A new time-scale for ray-finned fish evolution

Proceedings of the Royal Society B: Biological Sciences

Volumn 274, Issue 1609, 2007, Pages 489-498

  Hurley, Imogen A ^a   Mueller, Rachel Lockridge ^a   Dunn, Katherine A ^b   Schmidt, Eric J ^a   Friedman, Matt ^d   Ho, Robert K ^a,d   Prince, Victoria E ^a,d   Yang, Ziheng ^c   Thomas, Mark G ^c   Coates, Michael I ^a,d  

^a UNIVERSITY OF CHICAGO   (United States)

^b DALHOUSIE UNIVERSITY   (Canada)

^c UNIVERSITY COLLEGE LONDON   (United Kingdom)

^d UNIVERSITY OF CHICAGO   (United States)

Author keywords

Actinopterygii; Dating; Fishes; Fossils; Phylogeny; Whole genome duplication

Indexed keywords

CLADISTICS; DATING METHOD; DIVERGENCE; FINFISH; FOSSIL RECORD; GENETIC ANALYSIS; MITOCHONDRIAL DNA; MORPHOLOGY; NUCLEIC ACID ANALYSIS; PALEONTOLOGY; PHYLOGENY; TELEOST; TIMESCALE;

ACTINOPTERYGII; AMIA; ARTICLE; CLADISTICS; EVOLUTION; FISH; FOSSIL; GENE DUPLICATION; GENETIC VARIABILITY; GENOME; LEPISOSTEUS; NONHUMAN; PALEONTOLOGY; PHYLOGENY; PRIORITY JOURNAL; RAY FINNED FISH; TELEOST; ANIMAL; BAYES THEOREM; CLASSIFICATION; GENETICS; HISTOLOGY; TIME;

ACTINOPTERYGII; AMIA; AMIIDAE; LEPISOSTEUS; NEOPTERYGII; PISCES; TELEOSTEI; VERTEBRATA;

MITOCHONDRIAL DNA;

ANIMALS; BAYES THEOREM; DNA, MITOCHONDRIAL; EVOLUTION; FISHES; FOSSILS; GENOME; PHYLOGENY; TIME FACTORS;

EID: 34249943401     PISSN: 09628452     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rspb.2006.3749     Document Type: Article

References (60)

1. Amores, A. et al. 1998 Zebrafish hox clusters and vertebrate genome evolution. Science 282, 1711-1714.
2. Arratia, G. 1997 Basal teleosts and teleostean phylogeny. Palaeo Ichthyologica 7, 1-168.
3. Arratia, G. 2000 Remarkable teleostean fishes from the Late Jurassic of southern Germany and their phylogenetic relationships. Mitt. Mus. Nat.kd., Berl., Geozviss. Reihe 3, 137-179.
4. 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 semionotiforms. Palaeontology 49, 339-353.
5. Chiu, C. H., Amemiya, C., Dewar, K., Kim, C. B., Ruddle, F. H. & Wagner, G. P. 2002 Molecular evolution of the HoxA cluster in the three major gnathostome lineages. Proc. Natl Acad. Sci. USA 99, 5492-5497.
6. Christoffels, A., Koh, E. G., Chia, J. M., Brenner, S., Aparicio, S. & Venkatesh, B. 2004 Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. Mol. Biol. Evol. 21, 1146-1151.
7. Cloutier, R. & Arratia, G. 2004 Early diversification of actinopterygians. In Recent advances in the origin and early radiation of vertebrates (ed. G. Arratia, M. V. H. Wilson & R. Cloutier), pp. 217-270. München, Germany: Verlag Dr. Friedrich Pfeil.
8. Coates, M. I. 1999 Endocranial preservation of a Carboniferous actinopterygian from Lancashire, UK, and the interrelationships of primitive actinopterygians. Phil. Trans. R. Soc. B 354, 435-467. (doi:10.1098/rstb.1999.0396)
9. Crow, K. D. & Wagner, G. P. 2006 What is the role of genome duplication in the evolution of complexity and diversity? Mol. Biol. Evol. 23, 887-892.
10. 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. Mol. Biol. Evol. 23, 121-136.
11. DeBodt, S., Maere, S. & Van de Peer, Y. 2005 Genome duplication and the origin of angiosperms. Trends Ecol. Evol. 20, 591-597.
12. Dineley, D. L. & Metcalfe, S. J. 1999 Fossil fishes of Great Britain. Peterborough, UK: Joint Nature Conservation Committee.
13. Donoghue, P. C. J. & Purnell, M. A. 2005 Gene duplication, extinction, and vertebrate evolution. Trends Ecol. Evol. 20, 312-319.
14. Dunkle, D. H. 1939 A new paleoniscid fish from the Texas Permian. Am. J. Sci. 237, 262-274.
15. Gardiner, B. G. 1993 Osteichtythyes: basal actinopterygians. In Fossil record II (ed. M. J. Benton), pp. 611-619. London, UK: Chapman and Hall.
16. Gardiner, B. G. & Schaeffer, B. 1989 Interrelationships of lower actinopterygian fishes. Zool. J. Linn. Soc. 97, 135-187.
17. Gardiner, B. G., Maisey, J. G. & Littlewood, D. T. J. 1996 Interrelationships of basal neopterygians. In Interrelationships of fishes (ed. M. L. J. Stiassney, L. R. Parenti & G. D. Johnson), pp. 117-146. San Diego, IL: Academic Press.
18. Gardiner, B. G., Schaeffer, B. & Masserie, J. A. 2005 A review of the lower actinopterygian phylogeny. Zool. J. Linn. Soc. 144, 511-525.
19. Gradstein, F. M., Ogg, J. G. & Smith, A. G. 2004 A geologic time scale. Cambridge, UK: Cambridge University Press.
20. Grande, L. 2005 Phylogenetic study of gars and closely related species, based mostly on skeletal morphology. The resurrection of Holostei. In Fourth Int. Meeting on Mesozoic Fishes - Systematics, Homology and Nomenclature, Extended Abstracts (ed. F. J. Poyato-Ariza), pp. 119-121. Madrid, Spain: Servicio de Publicaciones de la Universidad Autónoma de Madrid/UAM Ediciones.
21. 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. J. Vertebr. Paleontol. 18(Suppl. 1), 1-690. Memoir 4
22. Graur, D. & Martin, W. 2004 Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends Genet. 20, 80-86.
23. Hoegg, S., Brinkmann, H., Taylor, J. S. & Meyer, A. 2004 Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish. J. Mol. Evol. 59, 190-203. (doi:10.1007/s00239-004-2613-z)
24. Huelsenbeck, J. P. & Ronquist, F. 2001 MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755. (doi:10.1093/bioinformatics/17.8.754)
25. Hurley, I., Hale, M. E. & Prince, V. E. 2005 Duplication events and the evolution of segment identity. Evol. Dev. 7, 556-567. (doi:10.1111/j.1525-142X.2005.05059.x)
26. Inoue, J. G., Miya, M., Tsukamoto, K. & Nishida, M. 2003 Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish". Mol. Phylogenet. Evol. 26, 110-120. (doi:10.1016/S1055-7903(02)00331-7)
27. 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 the two coelacanths. Gene 349, 227-235. (doi:10.1016/j.gene.2005.01. 008)
28. Jaillon, O. et al. 2004 Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431, 946-957. (doi:10.1038/nature03025)
29. Janvier, P. 1996 Early vertebrates. Oxford, UK: Oxford University Press.
30. Kikugawa, K., Katoh, K., Kuraku, S., Sakurai, H., Ishida, O., Iwabe, N. & Miyata, T. 2004 Basal jawed vertebrate phylogeny inferred from multiple nuclear DNA-coded genes. BMC Biol. 2, 3. (doi:10.1186/1741-7007-2- 3)
31. Kishino, H. & Hasegawa, M. 1989 Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J. Mol. Evol. 29, 170-179. (doi:10.1007/BF02100115)
32. Le, H. L. V., Lecointre, G. & Perasso, R. 1993 A 28S rRNA-based phylogeny of the gnathostomes: first steps in the analysis of conflict and congruence with morphologically based cladograms. Mol. Phylogenet. Evol. 2, 31-51. (doi:10.1006/mpev.1993.1005)
33. Lecointre, G., Philippe, H., Van Le, H. L. & Le Guyader, H. 1993 Species sampling has a major impact on phylogenetic inference. Mol. Phylogenet. Evol. 2, 205-224. (doi:10.1006/mpev.1993.1021)
34. Long, J. A. 2001 Rise of fishes. In Paleobiology II (ed. D. E. G. Briggs & P. R. Crowther), pp. 53-57. Oxford, UK: Blackwell Science Ltd.
35. Lund, R. 2000 The new Actinopterygian order Guildayichthyiformes from the Lower Carboniferous of Montana (USA). Geodiversitas 22, 171-206.
36. Mank, J. E. & Avise, J. C. 2006 Cladogenetic correlates of genomic expansions in the recent evolution of actinopterygiian fishes. Proc. R. Soc. B 273, 33-38. (doi:10.1098/rspb.2005.3295)
37. Muller, T. & Vingron, M. 2000 Modeling amino acid replacement. J. Comput. Biol. 7, 761-776. (doi:10.1089/10665270050514918)
38. Murray, A. M. 2000 Eocene cichlid fishes from Tanzania, East Africa. J. Vert. Paleont. 20, 651-664. (doi:10.1671/0272-4634(2000) 020[0651:ECFFTE]2.0.CO;2)
39. Nelson, J. S. 2006 Fishes of the world, 4th edn. New York, NY: Wiley.
40. Patterson, C. 1973 Interrelationships of holosteans. In Interrelationships of fishes (ed. P. H. Greenwood, R. S. Miles & C. Patterson), pp. 233-305. London, UK: Academic Press.
41. Peng, Z., He, S., Wang, J., Wang, W. & Diogo, R. 2006 Mitochondrial molecular clocks and the origin of the major Otocephalan clades (Pisces: Teleostei): a new insight. Gene 370, 113-124. (doi:10.1016/j.gene. 2005.11.024)
42. Peters, S. E. 2006 Macrostratigraphy of North America. J. Geol. 114, 391-412. (doi:10.1086/504176)
43. Posada, D. & Crandall, K. A. 1998 MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817-818. (doi:10.1093/ bioinformatics/14.9.817)
44. Prince, V. E., Joly, L., Ekker, M. & Ho, R. K. 1998 Zebrafish hox genes: genomic organization and modified colinear expression patterns in the trunk. Development 125, 407-420.
45. Quicke, D. L., Taylor, J. & Purvis, A. 2001 Changing the landscape: a new strategy for estimating large phylogenies. Syst Biol. 50, 60-66. (doi:10.1080/106351501750107477)
46. Regan, C. T. 1923 The skeleton of Lepidosteus, with remarks on the origin and evolution of the lower neopterygian fishes. Proc. Zool. Soc. 1923, 445-461.
47. Schaeffer, B. 1973 Interrelationships of chondrosteans. In Interrelationships of fishes (ed. P. H. Greenwood, R. S. Miles & C. Patterson), pp. 207-226. London, UK: Academic Press.
48. Schmidt, H. A., Strimmer, K., Vingron, M. & von Haeseler, A. 2002 TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18, 502-504. (doi:10.1093/bioinformatics/18.3.502)
49. Sepkoski Jr, J. J. 2002 A compendium of fossil marine animal genera. Bull. Am. Paleont. 363, 1-560.
50. Shimodaira, H. & Hasegawa, M. 1999 Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16, 1114-1116.
51. Smith, A. B. & Peterson, K. J. 2002 Dating the time of origin of major clades: molecular clocks and the fossil record. An. Rev. Earth Planet. Sci. 30, 65-88. (doi:10.1146/annurev.earth.30.091201.140057)
52. Smith, M. P. & Sansom, I. J. 2001 The origin of vertebrates. In Paleobiology II (ed. D. E. G. Briggs & P. R. Crowther), pp. 43-48. Oxford, UK: Blackwell Science, Ltd.
53. Steinke, D., Salzburger, W. & Meyer, A. 2006 Novel relationships among ten fish model species revealed based on a phylogenomic analysis using ESTs. J. Mol. Evol. 62, 772-784. (doi:10.1007/s00239-005-0170-8)
54. Swofford, D. L. 1998 PAUP*: Phylogenetic analysis using parsimony (* and other methods), v. 4.0. Sunderland, MA: Sinauer Associates.
55. Taylor, J. S., Van de Peer, Y., Braasch, I. & Meyer, A. 2001 Comparative genomics provides evidence for an ancient genome duplication event in fish. Phil. Trans. R. Soc. B 356, 1661-1679. (doi:10.1098/rstb.2001.0975)
56. Thorne, J. L. & Kishino, H. 2002 Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51, 689-702. (doi:10.1080/10635150290102456)
57. Vandepoele, K., De Vos, W., Taylor, J. S., Meyer, A. & Van de Peer, Y. 2004 Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates. Proc. Natl Acad. Sci. USA 101, 1638-1643. (doi:10.1073/pnas. 0307968100)
58. Venkatesh, B., Erdmann, M. V. & Brenner, S. 2001 Molecular synapomorphies resolve evolutionary relationships of extant jawed vertebrates. Proc. Natl Acad. Sci. USA 98, 11 382-11 387. (doi:10.1073/pnas. 201415598)
59. Yamanoue, Y., Miya, M., Inoue, J. G., Matsuura, K. & Nishida, M. 2006 The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes. Genes Genet. Syst. 81, 29-39. (doi:10.1266/ggs.81.29)
60. Yang, Z. 1997 PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 15, 555-556.