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Worthwhile reads on cladistic character coding

Some pointers to literature relevant to one of the most intellectually engaging topics I can think of in systematics – how to properly “code” cladistic characters. “Code” in quotation marks because there is more to it than a single verb or action might denote. For what it is worth, Olivier Rieppel’s (2007) “performance” paper is a must read in my assessment; he talks about the process of character “scoping”. Though practically all papers can be considered sincere (yes, that can matter) and scholarly contributions to advance the field, occasionally in an intellectual discourse setting overshadowed by too-easy dichotomies of pattern versus process, supposed methodological rigor versus eclecticism, or total evidence versus cherry picking (as I said, too easy, and no improvement here either in such a stenographic account).

Franz, N.M. 2014. Anatomy of a cladistic analysis. Cladistics 30: 294-321. pdf

I will update this listing, from time to time. My own current take is here, with corresponding WHS 2012 presentation:

Franz. Anatomy of a Cladistic Analysis. from taxonbytes

Agnarsson, I. & J.A. Miller. 2008. Is ACCTRAN better than DELTRAN? Cladistics 24: 1–7. Link

Kearney, M. 2002. Fragmentary taxa, missing data, and ambiguity: mistaken assumptions and conclusions. Systematic Biology 51: 369–381. Link

Kearney, M. & O. Rieppel. 2006. Rejecting “the given” in systematics. Cladistics 22: 369–377. Link

Mickevich, M.F. & S.J. Weller. 1990. Evolutionary character analysis: tracing character change on a cladogram. Cladistics 6: 137–170. Link

Patterson, C. & C.D. Johnson. 1997. The data, the matrix, and the message: comments on Begle’s “Relationships of the Osmeroid Fishes”. Systematic Biology 46: 358–365. Link

Pogue, M.G. & M.F. Mickevich. 1990. Character definitions and character state delineation: the bête noire of phylogenetic inference. Cladistics 6: 319–361. Link

Ramírez, M.J. 2007. Homology as a parsimony problem: a dynamic homology approach for morphological data. Cladistics 23: 588–612. Link

Richards, R. 2003. Character individuation in phylogenetic inference. Philosophy of Science 70: 264–279. Link

Rieppel, O. 2003. Semaphoronts, cladograms and the roots of total evidence. Biological Journal of the Linnean Society 80: 167–186. Link

Rieppel, O. 2007. The performance of morphological characters in broad-scale phylogenetic analyses. Biological Journal of the Linnean Society 92: 297–308. Link

Rieppel, O. & M. Kearney. 2002. Similarity. Biological Journal of the Linnean Society 75: 59–82. Link

Rieppel, O., Kearney, M., 2007. The poverty of taxonomic characters. Biology & Philosophy 22: 95–113. Link

Sereno, P.C. 2007. Logical basis for morphological characters in phylogenetics. Cladistics 23: 565–587. Link

Strong, E.E. & D. Lipscomb. 1999. Character coding and inapplicable data. Cladistics 15: 363–371. Link

Thiele, K. 1993. The holy grail of the perfect character: the cladistic treatment of morphometric data. Cladistics 9: 275-304. Link

Wenzel, J.W. & M.E. Siddall. 1999. Noise. Cladistics 15, 51–64. Link

Winther, R.G. 2009. Character analysis in cladistics: abstraction, reification, and the search for objectivity. Acta Biotheoretica 57: 129-162. Link

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