Monday, October 18, 2010

Bayesian NCPA?

Hi all,
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?


  1. I hadn't heard about that TREE paper, thanks for pointing it out. I will read, contemplate, and return.


  2. Hi, I think there is a bit of confusion here. Lemey et al 2009 (PLoS Comp Biol) is a discrete spatial model (not a Bayesian NCPA but an explicit model based approach). Lemey et al 2010 (Mol Biol Evol) is the continuous diffusion spatial model. There is also discussion of an approximate Bayesian modifications to NCPA by Manolopoulou in a PhD thesis.

  3. Ah yes- sorry for the confusion. I do know that they are separate methods and that the Lemey paper is not related to the Bayesian NCPA, I just wanted people's opinions on both. I haven't read the Manolopoulou phd thesis, but I do have it.