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. Yet no book has summarized this work until now. 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.

Inferring Phylogenies is intended for graduate-level courses, assuming some knowledge of statistics, mathematics (calculus and fundamental matrix algebra), molecular sequences, and quantitative genetics.

1. Parsimony methods
2. Counting evolutionary changes
3. How many trees are there?
4. Finding the best tree by heuristic search
5. Finding the best tree by branch and bound
6. Ancestral states and branch lengths
7. Variants of parsimony
8. Compatibility
9. Statistical properties of parsimony
10. A digression on history and philosophy
11. Distance matrix methods
12. Quartets of species
13. Models of DNA evolution
14. Models of protein evolution
15. Restriction sites, RAPDs, AFLPs, and microsatellites
16. Likelihood methods
17. Hadamard methods
18. Bayesian inference of phylogenies
19. Testing models, trees, and clocks
20. Bootstrap, jackknife, and permutation tests
21. Paired-sites tests
22. Invariants
23. Brownian motion and gene frequencies
24. Quantitative characters
25. Comparative methods
26. Coalescent trees
27. Likelihood calculations on coalescents
28. Coalescents and species trees
29. Alignment, gene families, and genomics
30. Consensus trees and distances between trees
31. Biogeography, hosts, and parasites
32. Phylogenies and paleontology
33. Tests based on tree shape
34. Drawing trees
35. Phylogeny software
Related Titles

Joseph Felsenstein

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. His current research interests include the development of coalescent-based Markov Chain Monte Carlo methods of computing likelihoods for models of evolution within species, and development of statistical methods for inferences about quantitative characters within and between species.

"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." -- AJ Drummond, Heredity

"The book is full of expert insights, as one would expect from an author who has made important original contributions to many of the areas he covers. Felsenstein provides beautiful and creative accounts of many topics. It will be a long time before there will be a comparable book; perhaps the field is now growing too fast for there to ever be one. The publication of Inferring Phylogenies is a milestone for evolutionary biology in general and phylogenetics in particular." -- Fredrik Ronquist, Science

"The author certainly sets out with an ambitious goal: to survey, in one book, the field of phylogenetics since computational methods entered the arena forty years ago, and he amply delivers on this promise. For researchers new to this area, the book describes contemporary methodology in a way that is both accessible and authoritative. For 'old hands,' it provides a wealth of background and commentary." -- Mike Steel, TRENDS in Ecology and Evolution

"Occasionally a book is a classic by the time it is published, and this is it. The breadth is very wide with all the main expected topics. It is hard to imagine how any lab could function without this book." -- David Penny, Systematic Biology

"Felsenstein's book represents a truly majestic discussion of the inference and applications of phylogenetic trees. The power of this volume lies in its unique combination of an accessible style with undoubted intellectual authority. Over 30 years ago Crow and Kimura produced what has become the cornerstone of theoretical population genetics. Felsenstein has now given us the definitive resource for anyone interested in phylogenetics. This volume is an outstanding achievement." -- Edward C. Holmes, The Quarterly Review of Biology