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Posts tagged ‘likelihood’

Weekly reading: Intermittent evolution and robustness of phylogenetic models

Models of evolution used in phylogenetic reconstruction make specific assumptions which (in their entirety, and globally applied) are ultimately wrong. They are also approximately right. What does this even mean? This week’s reading gets us into the notion of robustness of phylogenetic models to violations of their inherent assumptions. An important piece of the “which method should I use?” puzzle. Let’s see if we can identify other pieces too.

Nguyen, M.A.T., T. Gesell & A. von Haeseler. 2012. ImOSM: Intermittent evolution and robustness of phylogenetic methods. Molecular Biology and Evolution 29: 663-673. Available on-line here.

Weekly reading: Bayesian analysis outperforms parsimony for morphological data

We had a lively Weekly Discussion of Kumar et al. 2012, and are staying with the general theme (hereby undemocratically coined) of “new insights in statistical phylogenetics/phylogenomics”. Models, biases, assumptions, data. Thus, for next week:

Wright, A.M. & D.M. Hillis. 2014. Bayesian analysis using a simple likelihood model outperforms parsimony for estimation of phylogeny from discrete morphological data. PLoS ONE 9(10): e109210. Available on-line here.

Weekly reading: Philosophy of statistical phylogenetic methods

After a long summer hiatus, our Weekly Discussion series resumes for the Fall semester of 2014 (this time also as a one-credit under-/graduate seminar course “Current Topics in Systematics”). On the menu this semester we have the theory and practice of Next Generation Sequencing, but the corresponding papers will  have to wait a few weeks to make room for 2-3 unrelated topics on which new, intriguing papers have come out over the summer.

The first of these is on the philosophical correlates of statistical phylogenetic inference!

Barker, D. 2014. Seeing the wood for the trees: philosophical aspects of classical, Bayesian and likelihood approaches in statistical inference and some implications for phylogenetic analysis. Biology & Philosophy 29. (21 pp.). Available on-line here.

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: 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.