Last week we saw that coding inapplicables is tricky; essentially one must understand the limitations of the ‘square matrix’ and utilize reductive coding in such a way that logical and biological dependencies inherent in homology assessments are not distorted by the way in which global parsimony optimization occurs. We also saw a shift from a rather clear-cut stance about the boundaries between data and inference, to a more qualified position where inferences derived from an initial matrix and analysis should caution one to re-examine ‘the evidence’. Taking this dethroning of primary observations several steps further, next week we are reading:
Rieppel, O. 2007. The performance of morphological characters in broad-scale phylogenetic analyses. Biological Journal of the Linnean Society 92: 297–308. Available here.
For next week’s discussion in our budding coding cladistic characters series for this semester, we shall read a paper dealing with the ins and outs of coding “inapplicables”:
Strong, E.E. & D. Lipscomb. 1999. Character coding and inapplicable data. Cladistics 15: 363–371. Available here.
By popular demand, the Spring 2014 weekly lab discussion series will focus on the theory and practice of coding cladistic characters, and where and why this remains an essential task of systematics. This is a broad theme that has been treated by many authors and from different perspectives. We will start with a paper that is rife with issues that merit a more nuanced discussion; but at the same time reflects a suite of topics and positions advocated in the mid t0 late 1980s when the 1st- to 2nd-generation cladistic software packages (such as Hennig86) were in use.
Pimentel, R.A. & R. Riggins. 1987. The nature of cladistic data. Cladistics 3: 201-209. Available on-line here.