I thought it might help some of the engagement/core team to have a place with pointers to information about phylogenetics.
Inferring Phylogenies by Joe Felsenstein (on sale at Amazon for $54 ). Covers a lot of methods and history, generally pretty readable. Felsenstein is in the Trait Evolution group and is responsible for many methods in phylogenetics, such as independent contrasts, bootstrapping, and a dynamic programming algorithm for calculating tree likelihoods.
Computational Molecular Evolution by Ziheng Yang (Amazon $58 ). Covers a bit more detail of the math. Good to understand how some of the algorithms work. Despite its title, it covers a lot of phylogenetics, including much of relevance to trait evolution (such as ancestral state reconstruction).
Bodega Bay Workshop in Applied Phylogenetics (March 6-13, 2010). It covers many current methods for tree reconstruction, viewing trees, and looking at trait evolution on trees. It's taught by many of the people developing new approaches (including Mike Sanderson, an iPToL PI) and has students with a range of abilities and experiences in phylogenetics. Great chance to learn about the field and some of its culture and expectations while spending time on the stunning northern California coast. Registration just opened (Dec. 2009). Note that this course is cheap ($550 covers the course and room and board).
Workshop on Molecular Evolution (end of July/beginning of August, 2010). Goes into tree reconstruction in great depth, as well as topics in genomics and other areas. Many of the instructors are developers of relevant programs. Registration has not yet opened.