessment of its phylogenetic relationships. J Vert Paleontol. 1987, 7: 24-54. 10.1080/02724634.1987.10011636. · DOI
  76. Mo T: Anatomy, relationships and systematics of the Bagridae (Teleostei: Siluroidei) with a hypothesis of siluroid phylogeny. Theses Zoology. 1991, 17: 1-216.
  77. Arratia G: Development and variation of the suspensorium of primitive catfishes (Teleostei: Ostariophysi) and their phylogenetic relationships. Bonn Zool Monogr. 1992, 32: 1-148.
  78. De Pinna MCC: Phylogenetic relationships of Neotropical Siluriformes: History, overview and synthesis of hypotheses. Phylogeny and Classification of Neotropical Fishes. Edited by: Malabarba LR, Reis RE, Vari RP, Lucena ZM, Lucena CAS. 1998, Porto Alegre, Brasil: Edipucrs, 279-330.
  79. He S, Gayet M, Meunier FJ: Phylogeny of the Amphiliidae (Teleostei: Siluriformes). Ann Sci Natur. 1999, 20 (4): 117-146.
  80. Diogo R, Peng Z: State of the art of siluriform higher-level phylogeny. Gonorynchiformes and ostriophysan relationships: A comprehensive review. Edited by: Grande T, Poyato-Ariza FJ, Diogo R. 2010, Enfield, New Hampshire: Science Publishers, 465-515. · DOI
  81. Inoue JG, Miya M, Venkatesh B, Nishida M: The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanths. Gene. 2005, 349: 227-235. · DOI
  82. Yamanoue Y, Miya M, Inoue JG, Matsuura K, Nishida M: The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes. Genes Genet Syst. 2006, 81 (1): 29-39. 10.1266/ggs.81.29. · DOI
  83. Inoue JG, Kumazawa Y, Miya M, Nishida M: The historical biogeography of the freshwater knifefishes using mitogenomic approaches: a Mesozoic origin of the Asian notopterids (Actinopterygii: Osteoglossomorpha). Mol Phylogenet Evol. 2009, 51 (3): 486-499. 10.1016/j.ympev.2009.01.020. · DOI
  84. Arratia G: Basal teleosts and teleostean phylogeny. Palaeo-Ichthyology. 1997, 7: 5-168.
  85. Filleul A, Maisey JG: Redescription of Santanichthys diasii (Otophysi, Characiformes) from the Albian of the Santana Formation and comments on its implications for otophysan relationships. Am Mus Novit. 2004, 3455: 1-21. 10.1206/0003-0082(2004)455<0001:ROSDOC>2.0.CO;2. · DOI
  86. Kumazawa Y, Azuma Y, Nishida M: Tempo of mitochondrial gene evolution: Can mitochondrial DNA be used to date old divergences?. Endocytobiosis Cell Research. 2004, 15: 136-142.
  87. Santini F, Harmon LJ, Carnevale G, Alfaro ME: Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes. BMC Evol Biol. 2009, 9 (1): 194-10.1186/1471-2148-9-194. · DOI
  88. Reisz RR, Müller J: Molecular timescales and the fossil record: a paleontological perspective. Trends Genet. 2004, 20: 237-241. 10.1016/j.tig.2004.03.007. · DOI
  89. Müller J, Reisz RR: Four well-constrained calibration points from the vertebrate fossil record for molecular clock estimates. Bioessays. 2005, 1069-1075. 27 · DOI
  90. Hurley I, Mueller R, Dunn K, Schmidt E, Friedman M, Ho R, Prince V, Yang Z, Thomas M, Coates M: A new time-scale for ray-finned fish evolution. Proc R Soc B. 2007, 274 (1609): 489-498. 10.1098/rspb.2006.3749. · DOI
  91. Phillips MJ: Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny. Gene. 2009, 441 (1-2): 132-140. 10.1016/j.gene.2008.08.017. · DOI
  92. Miya M, Saitoh K, Wood R, Nishida M, Mayden RL: New primers for amplifying and sequencing the mitochondrial ND4/ND5 gene region of the Cypriniformes (Actinopterygii: Ostariophysi). Ichthyol Res. 2006, 53 (1): 75-81. 10.1007/s10228-005-0303-5. · DOI
  93. Buckup PA: The Characidiinae: a phylogenetic study of the South American darters and their relationships with other characiform fishes. Ph.D. thesis. 1991, Ann Harbor: The University of Michigan
  94. Storey BC: The role of mantle plumes in continental breakup: case histories from Gondwanaland. Nature. 1995, 377: 301-308. 10.1038/377301a0. · DOI
  95. Taverne L: Les poissons crétacés de Nardò. 16° Sorbinicharax verraesi gen. sp. nov. (Teleostei, Ostariophysi, Otophysi, Characiformes). Bollettino del Museo Civico di Storia Naturale di Verona. 2003, 27: 29-45.
  96. Otero O, Valentin X, Garcia G: Cretaceous characiform fishes (Teleostei: Ostariophysi) from Northern Tethys: description of new material from the Maastrichtian of Provence (Southern France) and palaeobiogeographic implications. Fishes and the break-up of Pangaea. Edited by: Cavin L, Longbottom A, Richter M. 2008, London: Geological Society, London, Special Publications, 295: 155-164.
  97. Lundberg JG, Sullivan JP, Rodiles-Hernández R, Hendrickson DA: Discovery of African roots for the Mesoamerican Chiapas catfish, Lacantunia enigmatica, requires an ancient intercontinental passage. Proc Acad Nat Sci Phila. 2007, 156 (1): 39-53. 10.1635/0097-3157(2007)156[39:DOARFT]2.0.CO;2. · DOI
  98. Sanderson MJ: r8s ver. 1.70. 2004
  99. Quental TB, Marshall CR: Diversity dynamics: molecular phylogenies need the fossil record. Trends Ecol Evol. 2010, 25 (8): 434-441. 10.1016/j.tree.2010.05.002. · DOI
  100. Benton MJ: Vertebrate palaeontology. 2005, Malden, MA: Blackwell, 3
  101. Benton MJ, Tverdokhlebov VP, Surkov MV: Ecosystem remodeling among vertebrates at the Permian-Triassic boundary in Russia. Nature. 2004, 432 (7013): 97-100. 10.1038/nature02950. · DOI
  102. Isozaki Y: Permo-Triassic boundary superanoxia and stratified superocean: records from lost deep sea. Science. 1997, 276 (5310): 235-238. 10.1126/science.276.5310.235. · DOI · Paper page
  103. Sperling EA, Ingle JC: A Permian-Triassic boundary section at Quinn River Crossing, northwestern Nevada, and implications for the cause of the Early Triassic chert gap on the western Pangean margin. Bull Geol Soc Am. 2006, 118 (5-6): 733-746. 10.1130/B25803.1. · DOI
  104. Grice K, Cao C, Love GD, B ttcher ME, Twitchett RJ, Grosjean E, Summons RE, Turgeon SC, Dunning W, Jin Y: Photic zone euxinia during the Permian-Triassic superanoxic event. Science. 2005, 307 (5710): 706-709. 10.1126/science.1104323. · DOI
  105. Jin YG, Wang Y, Wang W, Shang QH, Cao CQ, Erwin DH: Pattern of marine mass extinction near the Permian-Triassic boundary in South China. Science. 2000, 289 (5478): 432-436. 10.1126/science.289.5478.432. · DOI
  106. Chapelle G, Peck LS: Polar gigantism dictated by oxygen availability. Nature. 1999, 399 (6732): 114-115. · DOI
  107. Huynh TT, Poulsen CJ: Rising atmospheric CO2 as a possible trigger for the end-Triassic mass extinction. Palaeogeogr, Palaeoclimatol, Palaeoecol. 2005, 217 (3-4): 223-242. 10.1016/j.palaeo.2004.12.004. · DOI
  108. Dixon D, Jenkins I, Moody RTJ, Zhuravlev AY: Atlas of the evolving earth. Volume 2. From the Devonian to the Cretaceous. 2001, New York: Macmillan Reference USA
  109. Guex J, Bartolini A, Atudorei V, Taylor D: High-resolution ammonite and carbon isotope stratigraphy across the Triassic-Jurassic boundary at New York Canyon (Nevada). Earth Planet Sci Lett. 2004, 225 (1-2): 29-41. 10.1016/j.epsl.2004.06.006. · DOI
  110. López-Arbarello A: The record of Mesozoic fishes from Gondwana (excluding India and Madagascar). Mesozoic fishes 3. Edited by: Arratia G, Tintori A. 2004, München, Germany: Verlag Dr. Friedrich Pfeil, 597-624.
  111. Wilson MVH, Bruner JC, Arratia G, Tintori A: Mesozoic fish assemblages of North America. Mesozoic fishes 3. 2004, München, Germany: Verlag Dr. Friedrich Pfeil, 575-595.
  112. Chang MM, Miao D, Arratia G, Tintori A: An overview of Mesozoic fishes in Asia. Mesozoic fishes 3. Edited by: Arratia G, Tintori A. 2004, München, Germany: Verlag Dr. Friedrich Pfeil, 535-563.
  113. Milner ARC, Kirkland JI, Birthisel TA: The geographic distribution and biostratigraphy of Late Triassic-Early Jurassic freshwater fish faunas of the southwestern United States. New Mexico Museum of Natural History and Science Bulletin. 2006, 37: 522-529.
  114. Arratia G, Scasso R, Kiessling W: Late Jurassic fishes from Longing Gap, Antarctic Peninsula. J Vert Paleontol. 2004, 24 (1): 41-55. 10.1671/1952-4. · DOI
  115. Smith AG, Smith DG, Funnell BM: Atlas of Mesozoic and Cenozoic coastlines. 2004, Cambridge, UK: Cambridge University Press
  116. Ziegler A, Eshel G, Rees PMA, Rothfus T, Rowley D, Sunderlin D: Tracing the tropics across land and sea: Permian to present. Lethaia. 2003, 36 (3): 227-254. 10.1080/00241160310004657. · DOI
  117. Janvier P: Early vertebrates. 1996, Oxford, UK: Oxford University Press · DOI · Paper page
  118. Zhu M, Yu X, Wang W, Zhao W, Jia L: A primitive fish provides key characters bearing on deep osteichthyan phylogeny. Nature. 2006, 441 (7089): 77-80. 10.1038/nature04563. · DOI
  119. Patterson C: Osteichthyes: Teleostei. The fossil record 2. Edited by: Benton MJ. 1993, London, UK: Chapman & Hall, 621-656.
  120. Gayet M, Meunier FJ: Premiére découverte de Gymnotiformes fossiles (Pisces, Ostariophysi) dans le Miocène supérieur de Bolivie. CR Acad Sci Paris. 1991, 313 (4): 471-476.
  121. Gayet M, Meunier FJ: Paleontology and palaeobiogeography of catfishes. Catfishes. Edited by: Arratia G, Kapoor BG, Chardon M, Diogo R. 2003, Enfield, NH: Science Publishers, 491-522.
  122. Wilson MVH, Brinkman DB, Neuman AG: Cretaceous Esocoidei (Teleostei): early radiation of the pikes in North American fresh waters. J Paleontol. 1992, 66: 839-846. · DOI
  123. Tyler JC, Sorbini L: New superfamily and three new families of tetraodontiform fishes from the Upper Cretaceous: the earliest and most morphologically primitive plectognaths. Smith Contr Paleobio. 1996, 82: 1-59. · DOI
  124. Benton MJ, Donoghue PCJ, Asher RJ: Calibrating and constraining molecular clocks. Timetree of life. Edited by: Hedges SB, Kumar S. 2009, Oxford, UK: Oxford University Press, 35-86. · DOI

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Metadata

Authors
Nakatani, M., Miya, M., Mabuchi, K., Saitoh, K., & Nishida, M.
Venue
BMC Evolutionary Biology
Publisher
Springer Science and Business Media LLC
Published
2011-06-22
Volume
11
Issue
1
ISSN
1471-2148
DOI
10.1186/1471-2148-11-177
PMC
PMC3141434
Cited by
201
References
10
Language
en
Licence
www.springer.com/tdm (unspecified)

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