Reviews of "Inferring Phylogenies"
There were eight online and ten published reviews of the book.
As reviews appeared, I put some reactions here. I have provided
links to the actual reviews, but these may work only if your institution has
the appropriate subscription.
Ronquist's review is mostly fair-minded and says many nice things about the
book, though the large middle section of
the review is mostly devoted to complaining about things he doesn't like,
notably my failure to consider Willi Hennig and classification central to
the field. He also finds my coverage of Bayesian methods inadequate. Then
he finishes up by saying more nice things, almost as if to compensate. A few comments in reply to these
- A review by "wiredweird" on the Amazon.com web site
for my book.
This review is impressed by the book and calls it a "goldmine". The reviewer
gives it a full 5 stars, and mentions "this book's thud factor -- over
600 pages". It is a useful review which does not have much in the way of
criticisms of the book, except to mention that is "reads like an encyclopedia"
and that people who just want to run phylogeny programs may not want this
much detail. This is fair enough, and worth warning them about.
The review may be read here.
- Another review by "lynn" on the Amazon.com web site.
This review gives it four stars and otherwise is just a single statement, saying
only that "The book I bought is first printing version. Lots of typo inside..... I should correct them myself.-:( "
Having just finished correcting over 200 typos for the second printing, I can
only sympathize and hope that the buyers of the second printing will not
have reason to be concerned about the number of typos.
- A review in Science by Fredrik Ronquist:
- Ronquist, F. 2004. PHYLOGENETICS: A Broad Look at Tree-Building.
Science 303 (5659): 767-768 (Feb 6 2004).
- While Willi Hennig played a very important role in getting working
morphological systematists to appreciate the utility of well-defined logical
approaches, by the time his work was published in English, work on numerical
phylogenies was ongoing, and he had no substantial influence on numerical
methods, except through his influence on Farris and Kluge.
- Systematists get so worked up declaiming the centrality of classification
in systematics that I have argued the opposite. Well, we'll see what things
look like a few years from now.
- As to what should be called "Wagner parsimony" and what should be called
"Fitch parsimony", my terminology may be mistaken (or maybe not). "Fitch
parsimony" (in Ronquist's sense) was actually first used by Eck
and Dayhoff (1966),
though they did not explain their algorithms. Wagner didn't invent Wagner
Parsimony (as I note in the book), but Farris and Kluge called it that, and
gave algorithms that worked for ordinal scales and thus included the
unordered two-state case. Fitch gave the algorithms for the unordered 4 state
case (it works for n states too), and Hartigan (1973) for n states allowing
multifurcations, and he provided the first proof as well. It might be best to
use "Wagner parsimony" to denote the case of an ordinal scale, but it is not
obvious whose name should be used for the unordered n-state case.
Certainly Fitch's name is the leading contender.
A review in Trends in Ecology and Evolution by Mike Steel:
Mike Steel has been a major contributor to phylogenetic methodology, including
many contributions to quartets methods and Hadamard conjugation methods. His
gracious and strongly positive review emphasizes the detail and breadth of
my book. The only criticism he has is that is that it will be useful "less as
a textbook than as a repository of details, references and background". I
developed the book for use in a course, and it seems to work for that, but
perhaps most courses would not have the same level and concentration on
theory that my course does.
- Steel, M. 2004. Inferring phylogenies: an epic worth the wait.
Trends in Ecology and Evolution 19 (issue 4): 173-174 (April 2004).
A review by Stephen Wooding in the American Journal of Human Genetics:
A brief review, quite positive. Written in a rather clinical style, which is
perhaps appropriate for the journal. Wooding's only complaint is a justified
one: that I did not provide discussion of examples in which real data sets
- Wooding, S. 2004. Book review: Inferring Phylogenies, by Joseph
Felsenstein. American Journal of Human Genetics 74: 4074 (May 2004).
A review by Eddie Holmes in the Quarterly
Review of Biology:
A brief but glowingly positive review. I am particularly pleased with the
analogy to Crow and Kimura's classic text on theoretical population genetics.
I watched them write that book from the early 1960's on, critiqued some chapters
for Jim Crow,
and was pleased to be well-acknowledged in their Preface. I modelled my
level of presentation and writing
style in great measure on theirs, and hoped to have an effect similar to
theirs. It is gratifying to see that connection made.
- Holmes, E. C. 2004. Book review of "Inferring Phylogenies", by Joseph
Felsenstein. Quarterly Review of Biology 79: 204 (June, 2004).
A review by Jonathan Badger on the Amazon.com web site
for my book.
The review gives it four stars. It contains a brief description, but then
is primarily concerned with complaining about my treatment of Bayesian
methods. He is surprised at my "rather acrimonious treatment", and that I
complained about them "on philosophical grounds" when I had so often been
the target of philosophical arguments favoring parsimony methods. Well,
my perception of Chapter 18 is different. Badger argues that Bayesian methods
"will win or lose based on how well they work in practice". I don't think my
arguments are philosophical ones, except in the sense that everything
is philosophical. When I argue that your prior and mine might not be the same,
and when I argue that the only valid issue distinguishing Bayesian and
likelihood methods is the presence of a prior, those don't look like
philosophical arguments to me. And in making arguments in favor of statistical
methods (such as arguing about consistency) we are not simply withholding
judgement to see which method works well in practice.
A review by "folderol50" on the Amazon.com web site
for my book.
The review gives it only two stars, and consists, in its entirety, of the
I can't judge the matter objectively myself, of course, but I have gotten many
reactions from readers who find the book readable by people at elementary and
at advanced levels. My writing style is usually described as "clear", even
when I might rather aspire to having it be described as "elegant". I suspect
that this reaction is particular to this reader and not general.
"This book, although apparently containing everything, is written in a very
opaque style which makes it impossible to simply read through. It probably is a good reference to look in for particular topics, but it is not at all usable as an introduction."|
A review by David Penny in Systematic
This is a strongly positive review which says many nice things about the book.
I really couldn't ask for a more positive review.
Inspired perhaps by Laphroig, it meanders a bit in a charming way (I confess
I had never heard of Laphroig before).
I agree with Penny that I should have cited John Hartigan's important 1973
paper on the algorithm for counting steps on trees. Penny's argument for the
increasing importance of biases as opposed to statistical noise as a source
of incorrect phylogenies is a good and important point. I disagree with him
that the book probably cannot be used for teaching -- as I said above, in
response to a similar statement by Michael
Steel, I use the book for teaching myself, so it actually can
be used for teaching of a graduate course devoted entirely to phylogenies.
- Penny, D. 2004. Phylogeny in the comfort zone. Systematic Biology
53: 669-670 (August, 2004).
A review by Alexei Drummond in
As the title should make clear, this is an extremely favorable review. Drummond
says a great many very nice things. He does think that the book can be
used either as a teaching text or as a reference book. He
does have some criticisms, which he says he can list "if pressed". He finds
it "might be a tad sterile for the average biologist", as it lacks discussion
of analysis of actual data sets, and he is critical of the chapter on Bayesian
inference of phylogenies as too negative, saying that I do "a mild disservice to the continued development of statistical phylogenetics by downplaying one of the primary vehicles of recent progress." He points out the omission of MrBayes from the list of widely-used computer programs at the end of the book.
- Drummond, A. J. 2004. Inferring phylogenies: an instant classic. Heredity
93: 519. (November, 2004)
A review in Northeastern Naturalist by Barbara Fifield:
This review is simply a description of the topics the book covers. It is only
6 sentences long, and attempts no critique of the book.
- Fifield, B. 2004. Inferring Phylogenies. Northeastern Naturalist
11: 361. (September, 2004)
A review by Christine Petersen on the Amazon.com web
site for the book
The review gives the book a full 5 stars. It says that it might not be useable
as the text for a graduate course, but rather "functions well as a reference
book". It was used by a course she took, using the chapters as supplementary
readings. Because of its completeness, she says she would recommend this book
as "one title that most people working in phylogenetics would require for their
A review by Pascal Tassy in the Bulletin de la Société Français de Systématique, Février, 2005, No. 33, pages19-20.
This is a review in the internal society bulletin. The Bulletin is received
by the members of this society. It is a very gracious and entertaining
review which praises the book while noting that persons opposed to statistical
approaches to phylogenies may not find it satisfactory. The review
is in French. I am not
quite sure whether to count this as an on-line review or an in-print review
since I think the Bulletin may primarily be distributed on-line.
- Tassy wonders why I chose not to cover stratigraphic indices that measure
the fit between a phylogeny and stratigraphy of fossils. It was partly
laziness on my part and partly the feeling that it would not be easy to know
how to compromise fit between the phylogeny and the stratigraphy and
fit of the phylogeny and the change of characters, when these
were not all bookkept in a unified way. I mentioned this, saying (on
page 548) that
I will not describe these measures or the tests of which are best, preferring
to concentrate on methods that have some explicit means of compromising the
phylogeny and the stratigraphy.
- He also wonders with amusement whether my coverage of long branch
attraction is not excessive compared to coverage of charges that there are
countervailing phenomena called "short branch attraction" that favors
parsimony. In short: no, my coverage is the proper balance, at least, in
- In an effort to understand his review (as I only read French in a crude
way) I plugged the sentences into Google's French-to-English translator. One
of the results was extraordinary, and helps explain the incendiary nature of
debate in systematics. Tassy's sentence
Si vous voulez un manuel pour vous convaincre que la phylogénétique est d’essence statistique, c’est bien celui-là qu’il faut acheter.
was translated as
If you want a handbook to convince you that the phylogenetic one is of statistical gasoline, it is well that one which it is necessary to buy.
A review in Evolutionary Anthropology by Charles Lockwood:
A strongly positive review that agrees that the book has many strengths while
expressing some surprise that I did not spend time on character analysis and
polarity, issues of "cladistics" that Lockwood is surprised I did not include,
but at the same time he sees that this has its advantages. He ends up
by saying that "Felsenstein provides an essential and authoritative
reference that already has me thinking about phylogenetic questions
in a different way."
- Lockwood, C. 2005. Seeing the forest and the trees. Evolutionary Anthropology
A review in Journal of Classification by F. James Rohlf:
A positive review which describes the book as "important and useful", one
which "should be of interest to many readers of this journal" and which
"will be a rich source of ideas for future research". Rohlf has been a major
figure in the literature of numerical classification, and on occasion he
has contributed as well to the literature of phylogenetic inference. He
describes the chapters in some detail. One embarassing inaccuracy he points
out is my misattribution of the UPGMA method to Sokal and Michener's paper of
1957. It was apparently first published by Rohlf in 1962 and by Peter Sneath
in the same year.
- Rohlf, F. J. 2005. Book review: J. Felsenstein, Inferring Phylogenies, Sinauer Assoc., 2004, pp. xx + 664. Journal
of Classification 22: 139-142.
A review in Evolution by Mike Sanderson:
A review that praises the book for its clear explanations of
the mathematical and computational aspects of inference of phylogenies,
and for making these accessible to biologists. It contains a number of
thoughtful and serious criticisms. Mike is a gentleman and a scholar, with
firm views that he is not afraid to state, and this makes his review a
good starting point for a wider discussion of the state of systematics.
That aside, let me comment on the criticisms themselves:
- Sanderson, M. 2005. Where have all the clades gone? A systematist's take on Inferring Phylogenies. Evolution 59: 2056-2058.
Sanderson's is the most thoughtful and serious critique of the book yet
published, and will be very useful to the fields of systematics and
- Sanderson suggests that the book is not an adequate review of the
"large literature on parsimony-based phylogenetics". I guess I have so
little understanding that I don't get as much as he seems to out of the book
he suggests as an alternative there, Kitching et al.'s Cladistics: the
theory and practice of parsimony analysis. [On reading that book
more after writing this sentence I can see that I was being unfair to it --
it is wonderfully
clear and will be very useful to those who want an explanation of use
of the most widely-used kinds of parsimony methods, as long as they don't
want to use a statistical approach or inquire about other methods of
- He argues (as he
and Junhyong Kim have in a paper) that my confidence in methods with
fully-specified models is not adequately supported in the literature, which
he feels gives as least as much support to rougher and quicker approaches.
I think that the last word has not been said on this -- it depends on how
well those rougher methods will do in coping with tricky biases that may
be corrected by model-based methods. We shall see.
- He chides me for dismissing the importance of
classification (saying that my statements on that at the end of Chapter 11
are "a bizarre thumb in the eye to systematists" which is "badly out of
touch with reality"). He points as evidence to the heat generated by
controversies among systematists about the Phylocode: I would say that
the effort put into this controversy is further evidence that systematists do
not have their priorities straight. In their day-to-day work they really
do not make much use of higher taxa in classifications, but they show a
strange obsession with fighting about them for reasons that seem to me to be
an historical curiosity.
- Sanderson laments my "curious
omission of one of the central agendas of modern systematics: the discovery of
clades". Clades are very important, but are hard to infer with any degree of
certainty. He seems averse to incorporating our uncertainty about them into
conclusions we draw from them. I wonder whether that is not excessive
confidence in the clades.
- He says that my "one comment on the most
widely used method of rooting trees in real phylogenetic data analysis,
outgroup analysis, borders on dismissive" as I pointed out that it amounts to
knowing the answer in advance. Well, it does amount to this. If saying this
upsets Sanderson, he should ask whether he is not giving the inference
of the rooting a status that it does not deserve. (On further
consideration, this is too simple. If we have the ingroup and our method
gets only unrooted tree topology, then adding the outgroup does let us find
out where it connects. But if we are already have both the ingroup and the
outgroup in an unrooted tree topology, then using the outgroup method does
amount to knowing the answer in advance.)
- In his concern that I omit the importance of inferring clades, he noted
that "in one respect, Felsenstein implicitly acknowledges the importance
of clades, because his own bootstrap test delivers confidence levels on clades,
not trees." This is an interesting point, but a bit off the mark. For most
of our phylogeny methods, the tree specifies partitions (in effect branches
of the tree), not clades. To the extent that the rooting is uncertain,
bootstrap methods do not deliver confidence levels on clades.
A review by Roger Burks on the Amazon.com web
Burks credits the book with being good for computer scientists and
for biologists versed in biostatistics, but says that it "is very difficult
reading for other scientists who do not fully understand the complex math presented in the text. It also does not give a concinct summary of the assumptions and failings of each method." He feels that it is not good for "students who
don't have a good handle on such things." He gives it four stars.
A review by Aaron F. Goldberg on the Amazon.com web
site for the book
The review is the single sentence “Felsenstein's book is great as a
reference when looking up the major concepts and tests for phylogeny.”
It gives the book 5 stars.
A review by J. P. Drury on www.goodreads.com
This tantalizing review, in its entirety, says
[I] hate to use the pun, but felsenstein makes it impossible to see the forest
through the trees. i'm not sure for whom this text would be useful, honestly,
because it neither provides a solid intro for the lay reader nor gives anything
but a sort of nostalgic retrospective for those already in the know.
Since Drury is obviously "in the know" and I am obviously not, we can only wait, with growing excitement, for his book on the subject.
Drury rated the book 2 stars (out of 5). Ratings by others on that site
raised its rating to 3.79 stars.
A review by "M" on the Amazon.com web site
for my book.
The review calls it "a beautiful survey of phylogenetic algorithms and methods",
but complains that "There's unevenness in the details in this book, however. Some
mathematical or conceptual points are laid out with complete clarity, and others
require more insight on the part of the reader." The issue raised is that
some explanations require more mathematical or computer background than
others, and M wishes that "Felsenstein had included a few more intermediate steps in his
presentations of mathematical and conceptual points." M does say that "Nevertheless,
I think this is a classic" and assigns it 4 stars.
I wish I had some snappy reply to show why the complaints are not justified; I don't,
it seems to be an honest and heartfelt review.
Other reviews that were said to have been coming:
These reviews were at one point thought to be coming. However we have
passed the tenth anniversary of the publication of the book.
It is unusual to have reviews appear that late. One doubts whether
these reviews will ever appear.
For sheer entertainment value, the one I was waiting for
was the one in Cladistics (they were sent a review copy, and we
were told who it had been assigned to, but by now it is clear that
there will not be a review of the book there). For a while I was thinking of
offering a modest prize for the most outrageous parody of that imagined
review, but I finally decided that there was no point, as the actual review
would have inevitably won that competition.
- One was said to be coming in Plant Systematics and Evolution.
- Two reviewers were supposed to be writing reviews for
Molecular Phylogenetics and Evolution, though it is not clear yet
whether this was going to result in one, two, or zero reviews. Zero,
- A review is supposed to be be coming in
Theoretical Population Biology.
Incidentally, Amazon compiles a list of SIP's ("statistically improbable
phrases" that appear in my book). Their list turns out to be:
polymorphism parsimony, quartets methods, parsimony score, quartets distance, consensus supertree, multifurcating trees, least squares branch lengths, expected pattern frequencies, distance matrix methods, coalescent trees, short quartets, ancestral selection graph, unit branch length, unrooted tree topology, unrooted bifurcating trees, coalescent genealogy, given tree topology, tree rearrangement, character state tree, partial bootstrap, different tree topologies, least squares tree, phylogenetic invariants, same tree topology, postorder tree traversal
I think this is a great list -- it really gives you a sense of some things my
book covers that some others might not.
Those interested in a list of typos and their corrections
for the book should look at the web page here.
Those interested in the example data sets used in the book will find most of
them available for download here.