Molecular Evolution and Phylogenetics

Rating:
Summary: A valuable addition
Review: I don't look for any one book to answer all my questions. This one carries its weight, though, and maybe a bit more.

The first section gives the clearest and most detailed description of nucleotide sequence comparisons I've seen. I'm no biologist, but it really got me thinking about some new ways to talk about substitution matrices.

The bulk of the book covers what I hoped for originally: phylogenetic trees. The authors choose an unusual approach - it doesn't quite meet the authors' initial promise of math-minimization, but doesn't climb too far up the ivory tower, either. I find it a very practical, usable level of presentation. I'd be nervous about going beyond their formulas, since the math for real understanding isn't all there. Still, the phylogeny discussion covers a lot of material, and covers it well enough for me to write programs about most of it.

The final section addresses population genetics. I have nothing against population genetics, it just never seemed to point where I'm headed. Nei and Kumar corrected my mis-impression. Population gentics is the background model, the null hypothesis, behind the functions that score population differences. It really shows what happens when the tree of life branches out.

The book has some minor weaknesses. It emphasizes nucleotide sequences at the expense of peptides; I can't fault an author for writing what they want as opposed to what I want. On page one, the authors decline an intensely mathematical approach. By page 25, they're up to Poisson and gamma distances. The typography make the section breaks into a "Where's Waldo" experience. Nei's favorite author, based on citations, is Nei. Well, false modesty is no virtue. This book seems authoritative and Nei seems to be an authority, maybe not just in Nei's opinion.

This book really has given me a lot more to work with than most. Education isn't cheap these days, and this book is very educational. I just hope no one asks me to lend it any time soon.

Rating:
Summary: OK, until something better comes along
Review: Nei and Kumar's "Molecular Evolution and Phylogenetics" is basically an updated version of Nei's 1987 "Molecular Evolutionary Genetics" book. Accordingly, attention is shifted to reviewing many recent advances in methods of phylogenetic inference with an obvious bias towards distance methods, particularly those which the senior author devised. In fairness, they give decent coverage to the more popular parsimony and likelihood methods as well. The great strength of the book is the number of real examples used to illustrate properties of the methods, and their focus on statistical methodology without miring the reader in detailed mathematics. The disappointment is that while breadth of coverage is tolerable, depth is lacking. Expanding their views on the shortcomings of likelihood in choosing tree topology and likelihood ratio-tests in choosing models of sequence evolution would have been most enlightening, particularly as these issues have been brushed lightly aside by phylo-likelihoodists. Other methods (Hadamard transformations, Bayesian phylogenetic inference) were absent altogether. Further the chapter on molecular clocks was disappointing--old 1980s controversies were rehashed, while there was nothing on methods that relax the assumption of rate constancy while still allowing divergences to be dated. Admittedly some of this is very new and research is ongoing, but there isn't even a hint of these developments in this chapter. Another plus though is the addition of a chapter on inferring ancestral states of molecular sequences.

Unlike Molecular Evolutionary Genetics, far too little of the book is devoted to methods at the population level, and what is there again smacks of state-of-the-art 15-20 years ago. I was hoping for much more coverage of microsatellite and AFLP data. There was very little for either, while now rarely-used RFLPs were given extensive coverage.

In short, this book was too short, particularly for the price, and I almost gave it 3 stars rather than 4. However, if you are a phylogeneticist, you will probably want to have this book on your shelf. A lighter introduction for the uninitiated would be Rod Page's "Molecular Evolution" or Graur and Li's "Fundamentals of Molecular Evolution". However, my hopes for a good comprehensive text and reference on phylogenetic methods now rest on publication of Joseph Felsenstein's "Inferring Phylogenies".

Rating:
Summary: Top in its Field
Review: This book is an excellent text and reference for both graduate students and faculty. It covers several topics in molecular evolution and phylogenetic analysis, as the title suggests. It stands as a unique contribution because the authors explain the mathematical and conceptual framework of a given topic in molecular evolution or phylogenetic analysis and give subsequent examples to show how various analytical methods can be applied to the study of that topic. In that context, the explanation of concepts was exceptionally clear, which made it easy to understand potentially difficult subject matter. This book is highly recommended to those wishing to study the analysis of genes and proteins in an evolutionary framework.