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List 3 Jan. 31: Character analysis Buschbeck, E. K. 2000. Neurobiological constraints and fly systematics: how different types of neural characters can contribute to a higher level dipteran phylogeny. Evolution: 54: 888-898. Chappill, J. A. 1989. Quantitative characters in phylogenetic analysis. Cladistics 5: 217- 234. Goldman, N. 1988. Methods of discrete coding of morphological characters for numerical analysis. Cladistics 4:59-71. Hauser, D. L. and W. Presch. 1991. The effect of ordered characters on phylogenetic reconstruction. Cladistics 7: 243-265. Hibbett, D. S. and M. J. Donoghue. 2001. Analysis of character correlations among wood decay mechanisms, mating systems, and substrate ranges in Homobasidiomycetes. Systematic Biology 51: 215-242. Jenner, R. A. 2001. Bilaterian phylogeny and uncritical recycling of morphological data sets. Systematic Biology 50: 730-742. Le Quesne, W. J. 1969. A method of selection of characters in numerical taxonomy. Syst. Zool. 18:201-205. Lee, D.-C. and H. N. Bryant. 1999. A Reconsideration of the Coding of Inapplicable Characters: Assumptions and Problems. Cladistics 15: 373-378. Lipscomb, D. L. 1992. Parsimony, homology, and the analysis of multistate characters. Cladistics 8: 45-65. Mabee, P. M. 1989a. Assumptions underlying the ontogenetic use sequences for determining character state order. Trans. Amer. Fish. Soc. 118:159-166. ** Mishler, B. D.
2005. The logic of the data matrix in phylogenetic analysis. In V.A.
Albert (ed.), Parsimony, Phylogeny, and Genomics, pp. 57-70. ** Mishler, B. D. and E. De Luna. 1991. The use of ontogenetic data in phylogenetic analyses of mosses. Advances in Bryology 4:121-167. * Neff, N.A. 1986. A rational basis for a priori character weighting. Syst. Zool. 35:102-109. Monteiro, L. R. 2000. Why morphometrics is special: the problem with using partial warps as characters for phylogenetic analysis. Systematic Biology 49: 796-800. O'Keffe, F. R. and P. J. Wagner. 2001. Inferring and testing hypotheses of cladistic character independence by using character compatibility. Systematic Biology 50: 657-675. Pimentel, R.A. and Riggins, R. 1987. The nature of cladistic data. Cladistics 3:201-209. Pogue, M. G. and M. F. Mickevich. 1990. Character definitions and character state delineation: the bête noire of phylogenetic inference. Cladistics 6: 319-361. Rae, T. C. 1998. “The logical basis for the use of continuous characters in phylogenetic systematics.” Cladistics 14: 221-228. Schander, C. and P. Sundberg. Useful characters in gastropod phylogeny: soft information or hard facts? Systematic Biology 50: 136-141. Simmons, M. P. and H. Ochoterena. 2000. Gaps as characters in sequence-based phylogenetic analysis. Systematic Biology 49369-381. Simmons, M. P., H. Ochoterena, and T. G. Carr. 2001. Incorporation, relative homoplasy, and effect of gap characters in sequenced-based phylogenetic analysis. Systematic Biology 50: 454-461. Simmons, N. P. 2001. Misleading results from the use of ambiguity coding to score polymorphisms in higher-level taxa. Systematic Biology 50: 613-620. Slowinski, J. B. 1993. "Unordered" versus "ordered" characters. Syst. Biol. 42: 155- 165. Smith, E. N. and R. L. Gutberlet jr. 2001. Generalized frequency coding: a method of preparing polymorphic multistate characters for phylogenetic analysis. Systematic Biology 51: 156-169. * Stevens, P.F. 1991. Character states, morphological variation, and phylogenetic analysis: a review. Syst. Bot. 16:553-583. Strong, E. E. and D. Lipscomb. 1999. Character coding and inapplicable data. Caldistics 15: 363-371. Wagner, P. J. 2000. Exhaustion of morphologic character states among fossil taxa. Evolution 54: 365-386. Wagner, G. P. (ed.). 2001. The character concept in evolutionary biology. Academic Press, Wagner, P. J. 2000. Exhaustion of morphologic character states among fossil taxa. Evolution 54: 365-386. Wiens, J. J. 1995. Polymorphic characters in phylogenetic systematics. Syst. Biol. 44: 482-500. Wiens, J. J. 2001. Character analysis in morphological phylogenetics: problems and solutions. Systematic Biology 50 689-699. Wilkinson, M. 1992. Ordered versus unordered characters. Cladistics 8: 375-385. Feb. 2: Character coding * V.A. Albert, B.D. Mishler, and M.W. Chase. 1992. Character-state weighting for restriction site data in phylogenetic reconstruction, with an example from chloroplast DNA. In P. Soltis, D. Soltis, and J. Doyle (eds.), Molecular Systematics of Plants, pp. 369-403. Chapman and Hall. V.A. Albert and B.D. Mishler. 1992. On the rationale and utility of weighting nucleotide sequence data. Cladistics 8: 73-83. **V.A. Albert,
M.W. Chase, and B.D. Mishler. 1993. Character-state weighting for cladistic
analysis of protein-coding DNA sequences. Annals Missouri Botanical Broughton, R. E., S. E. Stanley, and R. T. Durrett. 2000. Quantification of homoplasy for nucleotide transitions and transversions and a reexamination of assumptions in weighted phylogenetic analysis. Systematic Biology 49: 617-627. Carpenter J.M.. 1994. Successive weighting, reliability and evidence. Cladistics 10(2): 215-220. Farris, J. S. 1969. A successive approximations approach to character weighting. Syst. Zool. 18: 374-385. Freudenstein, J. V., Pickett, K. M., Simmons, M. P. and Wenzel, J. W. From basepairs to birdsongs: Phylogenetic data in the age of genomics. Cladistics 19 (4) : 333-347 August 2003 Goloboff, P. A. 1993. Estimating character weights during tree searches. Cladistics 9: 83-91.
Taran Grant, Kirchoff, B. K.; Richter, S. J.; Remington, D. L., et al.
Complex data produce better characters. Systematic Biology 53 (1) : 1- Liebherr, J. K. and Zimmerman, E. C. 1998. Cladistic analysis, phylogeny and biogeography of the Hawaiian Platynin (Coleoptera: Carabidae). Systematic Entomology 23 (2) : 137-172. Maddison, W. P. 1993. Missing data versus missing characters in phylogenetic analysis. Systematic Biology 42 (4) : 576-581. Nixon K. C. and Sennblad, B and B. Bremer. 2000. Is ther a justification for differential a priori weighting in coding sequences? A case study from rbcL and Apocynaceae s.l. Systematic Biology 49: 101-113. Wheeler, Q.D. 1986. Character weighting and cladistic analysis. Syst. Zool. 35:110- 123. Whitehead D. R. and Ball G. E. 1975. Classification of the Middle American Genus (Cyrtolaus: Coleoptera: Carabidae pterostichini). Quaestiones Entomologicae 11 (4) : 591-619. Wilkinson, M. 1994. Weights and ranks in numerical phylogenetics. Cladistics 10(3): 321-329 Yeates, D. K. Groundplans and exemplars: Paths to the tree of life. Cladistics 11 (4) : 343-357 1995 |
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