I just read Three roads diverged? Routes to phylogeographic inference by Erik W. Bloomquist, Philippe Lemey, and Marc A. Suchard, out next month in TREE and I'm confused! They review some interesting work in phylogeography, but also talk up a "Bayesian NCPA" method. However, my understanding of the method they discuss is that although it takes into account uncertainty in reconstruction of the haplotype network, it doesn't modify the inference key at all, which seemed to me to be the most problematically inscrutable part of NCPA. Have any of you folks looked at this? Is there anything fresh there?
As well- what are your impressions of the method they describe as "spatial diffusion"? My understanding from the Lemey et al 2009 paper is that it is akin to reconstructing location as a continuous character on the phylogeny under a variety of models. Have any of you tried this method? What are your thoughts?