Molecular Evolution: A Phylogenetic Approach

Molecular Evolution: A Phylogenetic Approach. R. D. M. PAGE AND E. C. HOLMES. Blackwell Science, Inc., Maiden, Massachusetts, 1998. 352 pp., illus. (ISBN 0-865-42889-1 paper, $51.95)

Molecular phylogenetics, devoted to understanding the hierarchical structure of biological diversity through genetic data, is one of the fastest growing fields in biology, propelled by the polymerase chain reaction (PCR) as well as rapidly improving DNA sequencing technologies and other marker detection systems. One important outgrowth of the phylogenetic revolution is the recognition that evolutionary trees provide an important and appropriate context to address questions in a diversity of disciplines such as evolutionary biology, ecology, and developmental biology. In this book, the authors use the phylogenetic tree as a central metaphor in approaching the study of molecular evolution. Their central aim is to demonstrate what evolutionary information is contained in gene sequences and to show how this information can be recovered. The book is intended for senior undergraduate and graduate students taking courses in molecular evolution and/or phylogenetic reconstruction, or as a supplement for students taking wider courses in evolution. Each chapter begins with a concise table of contents that outlines the subject matter, and ends with a summary and a list of references for further reading. Tables and figures are abundant and extremely clear. Important concepts are discussed in greater detail in gray-shaded boxes. A comprehensive bibliography is included at the end of the book.

Four introductory chapters lay the groundwork for discussions in the rest of the book. After briefly describing the importance of trees in molecular evolution (Chapter 1:10 pages), the phylogenetic lexicon is disentangled in a clear and accessible form in Chapter 2 (26 pp.). Trees come in all shapes, sizes, and configurations, and sorting through the considerable descriptive jargon can be daunting. This chapter alone makes the book an excellent resource for any course in phylogenetic systematics.

Models of the evolution of repetitive sequences, multigene families, and differences in genome size and gene number among organisms are presented Chapter 3 (52 pp.). The authors intentionally emphasize the characteristics of genome function and organization that are most germane to phylogenetic reconstruction. Thus, some readers may be unsatisfied with the level of discussion for some topics. For example, mutation is clearly an important component of molecular evolution, but the authors do not present details about the mechanics of DNA mutation and repair. Instead, they devote more time to the genetic code, which differs not only between the nuclear and mitochondrial genome of an organism, but also between organisms. This knowledge is critical for building an accurate model of molecular evolution that can then be used to estimate a phylogenetic tree. Because the same molecular genetic processes operating within species give rise to the genetic patterns we detect among species, population genetics is a necessary foundation for an understanding of molecular phylogenetics. Population genetics is the focus of chapter 4 (46 pp.), and a good overview of classical Hardy-Weinberg theory is presented. But the biggest impact of a phylogenetic perspective on the molecular evolution of populations has been through coalescent theory, where the histories of extant genes are traced backwards through time. The coalescent receives relatively little treatment in this chapter. More discussion of this important conceptual tool would have been useful.

The analytical problems involved in reconstructing phylogenies from gene sequences are discussed in Chapters 5 (37 pp.) and 6 (56 pp.). A plethora of pairwise genetic distances have been published, and differences in the information content of each of these disparate measures is not always intuitive. Likewise, it is often difficult to decide how best to align divergent sequences containing gaps, and many solutions have been proposed in the primary literature. An exhaustive list of solutions and explanations was beyond the scope of this book. Instead, the authors discuss clearly the central problems involved in alignment and measuring genetic change, and present exemplary solutions. Chapter 6, the longest of the book, explains methods of phylogenetic inference, including distance methods, parsimony, and maximum likelihood. Methods for measuring confidence in trees, such as nonparametric and parametric bootstrapping, are discussed. These two chapters would be invaluable for any course in molecular systematics.

The book ends with two chapters that discuss the application of phylogenies in addressing a variety of evolutionary questions. Phylogenies have been useful in testing the long-standing neutralist-selectionist debate. In Chapter 7 (52 pp.), the ideas from both schools are presented. The final chapter deals with how to estimate an organismal tree from a gene tree, and whether it is best to combine data from different characters in reconstructing a phylogeny. Case studies in hostparasite cospeciation, on estimating the age of taxa, and on molecular epidemiology are then presented, enforcing the thesis of the book that phylogenies can elucidate a diversity of questions in biology.