Author Archives: Jeremy Brown

About Jeremy Brown

Assistant professor in the Dept. of Biological Sciences at Louisiana State University.

Bodega @ Evol2013


The schedule for the 2013 Evolution meeting was just released.  I’m sure there will be many Bodega instructors and former students (and future, too!) giving fascinating talks and posters.  Below are a few presentations that I found for instructors and students from Bodega2013.  Please add your own presentation time in the comments so that we can all work these into our meeting schedules.

Gideon Bradburd – Sun. at 5:00 – Disentangling the effects of geographic and ecological isolation on genetic differentiation

Jeremy Brown – Tues. at 4:45 – Variable phylogenetic signal in a forensically important HIV-1 transmission cluster

Tracy Heath – Sun. at 4:45 – The Fossilized Birth-Death Process: A Coherent Model of Fossil Calibration for Bayesian Divergence Time Estimation

Hannah Marx – Tues. at 2:30 – Alien encounters of the floral kind: interpreting patterns of community assembly on the San Juan Islands

Mike May – Sun. at 8:30 (am) – MCDUSA: A Monte Carlo method for more reliable detection of lineage-specific rates of diversification

Matt McGee – Sun. at 2:00 – The evolution of cichlid craniofacial diversity

Brian Moore – Tues. at 3:45 – Bayesian inference of phylogeny from partitioned data

Sam Price – Sat. at 9:30 – Assembly & early diversification of modern reef fishes

Glenn Seeholzer – Mon. at 7:00 (pm) – The phylogenetic signal and mode of climate-niche evolution in the Neotropical bird family Furnariidae

Bob Thomson – Tues. at 11:15 – Estimating Phylogeny from microRNA Data: A Critical Appraisal

Updated TreeSetViz

coverBetween the Bodega Bay workshop and my spring semester class on computational phylogenetics at LSU, I’ve been talking a lot about phylogenetic analyses recently.  In my opinion, one of the most underutilized approaches for summarizing phylogenetic information is to visualize collections of trees in tree space (or an approximation of tree space projected into 2 or 3 dimensions).  These visualizations can help with diagnosing MCMC convergence problems, comparing the phylogenetic signal coming from different genes, picking an appropriate burn-in, and a whole bunch of other stuff.  I widely recommend such visualizations to students.  There are some drawbacks (e.g., lots of information can be lost during the projection to such low-dimensional spaces), but on balance it seems to me that the advantages outweigh these drawbacks.  There really isn’t another way to summarize that amount of phylogenetic information in a single plot.  As far as I know, the first paper to describe this approach was by Hillis, Heath, and St. John (2005, Syst. Biol., 54: 471-482), which included the release of a Mesquite plug-in called TreeSetViz for performing such visualizations using multi-dimensional scaling (MDS). I used this tool quite a lot and was disappointed that it became incompatible with newer releases of Mesquite.  In fact, I maintained an outdated version of Mesquite just to run TreeSetViz.  Well, unbeknownst to me, an updated version of TreeSetViz was released last year that is compatible with the most recent versions of Mesquite (hat tip to Vinson Doyle for pointing this out) and includes a wide variety of new options for comparing and visualizing trees.  Strangely, this new release isn’t mentioned on the original TreeSetViz website, but it is announced, along with very simple installation instructions, on the Mesquite website.  More recently, additional tools that are independent of Mesquite (TreeScaper) have been developed that also perform tree set visualization and projection.  Give them a try!