A non-biologist friend of mine, on proofreading bits of the thesis-in-progress, got terribly excited about the program Mr Bayes.
"Mr Bayes!" she exclaimed. "That's the perfect name for a tabby cat!"
Her comments on the section where I actually described Bayesian methods in phylogenetics consisted mainly of 
and >.< faces. "The words seem to be in the right order for the English language?" was her concession.
Don't blame her, obviously. I periodically beat myself over the head with my notes about Bayesian & likelihood methods; this appears to be an effective means toward keeping the information in my head. Today I found a couple more implements of self-harm at Paul Agapow's site, the first his own primer, the second a link to Peter Foster's The Idiot's Guide to the Zen of Likelihood in a Nutshell in Seven Days for Dummies. Tee hee.
So browsing the talk titles for the Evolution 2006 meeting, I came to the conclusion that biologists, especially those who dabble in phylogenetics, tend to have a very specific sense of humour. By specific, I mean "take any opportunity to make a pun, an allusion, or maximise alliteration to the point of tongue-twisting" and dude, there's nothing wrong with that. You wrap your brain around priors and posteriors and your brain wants to crack a funny. It's just the way it is.
June 26, 2006
Doolittle, W.F. (1999) Phylogenetic classification and the universal tree. Science, 284, 2124-2128. [link]
Interesting review discussing recent findings which question a strict tree model for the universal tree of life. Lateral gene transfer is non-trivial, especial in archaeal and bacterial genomes. Doesn't dismiss the usefulness of molecular phylogenetics as a tool, but questions it as an end-goal (producing classifications).
If there were believable genealogies of all genes… one could then ask which genes have travelled together for how long in which genomes, without an obligation to marshal these data in the defense of one or another grander phylogenetic scheme for organisms.
Nifty figures, also.
May 3, 2006
Why is it with all the combined mac-love and technogeekery amongst phylogeneticists there isn’t a simple, friendly way to get my treefile into a presentable graphical form?
At present, it’s something torturous like from PAUP > Save As Pict. Then in Word, Import > Picture > File, and try to manipulate the individual bits. Until they start making random boxes, and I go blind.
All I want to do is colour code my taxa, add some node annotations, and not have to buy Illustrator! Photoshop won’t open the *.pict and let me manipulate the text, no matter what format it is converted to, because it rasterises the text.
TreeView wants me to save the file as an *.svg, which PS also doesn’t like. Searching Joe Felsenstein’s site, there appears to be some sort of program (TreeMe) which does these nifty things for the presentation of phylogenies, but it’s for PC! And also costs more than Illustrator.
Today I am Thwarted Lass.
March 3, 2006
Once upon a time I considered becoming an evolutionary bat biologist1. Bats are cool. They’re close to primates on the mammal phylogeny, they have interesting social systems, and some of them have astoundingly sophisticated echolocation systems.
Gareth Jones and Emma Teeling have a paper in TREE: The evolution of echolocation in bats, discussing the phylogenetic history of this trait. It may be quite flexible in the face of ecological constraints and challenges, as there seems to be convergent evolution when different types of calls are mapped onto the molecular phylogenies.
1. Now I just read comics.
February 9, 2006
A nifty little web-based applet for comparing the topology of two phylogenies and identifying where the differences lie. Could be useful in the future. Works for me on a G5 with Firefox. The paper referring to it is:
Nye, T. M. W., Lio, P. & Gilks, W. R. (2006) A novel algorithm and web-based tool for comparing two alternative phylogenetic trees. Bioinformatics, 22: 117-119.
February 6, 2006
Application of Phylogenetic Networks in Evolutionary Studies
Daniel H. Huson and David Bryant
Molecular Biology and Evolution 2006 23(2):254-267 [link]
The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees.
January 26, 2006
