Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families

PLoS ONE

Volumn 8, Issue 9, 2013, Pages

  Miya, Masaki ^a   Friedman, Matt ^b   Satoh, Takashi P ^c   Takeshima, Hirohiko ^d   Sado, Tetsuya ^a   Iwasaki, Wataru ^d   Yamanoue, Yusuke ^d   Nakatani, Masanori ^d   Mabuchi, Kohji ^d   Inoue, Jun G ^d   Poulsen, Jan Yde ^e   Fukunaga, Tsukasa ^d   Sato, Yukuto ^f   Nishida, Mutsumi ^d  

^a NATURAL HISTORY MUSEUM AND INSTITUTE   (Japan)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c DEPARTMENT OF BOTANY   (Japan)

^d UNIVERSITY OF TOKYO   (Japan)

^e UNIVERSITY OF BERGEN   (Norway)

^f TOHOKU UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTIVE RADIATION; ARTICLE; BIOINFORMATICS; CLADISTICS; END CRETACEOUS MASS EXTINCTION; EVOLUTION; EVOLUTIONARY ORIGIN; GEMPYLIDAE; GENE; MITOCHONDRIAL GENE; MONOPHYLY; MORPHOLOGICAL TRAIT; NONHUMAN; NUCLEAR GENE; NUCLEOTIDE SEQUENCE; PALEOGENE; PELAGIC FISH; PERCIFORMES; PHYLOGENY; SCOMBRIDAE; TRICHIURIDAE;

ANIMALS; BIODIVERSITY; COMPUTATIONAL BIOLOGY; ECOSYSTEM; EVOLUTION, MOLECULAR; GEOLOGICAL PROCESSES; PERCIFORMES; TUNA;

EID: 84883356664     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0073535     Document Type: Article

References (90)

1. Helfman GS, Collette BB, Facey DE, Bowen BW (2009) The diversity of fishes. Oxford, UK: Wiley-Blackwell. xviii +720 p.
2. Allen LG, Cross JN (2006) Surface waters. In: Allen LG, Pondella DJ, Horn MH, editors. The ecology of marine fishes: California and adjacent waters. Berkeley: University of California Press. 320-341.
3. Tyus HM (2012) Ecology and coservation of fishes. London: CRC Press. 529 p.
4. Froese R, Pauly D (2000) FishBase 2000: concepts, design and data sources. Los Baños, Laguna, Phillipines: ICLARM.
5. Magnuson JJ (1979) Locomotion by scombrid fishes: hydromechanics, morphology, and behavior. In: Hoar WS, Randall DJ, editors. Fish physiology. London: Academic Press. 239-313.
6. Miyake M, Guillotreau P, Sun CH, Ishimura G (2010) Recent developments in the tuna industry: stocks, fisheries, management, processing, trade and markets. Rome: FAO. 125 p.
7. Collette BB, Potthoff T, Richards WJ, Ueyanagi S, Russo JL, et al. (1984) Scombroidei: development and relationships. In: Moser HG, Richards WJ, Cohen DM, Fahay MP, Kendall Jr AW et al., editors. Ontogeny and systematics of fishes. Lawrence, KA: Am. Soc. Ichthyol. Herpetol. Spec. Publ. 591-620.
8. Johnson GD, (1986) Scombroid phylogeny: an alternative hypothesis. Bull Mar Sci 39: 1-41.
9. Block BA, Finnerty JR, Stewart AFR, Kidd J, (1993) Evolution of endothermy in fish: mapping physiological traits on a molecular phylogeny. Science 260: 210-210.
10. Orrell TM, Collette BB, Johnson GD, (2006) Molecular data support separate scombroid and xiphioid clades. Bull Mar Sci 79: 505-519.
11. Jondeung A, Karinthanyakit W, (2010) The complete mitochondrial DNA sequence of the short mackerel (Rastrelliger brachysoma), and its phylogenetic position within Scombroidei, Perciformes. Mitochondrial DNA 21: 36-47.
12. Nelson JS (2006) Fishes of the world. Hoboken, NJ: John Wiley & Sons. xx +601 p.
13. Regan CT, (1909) On the anatomy and classification of the scombroid fishes. Ann Mag Nat Hist 8: 66-75.
14. Tyler JC, Johnson GD, Nakamura I, Collette BB, (1989) Morphology of Luvarus imperialis (Luvaridae), with a phylogenetic analysis of the Acanthuroidei (Pisces). Smithson Contrib Zool 485: 1-78.
15. Little AG, Lougheed SC, Moyes CD, (2010) Evolutionary affinity of billfishes (Xiphiidae and Istiophoridae) and flatfishes (Plueronectiformes): Independent and trans-subordinal origins of endothermy in teleost fishes. Mol Phylogenet Evol 56: 897-904.
16. Near TJ, Eytan RI, Dornburg A, Kuhn KL, Moore JA, et al. (2012) Resolution of ray-finned fish phylogeny and timing of diversification. Proc Natl Acad Sci USA 109: 13698-13703.
17. Betancur-R R, Broughton RE, Wiley EO, Carpenter K, López JA, et al. (2013) The Tree of Life and a new classification of bony fishes. PLoS Currents: Tree of Life.
18. Li B, Dettaï A, Cruaud C, Couloux A, Desoutter-Meniger M, et al. (2009) RNF213, a new nuclear marker for acanthomorph phylogeny. Mol Phylogenet Evol 50: 345-363.
19. Yagishita N, Miya M, Yamanoue Y, Shirai SM, Nakayama K, et al. (2009) Mitogenomic evaluation of the unique facial nerve pattern as a phylogenetic marker within the percifom fishes (Teleostei: Percomorpha). Mol Phylogenet Evol 53: 258-266.
20. Chen WJ, Bonillo C, Lecointre G, (2003) Repeatability of clades as a criterion of reliability: a case study for molecular phylogeny of Acanthomorpha (Teleostei) with larger number of taxa. Mol Phylogenet Evol 26: 262-288.
21. Dettaï A, Lecointre G, (2008) New insights into the organization and evolution of vertebrate IRBP genes and utility of IRBP gene sequences for the phylogenetic study of the Acanthomorpha (Actinopterygii: Teleostei). Mol Phylogenet Evol 48: 258-269.
22. Smith WL, Craig MT, (2007) Casting the percomorph net widely: the importance of broad taxonomic sampling in the search for the placement of serranid and percid fishes. Copeia 2007: 35-55.
23. Wainwright PC, Smith WL, Price SA, Tang KL, Sparks JS, 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.
24. Schluter D (2000) The ecology of adaptive radiation. New York: Oxford University Press.
25. Simmons MP, Zhang LB, Webb CT, Reeves A, (2006) How can third codon positions outperform first and second codon positions in phylogenetic inference? An empirical example from the seed plants. Syst Biol 55: 245-258.
26. Saitoh K, Sado T, Mayden RL, Hanzawa N, Nakamura K, et al. (2006) 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 63: 826-841.
27. Strauss D, Sadler PM, (1989) Classical confidence intervals and Bayesian probability estimates for ends of local taxon ranges. Math Geol 21: 411-427.
28. Marshall CR, (1990) Confidence intervals on stratigraphic ranges. Paleobiol 16: 1-10.
29. Carpenter KE, Collette BB, Russo JL, (1995) Unstable and stable classifications of scombroid fishes. Bull Mar Sci 56: 379-405.
30. Okamoto M, Hoshino K, Jintoku T, (2011) First record of Amarsipus carlsbergi (Perciformes: Stromateoidei: Amarsipidae) from Japan and a northernmost range extension. Biogeography 13: 25-29.
31. Horn MH (1984) Stromateoidei: development and relationships. In: Moser HG, Richards WJ, Cohen DM, Fahay MP, Kendall AW Jr, et al., editors. Ontogeny and Systematics of Fishes. Lawrence, KA: Am. Soc. Ichthyol. Herpetol. Spec. Publ. 620-628.
32. Betancur-R R, Broughton RE, Wiley EO, Carpenter K, López JA, et al. (2013) The Tree of Life and a new classification of bony fishes. PLoS Currents: Tree of Life 5.
33. Broughton RE, Betancur-R R, Li C, Arratia G, Ortí G (2013) Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution. PLoS Currents: Tree of Life 5.
34. Marshall NB (1979) Development in deep-sea biology. Poole, Dorset, UK: Blandford Press.
35. Koblmüller S, Sefc KM, Sturmbauer C, (2008) The Lake Tanganyika cichlid species assemblage: recent advances in molecular phylogenetics. Hydrobiol 615: 5-20.
36. Glor RE, (2010) Phylogenetic insights on adaptive radiation. Annu Rev Ecol Evol Syst 41: 251-270.
37. Benfield MC, Caruso JH, Sulak KJ, (2009) In situ video observations of two manefishes (Perciformes: Caristiidae) in the mesopelagic zone of the northern Gulf of Mexico. Copeia 2009: 637-641.
38. Melo MRS, (2009) Revision of the genus Chiasmodon (Acanthomorpha: Chiasmodontidae), with the description of two new species. Copeia 2009: 583-608.
39. Jenkins RL, (1983) Observations on the commensal relationship of Nomeus gronovii with Physalia physalis. Copeia 1983: 250-252.
40. Janssen J, Harbison GR, (1981) Fish in salps: the association of squaretails (Tetragonurus spp.) with pelagic tunicates. J Mar Biol Assoc UK 61: 917-927.
41. Cavin L (2001) Effects of the Cretaceous-Tertiary boundary event on bony fishes. In: Buffetaut E, Koeberl C, editors. Geological and biological effects of impact events. Berlin, Germany: Springer Verlag. 141-158.
42. Friedman M, (2009) Ecomorphological selectivity among marine teleost fishes during the end-Cretaceous extinction. Proc Natl Acad Sci USA 106: 5218-5223.
43. Friedman M, Sallan LC, (2012) Five hundred million years of extinction and recovery: a Phanerozoic survey of large-scale diversity patterns in fishes. Palaeontol 55: 707-742.
44. Friedman M, (2010) Explosive morphological diversification of spiny-finned teleost fishes in the aftermath of the end-Cretaceous extinction. Proc R Soc B 277: 1675-1683.
45. Santini F, Carnevale G, Sorenson L, (2013) First molecular scombrid timetree (Percomorpha: Scombridae) shows recent radiation of tunas following invasion of pelagic habitat. Ital J Zool 80: 210-221.
46. Kriwet J, (2004) Neoselachian (Chondrichthyes, Elasmobranchii) diversity across the Cretaceous-Tertiary boundary. Palaeogeogr Palaeoclimatol Palaeoecol 214: 181-194.
47. Katoh K, Toh H, (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinformatics 9: 286-298.
48. Stamatakis A, (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
49. Lanave C, Preparata G, Sacone C, Serio G, (1984) A new method for calculating evolutionary substitution rates. J Mol Evol 20: 86-93.
50. Stamatakis A, Hoover P, Rougemont J, (2008) A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 57: 758-771.
51. Miya M, Nishida M, (1999) 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 1: 416-426.
52. 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 Evol Biol 8: 215.
53. Miya M, Nishida M, (2000) Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion. Mol Phylogenet Evol 17: 437-455.
54. Adachi J, Hasegawa M, (1996) Model of amino acid substitution in proteins encoded by mitochondrial DNA. J Mol Evol 42: 459-468.
55. Shimodaira H, (2002) An approximately unbiased test of phylogenetic tree selection. Syst Biol 51: 492-508.
56. Shimodaira H, Hasegawa M, (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 16: 1114-1116.
57. Shimodaira H, Hasegawa M, (2001) CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17: 1246-1247.
58. Yang Z, (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586-1591.
59. Brandley MC, Wang Y, Guo X, de Oca ANM, Fería-Ortíz M, et al. (2011) Accommodating heterogenous rates of evolution in molecular divergence dating methods: an example using intercontinental dispersal of Plestiodon (Eumeces) lizards. Syst Biol 60: 3-15.
60. Monsch KA, (2004) Revision of the scombroid fishes from the Cenozoic of England. Transactions of the Royal Society of Edinburgh: Earth Sciences 95: 445-489.
61. Monsch KA, Bannikov AF, (2011) New taxonomic synopses and revision of the scombroid fishes (Scombroidei, Perciformes), including billfishes, from the Cenozoic of territories of the former USSR. Earth and Environmental Science Transactions of the Royal Society of Edinburgh 102: 253-300.
62. Patterson C (1993) Osteichthyes: Teleostei. In: Benton MJ, editor. The fossil record 2. London, UK: Chapman & Hall. 621-656.
63. Marshall CR, (1997) Confidence intervals on stratigraphic ranges with nonrandom distributions of fossil horizons. Paleobiol 23: 165-173.
64. Marshall CR, Bleiweiss R, (1999) Fossil gap analysis supports early Tertiary origin of trophically diverse avian orders: Comment and Reply. Geology 27: 95-96.
65. Boettiger C, Lang DT, Wainwright PC, (2012) rfishbase: exploring, manipulating and visualizing FishBase data from R. J Fish Biol. 81: 2030-2039.
66. Team RDC (2007) R: A language and environment for statistical computing. Vienna, Austria: R Foundation Statistical Computing.
67. Revell LJ, (2012) phytools: an R package for phylogenetic comparative biology (and other things). Meth Ecol Evol 3: 217-223.
68. Felsenstein J, (1985) Phylogenies and the comparative method. Am Nat 125: 1-15.
69. Patterson C, (1964) A review of Mesozoic acanthopterygian fishes, with special reference to those of the English Chalk. Philos Trans R Soc Lond, Ser B: Biol Sci 247: 213-482.
70. Patterson C, (1993) An overview of the early fossil record of acanthomorphs. Bull Mar Sci 52: 29-59.
71. Owen E (1987) Palaeontological Association field guides to fossils. In: Smith AB, editor. Fossils of the Chalk. Oxford, UK: Oxford University Press. 9-14.
72. Rosen DE (1973) Interrelationships of higher euteleostean fishes. In: Greenwood PHJ, Miles RS, Patterson C, editors. Interrelationships of fishes. London: Academic Press. 397-513.
73. Bannikov AF, (1990) Fossil carangids and apolectids of the USSR. Trudy Paleontol Inst Akad Nauk SSSR 244: 1-108.
74. Smith-Vaniz WF (1984) Carangidae: relationships. In: Moser HG, Richards WJ, Cohen DM, Fahay MP, Kendall AW Jr, et al., editors. Ontogeny and Systematics of Fishes. Lawrence, KA: Am. Soc. Ichthyol. Herpetol. Spec. Publ. 522-533.
75. Bannikov AF, Parin NN, (1997) The list of marine fishes from Cenozoic (Upper Paleocene-Middle Miocene) localities in southern European Russia and adjacent countries. J Ichthyol 37: 133-146.
76. Gradstein FM, Ogg JG, Schmitz M (2012) A geologic time scale 2012. Amsterdam: Elsevier.
77. Marshall CR, (2008) A simple method for bracketing absolute divergence times on molecular phylogenies using multiple fossil calibration points. Am Nat 171: 726-742.
78. Friedman M, Johanson Z, (2012) †Opisthomyzon glaronensis (Wettstein, 1886) (Acanthomorpha, †Opisthomyzonidae), a junior synonym of †Uropteryx elongatus Agassiz, 1844. J Vert Paleontol 32: 1202-1206.
79. Micklich N, (1998) New information on the fishfauna of the Frauenweiler fossil site. Ital J Zool 65: 169-184.
80. Johnson GD (1984) Percoidei: development and relationships. In: Moser HG, Richards WJ, Cohen DM, Fahay MP, Kendall AW Jr, et al., editors. Ontogeny and Systematics of Fishes. Lawrence, KA: Am. Soc. Ichthyol. Herpetol. Spec. Publ. 464-498.
81. O'Toole B, (2002) Phylogeny of the species of the superfamily Echeneoidea (Perciformes: Carangoidei: Echeneidae, Rachycentridae, and Coryphaenidae), with an interpretation of echeneid hitchhiking behaviour. Can J Zool 80: 596-623.
82. Fischer H, Villa IM, (1990) Erste K/Ar-und 40Ar/39Ar-Hornblende-Mineralalter des Taveyannaz-Sandsteins. Schweiz Mineral Petrograph Mitteil 70: 73-75.
83. Gasser D, Den Brok B, (2008) Tectonic evolution of the Engi slates, Glarus alps, Switzerland. Swiss J Geosci 101: 311-322.
84. Micklich NR, Tyler JC, Johnson GD, Swidnicka E, Bannikov AF, (2009) First fossil records of the tholichthys larval stage of butterfly fishes (Perciformes, Chaetodontidae), from the Oligocene of Europe. Paläontol Zeits 83: 479-497.
85. Sorbini L, (1980) The Cretaceous fishes of Nardò. I°. Order Gasterosteiformes (Pisces). Boll Mus Civ Sto Nat Verona 8: 1-27.
86. Pietsch TW, (1978) Evolutionary relationships of the sea moths (Teleostei: Pegasidae) with a classification of gasterosteiform families. Copeia 1978: 517-529.
87. Orr JW (1995) Phylogenetic relationships of gasterosteiform fishes(Teleostei: Acanthomorpha) [Ph.D. thesis]. Seattle, WA: University of Washington.
88. Medizza F, Sorbini L (1980) Il giacimento del Salento (Lecce). I vertebrati fossili italiani Catalogo della Mostra, Verona. Verona, Italy: Museo Civico di Storia Naturale, Verona. 131-134.
89. Blot J, (1980) The ichthyofauna of the deposits of Monte Bolca (Province de Vérone, Italie). Catalogue systématique présentat l'état actuel des recherches concernant cette faune. Bull Mus Natl Hist Nat Paris 2: 339-396.
90. Andrea Papazzoni C, Trevisani E, (2006) Facies analysis, palaeoenvironmental reconstruction, and biostratigraphy of the "Pesciara di Bolca" (Verona, northern Italy): An early Eocene Fossil-Lagerstätte. Palaeogeogr Palaeoclimatol Palaeoecol 242: 21-35.