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Posts tagged ‘paper’

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: Diversification patterns in the Mediterranean tenebrionid genus Blaps

Another weekly reading, an empirical paper focusing on a Mediterrranean tenebrionid beetle radiation – genus Blaps Fabricius – using the DEC model by Ree et al. Reference: Condamine, F.L., L. Laurent Soldati, A.-L. Clamens, J.-Y. Rasplus & G.J. Kergoat. 2013. Diversification patterns and processes of wingless endemic insects in the Mediterranean Basin: historical biogeography of the genus Blaps (Coleoptera: Tenebrionidae). Journal of Biogeography 40: 1899–1913. Available here.

This paper’s group leader Gael Kergoat participated in the Third International Tenebrionoidea Symposium held earlier this year at ASU.

Weekly reading: Bayesian phylogeography finds its roots

This week’s reading, diving into geographic patterns below the species level: Lemey, P., A. Rambaut, A.J. Drummond & M.A. Suchard. 2009. Bayesian phylogeography finds its roots. PLoS Computational Biology 5(9): e1000520. Available here.

Weekly reading: Review of parametric methods in historical biogeography

Last week’s reading was a trip “back to the future” into MacArthur & Wilson (1967) style island biogeography – subtracting phylogeny and area cladograms from the equation and concentrating instead on island species richness and carrying capacities as a function of, well…(likely not just history and phylogeny). All this in a Bayesian framework. There was some question whether the current version of MrBayes can support such analyses. Next up for this week, more overview of parametric approaches: Ree, R.H. & I. Sanmartín. 2009. Prospects and challenges for parametric models in historical biogeographical inference. Journal of Biogeography 36: 1211–1220. Available here. 

Weekly reading: Bayesian island biogeography

Continuing our theme of reviewing novel, parametric methods for historical biogeography, this week’s (lengthy) read is: Sanmartín, I., P. van der Mark & F. Ronquist. 2008. Inferring dispersal: a Bayesian, phylogeny-based approach to island biogeography, with special reference to the Canary Islands. Journal of Biogeography 35: 428–449. PDF available here.

Weekly reading: more on maximum likelihood and ancestral geographic ranges – lagrange

Last week’s paper by Ree et al. (2005) introduced concepts and methods towards a likelihood framework for event-based historical biogeography (sensu Ronquist 1997). Area cladograms are no longer a central objective, and the assumptions of Ronquist’s (1997) parsimony-weighted model regarding absolute and relative rates of dispersal versus extinction in ancestral areas are exposed. This week’s reading is a direct follow-up which also introduces the software package lagrange:  Ree, R.H. & S.A. Smith. 2008. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Systematic Biology 57: 4-14. Available here.

Weekly reading: likelihood framework for the evolution of geographic range

Moving gradually into the parametric world of historical biogeographic inference, this week’s reading is: Ree, R.H., B.R. Moore, C.O. Webb & M.J. Donoghue. 2005. A likelihood framework for inferring the evolution of geographic range on phylogenetic trees. Evolution 59: 2299-2311. Available here.

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.