PREFACE         

To many zoology instructors, the phylogeny of animals is merely a convenience for organizing textbooks and courses, and not to be taken seriously. This approach was reasonable as long as there was no way of testing phylogenies. Moreover, until recently phylogenetics had few practical consequences. The past decade, however, has witnessed the flourishing of evolutionary developmental biology ("Evo Devo"), which promises for the first time to reveal the changes in developmental regulatory genes that led to the evolution of the different body plans that define animal phyla. Discovering the correct sequence of developmental genetic changes obviously depends on having the correct phylogeny to begin with, so animal phylogenetics has suddenly become crucial to a major area of research in zoology. In addition, having the correct phylogeny would permit quantitative tests of a variety of other evolutionary hypotheses regarding such questions as punctuated equilibrium and correlations between environmental and evolutionary changes (Heulsenbeck and Rannala 1997; Pagel 1999).

Molecular phylogenetics does not necessarily provide the correct phylogeny, but it can help eliminate incorrect ones and can suggest alternative hypotheses that otherwise might not have been considered. Molecular phylogenetics in a broad sense has been around since 1904, when G. H. F. Nuttall inferred the evolutionary relationships among primates and other mammals from their immunological compatibility. Libbie H. Hyman (1888-1969) often cited such serological studies favorably, while noting their technical limitations and the continuing need for studies based on traditional embryological and morphological characters. She would have been pleased with how far molecular phylogenetics has advanced, although she would undoubtedly have acerbic comments about some of the conclusions.

The current era of molecular phylogenetics began a few years before Hyman died, with the first comprehensive phylogenies reconstructed from the amino-acid sequences of cytochrome c (Fitch and Margoliash 1967). The availability of nucleic-acid sequences set off another revolution marked by the publication of a paper by Field et al. in 1988. Since then molecular phylogenetics has crawled, stumbled, and finally learned to stand and walk confidently (Adoutte et al. 2000). Molecular phylogenetic trees are now common in Science, Nature, and other journals, and a molecular phylogenetic tree is even the organizing principle of a popular book on diversity (Tudge 2000). Zoology instructors therefore have to be prepared to explain the discrepancy between the phylogenies common in textbooks and what students are likely to find elsewhere. Rather than being an added burden on the instructor, the introduction of molecular phylogenetics into teaching can be an opportunity to stimulate critical thinking.

Unfortunately, the jargon and methodology of molecular phylogenetics have made it difficult for the average zoology instructor to keep up with the flood of literature. Moreover, the often conflicting results of molecular phylogenetics have made many wonder whether learning about it is worth the trouble. In the1990s, however, the main outlines of animal molecular phylogeny have become fairly settled, so the time is now right for a concise introduction to its methods, terminology, and main conclusions.

This introduction has been organized to accommodate instructors with all levels of time and interest. It presupposes a basic understanding of cladistics, which is now the default method of representing phylogenies. Some of the terms of cladistics, as well as specialized terms in molecular phylogenetics, are explained in the glossary at the end of this document. A fuller treatment of cladistics can be found in references at the end of this document.

The main concepts and results of molecular phylogenetics can be gleaned in a few minutes by scanning the Table of Contents below. Clicking on a heading links to further discussion, which includes links to references and other sources on the web. Part I introduces the methods of molecular phylogenetics. This section can safely be deferred, or, for more detail, you may refer to books and web sites in the references or follow the links in this document. Many readers will want to jump to Part II, which describes what traditional morphological characters are supported or not, and Part III, which presents molecular-phylogenetic hypotheses as alternatives to the traditional morphology based hypotheses. These sections include historical sketches of traditional phylogenetic concepts, generally using Hyman's monumental The Invertebrates as a starting point. More recent morphological phylogenetic schemes are also outlined, especially the book length noncladistic study by Pat Willmer (1990) and the equally thorough cladistic study by Claus Nielsen (1995). Parts II and III may convince some zoology instructors that the organization of their syllabus according to traditional phylogenetics needs some revision. Part IV offers suggestions for such revision.

While molecular phylogenetics has developed considerably since its first conception, it is probably still in its larval stage. It will be apparent in Part III that controversies still remain unresolved. This web site will try to keep abreast of developments as they happen. In addition, feel free to email any corrections, suggestions, and questions to c.harris@plattsburgh.edu.

I am indebted to Marge Kemp, the Sponsoring Editor, for her insight in seeing the need for this project, Donna Nemmers, Developmental Editor, for guiding me in its creation, and Mark Christianson, the Media Developer, for its final execution. I am also grateful to Jan Pechenik and Ken Saladin for providing encouragement, stimulating discussions of phylogeny, and a due sense of caution.