Inferring Phylogenies

Explains clearly the assumptions and logic of making inferences about phylogenies, and using them to make inferences about evolutionary processes. Aspects covered include: discretely coded characters, molecular sequences, gene frequencies, quantitative traits, restriction sites, RAPDs and microsatellites. Intended for graduate level courses, assuming some knowledge of statistics, mathematics (calculus and fundamental matrix algebra), molecular sequences, and quantitative genetics.

Preface - Parsimony Methods - Counting Evolutionary Changes - How Many Trees Are There? - Finding the Best Tree by Heuristic Search - Finding the Best Tree-branch and Bound - Ancestral States and Branch Lengths - Variants of Parsimony - Compatibility - Statistical Properties of Parsimony - A Digression on History and Philosophy - Distance Matrix Methods - Quartets of Species - Models of DNA Evolution - Models of Protein Evolution - Restriction Sites, Rapds, and Microsatellites - Likelihood Methods - Hadamard Methods - Bayesian Inference of Phylogenies - Testing Trees by Likelihood - Bootstrap and Randomization Tests - Paired Sites Tests - Invariants - Continuous Characters and Gene Frequencies - Quantitative Characters - Comparative Methods - Coalescent Trees - Likelihood Calculations on Coalescents - Alignment, Gene Families and Genomics - Coalescents and Species Trees - Consensus Trees and Distances Between Trees - Biogeography, Hosts, and Parasites - Phylogenies and Paleontology - Tests Based on Tree Shape - Drawing Trees - Phylogeny Software