September 4

Fish exploitation:

* Darter tree from Near's paper generally have no exploitation data
* A couple are commercially exploited and generally have large adult body size.
* Reworking trait dispersion scripts to be a little bit more legible and faster
* Using ggplot2 where possible
* Need a better way to plot data: maybe artificially cluster tips together by rotating about nodes. Possibly misleading? Need to write a good caption + clear it with Mike
* Phlawd for the cods
* Going to run analyses with trees cut out from the 13 gene supertree
* Set up phlawd after SICB abstracts due when I have more time

Rate partitioning:

* On a per-locus basis, figure out what sequences are "probe" and "nonprobe", and, for nonprobe sequences, how far each site is from the probe region
* This can be approximated using "distance from center" as a lazy algorithm
* Build a heatmap for how many sites fall into each rate partition
* Average and 95% confidence intervals of estimated rate vs distance from center
* MrBayes run for UCE data

Miscellany:

* Rejected from PLoS Biology :(
* Read and comment on Raul's manuscript