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The Tree of Life: A Phylogenetic Classification

Article in Systematic Biology · August 2007

DOI: 10.1080/10635150701475605

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 696 SYSTEMATIC BIOLOGY
Downloaded By: [Morrison, David] At: 08:23 30 July 2007
basic things like input and output of phylogenetic data,
or even less basic things like defining models of DNA
substitution. As an algorithm developer, working in R
is likely to speed up your ability to turn an idea for an
algorithm into something that can be used by others. The
corollary of this is that R has the potential to be very good
for practitioners in that, once they have learned to navi-
gate the R environment, they get great flexibility and ac-
cess to an ever-increasing number of specialist packages.
Certainly, the cost in time of learning a language like R
Syst. Biol. 56(4):696–698, 2007
Copyright ! c Society of Systematic Biologists
ISSN: 1063-5157 print / 1076-836X online
DOI: 10.1080/10635150701475605
The Tree of Life: A Phylogenetic Classification.—Guillaume Lecointre
and Hervé Le Guyader. (Illustrated by Dominique Visset, translated
by Karen McCoy.) 2006. Belknap Press of Harvard University Press,
Cambridge MA. 560 pp. ISBN 978-0-674-02183-9 (ISBN-10 0-674-02183-
5). US$39.95, 34, £25.95 (hardback).
As the book review editor, it is obvious that I would
request from the publisher a copy of any book with this
title, with the intention of then sending it on to a reviewer.
However, I just couldn’t make myself do it in this case—I
loved the book too much to be able to part with it. So, I
am writing the review myself, and all of you will have
to buy your own copies.
There are, of course, a number of books around that
try to provide an overview of biodiversity, listing the
different taxonomic groups, along with an illustrated de-
scription of their distinguishing features, the best known
being that of Margulis and Schwarz (1997). If nothing
else, all introductory biology textbooks also do this, al-
though they never seem to present the other parts of
biology in the same style. This is a poor way to explain
biodiversity, because it smacks too much of natural his-
tory. Natural history is a very valuable thing, as cen-
turies of human study will attest, but it should never
be confounded with science. Science is about testing hy-
potheses, and in our business these hypotheses are about
evolutionary history. It has taken biologists a long time to
explicate the simple idea that it is the study of biodiver-
sity that makes biology different from other sciences—
the nature and scale of the interrelationships among or-
ganisms is something that has never been conceived of
within physics and chemistry. Evolutionary history is
our explanation for the origin of that biodiversity, and
so the best way to present biodiversity is in the context
of phylogenetic trees. That is what this new book does.
So, what makes this book different is its strictly (al-
most relentless) phylogenetic perspective. It is based on
trees, not only as metaphors but as the primary means
of communication—the text and the many excellent line
drawings are purely adjuncts to the trees. The book itself
VOL. 56
exceeds the cost of learning a program like PAUP*, but
the long-term benefits are also likely to be greater—and
the more people that get involved in doing phylogenetics
in R, then the more modules will become available. So
overcome that activation-energy hump, buy the book,
and get involved!
Barbara R. Holland, Institute of Fundamental Sciences, Massey Univer-
sity, Private Bag 11222, Palmerston North 5301, New Zealand; E-mail:
B.R.Holland@massey.ac.nz
is arranged as a set of nested clades, with each section
introduced by a tree along with a list of synapomorphies.
The clades within that tree then follow on the subsequent
pages, presented in the same manner, until the limit of
resolution of the book is reached. All of the putatively
monophyletic groups are numbered, for ease of locating
them within the book, and almost all of them are named.
Paraphyly and polyphyly are strictly excluded, no matter
how familiar the names of such groups might be.
This book thus demonstrates the art of making some-
thing very difficult look surprisingly easy. This is not
a feature of all books, because it requires great exper-
tise from the authors, but it would surely be a useful
synapomorphy if we could achieve it. In this case, the
straightforward arrangement, the simple writing style
(translated well) and the direct presentation of phylo-
genetic information all make the book accessible to the
reader, both expert and non-expert alike. In short, the
book is unique. It not only represents the first thor-
ough attempt to portray life from a purely phylogenetic
perspective, it is an excellent implementation of that
idea.
As an added bonus, there is a 35-page introduction to
phylogenetic systematics. This is among the best such in-
troductions in any language. The candid and unadorned
writing style comes to the fore, so that the ideas and in-
formation are comprehensible to the uninitiated without
alienating the experts by oversimplification. None of the
complications in phylogeny reconstruction are avoided
(although the methodology concentrates on parsimony
analysis), and yet the concepts are presented in a straight-
forward and logical manner, with suitable illustrated ex-
amples. The strengths and weaknesses of our current
methods are presented without excuses, and the conse-
quent classifications are presented without apologies to
the traditional approaches. Only long experience in this
line of work could produce a synthesis of this type. If
you ever need to explain phylogenetic systematics to an
interested member of the general public, then you can
safely direct them to this essay.
 2007 BOOK REVIEWS
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In the main body of the book, the authors have stuck
their necks out to produce one set of trees, and thus
“a” classification (as the title accurately indicates), rather
than taking a more Bayesian view of life and explic-
itly recognizing uncertainty in phylogeny reconstruc-
tion. You will therefore not be hard-pressed to find trees
with which you disagree—these are majority-rule trees,
not strict-consensus trees. In their favor, they are mostly
based on contemporary evidence, so that they reflect cur-
rent opinion rather than established tradition. On the
other hand, the overall impression is given that there is
no contention concerning any of the trees, which we all
know to be a distorted viewpoint (as do the authors).
Nevertheless, the trees have plenty of polychotomies,
and even the occasional dashed line, thus showing where
we are currently ignorant about relationships.
The authors also do not entertain the notion that the
history of life might not be particularly tree-like but may
instead be an anastomosing plexus of interrelationships.
The latter is certainly not a new idea, especially in mi-
crobiology and botany. The conception has even crept
into vertebrate biology. However, perhaps it is enough
that the authors have dealt so well with trees, without
asking them to delve into alternative metaphors such as
networks.
Among the most practically useful parts of the
book are those appendices entitled “Where are They?”
which indicate the position of most of the para-
phyletic/polyphyletic common names that still popu-
late the biological literature (algae, coelomates, reptiles,
etc). This is a real boon for non-experts in the particu-
lar groups concerned, or for those who are too young to
have been brought up with the older names (or are too
lazy to learn them). Interestingly, the named groups are
indicated as either including or not including their most
recent common ancestor, so that paraphyly and poly-
phyly are clearly distinguished from each other.
Most books on biodiversity still subscribe to the Great
Chain of Being, with evolutionary advancement pro-
ceeding inexorably from bacteria (at the beginning of the
book) to human beings (at the end). Phylogeneticists will
have no truck with this, however, as all branches on a
phylogenetic tree can be rotated ad libitum. So, although
bacteria are primal in this book, humans are penultimate,
with the ultimate lifeform being ray-finned fishes. This
neatly illustrates the fact that “Fishes” is a paraphyletic
group and thus fish should not be lumped together. It has
taken until the new millennium to get a general-purpose
book with a Darwinian-tree view of life rather than an
Aristotelian-linear one.
Nevertheless, the thing that will infuriate more read-
ers than anything else is the serious level of imbalance
in the treatments of the various clades. For example,
the Hexapoda get two pages in the main text and one
page in an appendix, whereas the Angiospermae get
two pages of main text and four pages of appendix. In
even sharper contrast, the Mollusca get 30 pages of main
text, and the Vertebrata get more than 150 pages. Al-
though this edition of the book is expanded from previ-
ous ones, where the imbalances generated some pointed
697
comments (e.g., Wendel, 2003), the primary expertise of
the authors still dominates the information content. The
authors justify the imbalance with the claim that they are
focusing on “groups that are most important for teaching
purposes” (page 7), but that depends very much on what
it is that you are teaching. We can hardly claim that we
shouldn’t be teaching about insects when we are teach-
ing about biodiversity, because they dominate it at the
macroscopic level. Only some serious excision of verte-
brate taxa would allow the treatments of the other groups
to be expanded (the book is large enough as it is).
Although most of the information seems to be accu-
rate, there are, as with any book, errors that will annoy
you as well as idiosyncrasies that may dismay you. These
include family names are not given initial capitals (con-
trary to the codes of nomenclature), the page on Arach-
nida has almost no common names (not even to note that
the Acari are ticks and mites), and in an appendix there
is the descriptive example “Proteaceae (plane)” (neither
aeroplanes, woodworking planes, nor plane trees are in
that particular plant family). Among the idiosyncrasies
are a sequence alignment that uses hyphens for identical
residues and asterisks for gaps (which is the convention
in some parts of molecular biology but not in phyloge-
netics), the failure to mention coccidiosis as a disease
caused by Apicomplexans (it is more widespread than
the other diseases listed), and some quaint cartoons to
illustrate Homo sapiens that are unfortunately all male.
Interestingly, the Tree of Life (page 49) remains unrooted,
so that technically none of the subsequent trees refer to
monophyletic groups!
For some of these quibbles, the authors should be
asked to stand in the corner of the classroom, facing
the wall, for a couple of hours; after that, they can cor-
rect the offending items in the next edition. For future
editions there will surely be—there have already been
three French editions (2001, 2002, 2006), an Italian edition
(2003), and a German one (2005). This first English edi-
tion has therefore been long overdue (see Wenzel, 2003).
This is a solidly constructed book that is clearly in-
tended for a long life even when subjected to frequent
consultation, which is its purpose. Nevertheless, its un-
doubted usefulness will ensure that future editions are
on the way, with revised and updated classifications.
There have already been a number of stylistic changes
throughout the editions, notably in the current French
and English editions, so that this version is well thought
out and very user friendly. All that really needs to hap-
pen in the future is for the book to remain up-to-date in
a field that prides itself on constant change. So (unlike
me), buy yourself a copy, and thus encourage the au-
thors to keep up their good work. You never know, they
may even branch out into the multimedia world, as did
Margulis and Schwarz (2002).
R EFERENCES
Lecointre, G., and H. Le Guyader. 2001. La classification phy-
logénétique du vivant. Éditions Belin, Paris.
Lecointre, G., and H. Le Guyader. 2002. La classification phy-
logénétique du vivant, 2e édition. Éditions Belin, Paris.
 698 SYSTEMATIC BIOLOGY
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Lecointre, G., and H. Le Guyader. 2003. La sistematica della vita: Una
guida alla classificazione filogenetica. (Tradotto da Carlo Brena.)
Zanichelli, Bologna.
Lecointre, G., and H. Le Guyader. 2005. Biosystematik: Alle Organis-
men im Überblick. (Von Claudia Schön übersetzt.) Springer-Verlag,
Berlin.
Lecointre, G., and H. Le Guyader. 2006. La classification phy-
logénétique du vivant, 3e édition (revue et augmentée). Éditions
Belin, Paris.
Margulis, L., and K. V. Schwartz (eds). 1997. Five kingdoms: An illus-
trated guide to the phyla of life on Earth, 3rd edition (revised). W.H.
Freeman, New York.
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VOL. 56
Margulis, L., and K. V. Schwartz (eds). 2002. Five kingdoms: A mul-
timedia guide to the phyla of life on Earth (Win/Mac CD-ROM),
version 2.0. Springer-Verlag, Berlin.
Wenzel, J. W. 2003. A user’s guide to the tree of life. Cladistics 19:376–
378.
David A. Morrison, Department of Parasitology (SWEPAR), National Vet-
erinary Institute and Swedish University of Agricultural Sciences, 751 89
Uppsala, Sweden; E-mail: David.Morrison@bvf.slu.se