I recently became aware of an October paper from Ian Holmes’s group at UC Berkeley describing a rich genome simulation toolset: “Tools for simulating evolution of aligned genomic regions with integrated parameter estimation” Besides their programs, what’s interesting about the paper is that they judged the quality of their work by comparing it to my own research. I have much respect for Holmes and to have him compete against a program from my dissertation research is an honor. Here is a choice quote from their paper:
We also compared our simulation methods, GSIMULATOR and SIMGENOME, to DAWG, a widely cited program for simulation of neutral substitution and indel events. We chose DAWG because it most closely exemplifies the goals we have identified here: it is clearly based on an underlying evolutionary model and provides tools for estimating the parameters of the indel model directly from sequence data. It appears to be the leading general-purpose simulator at the time of writing. Other simulators (such as PSPE) are richer, but do not provide the parameter-estimation functionality that DAWG does. (internal citations removed)
In other citation news, there is a new paper out in Genetics discussing the “hothead” mutation in Arabidopsis thaliana that made this blog semi-famous. This paper follows up on arguments that hothead’s revertant phenotype is due to unexpected outcrossing. They confirm that hothead does have a high outcrossing rate and that revertant phenotypes are due to outcrossed seeds.
When I first heard this argument, I kicked myself for not thinking about it first. What first characterized hothead plants was the lack of fusion in their flowers. Wild-type A. thaliana plants are complete selfers because their flowers are fused shut, preventing external pollen from reaching the stigma. This way, only pollen produced internally will pollinate A. thaliana. However, when the flower fails to close completely, external pollen is no longer excluded and outcrossing can occur. Duh!
Admittedly, this would have been hard to argue without having the actual plants because some observations reported in Lolle’s original paper conflict with outcrossing, but it appears that these observations cannot be replicated. Perhaps they were just artifacts.