Relative character-state space, amount of potential phylogenetic information, and heterogeneity of nucleotide and amino acid characters

Molecular Phylogenetics and Evolution

Volumn 32, Issue 3, 2004, Pages 913-926

  Simmons, Mark P ^a   Carr, Timothy G ^b   O'Neill, Kevin ^c  

^a Department of Environmental and Radiological Health Sciences   (United States)

^b Department of Obstetrics Gynecology   (United States)

^c Department of Computer Science and School of Operations Research and Information Engineering   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; NUCLEOTIDE; PROTEIN;

ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; COMPARATIVE STUDY; GENETIC VARIABILITY; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY;

AMINO ACIDS; CLASSIFICATION; EVOLUTION, MOLECULAR; MODELS, GENETIC; NUCLEOTIDES; PHYLOGENY; PROTEINS; RESEARCH DESIGN; VARIATION (GENETICS);

EID: 3843150595     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2004.04.011     Document Type: Article

References (91)

1. Agosti D., Jacobs D., DeSalle R. On combining protein sequences and nucleic acid sequences in phylogenetic analysis: the homeobox protein case. Cladistics. 12:1996;65-82
2. Albert V.A., Backlund A., Bremer K., Chase M.W., Manhart J.R., Mishler B.D., Nixon K.C. Functional constraints and rbc L evidence for land plant phylogeny. Ann. Mol. Bot. Gard. 81:1994;534-567
3. Albert V.A., Chase M.W., Mishler B.D. Character-state weighting for cladistic analysis of protein-coding DNA sequences. Ann. Mol. Bot. Gard. 80:1993;752-766
4. Anderson S.G.E., Sharp P.M. Codon usage and base composition in Rickettsia prowazekii. J. Mol. Evol. 42:1996;525-536
5. Archie J.W. A randomization test for phylogenetic information in systematic data. Syst. Zool. 38:1989;219-252
6. Bharathan G., Janssen B.-J., Kellogg E.A., Sinha N. Phylogenetic relationships and evolution of the KNOTTED class of plant homeodomain proteins. Mol. Biol. Evol. 16:1999;553-563
7. Björklund M. Are third positions really that bad? A test using vertebrate cytochrome. b Cladistics. 15:1999;191-197
8. Black W.C.I., Roehrdanz R.L. Mitochondrial gene order is not conserved in arthropods: prostriate and metastriate tick mitochondrial genomes. Mol. Biol. Evol. 15:1998;1772-1785
9. Blouin M.S., Yowell C.A., Courtney C.H., Dame J.B. Substitution bias, rapid saturation, and the use of mtDNA for nematode systematics. Mol. Biol. Evol. 15:1998;1719-1727
10. Broughton R.E., Stanley S.E., Durrett R.T. Quantification of homoplasy for nucleotide transitions and transversions and a reexamination of assumptions in weighted phylogenetic analysis. Syst. Biol. 49:2000;617-627
11. Burmester T. Molecular evolution of the arthropod hemocyanin superfamily. Mol. Biol. Evol. 18:2001;184-195
12. Campbell D.L., Brower A.V.Z., Pierce N.E. Molecular evolution of the Wingless gene and its implications for the phylogenetic placement of the butterfly family Riodinidae (Lepidoptera: Papilionoidea). Mol. Biol. Evol. 17:2000;684-696
13. Chang B.S.W., Campbell D.L. Bias in phylogenetic reconstruction of vertebrate rhodopsin sequences. Mol. Biol. Evol. 17:2000;1220-1231
14. Conant G.C., Lewis P.O. Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inference. Mol. Biol. Evol. 18:2001;1024-1033
15. Dayhoff, M.O., Eck, R.V., Park, C.M., 1972. A model of evolutionary change in proteins. In: Dayhoff, M.O. (Ed.), Atlas of protein sequence and structure. National Biomedical Research Foundation, Washington, DC, pp. 89-99
16. Durnford D.G., Deane J.A., Tan S., McFadden G.I., Gantt E., Green B.R. A phylogenetic assessment of the eukaryotic light-harvesting antenna proteins, with implications for plastid evolution. J. Mol. Evol. 48:1999;59-68
17. Faith D., Cranston P. Could a cladogram this short have arisen by chance alone? Cladistics. 7:1991;1-28
18. Farris J.S. On comparing the shapes of taxonomic trees. Syst. Zool. 22:1973;50-54
19. Farris J.S. The retention index and the rescaled consistency index. Cladistics. 5:1989;417-419
20. Farris J.S., Albert V.A., Källersjö M., Lipscomb D., Kluge A.G. Parsimony jackknifing outperforms neighbor-joining. Cladistics. 12:1996;99-124
21. Felsenstein J. Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Syst. Zool. 22:1973;240-249
22. Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:1978;401-410
23. Felsenstein J. Parsimony in systematics: biological and statistical issues. Ann. Rev. Ecol. Syst. 14:1983;313-333
24. Foster P.G., Jermiin L.S., Hickey D.A. Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria. J. Mol. Evol. 44:1997;282-288
25. Friedlander T.P., Regier J.C., Mitter C., Wagner D.L. A nuclear gene for higher level phylogenetics: phosphoenolpyruvate carboxykinase tracks mesozoic-age divergences within Lepidoptera (Insecta). Mol. Biol. Evol. 13:1996;594-604
26. Freudenstein J.V., Pickett K.M., Simmons M.P., Wenzel J.W. From basepairs to birdsongs: phylogenetic data in the age of genomics. Cladistics. 19:2003;333-347
27. Frohlich M.W., Parker D.S. The mostly male theory of flower evolutionary origins: from genes to fossils. Syst. Bot. 25:2000;155-170
28. Goffinet B., Cox C.J., Shaw A.J., Hedderson T.A.J. The Bryophyta (mosses): systematic and evolutionary inferences from an rps4 gene (cpDNA) phylogeny. Ann. Bot. 87:2001;191-208
29. Goodman M., Czelusniak J., Moore G.W., Romero-Herrera A.E., Matsuda G. Fitting the gene lineage into its species lineage: a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Zool. 28:1979;132-163
30. Graybeal A. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol. 47:1998;9-17
31. Gu X., Hewett-Emmett D., Li W.-H. Directional mutational pressure affects the amino acid composition and hydrophobicity of proteins in bacteria. Genetica. 102-103:1998;383-391
32. Hasebe M., Kofuji R., Ito M., Kato M., Iwatsuki K., Ueda K. Phylogeny of gymnosperms inferred from rbc L gene sequences. Bot. Mag. Tokyo. 105:1992;673-679
33. Hasegawa M., Hashimoto T., Adachi J., Iwabe N., Miyata T. Early branchings in the evolution of eukaryotes: ancient divergence of Entamoeba that lacks mitochondria revealed by protein sequence data. J. Mol. Evol. 36:1993;380-388
34. Hashimoto T., Nakamura Y., Nakamura F., Shirakura T., Adachi J., Goto N., Okamoto K., Hasegawa M. Protein phylogeny gives a robust estimation for early divergences of eukaryotes: phylogenetic place of a mitochondrial-lacking protozoan, Giardia lamblia. Mol. Biol. Evol. 11:1994;65-71
35. Hassanin A., Lecointre G., Tillier S. The 'evolutionary signal' of homoplasy in protein-coding gene sequences and its consequences for a priori weighting in phylogeny. CR Acad. Sci. III. 321:1998;611-620
36. Hendy M.D., Penny D. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:1989;297-309
37. Hillis D.M. Inferring complex phylogenies. Nature. 383:1996;130-131
38. Hillis D.M. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47:1998;3-8
39. Hillis D.M., Bull J.J., White M.E., Badgett M.R., Molineux I.J. Experimental phylogenetics: generation of a known phylogeny. Science. 255:1992;589-592
40. Ivics, Z., Izsvak, Z., Minter, A., Hackett, P.B., 1996. Identification and evolution of functional domains of Tcl-like transposable elements. 93, 5008-5013
41. Jermiin, L.S., Ho, S.Y.W., Ababneh, F., Robinson, J., Larkum, A.W.D., in press. The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated. Systematic Biology
42. Jukes T.H., Bhushan V. Silent nucleotide substitutions and G. + C content of some mitochondrial and bacterial genes J. Mol. Evol. 24:1986;39-44
43. Källersjö M., Albert V.A., Farris J.S. Homoplasy increases phylogenetic structure. Cladistics. 15:1999;91-93
44. Kimura M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:1980;111-120
45. Kluge A.G., Farris J.S. Quantitative phyletics and the evolution of Anurans. Syst. Zool. 18:1969;1-32
46. Kumar S., Gadagkar S.R. Disparity index: a simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences. Genetics. 158:2001;1321-1327
47. Kumar S., Tamura K., Jakobsen I.B., Nei M. MEGA2: Molecular Evolutionary Genetics Analysis software. Bioinformatics. 17:2001;1244-1245
48. Lewis L.A., Mishler B.D., Vilgalys R. Phylogenetic relationships of the liverworts (Hepaticeae), a basal embryophyte lineage, inferred from nucleotide sequence data of the chloroplast gene rbc L. Mol. Phylogenet. Evol. 7:1997;377-393
49. Lieckfeldt E., Cavignac Y., Fekete C., Börner T. Endochitinase gene-based phylogenetic analysis of Trichoderma. Microbiol. Res. 155:2000;7-15
50. Lockhart P.J., Howe C.J., Bryant D.A., Beanland T.J., Larkum A.W.D. Substitutional bias confounds inference of cyanelle origins from sequence data. J. Mol. Evol. 34:1992;153-162
51. Lockhart P.J., Penny D., Hendy M.D., Howe C.J., Beanland T.J., Larkum A.W.D. Controversy on chloroplast origins. FEBS Lett. 301:1992;127-131
52. Loomis W.F., Smith D.W. Molecular phylogeny of Dictyostelium discoideum by protein sequence comparison. Proc. Natl. Acad. Sci. USA. 87:1990;9093-9097
53. Maddison, W.P., Maddison, D.R., 1992. MacClade: Analysis of phylogeny and character evolution. Sinauer Associates, Inc., Sunderland, Massachusetts
54. Manhart J.R. Phylogenetic analysis of green plant rbc L sequences. Mol. Phylogenet. Evol. 3:1994;114-127
55. McArthur A.G., Knodler L.A., Silberman J.D., Davids B.J., Gillin F.D., Sogin M.L. The evolutionary origins of eukaryotic protein disulfide isomerase domains: new evidence from the amitochondriate protist Giardia lamblia. Mol. Biol. Evol. 18:2001;1455-1463
56. Meyer A. Shortcomings of the cytochrome b gene as a molecular marker. Trends Ecol. Evol. 9:1994;278-280
57. Mishler B.D., Bremer K., Humphries C.J., Churchill S.P. The use of nucleic acid sequence data in phylogenetic reconstruction. Taxon. 37:1988;391-395
58. Mitchell A., Mitter C., Regier J.C. More taxa or more characters revisited: combining data from nuclear protein-encoding genes for phylogenetic analyses of Noctuoidea (Insecta: Lepidoptera). Syst. Biol. 49:2000;202-224
59. Miyamoto M.M., Fitch W.M. Testing the covarion hypothesis of molecular evolution. Mol. Biol. Evol. 12:1995;503-513
60. Moritz C., Dowling T.E., Brown W.M. Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Ann. Rev. Ecol. Syst. 18:1987;269-292
61. Naylor G.J.P., Collins T.M., Brown W.M. Hydrophobicity and phylogeny. Nature. 373:1995;565-566
62. Naylor G.J.P., Gerstein M. Measuring shifts in function and evolutionary opportunity using variability profiles: a case study of the globins. J. Mol. Evol. 51:2000;223-233
63. Nixon, K.C., 2002. Winclada version 1.00.08. Published by the author, Ithaca, New York
64. Olmstead R.G., Reeves P.A., Yen A.C. Patterns of sequence evolution and implications for parsimony analysis of chloroplast DNA. Soltis D.S., Soltis P.S., Doyle J.J. Molecular Systematics of Plants II DNA Sequencing. 1998;164-187 Kluwer, Boston
65. Philippe H., Lecointre G., Lê H.L.V., Le Guyader H. A critical study of homoplasy in molecular data with the use of a morphologically based cladogram, and its consequences for character weighting. Mol. Biol. Evol. 13:1996;1174-1186
66. Prager E.M., Wilson A.C. Ancient origin of lactalbumin from lysozyme: analysis of DNA and amino acid sequences. J. Mol. Evol. 27:1988;326-335
67. Rannala B., Yang Z. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43:1996;304-311
68. Rodríguez-Trelles F., Tarrío R., Ayala F.J. Switch in codon bias and increased rates of amino acid substitution in the Drosophila saltans species group. Genetics. 153:1999;339-350
69. Rodríguez-Trelles F., Tarrío R., Ayala F.J. Fluctuating mutation bias and the evolution of base composition in Drosophila. J. Mol. Evol. 50:2000;1-10
70. Rosenberg M.S., Kumar S. Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference. Mol. Biol. Evol. 20:2003;610-621
71. SAS Institute, 1992. SAS/STAT software: changes and enhancements, release 6.07. SAS Technical Report P-229, SAS Institute, Inc., Cary, North Carolina
72. Simmons M.P. A fundamental problem with amino-acid-sequence characters for phylogenetic analyses. Cladistics. 16:2000;274-282
73. Simmons, M.P. Accepted. Amino acid versus nucleotide characters for phylogenetic inference of the basal angiosperms. In: Sharma, A.K., Sharma, A. (Eds.), Plant genome biodiversity and function: phanerogams volume 1B. Science Publishers, Inc., Enfield, New Hampshire
74. Simmons M.P., Freudenstein J.V. Artifacts of coding amino acids and other composite characters for phylogenetic analysis. Cladistics. 18:2002;354-365
75. Simmons M.P., Ochoterena H. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 49:2000;369-381
76. Simmons M.P., Ochoterena H., Freudenstein J.V. Conflict between amino acid and nucleotide characters. Cladistics. 18:2002;200-206
77. Simmons M.P., Ochoterena H., Freudenstein J.V. Amino acid vs. nucleotide characters: challenging preconceived notions. Mol. Phylogenet. Evol. 24:2002;78-90
78. Simmons, M.P., Reeves, A., Davis, J.I., 2004. Character-state space versus rate of evolution for phylogenetic inference. Cladistics, in press
79. Simon C., Frati F., Beckenbach A., Crespi B., Liu H., Flook P. Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann. Entomol. Soc. Am. 87:1994;651-701
80. Sokal R.R., Rohlf F.J. Biometry. second ed.:1981;W.H. Freeman, New York
81. Steel M., Penny D. Parsimony, likelihood, and the role of models in molecular phylogenetics. Mol. Biol. Evol. 17:2000;839-850
82. Swofford, D.L., 1998. PAUP*: phylogenetic analysis using parsimony (* and other methods). Sinauer Associates, Inc., Sunderland, Massachusetts
83. SYSTAT, 1992. SYSTAT for the Macintosh, version 5.2.1. SYSTAT, Inc., Evanston, Illinois
84. Tsukiyama S., Ide M., Ariyoshi H., Shirakawa I. A new algorithm for generating all the maximal independent sets. SIAMJ. Comput. 6:1977;505-517
85. Wenzel J.W., Siddall M.E. Noise. Cladistics. 15:1999;51-64
86. Whelan S., de Bakker P.I.W., Goldman N. Pandit: a database of protein and associated nucleotide domains with inferred trees. Bioinformatics. 19:2003;1556-1563
87. Wilkinson M. A comparison of two methods of character construction. Cladistics. 11:1995;297-308
88. Wilson W.C., Ma H.-C., Venter E.H., van Dijk A.A., Seal B.S., Mecham J.O. Phylogenetic relationships of bluetongue viruses based on gene S7. Virus Res. 67:2000;141-151
89. Wirth T., Le Guellec R., Veuille M. Directional substitution and evolution of nucleotide content in the cytochrome oxidase II gene in earwigs (dermapteran insects). Mol. Biol. Evol. 16:1999;1645-1653
90. Woese C.R., Achenbach L., Rouviere P., Mandelco L. Archael phylogeny: reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts. Syst. Appl. Microbiol. 14:1991;364-371
91. Yang Z. On the best evolutionary rate for phylogenetic analysis. Syst. Biol. 47:1998;125-133