HENRY

New issues of Systematic Biology, Molecular Biology and Evolution and Bioinformatics mean that it’s about time I did a phylogenetics round-up.

1. The first study, “Experimental Design Criteria in Phylogenetics: Where to Add Taxa” by Geuten et al, investigates the best places to add taxa to enhance phylogenetic accuracy. This is quickly becoming a non-trivial problem in phylogenetics work, as the amount of sequence data we have far surpasses the amount of computing iron we have to throw at it. Using a Fisher information approach, the authors conclude that:
   

   (our) criteria show a general preference for augmenting the tree at deep internal nodes connected to long branches, increasing information about the more uncertain regions of the tree. For more extreme phylogenetic trees, with combinations of branch lengths that make them difficult to reconstruct accurately (…), the information criteria do not necessarily choose nodes as their optimal location in the tree for targeted taxon addition. In these cases, targeting a long branch for subdivision can be the most optimal strategy.

2. This is followed by Barbara Holland reviewing Emmanuel Paradis’ new book Analysis of Phylogenetics and Evolution with R. Paradies has written the APE (Analysis of Phylogenetics and Evolution) library for the R statistical framework, and this book appears to be a expanded tutorial to both R and APE etc.Barbara argues that the book, APE and R provide a really good opportunity to step away from the black boxes of PAUP* and Phylip and get real hands-on experience doing phylogenetics, as well as a good framework for implementing new algorithms. Sounds fun.
3. Just to cherry-pick a few more interesting articles from Syst. Bio this month, Brown and Lemmon who explore “The Importance of Data Partitioning and the Utility of Bayes Factors in Bayesian Phylogenetics“, and Nicolas Galtier’s A Model of Horizontal Gene Transfer and the Bacterial Phylogeny Problem which shows that supertree methods are actually quite robust to horizontal gene transfer. I’m adding both of these to my “to cite” pile.
4. Ok, on to MBE, where some of the Alan Wilson center folk (including the aforementioned Barbara Holland) introduce Treeness Triangles, a method of visualizing the loss of phylogenetic signal. The software is here.
5. ..and another paper touching on a really important issue that I’ve been encountering recently, the accuracy of Bayesian phylogenetic methods at estimating posterior probabilities and branch lengths. Bryan Kolaczkowski and Joseph W. Thornton investigate the Effects of Branch Length Uncertainty on Bayesian Posterior Probabilities for Phylogenetic Hypotheses and find that:
   

   The pattern of branch lengths on the true tree determines whether integrating over uncertainty pushes posterior probabilities upward or downward. The magnitude of the effect depends on the specific prior distributions used and the length of the sequences analyzed. Under realistic conditions, however, even extraordinarily long sequences are not enough to prevent frequent inference of incorrect clades with strong support.

6. Finally, AWTY or (Are We There Yet?) is a piece of software that a number of people have recommended to me recently, as a means of assessing convergence in Bayesian MCMC runs:
   

   AWTY is a system for graphical exploration of Markov chain Monte Carlo (MCMC) convergence in Bayesian phylogenetic inference. The graphics produced by AWTY are designed to help assess whether an MCMC analysis has run long enough, such that tree topologies are being sampled in proportion to their true posterior probability distribution. In other words, “Are We There Yet?” or AWTY for short. Admittedly, the results generated by AWTY will never be able to answer this question with a definitive yes; however, in some cases results will point confidently to the answer no.

   The full write-up is available here: AWTY (Are We There Yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics, and the online web-app is available at AWTY online.

Posted on September 1st, 2007 by Simon Greenhill