Login

Join for Free!
116996 members
table of contents table of contents

An alternative source of time constraints in teleostean phylogeny by evaluating a …


Biology Articles » Biogeography » Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences » References

References
- Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences

  1. Yang Z: Computational Molecular Evolution. New York: Oxford University Press; 2006.

  2. Benton MJ, Donoghue PC: Paleontological evidence to date the tree of life.

    Mol Biol Evol 2007, 24:26-53. 

  3. Hedges SB, Kumar S: Precision of molecular time estimates.

    Trends Genet 2004, 20:242-247.

  4. Benton MJ: The Fossil Record. Volume 2. London: Chapman & Hall; 1993. 

  5. Kumazawa Y, Yamaguchi M, Nishida M: Mitochondrial molecular clocks and the origin of euteleostean biodiversity: Familial radiation of perciforms may have predated the Cretaceous/Tertiary boundary. In The biology of biodiversity. Edited by: Kato M. Tokyo: Springer; 1999:35-52. 

  6. Kumazawa Y, Nishida M: Molecular phylogeny of osteoglossoids: A new model for Gondwanian origin and plate tectonic transportation of the Asian arowana.

    Mol Biol Evol 2000, 17:1869-1878.

  7. Genner MJ, Seehausen O, Lunt DH, Joyce DA, Shaw PW, Carvalho GR, Turner GF: Age of cichlids: new dates for ancient lake fish radiations.

    Mol Biol Evol 2007, 24:1269-1282. 

  8. Banarescu P: Zoogeography of fresh waters. Wiesbaden: AULA-Verlag; 1990.

  9. Lundberg JG: African-South American freshwater fish clades and continental drift: Problems with a paradigm. In Biological relationships between Africa and South America. Edited by: Goldblatt P. New Haven: Yale University Press; 1993:156-198.

  10. Avise JC: Phylogeography: The History and Formation of Species. Cambridge: Harvard University Press; 2000.

  11. Nelson JS: Fishes of the world. 4th edition. Hoboken: John Wiley & Sons; 2006.

  12. Kocher TD: Adaptive evolution and explosive speciation: the cichlid fish model.

    Nat Rev Genet 2004, 5:288-298. 

  13. Stiassny MLJ: Phylogenetic intrarelationships of the family Cichlidae: an overview. In Cichlid Fishes: behaviour, ecology and evolution. Edited by: Keenleyside MHA. London: Chapman & Hall; 1991:1-35.

  14. Zardoya R, Vollmer DM, Craddock C, Streelman JT, Karl S, Meyer A: Evolutionary conservation of microsatellite flanking regions and their use in resolving the phylogeny of cichlid fishes (Pisces: Perciformes).

    Proc R Soc Lond B 1996, 263:1589-1598. 

  15. Farias IP, Orti G, Meyer A: Total evidence: molecules, morphology, and the phylogenetics of cichlid fishes.

    J Exp Zool 2000, 288:76-92. 

  16. Sparks JS, Smith WL: Phylogeny and biogeography of cichlid fishes (Teleostei: Perciformes: Cichlidae).

    Cladistics 2004, 20:501-517. 

  17. Chakrabarty P: Cichlid biogeography: comment and review.

    Fish Fish 2004, 5:97-119.

  18. Sparks JS, Smith WL: Freshwater fishes, dispersal ability, and nonevidence: "Gondwana Life Rafts" to the rescue.

    Syst Biol 2005, 54:158-165. 

  19. Vences M, Freyhof J, Sonnenberg R, Kosuch J, Veith M: Reconciling fossils and molecules: Cenozoic divergence of cichlid fishes and the biogeography of Madagascar.

    J Biogeogr 2001, 28:1091-1099.

  20. Murray AM: The fossil record and biogeography of the Cichlidae (Actinopterygii : Labroidei).

    Biol J Linn Soc 2001, 74:517-532.

  21. 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, 1:416-426.

  22. 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, 17:437-455.

  23. Inoue JG, Miya M, Tsukamoto K, Nishida M: Complete mitochondrial DNA sequence of the Japanese sardine Sardinops melanostictus.

    Fish Sci 2000, 66:924-932.

  24. Inoue JG, Miya M, Tsukamoto K, Nishida M: A mitogenomic perspective on the basal teleostean phylogeny: resolving higher-level relationships with longer DNA sequences.

    Mol Phylogenet Evol 2001, 20:275-285. 

  25. Ishiguro N, Miya M, Nishida M: Complete mitochondrial DNA sequence of ayu, Plecoglossus altivelis.

    Fish Sci 2001, 67:474-481.

  26. Kawaguchi A, Miya M, Nishida M: Complete mitochondrial DNA sequence of Aulopus japonicus (Teleostei : Aulopiformes), a basal Eurypterygii: longer DNA sequences and higher-level relationships.

    Ichthyol Res 2001, 48:213-223.

  27. Inoue JG, Miya M, Aoyama J, Ishikawa S, Tsukamoto K, Nishida M: Complete mitochondrial DNA sequence of the Japanese eel Anguilla japonica.

    Fish Sci 2001, 67:118-125.

  28. Inoue JG, Miya M, Tsukamoto K, Nishida M: Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish".

    Mol Phylogenet Evol 2003, 26:110-120.

  29. Kumazawa Y, Nishida M: Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics.

    J Mol Evol 1993, 37:380-398. 

  30. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG: The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.

    Nucleic Acids Res 1997, 25:4876-4882. 

  31. Maddison WP, Maddison DR: MacClade 4.0: analysis of phylogeny and character evolution. Sunderland: Sinauer Associates; 2000. 

  32. Huelsenbeck JP, Ronquist F: MRBAYES: Bayesian inference of phylogenetic trees.

    Bioinformatics 2001, 17:754-755.

  33. Yang ZH: Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods.

    J Mol Evol 1994, 39:306-314. 

  34. Nylander JA, Ronquist F, Huelsenbeck JP, Nieves-Aldrey JL: Bayesian phylogenetic analysis of combined data.

    Syst Biol 2004, 53:47-67. 

  35. Stamatakis A: RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.

    Bioinformatics 2006, 22:2688-2690. 

  36. Schmidt HA, Strimmer K, Vingron M, von Haeseler A: TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing.

    Bioinformatics 2002, 18:502-504.

  37. 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, 29:170-179.

  38. Shimodaira H, Hasegawa M: Multiple comparisons of log-likelihoods with applications to phylogenetic inference.

    Mol Biol Evol 1999, 16:1114-1116.

  39. Kass RE, Raftery AE: BAYES FACTORS.

    J Am Stat Assoc 1995, 90:773-795.

  40. Brandley MC, Schmitz A, Reeder TW: Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards.

    Syst Biol 2005, 54:373-390.

  41. Thorne JL, Kishino H, Painter IS: Estimating the rate of evolution of the rate of molecular evolution.

    Mol Biol Evol 1998, 15:1647-1657. 

  42. Yang ZH: PAML: a program package for phylogenetic analysis by maximum likelihood.

    Comput Appl Biosci 1997, 13:555-556.

  43. Mabuchi K, Miya M, Azuma Y, Nishida M: Independent evolution of the specialized pharyngeal jaw apparatus in cichlid and labrid fishes.

    BMC Evol Biol 2007, 7:10.

  44. Asakawa S, Kumazawa Y, Araki T, Himeno H, Miura K, Watanabe K: Strand-specific nucleotide composition bias in echinoderm and vertebrate mitochondrial genomes.

    J Mol Evol 1991, 32:511-520. 

  45. Miya M, Takeshima H, Endo H, Ishiguro NB, Inoue JG, Mukai T, Satoh TP, Yamaguchi M, Kawaguchi A, Mabuchi K, Shirai SM, Nishida M: Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences.

    Mol Phylogenet Evol 2003, 26:121-138.

  46. Kikugawa K, Katoh K, Kuraku S, Sakurai H, Ishida O, Iwabe N, Miyata T: Basal jawed vertebrate phylogeny inferred from multiple nuclear DNA-coded genes.

    BMC Biol 2004, 2:3. 

  47. Patterson C: Interrelationships of holosteans. In Interrelationships of fishes. Edited by: Greenwood PH, Miles RS, Patterson C. London: Academic Press; 1973:233-305.

  48. Streelman JT, Karl SA: Reconstructing labroid evolution with single-copy nuclear DNA.

    Proc R Soc Lond B 1997, 264:1011-1020.

  49. Briggs JC: Fishes and birds: Gondwana life rafts reconsidered.

    Syst Biol 2003, 52:548-553.

  50. Smith AG, Smith DG, Funnell BM: Atlas of Mesozoic and Cenozoic coastlines. New York: Cambridge University Press; 1994.

  51. Storey BC: The role of mantle plumes in continental breakup: case histories from Gondwanaland.

    Nature 1995, 377:301-308.

  52. Masters JC, de Wit MJ, Asher RJ: Reconciling the origins of Africa, India and Madagascar with vertebrate dispersal scenarios.

    Folia Primatol 2006, 77:399-418. 

  53. Malabarba MC, Zuleta O, Del Papa C: Proterocara argentina, a new fossil cichlid from the Lumbrera Formation, Eocene of Argentina.

    J Vertebr Paleontol 2006, 26:267-275. 

  54. 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.

  55. 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, 81:29-39. 

  56. Steinke D, Salzburger W, Meyer A: Novel relationships among ten fish model species revealed based on a phylogenomic analysis using ESTs.

    J Mol Evol 2006, 62:772-784.

  57. Hurley IA, Mueller RL, Dunn KA, Schmidt EJ, Friedman M, Ho RK, Prince VE, Yang ZH, Thomas MG, Coates MI: A new time-scale for ray-finned fish evolution.

    Proc R Soc Lond B 2007, 274:489-498. 

  58. Kumar S, Hedges SB: A molecular timescale for vertebrate evolution.

    Nature 1998, 392:917-920.

  59. Wray GA, Levinton JS, Shapiro LH: Molecular evidence for deep precambrian divergences among metazoan phyla.

    Science 1996, 274:568-573.

  60. Benton MJ, Ayala FJ: Dating the tree of life.

    Science 2003, 300:1698-1700. 

  61. Kumazawa Y, Azuma Y, Nishida M: Tempo of mitochondrial gene evolution: Can mitochondrial DNA be used to date old divergences?

    Endocytobiosis Cell Res 2004, 15:136-142.

  62. Martin AP, Palumbi SR: Body size, metabolic rate, generation time, and the molecular clock.

    Proc Natl Acad Sci USA 1993, 90:4087-4091.

  63. Sparks JS, Smith WL: Phylogeny and biogeography of the Malagasy and Australasian rainbowfishes (Teleostei : Melanotaenioidei): Gondwanan vicariance and evolution in freshwater.

    Mol Phylogenet Evol 2004, 33:719-734.

  64. Botella H, Blom H, Dorka M, Ahlberg PE, Janvier P: Jaws and teeth of the earliest bony fishes.

    Nature 2007, 448:583-586. 


rating: 0.00 from 0 votes | updated on: 27 Oct 2008 | views: 11240 |

Rate article:







excellent!bad…