Book Review
Syst. Biol. 61(6):1087–1088, 2012
© The Author(s) 2012. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved.
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DOI:10.1093/sysbio/sys065
Advance Access publication on July 20, 2012
Phylogenetics: The Theory and Practice of
Phylogenetic Systematics, 2nd edition. E. O. Wiley
and Bruce S. Lieberman. Hoboken, NJ: Wiley-
Blackwell, 2011. xvi + 406 pp. ISBN 978-0-470-90596-
8. $99.95/£66.95/E80.40 (hardback). ISBN 978-1-1180-
1787-6. $79.99/£54.99/E64.99 (e-book).
This is a difficult book to review, as it has a long
history. The first edition (by Edward O. Wiley alone)
appeared in 1981, when I was a PhD student, and the
contemporary reviews varied from cautious enthusiasm
by cladists (Brooks 1982; Humphries 1982; Watrous
1982), to doubt by evolutionists (Felsenstein 1983a) to
outright rejection by pheneticists (Colless 1982). (The
latter review, incidentally, must be one of the most
cited reviews ever published by Systematic Zoology, as
it contains the original publication of Colless’ tree-
imbalance index.)
The original book was part of a triumvirate, along
with the books by Eldredge and Cracraft (1980) and
Nelson and Platnick (1981), that summarized from
different perspectives the changes in systematics that
had occurred during the preceding 15 years, when
Hennigian cladistics replaced narrative systematics.
However, systematics has changed as much in the 30
years since 1981 as it did in those 15 years (parsimony-
based cladistics has been supplanted by likelihood-
based statistical phylogenetics, and morphological data
have been swamped by molecular systematics), and this
new edition of Phylogenetics accurately reflects the 15
years but not the 30 years.
This is not to say that the book hasn’t been updated
for this second edition, as it most surely has. Almost
every page has been revised, new sections have been
written, some sections have been deleted, and hundreds
of new references have been added. The book still focuses
on phylogenetics (Chapters 1–8) much more than on
systematics (Chapters 9–11), as it did before. The point,
however, is that the issues that were important for
phylogenetic systematics in 1981 are not the ones that are
important now, and we need a new book not a revised
one. It cannot be accidental that neither of the books by
Eldredge and Cracraft (1980) nor Nelson and Platnick
(1981) has been revised for a modern audience—they
were very relevant in their time, but that time was 30
years ago.
Perceptively, Felsenstein (1983a, p. 62) noted in his
original book review that: “Wiley’s book, together with
Eldredge and Cracraft’s, are beacons, lighting the way
out of the fog of inexplicit and intuitive methods, but
revealing all too clearly that the path does not lead
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much farther, and that a different way must be taken.”
This was part of his campaign “to persuade biologists
to think of the problem of inferring phylogenies as
being basically statistical, and to abandon deductive
frameworks that are used as a justification for parsimony
methods” (Felsenstein 1983b, p. 246). This campaign
was ultimately successful and, in combination with the
widespread availability of molecular data, phylogenetics
was transformed from a specialist discipline into a
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mainstream part of biological science. Systematics is
now only one of many fields that are closely associated
with phylogenetics, which itself now stands at a central
position within biology. Phylogenetics reflects little of this
change.
There are many things to like about this book,
as there were in the first edition. The phylogenetic
approach to systematics is what makes it a part
of science rather than simply natural history, which
it was for centuries. The book is a very readable
(although perhaps overly pedantic) summary of much
of phylogenetic systematics, covering both theory and
practice. Along with tree-building, there is much
discussion of the nature of species and speciation,
methods of species recognition and delimitation, the
logical basis of phylogenetic classification and the
recognition of supra-specific taxa, character analysis
and homology, historical biogeographical analysis, and
methods for alpha taxonomic research. It certainly
covers more of systematics than does the competing
book by Schuh and Brower (2009), which is very
strictly cladistic in viewpoint, and it provides a broader
perspective than the botanically focused book by Stuessy
(2009), which adopts a somewhat idiosyncratic phyletic
viewpoint.
However, this book’s origin in late 1970s cladistics is
still painfully obvious, in spite of the extensive revisions.
For example, parsimony analysis is given 50 pages
of treatment (Chapter 6) but statistical phylogenetics
gets only 25 pages (Chapter 7), and much is made
of the theoretical distinction between cladograms and
phylogenetic trees. Unfortunately, the discussion of
graph theory (Chapter 4) is rather confused, and
trees are treated as the “expected” paradigm for most
organismal groups (see also Wiley 2010), even though
modern phylogenetics recognizes that plants (due to
hybridization) and bacteria (due to horizontal gene
transfer) do not fit this paradigm. Most of the illustrative
examples are based on animals (which seem to fit
the tree paradigm much better), although this is not
unexpected from authors who are a zoologist and an
animal paleontologist, respectively.
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 1088 SYSTEMATIC BIOLOGY
Given the increasing prevalence of molecular data in
systematics, it is rather surprising that so little attention
is given to molecules in this book. For example, gene
homology and the homology of DNA sequences are
clearly important issues for both theory and practice, but
these topics get only four pages of separate discussion
(under the heading “Similarity in Position” as a criterion
for homology), with a reference to a 1994 paper by David
Hillis that considers primarily gene homology.
One of the most prominently annoying characteristics
of cladists has been the cult of the individual—
the reverence for named authority. Cladists usually
introduce and discuss ideas in terms of who allegedly
first thought of them, rather than in terms of the
ideas themselves. The ideas apparently do not stand
independently of the people, and this is a weakness that
permeates this book. Most scientists couldn’t tell you
who developed the concept of maximum likelihood (it
was Ronald Fisher), and though they have a vague idea
who introduced Bayesian thinking they couldn’t tell you
the name of the person who pioneered and developed
it in its modern form (it was Pierre-Simon Laplace).
Cladists, on the other hand, can name everyone, and
they do so first. It has gotten to the stage that the
mere mention of Willi Hennig’s name, for example, can
cause a phylogeneticist’s eyes to glaze over. Hennig was
historically important as a catalyst, particularly within
the systematics community, but he was a synthesizer
of previous ideas (e.g. from Abel, Naef, Tschulok and
Zimmerman) rather than an innovator. There are plenty
of other names in non-cladistic phylogenetics, and many
of them are missing from this book. [Charles Darwin is
another name that seems to need a moratorium within
phylogenetics!]
Mind you, statistical phylogenetics on its own
does not actually provide an explicit logic for
phylogeny reconstruction. Hennig’s logical use of
synapomorphy provides the explanatory connection
between a mathematical tree and an evolutionary
history—a tree is a convenient mathematical summary
of the data and becomes a representation of history only
when one considers the synapomorphic information.
So, cladistics does still have a theoretical relevance to
modern systematics even if it is no longer widely used
in practice.
This distinction is particularly relevant for
Phylogenetics. The book professes to be about both
“the theory and practice of phylogenetic systematics”
but it focuses mainly on the former and says relatively
little about modern practice. Indeed, the book actually
concentrates on the logic of phylogenetic inference in
relation to systematics (as noted on p. xv), which is
only part of the theory and practice. This is probably
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VOL. 61
the book’s principal weakness, that it focuses on logical
inference (which was a big issue in 1981) rather than on
modern systematic practice and its current theoretical
justifications (of which logical inference is not the least
important part). The authors apparently felt that the
logic of phylogenetic systematics has not changed much
in the past 30 years (there has been no philosophical
revolution), and so their philosophical approach to the
subject did not need changing from the first edition of
the book. This overlooks the fact that the theory and
practice have both changed rather a lot (there has been a
technical revolution in data and methods), leaving this
book looking rather antiquated.
I have a great deal of sympathy for the authors, as
they have clearly put a lot of work into a book that
is unfortunately out of kilter with so many parts of
modern systematics. It seems to me that the hard-core
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cladists won’t like this book much and neither will the
statistical crowd. There is too much Hennigian baggage
from the 1970s to interest molecular phylogeneticists, too
much statistics for the cladists, too much focus on logical
inference for practicing systematists, and far too many
typographical errors to justify the price. This ultimately
leaves me wondering who is the audience for this book
in the 21st century.
REFERENCES
Brooks D.R. 1982. [Review of] Phylogenetics: the theory and practice
of phylogenetic systematics. J. Parasitol. 68:724–726.
Colless D.H. 1982. [Review of] Phylogenetics: the theory and practice
of phylogenetic systematics. Syst. Zool. 31:100–104.
Eldredge N., Cracraft J. 1980. Phylogenetic patterns and the
evolutionary process: method and theory in comparative biology.
New York (NY): Columbia Uni. Press.
Felsenstein J. 1983a. Another beacon in the fog. Quart. Rev. Biol.
58:60–62.
Felsenstein J. 1983b. Statistical inference of phylogenies. J. Roy. Stat.
Soc., A 146:246–272.
Humphries C.J. 1982. [Review of] Phylogenetics: the theory and
practice of phylogenetic systematics. Watsonia 14:209–210.
Nelson G., Platnick N. 1981. Systematics and biogeography: cladistics
and vicariance. New York (NY): Columbia Uni. Press.
Schuh R.T., Brower A.V.Z. 2009. Biological systematics: principles and
applications. 2nd ed. Ithaca (NY): Cornell Uni. Press.
Stuessy T.F. 2009. Plant taxonomy: the systematic evaluation of
comparative data. 2nd ed. New York (NY): Columbia Uni. Press.
Watrous L.E. 1982. [Review of] Phylogenetics: the theory and practice
of phylogenetic systematics. Syst. Zool. 31:98–100.
Wiley E.O. (2010) Why trees are important. Evolution: Educ. Outreach
3:499–505.
David A. Morrison, Section for Parasitology (SWEPAR), Swedish
University of Agricultural Sciences, 751 89 Uppsala, Sweden;
Email: David.Morrison@slu.se.
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