Inferring Phylogenies

by Joseph Felsenstein

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 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.

Genres: Evolution, Science, Biology, Reference, Textbooks, Computer Science, Nonfiction

580 pages, Paperback

First published August 1, 2003

Reviews

[Bill Tyne · Rating 2 out of 5]

After several false starts I finally read this cover to cover. There is a lot of useful information on approaches to phylogeny and how to test various hypothesis and parameters related to evolutionary processes using phylogenetic approaches. The major problem with the book is in the presentation. It assume a lot of prior knowledge that disbars it from all but a specialised audience, this is not for the general biologist or even the molecular biologist who might be interested in phylogenetics - it is aim firmly at bioinformaticians with a strong background in statistics and probability (this includes the application of calculus and matrix algebra to equations exploring likelihood etc.). There are not enough worked examples in the text to clarify the endless equations presented. The odd occasion a worked example was present it was very helpful which underscores the point that a wider application of such examples would have improved the book no end. In addition some terms were introduced with little or know explanation (again an assumption of pre-existing knowledge that may not be present) - perhaps a glossary would help sort this issue out, it would certainly have been useful in keeping up with the plethora of technical terms bandied about. Finally the attitude of the author strike one as arrogant and contemptuous one can really sense the sneer as he mentions we mere biologists - an attitude that sadly does the bioinformaticians no favours.

[J.P. Drury · Rating 2 out of 5]

hate to use the pun, but felsenstein makes it impossible to see the forest through the trees. i'm not sure for whom this text would be useful, honestly, because it neither provides a solid intro for the lay reader nor gives anything but a sort of nostalgic retrospective for those already in the know.

[Michiel · Rating 4 out of 5]

An impressive overview on the statistical methods used in phylogeny. Not for the faint of heart!