Inferring Phylogenies

JOSEPH FELSENSTEIN is Professor in the Department of Genome Sciences at the University of Washington.

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.