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Reading List 3
The required readings are marked with two asterisks**. Highly recommended readings
are marked with one asterisk*; the rest are for background information and to allow
you an entrance into the literature.


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. Oxford University Press.

 

** 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. Oxford University Press.

References

 

** 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 bÍte 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, San Diego.

 

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

Garden 80: 752-766.

 

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, Arnold G. Kluge. Transformation Series as an Ideographic Character Concept. Cladistics 20(1). February 2004

 

Kirchoff, B. K.; Richter, S. J.; Remington, D. L., et al. Complex data produce better characters. Systematic Biology 53 (1) : 1-17 February 2004

 

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 Davis J. I. 1991. Polymorphic taxa missing values and cladistic analysis. 1991 Annual meeting of the Botanical Society of America with the American Institute of Biological Sciences, San Antonio, Texas, USA, AUGUST 4-8, 1991. AM J BOT. American Journal of Botany 78 (6 SUPPL) : 206.

 

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