Conflict between amino acid and nucleotide characters

Cladistics

Volumn 18, Issue 2, 2002, Pages 200-206

  Simmons, Mark P ^a,c   Ochoterena, Helga ^b   Freudenstein, John V ^a  

^a OHIO STATE UNIVERSITY   (United States)

^b UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

^c Immunology and Pathology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; EVOLUTIONARY BIOLOGY; PHYLOGENETICS;

SPERMATOPHYTA;

EID: 0036557785     PISSN: 07483007     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1096-0031.2002.tb00148.x     Document Type: Article

References (32)

1. Albert, V. A., Chase, M. W., and Mishler, B. D. (1993). Character-state weighting for cladistic analysis of protein-coding DNA sequences. Ann. Mo. Bot. Gard. 80, 752-766.
2. Árnason, Ú., and Gullberg, A. (1994). Relationship of baleen whales established by cytochrome b gene sequence comparison. Nature 367, 726-728.
3. Baker, R. H., and DeSalle, R. (1997). Multiple sources of character information and the phylogeny of Hawaiian drosophilids. Syst. Biol. 46, 654-673.
4. Baker, W. J., Asmussen, C. B., Barrow, S. C., Dransfield, J., and Hedderson, T. A. (1999). A phylogenetic study of the palm family (Palmae) based on chloroplast DNA sequences from the trnL-trnF region. Plant Syst. Evol. 219, 111-126.
5. Baker, W. J., Hedderson, T. A., and Dransfield, J. (2000). Molecular phylogenetics of subfamily Calamoideae (Palmae) based on nrDNA ITS and cpDNA rps16 intron sequence data. Mol. Phylogenet. Evol. 14, 195-217.
6. Blouin, M. S., Yowell, C. A., Courtney, C. H., and Dame, J. B. (1998). Substitution bias, rapid saturation, and the use of mtDNA for nematode systematics. Mol. Biol. Evol. 15, 1719-1727.
7. Dahlgren, R. M. T. (1980). A revised system of classification of the angiosperms. Bot. J. Linn. Soc. 80, 91-124.
8. Edwards, S. V., Arctander, P., and Wilson, A. C. (1991). Mitochondrial resolution of a deep branch in the genealogical tree for perching birds. Proc. R. Soc. London Ser. B 243, 99-107.
9. Farris, J. S. (1989). The retention index and the rescaled consistency index. Cladistics 5, 417-419.
10. Farris, J. S., Albert, V. A., Källersjö, M., Lipscomb, D., and Kluge, A. G. (1996). Parsimony jackknifing outperforms neighbor-joining. Cladistics 12, 99-124.
11. Friedlander, T. P., Regier, J. C., and Mitter, C. (1994). Phylogenetic information content of five nuclear gene sequences in animals: Initial assessment of character sets from concordance and divergence studies. Syst. Biol. 43, 511-525.
12. Goloboff, P. A. (1993). Nona, version 1.6. Distributed by the author, Tucuman, Argentina.
13. Källersjö, M., Albert, V. A., and Farris, J. S. (1999). Homoplasy increases phylogenetic structure. Cladistics 15, 91-93.
14. Karol, K. G., Suh, Y., Schatz, G. E., and Zimmer, E. A. (2000). Molecular evidence for the phylogenetic position of Takhtajania in the Winteraceae: Inference from nuclear ribosomal and chloroplast gene spacer sequences. Ann. Mo. Bot. Gard. 87, 414-432.
15. Maddison, W. P., and Maddison, D. R. (1992). MacClade: Analysis of Phylogeny and Character Evolution. Sinauer, Sunderland, MA.
16. McDade, L. A., Masta, S. E., Moore, M. L., and Waters, E. (2000). Phylogenetic relationships among Acanthaceae: Evidence from two genomes. Syst. Bot. 25, 106-121.
17. Meyer, A. (1994). Shortcomings of the cytochrome b gene as a molecular marker. Trends Ecol. Evol. 9, 278-280.
18. Meyer, A., and Wilson, A. C. (1990). Origin of tetrapods inferred from their mitochondrial DNA affiliation to lungfish. J. Mol. Evol. 31, 359-364.
19. Mindell, D. P., Shultz, J. W., and Ewald, P. W. (1995). The AIDS pandemic is new, but is HIV new? Syst. Biol. 44, 77-92.
20. Montgelard, C., Catzeflis, F. M., and Douzery, E. (1997). Phylogenetic relationships of artiodactyls and cetaceans as deduced from the comparison of cytochrome b and 12S rRNA mitochondrial sequences. Mol. Biol. Evol. 14, 550-559.
21. Moritz, C., Dowling, T. E., and Brown, W. M. (1987). Evolution of animal mitochondrial DNA: Relevance for population biology and systematics. Annu. Rev. Ecol. Syst. 18, 269-292.
22. Nandi, O. I., Chase, M. W., and Endress, P. K. (1998). A combined cladistic analysis of angiosperms using rbcL and non-molecular data sets. Ann. Mo. Bot. Gard. 85, 137-212.
23. Nixon, K. C. (1999). Winclada (BETA). Distributed by the author, Ithaca, NY.
24. Olmstead, R. G., and Sweere, J. A. (1994). Combining data in phylogenetic systematics: An empirical approach using three molecular data sets in the Solanaceae. Syst. Biol. 43, 467-481.
25. Olmstead, R. G., Kim, K.-J., Jansen R. K., and Wagstaff, S. J. (2000). The phylogeny of the Asteridae sensu lato based on chloroplast ndhF gene sequences. Mol. Phylogenet. Evol. 16, 96-112.
26. Rodman, J. E. (1991). A taxonomic analysis of glucosinolate-producing plants. Part 2. Cladistics. Syst. Bot. 16, 619-629.
27. Simmons, M. P. (2000). A fundamental problem with amino-acid-sequence characters for phylogenetic analyses. Cladistics 16, 274-282.
28. Simmons, M. P., and Freudenstein, J. V. (In press) Artifacts of coding amino acids and other composite characters for phylogenetic analysis. Cladistics.
29. Simmons, M. P., Savolainen, V., Clevinger, C. C., Archer, R. H., and Davis, J. I. (2001). Phylogeny of the Celastraceae inferred from 26S nrDNA, phytochrome B, atpB, rbcL, and morphology. Mol. Phylogenet. Evol. 19, 353-366.
30. Simon, C., Frati, F., Beckenbach, A., Crespi, B., Liu, H., and Flook, P. (1994). Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann. Entomol. Soc. Am. 87, 651-701.
31. Soltis, D. E., et al. (2000). Angiosperm phylogeny inferred from a combined data set of 18S rDNA, rbcL, and atpB sequences. Bot. J. Linn. Soc. 133, 381-461.
32. Wilkinson, M. (1995). A comparison of two methods of character construction. Cladistics 11, 297-308.