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New publication: Anatomy of a cladistic analysis

CodingCladisticCharacters

My “Anatomy” paper went from on-line only preprint to officially published. I intended this to serve as a use case-centered companion paper to this:

Franz, N.M. 2005. Outline of an explanatory account of cladistic practice. Biology & Philosophy 20: 489-515. PDF

There is an interesting, still insufficiently explored interaction between reliable character individuation and parsimony in systematics. And understanding and maximizing the positive effects of this interaction is relevant to improving the language of systematics.

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

Abstract. The sequential stages culminating in the publication of a morphological cladistic analysis of weevils in the Exophthalmus genus complex (Coleoptera: Curculionidae: Entiminae) are reviewed, with an emphasis on how early-stage homology assessments were gradually evaluated and refined in light of intermittent phylogenetic insights. In all, 60 incremental versions of the evolving character matrix were congealed and analysed, starting with an assembly of 52 taxa and ten traditionally deployed diagnostic characters, and ending with 90 taxa and 143 characters that reflect significantly more narrow assessments of phylogenetic similarity and scope. Standard matrix properties and analytical tree statistics were traced throughout the analytical process, and series of incongruence length indifference tests were used to identify critical points of topology change among succeeding matrix versions. This kind of parsimony-contingent rescoping is generally representative of the inferential process of character individuation within individual and across multiple cladistic analyses. The expected long-term outcome is a maturing observational terminology in which precise inferences of homology are parsimony-contingent, and the notions of homology and parsimony are inextricably linked. This contingent view of cladistic character individuation is contrasted with current approaches to developing phenotype ontologies based on homology-neutral structural equivalence expressions. Recommendations are made to transparently embrace the parsimony-contingent nature of cladistic homology.

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