Inferring Phylogenies

Joe Felsenstein is Professor in the Department of Genome Sciences at the University of Washington, Seattle, where he has taught for more than thirty years. He earned a B.S. (Honors) in Zoology from the University of Wisconsin, Madison, and a Ph.D. in Zoology from the University of Chicago. Dr. Felsenstein is the author of the widely used PHYLIP package of programs for inferring phylogenies. He served as President of the Society for the Study of Evolution in 1993 and has received numerous awards, including: election to membership in the American Academy of Arts and Sciences (1992); the Sewall Wright Award, American Society of Naturalists (1993; election to membership in the National Academy of Sciences (1999); and the Weldon Memorial Prize, Oxford University (2000). His work has ranged from theoretical evolutionary genetics to statistical methods for inferring phylogenies.

• 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.

Joe Felsenstein has had more positive influence on the statistical revolution of phylogenetics than any other researcher in the field. For that reason, many biologists view him as the father of statistical phylogenetics. It was with this in mind that I finally got my hands on his long-awaited book, Inferring Phylogenies. The short answer is: it delivers. Inferring Phylogenies is quite simply an instant classic.