Inferring Phylogenies [Paperback]

Joseph Felsenstein (Author)

Book Description

ISBN-10: 0878931775 | ISBN-13: 978-0878931774 | Publication Date: September 4, 2003 | Edition: 2

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

Editorial Reviews

Review

"FelsensteinÂ’s book Â… represents a truly majestic discussion of the inference and applications of phylogenetic trees." -- Edward C. Holmes, The Quarterly Review of Biology<br /><br />"Occasionally a book is a classic by the time it is published, and this is it. Â… " -- David Penny, Systematic Biology<br /><br />"The publication of Inferring Phylogenies is a milestone for evolutionary biology in general and phylogenetics in particular." --Fredrik Ronquist, Science

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

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

About the Author

JOSEPH FELSENSTEIN is Professor in the Department of Genome Sciences at the University of Washington.

Product Details

• Paperback: 664 pages
• Publisher: Sinauer Associates; 2 edition (September 4, 2003)
• Language: English
• ISBN-10: 0878931775
• ISBN-13: 978-0878931774
• Product Dimensions: 8.9 x 7 x 1.2 inches
• Shipping Weight: 1.9 pounds (View shipping rates and policies)
• Average Customer Review: 4.1 out of 5 stars  See all reviews (7 customer reviews)
• Amazon Best Sellers Rank: #327,922 in Books (See Top 100 in Books)

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Customer Reviews

Most Helpful Customer Reviews

41 of 45 people found the following review helpful:

5.0 out of 5 stars The encyclopedia, January 5, 2004

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wiredweird "wiredweird" (Earth, or somewhere nearby) - See all my reviews
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This review is from: Inferring Phylogenies (Paperback)

It's fairly common to start with a few protein or DNA sequences from different species, and to try to figure out what the various lines of descent are that connect them. This book is about the computations that find the "family trees" based on molecular (or other) data.

The book is a goldmine. Among phylogeny programs, PHYLIP (supported since 1980) could well be the most popular - Felsenstein wrote it. In this, he covers an incredible number of techniques, drawn from dozens of fundamentally different insights into the problem of relatedness. Felsentein desribes many techniques, their variations, and their relationships to others. He describes every phase of the analysis, from interpreting raw data, through deducing trees and evaluating them statistically, to displaying them visually. Despite this book's thud factor - ove 600 pages - it can not cover every topic in full detail. That's when the book's references, about 50 pages of them, become valuable. Felsenstein welcomes the interested reader into every aspect of the field's literature.

Despite the huge body of theory and practice, there are still many disputes about the proper interpretations or approaches to some thorny issues. Felsenstein goes over the issues in some detail, and is not afraid to take sides when he sees reason to.

Felsenstein gives clear descriptions of many basic algorithms. There's no code here, but a diligent reader should be able to develop implementations of them. I could have hoped for better indexing of algorithms, but the chapter organization is clear enough to make any search brief. I could also have asked for more of the algorithms to be spelled out in implementable detail, but the book would have needed thousands of pages to include them all. He seems to have chosen a variety of well-known and important algorithms for full description, and left the minor or complex ones for the references.

If you just want to use one of the common phylogeny programs, you came to the wrong place. This is about fundamental techniques for creating programs - there's almost nothing here for the user who just wants the results. Such users won't even learn much more about the results they do get. Developers and statisticians who need detailed analyses will probably find what they they want, and lots more.

The only problem with the book is that it reads like an encyclopedia. Lots of developers can get lots of good work done without this level of knowledge. It will take a truly devoted reader to plow though it, as well as a good foundation in algorithm development and in probability and stats. If you are dedicated to becoming an expert in the practice and problems of phylogenetic analysis, though, I doubt that any other book will give you a third of the knowledge or a tenth of the breadth.

18 of 18 people found the following review helpful:

4.0 out of 5 stars Good as a refresher for the initiated, but not for beginners at all, May 29, 2006

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Roger Burks (Riverside, CA United States) - See all my reviews
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This review is from: Inferring Phylogenies (Paperback)

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.

24 of 27 people found the following review helpful:

4.0 out of 5 stars More than what the title implies, July 5, 2004

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Jonathan Badger (Washington, DC United States) - See all my reviews
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This review is from: Inferring Phylogenies (Paperback)

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.