ASBS Newsletter – Book Review
Principles and Techniques of Contemporary Taxonomy
written by Donald L. J. Quicke
(From ASBS Newsletter Number 93, December 1997)
Publisher: Blackie Academic & Professional [Chapman & Hall], London. 1993. xii+311 pi). ISBN 0 7514 00293.
It has been some time since the last of my book reviews appeared in this Newsletter; nearly three years, in fact. This hiatus has not been because I have not been reading, but because I have been reading and writing other things instead.
However, I have recently returned to perusing systematics-type books on the long train-trip to and from my work, and it seemed appropriate to celebrate the upcoming anniversary of my last review by starting to produce a new one. Actually, I also have two more systematics books sitting on my bedroom floor waiting to be read, and so I expect that you will be subjected to another couple of reviews before too long.
As you may recall, in 1992 I started a series of reviews aimed at assessing the ability of the then-current crop of botanical textbooks to present systematics as an exciting modern science, rather than as simply being a traditional scholarly exercise. The six books that I reviewed varied widely in intent, including generalist introductory ones (A.S.B.S. Newsletter 70: 30-33), taxonomy-based ones concentrating on the practice (A.S.B.S. Newsletter 71: 32-36), and more systematics-oriented ones focussing on the principles (A.S.B.S. Newsletter 72: 24-27, 74: 21-27). These books all have their own strengths and weaknesses, but none of them seemed to be just right for modern university classes. So, I have now returned to the fray, to look at a few of the more-recent contenders.
In this case, I have broadened the field to include a book on biological systematics in general, as opposed to botanical systematics alone. This approach to the subject has the potential to emphasize the broad nature of systematic principles, because botanists, zoologists, mycologists, phycologists, parasitologists, bacteriologists, virologists, etc all have common goals, methodologies and difficulties. However, it also has the potential to down-play those parts of systematics that may be particularly relevant to botanists but which seem to be less important to other types of taxonomists. We shall see.
The book by Donald Quicke is aimed at university biology undergraduates who have already had an introductory biology subject. The stated aim of the book is "to stem [the] trend" in which "university biology courses have been progressively marginalizing taxonomy in favour of more 'trendy' areas". It thus discusses the principles rather than the practice of systematics, by which I mean that it covers the theoretical foundations of systematics rather than containing descriptions of particular taxonomic schemes. It is organized into 13 logically-arranged chapters, plus a lengthy (26 pages) Glossary. The publication quality is generally good, although there are quite a few typographical errors (including erratic plurals and tenses, and missing references), and there are some very long unpunctuated sentences because commas seem to have been eschewed. Unfortunately, there are not that many line figures or tables to break up the text, presumably because of cost. The Index is rather brief, and the Bibliography is not meant to be extensive, although it is up-to-date.
Overall, the book provides a pretty good balance between "Principles" (e.g. classification, phylogeny reconstruction) and "Techniques" (e.g. identification, data collection). However, the word "Contemporary" in the title means that there is no historical component to the presentations. Systematics is presented as just this-is-the-way-it-is, with little regard for alternative approaches, and with almost no explanation of the intellectual debates that have occurred and are continuing to occur. The book will thus appeal to those students who want nothing more from their degree than "the answer", but it may seem a bit dry to the more advanced students who want their science to be intellectually stimulating.
This is not to say that the author is unaware of the development of taxonomic ideas; and, indeed, the brief Preface expounds enthusiastically on this topic, describing taxonomy as "an ever-changing, controversial and exciting field of biology". Unfortunately, the enthusiasm is largely confined to this Preface, with a bit more in the first chapter. However, I particularly liked the description of taxonomy as "a complex mixture of 'biology, philosophy and mathematics" (although most of my own students assiduously try to avoid the latter two topics).
The book starts, not unexpectedly, with a brief Introduction (10 pages). This describes the "compass of taxonomy and systematics", in which the author admits that the book is actually about systematics (broadly defined) rather than taxonomy (more narrowly defined). It also implies rather strongly that phylogeneties is the main part of systematics; and this is a theme that runs throughout the rest of the book, with all non-phylogenetic evolutionary topics (e.g. biogeography, evolutionary processes, coevolution) being relegated to a single chapter. The brief historical background is also rather weak, with some very naive introductions to phenetics and cladistics (for example, parsimony is treated as producing the best hypothesis in cladistics, rather than as being a methodological criterion for choosing the working hypothesis that will be subjected to further test).
Chapter 2 is the longest chapter (41 pages), being a competent introduction to Characters, Taxa and Species. Characters and character states are introduced well, with particular attention to decisions about primitive versus advanced (although functional outgroup analysis is ignored), and those classes of characters that require special consideration. However, we are also introduced to the usual cliches about how many thousands of "independent" characters molecular data are going to provide us with (if evolution has occurred, and molecular sequences represent functional biological molecules, then the gene sequences cannot be any more independent than are morphological characters). It is also at this stage that the biggest bias in the book becomes apparent: Donald Quicke is an entomologist, and thus insect examples dominate most of the discussions (both with regard to the theory chosen for discussion and the actual examples used), followed by vertebrates (sections 2.3.5 - 2.3.8 are entirely animal-related, for example). Plants are not ignored, but they definitely run a poor third.
Monophyletic and non-monophyletic groups are also discussed, along with various concepts of species. Unfortunately, the example in Figure 2.10 has the paraphyletic and polyphyletic groups being identical, in spite of the clear distinction made in the text; and the problem of the ancestral species being paraphyletic when a new daughter species is recognized is treated as a special case for one class of species, rather than being true for all species (as originally discussed by Willi Hennig).
Chapter 3 concerns Phylogenctic Reconstruction: Cladistics and Related Methods (33 pages). This is a somewhat inconsistent chapter, with many of the descriptions being very simplistic, and therefore potentially misleading to the uninitiated. Furthermore, cladistics is treated as being more-or-less synonymous with character-based parsimony. Thus, compatibility methods occupy a large place in the chapter, but distance-related treebuilding methods are relegated to an aside (with neighbor-joining, the most popular of these methods, being completely ignored), and the actual distance calculations not being discussed at all. This is at variance with the emphasis elsewhere in the book, because molecular methods are treated extensively elsewhere and in practice distance-related methods are commonly used for the analysis of molecular data. The popular use of distance methods in molecular studies stems from the fact that it is possible to "correct" the distances for various biases that are known to exist (such as multiple substitutions, transition : transversion ratios, GC content), and this improves the consistency of the phylogeny estimation; such corrections are not straightforward for the character-based parsimony methods. However, parsimony is still the predominant method for analyses of morphological and anatomical data.
The thorny topic of the relationship between phylogeny and classification is also addressed, with the author coming out in favour of recognizing paraphyletic groups, such as the Reptilia, when it is convenient but completely rejecting polyphylctic groups. However, this is a difficult position to justify, given that it is very hard to clearly define a practical distinction between these two concepts (the usual theoretical distinction concerns whether the most recent common ancestor of the taxa is included in the group or not, which is rather a difficult decision to make in practice if only contemporary taxa are being studied).
Chapter 4 is an effective introduction to Phenetic Methods in Taxonomy (13 pages), although it is a bit weak on why such methods are useful, considering mainly their use in automated identification. The most obvious other use of phenetics is in looking at relationships that are not necessarily strictly hierarchical, such as intraspecific variation where gene flow means that the relationships are likely to be a network (rather than a dichotomous tree).
Chapter 5, covering Keys and Identification (17 pages), is justifiably the most practically oriented part of the book, but as a result it does give little insight into the theoretical background of the various techniques discussed. Unfortunately, the example of an indented key in section 5.2.1 is not actually indented (it is the Dallwitz version of an indented key), which may confuse the newcomer.
Chapter 6 includes a generally good overview of Nomenclature and Classification (21 pages). Nevertheless, it is also rather erratic, possibly because of a need to cover such a broad range of organisms and thus rules of nomenclatlure (we are also incorrectly told that the Codes "result from the occasional Congresses" when there hasn't been a Zoological Congress for decades), but also because this chapter is intellectually isolated from all of the previous ones. In particular, there is no discussion of the fact that recent evidence suggests that the protists, fungi and algae as traditionally defined are polyphyletic, and so may create all sorts of inconsistencies when the Codes of Nomenclature are applied (or ignored, as is often the case for protists). There is also a tendency to use words without explaining their meaning; and the use of the expression "specific name" instead of "specific epithet" may not help novices. The author is also apparently unaware that there is (and has been for nearly a decade) an "authoritative list of authors and their abbreviations" for botanical nomenclature. The chapter ends with some suggestions for deciding priorities as to what new species should be described first but these are unfortunately at variance with the considerations for conservation of biodiversity.
Chapters 7 (Cytotaxonomy, 10 pages), 8 (Chemotaxonomy and Related Topics, 9 pages),9 (Immunotaxonomy, 12 pages), 10 (Proteins and Taxonomy, 23 pages), and 11 (Nucleic Acid Methods, 35 pages) provide practical details (i.e. techniques) about various sources of taxonomic data. Morphology and anatomy are ignored, presumably as a result of the focus on biology rather than zoology or botany (for example), although this is never spelled out. Most of these chapters are good introductions to their topics for non-experts, although there is, once again, a tendency to use words without explaining their meaning or to use them several pages before their meaning is explained. Also, the section on the analysis of protein data does not discuss the use of BLOSUM matrices, and that on the analysis of nucleotide data does not discuss the corrections for biases (noted above); in fact, the use of distances is treated as "largely historical". Furthermore, the section on sequence alignment incorrectly treats it as a parsimony problem rather than a phenetic problem (computer alignment is based on overall similarity), and ignores the possibility of using functional criteria to align the sequences.
Chapter 12 covers Palaeotaxoiiomy, Biogeography, Evolution and Extinction (16 pages). These topics are apparently lumped together because they are all non-phylogenctic evolutionary topics; and clearly each of these topics could be dramatically, and usefully, amplified from the brief coverage given here. Furthermore, the discussion of biogeography is abysmal, and that of co-evolution is not much better (but we are finally told about cladogenesis and anagenesis, which should have been mentioned in Chapter 2). This is thus far-and-away the weakest part of this book. This is a pity, because this is the one chapter where it is possible to emphasize and expand on the usefulness of systematics to biology in general, rather than merely having this point tucked away in the Preface.
The book ends with a chapter on Museums, Herbaria, Biodiversity, Conservation and the Future of Taxonomy (19 pages). The first part of the chapter is about museums only, in spite of the title, and it is thus another example of the zoological bias in the book. The second part of the chapter would be much better as an enthusiastic introduction to the book rather than as a hopeful conclusion.
So, in the final analysis, this book is probably quite acceptable as an introductory textbook, provided that its biases are acknowledged (i.e. entomology, parsimony cladistics) and its weaknesses accepted (i.e. typographical errors, poor coverage of some important topics). It is, in many ways, a compromise between several competing influences (e.g. botany versus zoology, detailed versus broad coverage), and the author has made his own decisions about which way to go, based presumably on his own erudition and inclination. We should not hold this against him. However, this book would certainly be better as a textbook for a class of biologists rather than for a class of botanists.
Reviewer: David Morrison