@mlandis, yes we have been looking at the frequency of traffic between trees as well and have tried visualizing this by making the edges thicker in proportion to the number of transitions. This also couldn't fit into the talk and is very much a work in progress.
One issue with directly looking at tree transitions is that sampling density affects the quality of tree transition statistics, but some of these tree islands require a large number of iterations to reach (and then get stuck in for a large number of iterations). I was filling up all of @ematsen 's hard drive space before I switched to sampling every 100 or 1000 iterations. Commute time statistics are an alternative way of looking at this.
Also, that last comment was @alexei_drummond, in case it wasn't clear from the context.