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Inferring Phylogenies, by Joseph Felsenstein
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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.
- Sales Rank: #1250252 in Books
- Brand: Brand: Sinauer Associates
- Published on: 2003-09-04
- Original language: English
- Number of items: 1
- Dimensions: 7.00" h x .90" w x 9.00" l, 1.10 pounds
- Binding: Paperback
- 580 pages
- Used Book in Good Condition
Review
"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
About the Author
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.
Most helpful customer reviews
20 of 21 people found the following review helpful.
Good as a refresher for the initiated, but not for beginners at all
By Roger Burks
This new explanation of phylogenetic methods contains a good discussion of the merits and potential failings of many of the methods currently used to study phylogenetics. It may be very good for computer science students, who have a better grasp of the mathematics. It may also be good for biologists well versed in biostatistics, who want to know why systematists use certain, less easily handled, analytical methods. However, it is very difficult reading for other scientists who do not fully understand the complex math presented in the text. It also does not give a concinct summary of the assumptions and failings of each method. The bottom line is that this book is good for experts who easily understand algorithms, but not good for students who don't have a good handle on such things.
29 of 33 people found the following review helpful.
More than what the title implies
By Jonathan Badger
As one would expect, the majority of this book deals with the various algorithms for phylogenetic analysis (such as the various versions of parsimony, distance based methods, and likelihood methods), but the book covers more topics that this. In particular, the book covers methods of tree comparison such as the KHT and SH tests, which I found particularly welcome because the current literature covering these tests often are rather opaque to those who haven't followed it since their conception.
The only weak thing about about the book (besides the many typos, which should be fixed in the new printing anyway), is Felsenstein's rather acrimonious treatment of Bayesian methods, in which the Bayesian use of priors is criticized on philosophical grounds.
I was annoyed by this not because I'm a card-carrying Bayesian (which I'm certainly not), but rather because I would have thought that Felsenstein of all people, whose primary opponents in the 1980's were the members of the philosophically-minded Willi Hennig crowd (who always claimed that parsimony was "philosophically right" even when it gave the wrong answer), would realize the futility of arguing scientific issues on philosophical grounds. Bayesian methods, as all scientific methods, will win or lose based on how well they work in practice, despite turgid philosophizing on both sides of the issue.
0 of 0 people found the following review helpful.
Five Stars
By Amazon Customer
great
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