Next week’s reading in our quickly ending series on coding characters and (most recently) dynamic homology.
Ramírez, M.J. & P. Michalik. 2014. Calculating structural complexity in phylogenies using ancestral ontologies. Cladistics (Early View). Available here.
Update: Wonderful paper! Love the innovative and somewhat irreverent use of ontologies specifically to address and answer a genuine systematic question complex, outside of the “Protégé paradigm” (and in fact without formal reasoning, period). Ramírez and co-authors are onto something novel and impactful.
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.
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.
I will update this listing, from time to time. My own current take is here, with corresponding WHS 2012 presentation: