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Inferring Phylogenies

Joseph Felsenstein

September 2003

ISBN: 9780878931774

580 pages

Price: £85.00

Clearly explains the assumptions and logic of making inferences about phylogenies, and using them to make inferences about evolutionary processes. If you are a lecturer interested in adopting this title for your course, please contact your Oxford representative to arrange a local price.



Published by Sinauer Associates, an imprint of Oxford University Press.

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.

About the Author(s)

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.

Table of Contents

    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
    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
    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


"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

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