Novel relationships among ten fish model species revealed based on a phylogenomic analysis using ESTs

Journal of Molecular Evolution

Volumn 62, Issue 6, 2006, Pages 772-784

  Steinke, Dirk ^a   Salzburger, Walter ^a   Meyer, Axel ^a  

^a UNIVERSITY OF KONSTANZ   (Germany)

Author keywords

EST; Euteleostei; Gondwana; Molecular clock; Pangea; Phylogenomics; Teleost phylogeny

Indexed keywords

AQUACULTURE; ARTICLE; BELONIFORMES; CLADISTICS; CYPRINIFORMES; CYPRINODONTIFORMES; EXPRESSED SEQUENCE TAG; FISH; GENE; GENETIC VARIABILITY; GENOMICS; JURASSIC; NONHUMAN; NUCLEOTIDE SEQUENCE; PERCIFORMES; PHYLOGENY; PUFFER FISH; RELIABILITY; SALMONIFORMES; SILURIFORMES; TELEOST; TETRAODONTIFORMES; UNINDEXED SEQUENCE;

ANIMALS; EXPRESSED SEQUENCE TAGS; FISHES; HUMANS; MODELS, GENETIC; PHYLOGENY;

ACANTHOPTERYGII; BELONIFORMES; CICHLIDAE; CYPRINIFORMES; CYPRINODONTIFORMES; EUTELEOSTEI; FUNDULUS HETEROCLITUS; OSTARIOPHYSI; PERCIFORMES; PROTACANTHOPTERYGII; SALMONIFORMES; SILURIFORMES; TETRAODONTIDAE; TETRAODONTIFORMES;

EID: 33646878378     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-005-0170-8     Document Type: Article

References (72)

1. Abascal F, Zardoya R, Posada D (2005) ProtTest: Selection of best-fit models of protein evolution. Bioinformatics 21:2104-2015
2. Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, Gelpke MD, Roach J, Oh T, Ho IY, Wong M, Detter C, Verhoef F, Predki P, Tay A, Lucas S, Richardson P, Smith SF, Clark MS, Edwards YJ, Doggett N, Zharkikh A, Tavtigian SV, Pruss D, Barnstead M, Evans C, Baden H, Powell J, Glusman G, Rowen L, Hood L, Tan YH, Elgar G, Hawkins T, Venkatesh B, Rokhsar D, Brenner S (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297:1283-1285
3. Arratia G (1999) The monophyly of teleostei and stem-group teleosts. In: Arratia G, Schultze HP (eds) Mesozoic fish 2: Systematics and fossil record. Pfeil, Munich
4. Benton MJ (1993) The fossil record, vol. 2 Chapman and Hall, London
5. Berg LS (1958) System der rezenten und fossilen Fischartigen und Fische. Verlag der Wissenschaften, Berlin
6. Cavender (1991) The fossile record of the Cyprinidae. In: Winfield IJ, Nelson JS (eds) Cyprinid fish: Systematics, biology and exploitation. Fish and Fisheries Series 3. Chapman and Hall, London
7. 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
8. Chen WJ, Orti G, Meyer A (2004) Novel evolutionary relationship among four fish model systems. Trends Genet 20:424-431
9. Collette BB (2003) Family Belonidae Bonaparte 1832 - needlefish. Calif Acad Sci Annot Checklists Fish 16:1-22
10. Cummings MP, Meyer A (2005) Magic bullets and golden rules: data sampling in molecular phylogenetics. Zoology 108:329-336
11. Cummings MP, Otto SP, Wakeley J (1995) Sampling properties of DNA sequence data in phylogenetic analysis. Mol Biol Evol 12:814-822
12. De Pinna MCC (1996) Teleostean monophyly. In: Stiassny MLJ, Parenti LR, Johnson GD (eds) Interrelationships of fish. Academic Press, San Diego
13. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
14. Felsenstein J (1989) Phylogenetic inference programs (PHYLIP). University of Washington, Seattle, and University Herbarium, University of California, Berkeley
15. Fink SV, Fink WL (1996) Interrelationships of ostariophysan fish (Teleostei). In: Stiassny MLJ, Parenti LR, Johnson GD (eds) Interrelationships of fish. Academic Press, San Diego
16. Gadagkar SR, Rosenberg MS, Kumar S (2005) Inferring species phylogenies from multiple genes:Concatenated sequence tree versus consensus gene tree. Mol Dev Evol 304B:64-74
17. Gerhold D, Caskey CT (1996) It's the genes! EST access to human genome content. Bioessays 18:973-981
18. Greenwood PH, Rosen DE, Weitzman SH, Mayers GS (1966) Phyletic studies of teleostean fish, with a provisional classification of living forms. Bull Am Mus Nat Hist 131:339-455
19. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696-704
20. Helfman GS, Collette BB, Facey DE (1997) The diversity of fish Blackwell Science, Cambridge, MA
21. Hillis DM (1998) Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst Biol 47:3-8
22. Hillis DM, Pollock DD, McGuire JA, Zwickl DJ (2003) Is sparse taxon sampling a problem for phylogenetic inference? Syst Biol 52:124-126
23. Hoegg S, Brinkmann H, Taylor JS, Meyer A (2004) Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish. J Mol Evol 59:190-203
24. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17:754-755
25. Hughes J, Longhorn SJ, Papadopoulou A, Theodorides K, de Riva A , Mejia-Chang M, Foster PG, Vogler AP (2006) Dense taxonomic EST sampling and its applications for molecular systematics of the Coleoptera (beetles). Mol Biol Evol 23:268-278
26. Inoue JG, Miya M, Tsukamoto K, Nishida M (2004) Mitogenomic evidence for the monophyly of elopomorph fish (Teleostei) and the evolutionary origin of the leptocephalus larva. Mol Phylogenet Evol 32:274-286
27. Inoue JG, 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
28. Ishiguro NB, Miya M, Nishida M (2003) Basal euteleostean relationships: a mitogenomic perspective on the phylogenetic reality of the " Protacanthopterygii." Mol Phylogenet Evol 27:476-488
29. Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, Nicaud S, Jaffe D, Fisher S, Lutfalla G, Dossat C, Segurens B, Dasilva C, Salanoubat M, Levy M, Boudet N, Castellano S, Anthouard V, Jubin C, Castelli V, Katinka M, Vacherie B, Biemont C, Skalli Z, Cattolico L, Poulain J, De Berardinis V, Cruaud C, Duprat S, Brottier P, Coutanceau JP, Gouzy J, Parra G, Lardier G, Chapple C, McKernan KJ, McEwan P, Bosak S, Kellis M, Volff JN, Guigo R, Zody MC, Mesirov J, Lindblad-Toh K, Birren B, Nusbaum C, Kahn D, Robinson-Rechavi M, Laudet V, Schachter V, Quetier F, Saurin W, Scarpelli C, Wincker P, Lander ES, Weissenbach J, Roest Crollius H (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431:946-957
30. Johnson GD, Patterson C (1993) Percomorph phylogeny: a survey of acanthomorphs and a new proposal. Bull Mar Sci 52:554-626
31. Johnson GD, Patterson C (1996) Relationships of lower euteleostean fish. In: Stiassny MLJ, Parenti LR, Johnson GD (eds) Interrelationships of fish. Academic Press, San Diego
32. Kruiswijk CP, Hermsen TT, Westphal AH, Savelkoul FJ, Steti RJM (2002) A novel functional class I cineage in Zebrafish (Danio rerio), Carp (Cyprinus carpio), and large Barbus (Barbus intermedius) showing an unusual conservation of the peptide binding domains. J Immunol 169:1936-1947
33. Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 5:150-163
34. Kumar S, Gadagkar SR (2000) Efficiency of the neighbor-joining method in reconstructing deep and shallow evolutionary relationships in large phylogenies. J Mol Evol 51:544-553
35. Kumazawa Y, Yamaguchi M, Nishida M (1999). Mitochondrial molecular clocks and the origin of euteleostean biodiversity: familial radiation of Perciforms may have predated the Cretaceous/Tertiary boundary. In: Kato M (ed) The biology of biodiversity. Springer, Hong Kong
36. Lake LA, Moore JE (1998) Phylogenetic analysis and comparative genomics. Trends guide to Bioinformatics, Trends Supplement 1998:22-23
37. Larget B, Simon DL (1999) Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol Biol Evol 16:750-759
38. Mitchell A, Mitter C, Regier JC (2000) More taxa or more characters revisited: combining data from nuclear protein-encoding genes for phylogenetic analyses of Noctuoidea (Insecta: Lepidoptera). Syst Biol 49:202-224
39. Miya M, Nishida M (2000) Use of mitogenomic information in teleostean molecular pyhlogenetics: a tree-based exploration under the maximum-parsimony optimality criterion. Mol Phylogenet Evol 17:437-455
40. Miya M, Takeshima H, Endo H, Ishiguro NB, Inoue JG, Mukai T, Satoh TP, Yamaguchi M, Kawaguchi A, Mabuchi K, Shirai SM, Nishida M (2003) Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol Phylogenet Evol 26:121-138
41. Mossel E, Vigoda E (2005) Phylogenetic MCMC algorithms are misleading on mixtures of trees. Science 309:2207-2209
42. Near TJ, Sanderson MJ (2004) Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection. Phil Trans R Soc Lond B Biol Sci 359:1477-1483
43. Near TJ, Meylan PA, Shaffer HB (2005) Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles. Am Nat 165:137-146
44. Nelson J (1994) Fishes of the world. Wiley, New York
45. Notredame C, Higgins DG, Heringa J (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 302:205-217
46. Renn SCP, Aubin-Horth N, Hofmann HA (2004) Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray. BMC Genomics 5:42
47. Resetnikov JS (1988) Coregonid fish in recent conditions. Finnish Fish Res 9:11-16
48. Rokas A, Carroll SB (2005) More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol Biol Evol 22:1337-1344
49. Rokas A, William BL, King N, Carroll SB (2003) Genome scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804
50. Rokas A, Kruger D, Carroll SB (2005) Animal evolution and the molecular signature of radiations compressed in time. Science 310:1933-1938
51. Rosen DE (1973) Interrelationships of higher teleostean fish. In: Greenwood PH, Miles RS, Patterson C (eds) Interrelationships of fish. Academic Press, London
52. Rosen DE (1974) Phylogeny and zoogeography of salmoniform fish and relationships of Lepidogalaxias salamandroides. Bull Am Mus Nat Hist 153:265-326
53. Rosen DE, Greenwood PH (1970) Origin of the Weberian apparatus and the relationships of the ostariophysan and gonorynchiform fish. Am Mus Novit 2428:1-25
54. Rosen DE, Patterson C (1969) The structure and relationships of the paracanthopterygian fish. Bull Am Mus Nat Hist 141:357-474
55. Rosenberg MS, Kumar S (2001) Incomplete taxon sampling is not a problem for phylogenetic inference. Proc Natl Acad Sci USA 98:10751-10756
56. Rosenberg MS, Kumar S (2003) Taxon sampling, bioinformatics, and phylogenomics. Syst Biol 52:119-124
57. Saitoh K, Miya M, Inoue JG, Ishiguro NB, Nishida M (2003) Mitochondrial genomics of ostariophysan fish:Perspectives on phylogeny and biogeography. J Mol Evol 56:464-472
58. Sanderson MJ (2003) r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19:301-302
59. Santini F, Tyler JC (2003) A phylogeny of the families of fossil and extant tetraodontiform fish (Acanthomorpha, Tetraodontiformes), Upper Cretaceous to Recent. Zool J Linn Soc 139:565-617
60. Shevchuk NA, Allard MW (2001) Sources of incongruence among mammalian mitochondrial sequences: COII, COIII, and ND6 genes are main contributors. Mol Phylogenet Evol 21:43-54
61. Shimodaira H (2002) An approximately unbiased test of phylogenetic tree selection. Syst Biol 51:492-508
62. Shimodaira H, Hasegawa M (2001) CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246-1247
63. Simmons MP, Miya M (2004) Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches: a case study using mitogenomic data from 100 higher teleost fish. Mol Phylogenet Evol 31:351-362
64. Steinke D, Salzburger W, Meyer A (2004) EverEST - A phylogenomic EST database approach. Phyloinformatics 6:1-4
65. Stepien CA, Kocher TD (1997) Molecules and morphology in studies of fish evolution. In: Kocher TD, Stepien CA (eds) Molecular systematics of fish. Academic Press, San Diego
66. Swofford DL (2002) PAUP*. Phylogenetic analysis using parsimony (*and other methods), version 4.10b Sinauer Associates, Sunderland, MA
67. Takezaki N, Figueroa F, Zaleska-Rutczynska Z, Klein J (2003) Molecular phylogeny of early vertebrates: monophyly of the Agnathans as revealed by sequences of 35 genes. Mol Biol Evol 20:287-292
68. Takezaki N, Figueroa F, Zaleska-Rutczynska Z, Takahata N, Klein J (2004) The phylogenetic relationship of tetrapod, coelacanth, and lungfish revealed by the sequences of forty-four nuclear genes. Mol Biol Evol 21:1512-1524
69. Taylor JS, Braasch I, Frickey T, Meyer A, van de Peer Y (2003) Genome duplication, a trait shared by 22,000 species of ray-finned fish. Genome Res 13:382-390
70. Watanabe M, Kobayashi N, Shin-i T, Horiike T, Tateno Y, Kohara Y, Okada N (2004) Extensive analysis of ORF sequences from two different cichlid species in Lake Victoria provides molecular evidence for a recent radiation event of the Victoria species flock identity of EST sequences between Haplochromis chilotes and Haplochromis sp. "Redtailsheller." Gene 343:263-269
71. Whelan S, Goldman N (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18:691-699
72. Wiley EO, Johnson GD, Dimmick WW (2000) The interrelationships of Acantomorph fish: a total evidence approach using molecular and morphological data. Biochem Syst Ecol 28:319-350