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Posts tagged ‘parsimony’

Weekly reading: Cladistic matrices, Wagner trees, and optimizations “by hand”

This week our weekly lab discussion group shifts gears from the empiricism/realism debate to actual, and mostly still “manual” (as if hands could think), character matrix assembly, Wagner tree construction, and upward-/downward-pass parsimony-based character state optimization. Consistency and retention indices. And WinClada and NONA. Let’s see how far the first session will take us towards understanding the interaction between characters, parsimony, optimizations, and trees.

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:

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Weekly reading: reconciled trees and New Guinean historical biogeography

This week we are discussing an empirical paper that makes use of Page’s (1994) reconciled trees and TreeMap programs: van Welzen, P.C., H. Turner & M.C. Roos. 2001. New Guinea: a correlation between accreting areas and dispersing Sapindaceae. Cladistics 17: 242-247.

Weekly reading: Maps between trees of genes, organisms, and areas

This week we will read one of the introductory paper’s for Roderic Page’s Component 2.0 software program: Page, R.D.M. 1994. Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Systematic Biology 43: 58-77.

Weekly reading: Page (1988) on assumptions 0, 1, 2

Today we read Page (1988): Quantitative Cladistic Biogeography: Constructing and Comparing Area Cladograms. In this paper, the author presented algorithms that implement Assumptions 1 and 2 previously proposed by Nelson and Platnick (1981).  Together with Assumption 0 (Zandee, 1987), these so-called ‘assumptions’ are used to resolve fundamental/individual area cladograms involving missing taxa, widespread taxa, and redundant distributions. They provide different sets of solutions for a given taxon-area cladogram with such conflicts, with Assumption 0 typically yielding the least and Assumption 2 the most area cladograms.

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Weekly reading: Quantitative cladistic biogeography – area cladograms

Ronquist (1997) is a “classic” at this point (though see RASP), but one can reach further back in time with quantitative biogeographic methods (read: computer programs). Though not much further than this: R.D.M. Page (1988) – Quantitative cladistic biogeography: Constructing and comparing area cladograms. Systematic Zoology 37: 254-270. Our reading for this week’s discussion. Link to JSTOR.

Weekly reading: Dispersal-vicariance analysis

Last week’s paper on parametric biogeography methods by Ronquist & Sanmartín (2012) was densely written and programmatic as much as it was a review. It presents and assumes a fair amount of prior understanding. In subsequent weekly discussions we will trace back and understand the different models and methods covered by these leading authors. The general theme is event-based methods in biogeography. Likely a good place to start retracing the development of this field is Ronquist (1997): Dispersal-vicariance analysis: a new approach to the quantification of historical biogeography. This will be our reading paper for next week.