A New Paradigm? Species Trees From Gene Trees

Lots of talk about a 'new paradigm' today at a symposium on generating species trees from gene trees at the Minnesota evolution meetings. If most of the speakers in this symposium have their way, the days of generating individual gene trees or trees from concatenated datasets will soon be in the past. Talk of such an advance dates back more than a decade, but things have moved very quickly over the past two years. This seems due in large part to the emergence of the software package BEST by Liang Liu. I've received mixed reports about BEST's accessibility and limitations. As one might expect from a new package it's a bit buggy and may be a bit less user-friendly than you'd like, but is working for most people. Liang Liu said during his presentation that version 2.0 posted on June 18, 2008 is considerably better than the previous iteration, so you'd be well-served to upgrade if you've already been messing with it. More generally, there are some potentially significant assumptions of the existing methods for generating species trees from gene trees (e.g., horizontal gene transfer) whose violations are not well understood. In any case, you'd better move BEST to the top fo the list of programs you need to learn...