Character-state space versus rate of evolution in phylogenetic inference

Cladistics

Volumn 20, Issue 2, 2004, Pages 191-204

  Simmons, Mark P ^a   Reeves, Aaron ^a   Davis, Jerrold I ^b  

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

^b Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHARACTER DISPLACEMENT; CLADISTICS; EVOLUTION; PHYLOGENY;

EID: 2942556943     PISSN: 07483007     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1096-0031.2004.00014.x     Document Type: Article

References (70)

1. Albert, V.A., Backlund, A., Bremer, K., Chase, M.W., Manhart, J.R., Mishler, B.D., Nixon, K.C., 1994. Functional constraints and rbcL evidence for land plant phylogeny. Ann. Mo. Bot. Gard. 81, 534-567.
2. Archie, J.W., 1989. A randomization test for phylogenetic information in systematic data. Syst. Zool. 38, 219-252.
3. Baldauf, S.L., 2003. The deep roots of eukaryotes. Science 300, 1703-1706.
4. Björklund, M., 1999. Are third positions really that bad? A test using vertebrate cytochrome b. Cladistics 15, 191-197.
5. Black, W.C., Roehrdanz, R.L., 1998. Mitochondrial gene order is not conserved in arthropods: prostriate and metastriate tick mitochondrial genomes. Mol. Biol. Evol. 15, 1772-1785.
6. Brooks, D.R., McLennan, D.A., 1994. Historical ecology as a research programme: scope, limitations and the future. In: Eggleton, P., Vane-Wright, R.I. (Eds.), Phylogenetics and Ecology. The Linnean Society of London, London, pp. 1-27.
7. Broughton, R.E., Stanley, S.E., Durrett, R.T., 2000. Quantification of homoplasy for nucleotide transitions and transversions and a reexamination of assumptions in weighted phylogenetic analysis. Syst. Biol. 49, 617-627.
8. Campbell, D.L., Brower, A.V.Z., Pierce, N.E., 2000. Molecular evolution of the Wingless gene and its implications for the phylogenetic placement of the butterfly family Riodinidae (Lepidoptera: Papilionoidea). Mol. Biol. Evol. 17, 684-696.
9. Chapman, R.W., Avise, J.C., Asmussen, M.A., 1979. Character state restrictions and boundary conditions in the evolution of quantitative multistate characters. J. Theor. Biol. 80, 51-64.
10. Collins, D.W., Jukes, T.H., 1994. Rates of transition and transversion in coding sequences since the human-rodent divergence. Genomics 20, 386-396.
11. Collins, T.M., Wimberger, P.M., Naylor, G.J.P., 1994. Compositional bias, character-state bias, and character-state reconstruction using parsimony. Syst. Biol. 43, 482-496.
12. Davis, J.I., Simmons, M.P., Stevenson, D.W., Wendel, J.F., 1998. Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atpA sequences. Syst. Biol. 47, 282-310.
13. 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.
14. Edwards, S.V., Arctander, P., Wilson, A.C., 1991. Mitochondrial resolution of a deep branch in the genealogical tree for perching birds. Proc. Roy. Soc., London, Ser. B 243, 99-107.
15. Eyre-Walker, A., 1998. Problems with parsimony in sequences of biased base composition. J. Mol. Evol. 47, 686-690.
16. Faith, D., Cranston, P., 1991. Could a cladogram this short have arisen by chance alone? Cladistics 7, 1-28.
17. Farris, J.S., 1989. The retention index and the rescaled consistency index. Cladistics 5, 417-419.
18. Felsenstein, J., 1978a. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27, 401-410.
19. Felsenstein, J., 1978b. The number of evolutionary trees. Syst. Zool. 27, 27-33.
20. Felsenstein, J., 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368-376.
21. Fitch, W.F., 1967. Evidence suggesting a non-random character to nucleotide replacements in naturally occurring mutations. J. Mol. Biol. 26, 499-507.
22. Fitch, W.M., Markowitz, E., 1970. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem. Genet. 4, 579-593.
23. Freudenstein, J.V., Pickett, K.M., Simmons, M.P., Wenzel, J.W., 2003. From basepairs to birdsongs: phylogenetic data in the age of genomics. Cladistics 19, 333-347.
24. Frohlich, M.W., Parker, D.S., 2000. The mostly male theory of flower evolutionary origins: from genes to fossils. Syst. Bot. 25, 155-170.
25. Graur, D., Li, W.-H., 2000. Fundamentals of Molecular Evolution, 2nd edn. Sinauer Associates, Sunderland, MA.
26. Hasegawa, M., Hashimoto, T., Adachi, J., Iwabe, N., Miyata, T., 1993. Early branchings in the evolution of eukaryotes: ancient divergence of Entamoeba that lacks mitochondria revealed by protein sequence data. J. Mol. Evol. 36, 380-388.
27. Hillis, D.M., 1987. Molecular versus morphological approaches. Ann. Rev. Ecol. Syst. 18, 23-42.
28. Hillis, D.M., 1996. Inferring complex phylogenies. Nature 383, 130-131.
29. Hillis, D.M., 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47, 3-8.
30. Irwin, D.M., Kocher, T.D., Wilson, A.C., 1991. Evolution of the cytochrome b gene of mammals. J. Mol. Evol. 32, 128-144.
31. Jukes, T.H., Cantor, C.R., 1969. Evolution of protein molecules. In: Munro, H.N. (Ed.), Mammalian Protein Metabolism. Academic Press, New York, pp. 21-132.
32. Källersjö, M., Albert, V.A., Farris, J.S., 1999. Homoplasy increases phylogenetic structure. Cladistics 15, 91-93.
33. Källersjö, M., Farris, J.S., Kluge, A.G., Bult, C., 1992. Skewness and permutation. Cladistics 8, 275-287.
34. Kimura, M., 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111-120.
35. Klenk, H.-P., Zillig, W., 1994. DMA-dependent RNA polymerase subunit B as a tool for phylogenetic reconstructions: branching topology of the archaeal domain. J. Mol. Evol. 38, 420-432.
36. Kluge, A.G., Farris, J.S., 1969. Quantitative phyletics and the evolution of Anurans. Syst. Zool. 18, 1-32.
37. Lanyon, S.M., 1988. The stochastic mode of molecular evolution: what consequences for systematic investigations? Auk 105, 563-573.
38. Lewis, L.A., Mishler, B.D., Vilgalys, R., 1997. Phylogenetic relationships of the liverworts (Hepaticeae), a basal embryophyte lineage, inferred from nucleotide sequence data of the chloroplast gene rbcL. Mol. Phylogenet. Evol. 7, 377-393.
39. Lockhart, P.J., Howe, C.J., Bryant, D.A., Beanland, T.J., Larkum, A.W.D., 1992. Substitutional bias confounds inference of cyanelle origins from sequence data. J. Mol. Evol. 34, 153-162.
40. Manhart, J.R., 1994. Phylogenetic analysis of green plant rbcL sequences. Mol. Phylogenet. Evol. 3, 114-127.
41. Meyer, A., 1994. Shortcomings of the cytochrome b gene as a molecular marker. Trends Ecol. Evol. 9, 278-280.
42. Meyer, A., Wilson, A.C., 1990. Origin of tetrapods inferred from their mitochondrial DNA affiliation to lungfish. J. Mol. Evol. 31, 359-364.
43. Mishler, B.D., Bremer, K., Humphries, C.J., Churchill, S.P., 1988. The use of nucleic acid sequence data in phylogenetic reconstruction. Taxon 37, 391-395.
44. Miyamoto, M.M., Fitch, W.M., 1995. Testing the covarion hypothesis of molecular evolution. Mol. Biol. Evol. 12, 503-513.
45. Moriyama, E.N., Powell, J.R., 1997. Synonymous substitution rates in Drosophila: mitochondrial versus nuclear genes. J. Mol. Evol. 45, 378-391.
46. Naylor, G.J.P., Collins, T.M., Brown, W.M., 1995. Hydrophobicity and phytogeny. Nature 373, 565-566.
47. Naylor, G.J.P., Gerstein, M., 2000. Measuring shifts in function and evolutionary opportunity using variability profiles: a case study of the globins. J. Mol. Evol. 51, 223-233.
48. Nishiyama, T., Kato, M., 1999. Molecular phylogenetic analysis among bryophytes and tracheophytes based on combined data of plastid coded genes and the 18S rRNA gene. Mol. Biol. Evol. 16, 1027-1036.
49. Ortí, G., Meyer. A., 1996. Molecular evidence of ependymin and the phylogenetic resolution of early divergences among euteleost fishes. Mol. Biol. Evol. 13, 556-573.
50. Perna, N.T., Kocher, T.D., 1995. Unequal base frequencies and the estimation of substitution bias. Mol. Biol. Evol. 12, 359-361.
51. Prager, E.M., Wilson, A.C., 1988. Ancient origin of lactalbumin from lysozyme: analysis of DNA and amino acid sequences. J. Mol. Evol. 27, 326-335.
52. Prychitko, T.M., Moore, W.S., 2000. Comparative evolution of the mitochondrial cytochrome b gene and nuclear B-fibrinogen intron 7 in woodpeckers. Mol. Biol. Evol. 17, 1101-1111.
53. Schuh, R.T., Polhemus, J.T., 1980. Analysis of taxonomic congruence among morphological, ecological, and biogeographic data sets for the Leptopodomorpha (Hemiptera). Syst. Zool. 29, 1-26.
54. Sennblad, B., Bremer, B., 2000. Is there a justification for differential a priori weighting in coding sequences? A case study from rbcL and Apocynaceae s.l. Syst. Biol. 49, 101-113.
55. Simmons, M.P., 2000. A fundamental problem with amino-acid-sequence characters for phylogenetic analyses. Cladistics 16, 274-282.
56. Simmons, M.P., In press. Amino acid versus nucleotide characters for phylogenetic inference of the 'basal' angiosperms. In: Sharma, A.K., Sharma, A. (Eds.), Plant Genome Biodiversity and Evolution: Vol. 1, Part B: Phanerogams. Science Publishers, Enfield, NH.
57. Simmons, M.P., Carr, T.G., O'Neill, K., In press. Relative character-state space, amount of potential phylogenetic information, and heterogeneity of nucleotide and amino acid characters. Mol. Phylogenet. Evol.
58. Simmons, M.P., Freudenstein, J.V., 2002. Artifacts of coding amino acids and other composite characters for phylogenetic analysis. Cladistics 18, 354-365.
59. Simmons, M.P., Miya, M., in press. Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches: a case study using mitogenomic data from 100 higher teleost fishes. Mol. Phylogenet. Evol. 00, 000-000.
60. Simmons, M.P., Ochoterena, H., Freudenstein, J.V., 2002. Amino acid vs. nucleotide characters: challenging preconceived notions. Mol. Phylogenet. Evol. 24, 78-90.
61. Sokal, R.R., Rohlf, F.J., 1981. Taxonomic congruence in the Leptopodomorpha re-examined. Syst. Zool. 30, 309-325.
62. Steel, M., Penny, D., 2000. Parsimony, likelihood, and the role of models in molecular phylogenetics. Mol. Biol. Evol. 17, 839-850.
63. Swofford, D.L., 2002. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods) 4.0 beta 10. Sinauer, Sunderland, MA.
64. Wenzel, J.W., Siddall, M.E., 1999. Noise. Cladistics 15, 51-64.
65. Wirth, T., Le Guellec, R., Veuille, M., 1999. Directional substitution and evolution of nucleotide content in the cytochrome oxidase II gene in earwigs (dermapteran insects). Mol. Biol. Evol. 16, 1645-1653.
66. Yang, Z., 1993. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10, 1396-1401.
67. Yang, Z., 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS 13, 555-556.
68. Yang, Z., 1998. On the best evolutionary rate for phylogenetic analysis. Syst. Biol. 47, 125-133.
69. Yang, Z., Nielsen, R., Hasegawa, M., 1998. Models of amino acid substitution and applications to mitochondrial protein evolution. Mol. Biol. Evol. 15, 1600-1611.
70. Zujko-Miller, C., Miller, J.A., 2003. PEST: Precision estimated by sampling traits. Program distributed by the authors, 〈http://www.gwu.edu/ ~clade/spiders/pestDocs.htm〉.