Dealing with saturation at the amino acid level: A case study based on anciently duplicated zebrafish genes

Gene

Volumn 295, Issue 2, 2002, Pages 205-211

  Van De Peer, Yves ^a   Frickey, Tancred ^b   Taylor, John S ^b   Meyer, Axel ^b  

^a DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^b UNIVERSITY OF KONSTANZ   (Germany)

Author keywords

Amino acid sequences; Duplicate fish genes; Mutational saturation

Indexed keywords

AMINO ACID;

AMINO ACID SEQUENCE; CHICKEN; CONFERENCE PAPER; FROG; GENE DUPLICATION; GENETIC VARIABILITY; GENOME; HUMAN; HYPOTHESIS; MOLECULAR EVOLUTION; MUTATION; NONHUMAN; PRIORITY JOURNAL; PROBABILITY; ZEBRA FISH;

AMINO ACIDS; ANIMALS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENOME; MODELS, GENETIC; PHYLOGENY; ZEBRAFISH;

ACTINOPTERYGII; ANURA; DANIO RERIO; GALLUS GALLUS; PISCES; SARCOPTERYGII; TETRAPODA;

EID: 0037036943     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(02)00689-3     Document Type: Conference Paper

References (42)

1. Adachi J., Hasegawa M. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J. Mol. Evol. 42:1996;459-468.
2. Amores A., Force A., Yan Y.L., Joly L., Amemiya C., Fritz A., Ho R.K., Langeland J., Prince V., Wang Y.L., Westerfield M., Ekker M., Postlethwait J.H. Zebrafish hox clusters and vertebrate genome evolution. Science. 282:1998;1711-1714.
3. Barbazuk W.B., Korf I., Kadavi C., Heyen J., Tata S., Wun E., Bedell J.A., McPherson J.D., Johnson S.L. The syntenic relationships of the zebrafish and human genomes. Genome Res. 10:2000;1351-1358.
4. Brinkmann H., Philippe H. Archaea sister group of bacteria? Indications from tree reconstruction artifacts in ancient phylogenies. Mol. Biol. Evol. 16:1999;817825.
5. Brown W.M., Prager E.M., Wang A., Wilson A.C. Mitochondrial DNA sequences of primates: tempo and mode of evolution. J. Mol. Evol. 18:1982;225-239.
6. Chaw S.M., Parkinson C.L., Cheng Y., Vincent T.M., Palmer J.D. Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers. Proc. Natl. Acad. Sci. USA. 97:2000;4086-4091.
7. Dayhoff M.O., Schwartz R.M., Orcutt B.C. A model of evolutionary change in proteins. Dayhoff M.O., Atlas of Protein Sequence and Structure. 1978;345-352 National Biomedical Research Foundation, Washington, DC.
8. Felsenstein J. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27:1978;401-410.
9. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 39:1985;783-791.
10. Forterre P., Philippe H. Where is the root of the universal tree of life? BioEssays. 21:1999;871-879.
11. Hansmann S., Martin W. Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis. Int. J. Syst. Evol. Microbiol. 50:2000;1655-1663.
12. Henikoff S., Henikoff J.G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA. 89:1992;10915-10919.
13. Holland P.W.H. Major transitions in animal evolution: a developmental genetic perspective. Am. Zool. 38:1998;829-842.
14. Hughes A. Phylogenies of developmentally important proteins do not support the hypothesis of two rounds of genome duplication early in vertebrate history. J. Mol. Evol. 48:1999;565-576.
15. Jones D.T., Taylor W.R., Thornton J.M. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:1992;275-282.
16. Kimura M., The Neutral Theory of Molecular Evolution. 1983;Cambridge University Press, Cambridge, UK.
17. Meyer A., Schartl M. Gene and genome duplications in vertebrates: the one-to-four (to-eight in fish) rule and the evolution of novel gene functions. Curr. Opin. Cell Biol. 11:1999;699-704.
18. Meyer T.E., Cusanovich M.A., Kamen M.D. Evidence against use of bacterial amino acid sequence data for construction of all-inclusive phylogenetic trees. Proc. Natl. Acad. Sci. USA. 83:1986;217-220.
19. Moriyama E.N., Powell J.R. Synonymous substitution rates in Drosophila: mitochondrial versus nuclear genes. J. Mol. Evol. 45:1997;378-391.
20. Nei M., Kumar S., Molecular Evolution and Phylogenetics. 2000;Oxford University Press, Oxford, UK.
21. Nickrent D.L., Parkinson C.L., Palmer J.D., Duff R.J. Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants. Mol. Biol. Evol. 17:2000;1885-1895.
22. Olsen G.J. Earliest phylogenetic branchings: comparing rRNA-based evolutionary trees inferred with various techniques. Cold Spring Harbor Symp. Quant. Biol. 52:1987;825-837.
23. Page R.D.M., Holmes E.C., Molecular Evolution, A Phylogenetic Approach. 1998;Blackwell Science, Oxford, UK.
24. Postlethwait J.H., Woods I.G., Ngo-Hazelett P., Yan Y.L., Kelly P.D., Chu F., Huang H., Hill-Force A., Talbot W.S. Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Res. 10:2000;1890-1902.
25. Robinson-Rechavi M., Marchand O., Escriva H., Bardet P.L., Zelus D., Hughes S., Laudet V. Euteleost fish genomes are characterized by expansion of gene families. Genome Res. 11:2001;781-788.
26. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:1987;406-425.
27. Spring J. Vertebrate evolution by interspecific hybridization - are we polyploid? FEBS Lett. 400:1997;2-8.
28. Skrabanek L., Wolfe K.H. Eukaryote genome duplication where's the evidence? Curr. Opin. Gen. Dev. 8:1998;694-700.
29. Strimmer K., von Haeseler A. Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:1996;964-969.
30. Swofford D.L., PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. 1998;Sinauer Associates, Sunderland, MA.
31. Swofford D.L., Olsen G.J., Waddell P.J., Hillis D.M. Phylogenetic inference. Hillis D.M., Moritz C., Mable B.K., Molecular Systematics. 1996;407-514 Sinauer Associates, Sunderland, MA.
32. Tang K.L., Berendzen P.B., Wiley E.O., Morrissey J.F., Winterbottom R., Johnson G.D. The phylogenetic relationships of the suborder Acanthuroidei (Teleostei: Perciformes) based on molecular and morphological evidence. Mol. Phylogenet. Evol. 11:1999;415-425.
33. Taylor J.S., Brinkmann H. 2R or not 2R? Trends Genet. 17:2001;488-489.
34. Taylor J.S., Van de Peer Y., Braach I., Meyer A. Comparative genomics provides evidence for an ancient genome duplication event in fish. Phil. Trans. R. Soc. Lond. B. 356:2001;119.
35. Van de Peer Y., Ben Ali A., Meyer A. Microsporidia: accumulating molecular evidence that a group of amitochondriate and suspectedly primitive eukaryotes are just curious fungi. Gene. 246:2000;1-8.
36. Van de Peer Y., Taylor J.S., Braasch I., Meyer A. The ghost of selection past: rates of evolution and functional divergence in anciently duplicated genes. J. Mol. Evol. 53:2001;434-444.
37. Wang Y., Gu X. Evolutionary patterns of gene families generated in the early stage of vertebrates. J. Mol. Evol. 51:2000;88-96.
38. Wakeley J. The excess of transitions among nucleotide substitutions: new methods of estimating transition bias underscore its significance. Trends Ecol. Evol. 11:1996;158-163.
39. Wittbrodt J., Meyer A., Schartl M. More genes in fish? BioEssays. 20:1998;511-512.
40. Woods I.G., Kelly P.D., Chu F., Ngo-Hazelett P., Yan Y.L., Huang H., Postlethwait J.H., Talbot W.S. A comparative map of the zebrafish genome. Genome Res. 10:2000;1903-1914.
41. Yang Z. Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol. Evol. 11:1996;367-372.
42. Zardoya R., Meyer A. Vertebrate phylogeny: limits of inference of mitochondrial genome and nuclear rDNA data due to an adverse phylogenetic signal/noise ratio. Ahlberg P., Major Events in Early Vertebrate Evolution. 2001;135-155 Taylor and Francis, London.