Revealing Less Derived Nature of Cartilaginous Fish Genomes with Their Evolutionary Time Scale Inferred with Nuclear Genes

PLoS ONE

Volumn 8, Issue 6, 2013, Pages

  Renz, Adina J ^a   Meyer, Axel ^a   Kuraku, Shigehiro ^a,b  

^a UNIVERSITY OF KONSTANZ   (Germany)

^b RIKEN Center for Biosystems Dynamics Research   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE BINDING OLIGOMERIZATION DOMAIN LIKE RECEPTOR;

ARTICLE; CARTILAGINOUS FISH; CONTROLLED STUDY; ELASMOBRANCH; EXPRESSED SEQUENCE TAG; GENE MAPPING; GENE SEQUENCE; GENOME; GENOMICS; HOLOCEPHALI; MOLECULAR EVOLUTION; MORPHOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PALEONTOLOGY; PHENOTYPE; PHYLOGENY; SEQUENCE ALIGNMENT; SPECIES DIVERSITY; TRANSCRIPTOMICS;

ANIMALS; CELL NUCLEUS; DATA MINING; EVOLUTION, MOLECULAR; FISHES; GENE EXPRESSION PROFILING; GENOMICS; MOLECULAR SEQUENCE DATA; NUCLEAR PROTEINS; SEQUENCE ANALYSIS;

CHIMAERIFORMES; CHONDRICHTHYES; ELASMOBRANCHII; HOLOCEPHALI; TETRAPODA; VERTEBRATA;

EID: 84879330929     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0066400     Document Type: Article

References (69)

1. Kikugawa K, Katoh K, Kuraku S, Sakurai H, Ishida O, et al. (2004) Basal jawed vertebrate phylogeny inferred from multiple nuclear DNA-coded genes. BMC Biol 2: 3.
2. Janvier P (1996) Early vertebrates. Oxford: Oxford University Press.
3. Nelson JM (1994) Fishes of the world. New York: Wiley.
4. Maisey JG, (1984) Higher Elasmobranch Phylogeny and Biostratigraphy. Zool J Linn Soc-Lond 82: 33-54.
5. Coates MI, Sequeira SEK (2001) Early sharks and primitive gnathostome interrelationships. In: Ahlberg PE, editor. Major Events in Early Vertebrate Evolution Palaeontology, phylogeny, genetics and development. London: Taylor & Francis. 241-262.
6. Grogan ED, Lund R (2004) The origin and relationships of early chondrichthyes. In: Carrier JC, Musick JA, Heithaus MR, editors. Biology of sharks and their relatives. Boca Raton: CRC Press. 3-32.
7. Maisey JG, (1986) Heads and tails: A chordate phylogeny. Cladistics 2: 201-256.
8. Arnason U, Gullberg A, Janke A, (2001) Molecular phylogenetics of gnathostomous (jawed) fishes: old bones, new cartilage. Zool Scr 30: 249-255.
9. Mallatt J, Winchell CJ, (2007) Ribosomal RNA genes and deuterostome phylogeny revisited: more cyclostomes, elasmobranchs, reptiles, and a brittle star. Mol Phylogenet Evol 43: 1005-1022.
10. Bigelow HB, Schroeder WC (1948) Sharks. In: Tee-Van J, Breder CM, Hildebrand SF, Parr AE, Schroeder WC, editors. Fishes of the western North Atlantic Part 1. New Haven: Sears Foundation for Marine Research, Yale University. 59-546.
11. Bigelow HB, Schroeder WC (1953) Sawfishes, guitarfishes, skates and rays. In: Tee-Van J, Breder CM, Hildebrand SF, Parr AE, Schroeder WC, editors. Fishes of the western North Atlantic Part 2. New Haven: Sears Foundation for Marine Research, Yale University.
12. Shirai S (1992) Squalean phylogeny: a new framework of "squaloid" sharks and related taxa. Sapporo: Hokkaido University Press.
13. de Carvalho MR (1996) Higher-level elasmobranch phylogeny, basal squaleans, and paraphyly. In: Stiassny MLJ, Parenti LR, Johnson GD, editors. Interrelationships of fishes. San Diego: Academic Press. 35-84.
14. Douady CJ, Dosay M, Shivji MS, Stanhope MJ, (2003) Molecular phylogenetic evidence refuting the hypothesis of Batoidea (rays and skates) as derived sharks. Mol Phylogenet Evol 26: 215-221.
15. Inoue JG, Miya M, Lam K, Tay BH, Danks JA, et al. (2010) Evolutionary origin and phylogeny of the modern holocephalans (Chondrichthyes: Chimaeriformes): a mitogenomic perspective. Mol Biol Evol 27: 2576-2586.
16. Velez-Zuazo X, Agnarsson I, (2011) Shark tales: a molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes). Mol Phylogenet Evol 58: 207-217.
17. Winchell CJ, Martin AP, Mallatt J, (2004) Phylogeny of elasmobranchs based on LSU and SSU ribosomal RNA genes. Mol Phylogenet Evol 31: 214-224.
18. Maisey JG, Naylor GJP, Ward DJ (2004) Mesozoic elasmobranchs, neoselachian phylogeny and the rise of modern elasmobranch diversity. In: Arratia G, Tintori A, editors. Mesozoic fishes 3- systematics, paleoenvironments and biodiversity. München: Verlag Dr. Friedrich Pfeil. 17-56.
19. Klug S, (2010) Monophyly, phylogeny and systematic position of the dagger Synechodontiformes (Chondrichthyes, Neoselachii). Zool Scr 39: 37-49.
20. Heinicke M, Naylor G, Hedges S (2009) Cartilaginous fishes (Chondrichthyes). In: Kumar S, Hedges S, editors. The Timetree of Life. New York: Oxford University Press. 320-327.
21. Martin AP, Naylor GJ, Palumbi SR, (1992) Rates of mitochondrial DNA evolution in sharks are slow compared with mammals. Nature 357: 153-155.
22. Mulley JF, Zhong YF, Holland PW, (2009) Comparative genomics of chondrichthyan Hoxa clusters. BMC Evol Biol 9: 218.
23. Wang J, Lee AP, Kodzius R, Brenner S, Venkatesh B, (2009) Large number of ultraconserved elements were already present in the jawed vertebrate ancestor. Mol Biol Evol 26: 487-490.
24. Martin AP, (1999) Substitution rates of organelle and nuclear genes in sharks: implicating metabolic rate (again). Mol Biol Evol 16: 996-1002.
25. Martin AP, Palumbi SR, (1993) Body Size, Metabolic-Rate, Generation Time, and the Molecular Clock. Proc Natl Acad Sci U S A 90: 4087-4091.
26. Hedges SB, Kumar S (2009) The Timetree of Life. New York: Oxford University Press.
27. Iglesias SP, Lecointre G, Sellos DY, (2005) Extensive paraphylies within sharks of the order Carcharhiniformes inferred from nuclear and mitochondrial genes. Mol Phylogenet Evol 34: 569-583.
28. Delsuc F, Brinkmann H, Philippe H, (2005) Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 6: 361-375.
29. Philippe H, Delsuc F, Brinkmann H, Lartillot N, (2005) Phylogenomics. Annu Rev Ecol Evol Syst 36: 541-562.
30. Li C, Orti G, Zhang G, Lu G, (2007) A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study. BMC Evol Biol 7: 44.
31. Townsend TM, Alegre RE, Kelley ST, Wiens JJ, Reeder TW, (2008) Rapid development of multiple nuclear loci for phylogenetic analysis using genomic resources: an example from squamate reptiles. Mol Phylogenet Evol 47: 129-142.
32. Shen XX, Liang D, Wen JZ, Zhang P, (2011) Multiple genome alignments facilitate development of NPCL markers: a case study of tetrapod phylogeny focusing on the position of turtles. Mol Biol Evol 28: 3237-3252.
33. Aschliman NC, Nishida M, Miya M, Inoue JG, Rosana KM, et al. (2012) Body plan convergence in the evolution of skates and rays (Chondrichthyes: Batoidea). Mol Phylogenet Evol 63: 28-42.
34. Li C, Matthes-Rosana KA, Garcia M, Naylor GJ, (2012) Phylogenetics of Chondrichthyes and the problem of rooting phylogenies with distant outgroups. Mol Phylogenet Evol 63: 365-373.
35. Benton M, Donoghue P, Asher R (2009) Calibrating and constraining molecular clocks. In: Kumar S, Hedges S, editors. The Timetree of Life. Oxford: Oxford University Press. 35-86.
36. Ivanov A, (2005) Early Permian chondrichthyans of the Middle and South Urals. Revista Brasileira de Paleontologia 8: 127-138.
37. Dessimoz C, Zoller S, Manousaki T, Qiu H, Meyer A, et al. (2011) Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes). Brief Bioinform 12: 474-484.
38. Ravi V, Venkatesh B, (2008) Rapidly evolving fish genomes and teleost diversity. Curr Opin Genet Dev 18: 544-550.
39. King BL, Gillis JA, Carlisle HR, Dahn RD, (2011) A natural deletion of the HoxC cluster in elasmobranch fishes. Science 334: 1517.
40. Hay JM, Subramanian S, Millar CD, Mohandesan E, Lambert DM, (2008) Rapid molecular evolution in a living fossil. Trends Genet 24: 106-109.
41. Miller HC, Moore JA, Allendorf FW, Daugherty CH, (2009) The evolutionary rate of tuatara revisited. Trends Genet 25: 13-15.
42. Amemiya CT, Powers TP, Prohaska SJ, Grimwood J, Schmutz J, et al. (2010) Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome. Proc Natl Acad Sci U S A 107: 3622-3627.
43. Casane D, Laurenti P, (2013) Why coelacanths are not 'living fossils': A review of molecular and morphological data. Bioessays 35: 332-338.
44. Ballard WW, Mellinger J, Lechenault H, (1993) A Series of normal stages for development of Scyliorhinus canicula, the lesser spotted dogfish (Chondrichthyes, Scyliorhinidae). J Exp Zool 267: 318-336.
45. Didier DA, Leclair EE, Vanbuskirk DR, (1998) Embryonic staging and external features of development of the chimaeroid fish, Callorhinchus milli (Holocephali, Callorhinchidae). J Morphol 236: 25-47.
46. Luer CA, Walsh CJ, Bodine AB, Wyffels JT, (2007) Normal embryonic development in the clearnose skate, Raja eglanteria, with experimental observations on artificial insemination. Environ Biol Fish 80: 239-255.
47. Parton A, Bayne CJ, Barnes DW, (2003) Analysis and functional annotation of expressed sequence tags from in vitro cell lines of elasmobranchs: Spiny dogfish shark (Squalus acanthias) and little skate (Leucoraja erinacea). Comp Biochem Physiol Part D Genomics Proteomics 5: 199-206.
48. Gordon D (2003) Viewing and editing assembled sequences using Consed. Curr Protoc Bioinformatics Unit 11.2. doi: 10.1002/0471250953.bi1102s02.
49. Gordon D, Abajian C, Green P, (1998) Consed: a graphical tool for sequence finishing. Genome Res 8: 195-202.
50. Burge C, Karlin S, (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol 268: 78-94.
51. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
52. Katoh K, Kuma K, Toh H, Miyata T, (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33: 511-518.
53. Saitou N, Nei M, (1987) The neighbor-joining method - a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
54. Felsenstein J, (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368-376.
55. Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
56. Daubin V, Gouy M, Perriere G, (2001) Bacterial molecular phylogeny using supertree approach. Genome Inform 12: 155-164.
57. Gribaldo S, Philippe H, (2002) Ancient phylogenetic relationships. Theor Popul Biol 61: 391-408.
58. Dehal P, Boore JL, (2005) Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol 3: e314.
59. Kuraku S, (2010) Palaeophylogenomics of the vertebrate ancestor - impact of hidden paralogy on hagfish and lamprey gene phylogeny. Integr Comp Biol 50: 124-129.
60. Kuraku S, Meyer A, (2009) The evolution and maintenance of Hox gene clusters in vertebrates and the teleost-specific genome duplication. Int J Dev Biol 53: 765-773.
61. Schmidt HA, Strimmer K, Vingron M, von Haeseler A, (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502-504.
62. Yang Z, (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586-1591.
63. Rannala B, Yang Z, (2007) Inferring speciation times under an episodic molecular clock. Syst Biol 56: 453-466.
64. Jones DT, Taylor WR, Thornton JM, (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8: 275-282.
65. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW, (2011) GenBank. Nucleic Acids Res 39: D32-37.
66. Flicek P, Amode MR, Barrell D, Beal K, Brent S, et al. (2011) Ensembl 2011. Nucleic Acids Res 39: D800-806.
67. VISTA Genome Browser. Available: http://genome.lbl.gov/vista/index.shtml Accessed 2013 June 1.
68. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 28: 2731-9.
69. Compagno LJV, Didier DA, Burgess GH (2005) Classification of Chondrichthyan Fish. In: Fowler SL editor. Sharks, Rays, and Chimaeras, the Status of the Chondrichthyan Fishes. Gland: IUCN/SSC Shark Specialist Group. 4-11.