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CLADISTICS: A PRACTICAL PRIMER ON CD-ROM

Phylogenetic systematics has become increasingly recognized as the most powerful method available for reconstructing phylogeny and therefore a necessary part of the tool kit of all practicing paleontologists. However, until recently there have been few texts that explain the principles of cladistic analysis at other than an advanced level and there has been a distinct lack of resources for undergraduate courses. This was partly remedied by the text produced by Kitching et al. (1998), which did provide an extensive overview of the principles and practice of cladistics although it was hampered by its format in providing effective exercises. This gap has now been filled by the publication reviewed here in which a CD-ROM authored by Peter Skelton and Andrew Smith is accompanied by a text by Neale Monk. One wonders why this has not been tried before, because CD-ROM provides an extremely flexible and interactive method of conveying information and has the added advantage of being able to incorporate multimedia. In this case the CDROM and the text provide the same information although the format is slightly different and the exercises are not dealt with quite as fully in the text as they are in the CD-ROM. This publication was apparently not produced specifically for paleontologists (although Andrew Smith's background in echinoid paleobiology is often strongly evident in the examples used) and so to assess it from several perspectives this review was carried out by a vertebrate paleontologist (DKE), an undergraduate (RBI), and a geologist with an interest in cladistics (JHW). The publication is organized in chapters that take the student through first principles and then into characters and homology before dealing with cladograms and trees and finally the tests of robustness of trees. Students can then evaluate themselves through an exercise (on echinoids of course!) that uses the principles introduced in the text. One of the distinct advantages of this publication is that both morphological and molecular data are dealt with in methodologically the same way throughout, an approach that demystifies the molecular data that many of us in paleontology rarely deal with and demonstrates its uses and its limitations. This is brought together particularly well in the final exercise in which both morphological and molecular data are developed, manipulated, and combined and it is shown how one set of data can be used to provide a check on the other. Chapter one dealing with first principles takes us straight into the classic three-taxon problem using the horse, zebra, and cow and demonstrates how the distribution of characters provides a means of grouping these organisms. Immediately the concept of using nucleotide bases in the same way is introduced and mutations are discussed. It appears to us that in the CD-ROM this is introduced a little quickly, after all for most of us it is easier to grasp the homology of morphological data than nucleotide bases, but it is supported by a series of exercises that consolidate the information. This information is followed by an explanation of parsimony and the development of trees. Chapter two deals with the concepts of homology and homoplasy and then continues with character definition and weighting. It might have helped here if weighting, once introduced, had been dealt with in more detail because, although the concept is clearly explained, one is left without an understanding of how weighting is carried out in practice. The third chapter covers cladograms and trees and provides a particularly clear overview of how polarity can be determined through ontogenetic criteria and outgroup comparison. One problem that becomes apparent in this chapter is that, in order to carry out the exercises, pages of trees have to be copied or printed off and then worked on by hand. In one case 15 trees need to be copied. It seems as though this is one area where the interactive capabilities of the CD-ROM are not fully utilized. The final chapter deals with fit and robustness and explains more clearly than we have seen in other publications what the bootstrap and Bremer support tests actually do and how to evaluate the results. The final section is a series of exercises on the coding of matrices of morphological and molecular data, using previously published material on the relationships of regular and irregular sea urchins. Perhaps at this stage it might have been interesting to provide data that could be run separately using one of the computational programs available for cladistic analysis or at least provide some discussion of how these programs are used, but that would perhaps necessitate a second book. The three of us found that the CD-ROM operated well on both a Mac and a PC and on machines of varying vintage and was easy to use other than in the one or two minor areas commented on previously. The accompanying book is easy to follow and provides useful back-up if used with the CD. It lacks a bibliography so it cannot act as a source to the literature, however, it does provide a list of links to various sources for software programs although it does not discuss them or their relative merits, which would have been helpful. As a teaching tool for courses in which no previous knowledge of cladistics is expected, this publication would be extremely effective. It would also be useful for those of us who need to review cladistic methodology. At $55 it is not too expensive to buy for either of these reasons. For graduate classes this would be too elementary, but it would provide the thorough grounding necessary to understand more advanced concepts. Maybe the next step should be the production of a companion publication suitable for graduate classes that deals with higher level topics such as detailed discussions of character coding and explanations of other complex statistical analyses used. Until that time, Cladistics:A Practical Primer is the best general teaching resource available. DAVID K. ELLIOTT RANDALL B. IRMIS JAMES H. WITTKE