Phylogenies (evolutionary trees) are basic to thinking about and analyzing differences between species. Statistical, computational, and algorithmic work on them has been ongoing for four decades, with great advances in understanding. "Inferring Phylogenies" explains clearly the assumptions and logic of making inferences about phylogenies, and using them to make inferences about evolutionary processes. It is an essential text and reference for anyone who wants to understand how phylogenies are reconstructed and how they are used. As phylogenies are inferred with various kinds of data, this book concentrates on some of the central ones: discretely coded characters, molecular sequences, gene frequencies, and quantitative traits. Also covered are restriction sites, RAPDs, and microsatellites. This work is intended for graduate level courses, assuming some knowledge of statistics, mathematics (calculus and fundamental matrix algebra), molecular sequences, and quantitative genetics.
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
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