Wednesday, April 30, 2008

How shalt thou partition a Bayesian analysis?

Partitioned Bayesian phylogenetic analysis is all the rage. In a partitioned analysis, the data is divided a priori into regions of DNA that are thought to be evolving at different rates (e.g., first, second, and third codon positions). It makes sense to partition datasets: we know that different types of DNA evolve at different rates. How many partitions, and of which, should be used is somewhat more controversial. Matt Brandley et al. (Sys. Bio. 54:373-390) was among the first to address this question with an empirical dataset. They used Bayes factors to assess alternative partitioning strategies. They ultimately selected the most heavily partitioned analysis because it resulted in significantly better likelihood score than alternatives, even when penalizing for overparameterization. Most subsequent analyses have come to a similar conclusion: the most heavily partitioned dataset is nearly always favored by Bayes factors. McGuire et al. (Sys. Bio. 56:837-856) consider other possible means for selecting among alternative partitioning strategies (e.g., decision theoretic methodology). They found that not all methods share the Bayes factors tendency to select the most heavily partitioned framework. Although they favor a method that selects a somewhat less heavily partitioned analysis (DT), the various partitioning strategies appear to have little impact on their overall conclusions. Always good to do the most sophisticated analyses, but it can be a bit frustrating when you find you would have gotten the same answer with lots less effort...

Tuesday, April 29, 2008

Apple Remote and PowerPoint

You got your free Apple Remote controller, but it doesn't work with PowerPoint? Bummer, eh? No more! iRed Lite, a free application for OS X lets you program your remote buttons or just use the default ones. Just in time for the summer meeting season.


Unbelievable. After years of waiting a GUI interface for the most popular program in phylogenetics - PAUP* - is finally available for Mac OSX on the intel platform! It appeared without fanfare on a page for the CDC's Workshop on Molecular Evolution. Not sure yet how buggy its going to be, but I'm playing with it right now. I can't even remember how to use it; it's been that long.

Updated: Our hopes and dreams must once again be put on hold, the link to the PAUP GUI is gone and the installed version has expired. The link has been updated with a new version for 2009.

Everyone gets excited about rapid evolution

No discoveries in evolution attract more attention than examples of rapid phenotypic change via natural selection. When we observe impressive evolutionary changes happening over an interval of time that's shorter than a typical human life-span, the abstract power of natural selection becomes tangible. Excitement about rapid evolution often leads to publication in top tier journals, in some cases before other alternatives have been adequately considered.

In 1997 my PhD supervisor - Jonathan Losos - published a paper in Nature that suggested rapid evolution via natural selection in a population of lizards introduced to a Bahamian island only a few decades ago. It was more than ten years before follow-up experiments demonstrated that this observation could be the result of phenotypic plasticity. In spite of this finding, the work continue to be cited as an example of rapid evolution via natural selection.

I was surprised, however, to see it cited in this context by another paper purporting to have observed rapid evolution in another island lizard population. In the pages PNAS, Herrel et al. report dramatic phenotypic changes in a lizard population introduced to a Croatian island in the Adriatic Sea. They observe significant changes in both morphology and performance; perhaps the most striking of these is the appearance of cecal valves, which are thought to increase efficiency of digestion in herbivorous lizards (the introduced population appears to be more herbivorous than the population from which it was derived). Although one could reasonably argue that the types of changes seen in this population are unlikely to represent a plastic response, this possibility cannot, and should not, be brushed under the table too rapidly.