Survey philosophical piece on phylogenetic inference:
The piece we are reading by Matt Haber is a direct response to the following:
The Farris piece below is perhaps the most famous piece defending the Parsimony method. The Felsenstein is the first two chapters from Inferring Phylogenies and describes the Parimony method in a very clear way.
Foster is an attempt to make more perspicuous what is going on. Howson and Urbach is a short, general introduction to Bayesian reasoning, the Lewis piece is a survey of some work in phylogenetics including Bayesian methods and the Velasco piece is a very basic introduction to Bayesian methods in phylogenetics, but is a more philosophical piece which discusses the assignent of prior probabilities to trees.