Typos in "Inferring Phylogenies"

The fourth printing has now appeared. To see which printing you have, look on the copyright page (the page after the title page). At the bottom is a row of digits (5 4 3 2 etc.). The last one is the number of the printing. The third printing also has a light blue background in the cover photo of the Far Flung Fir sculpture (the first, second and fourth editions have an olive-colored background). The first printing can also be distinguished by the absence of quotes from reviewers on the back cover, which is mostly just black.

Contents of this web page:

Typos in the fourth and third printings (also found in the first two printings)

Typos in the second printing (also found in the first printing)

Typos in the first printing

References that should have been in the book

Erroneous statements in the book

A second edition?

The following typographical or algebraic errors are known. They are given by page.

Typos in the third and fourth printings

The following typos are in the first, second, third and fourth printings. For some reason I was not asked to make any corrections when the fourth printing was done.

Corrections in book text, figures, or index
page phrase (or location): should be:
  20 We will consider a building up We will consider building up
  22 (in Figure 3.3) The branch of the top two-species tree where
species c is added to get the center
three-species tree is the wrong one.
  66there are not or more two states that both occur
(this one was different in the first edition)
there are not two or more states that occur
107 homplasious homoplasious
113 that the probability becomes 1 the probability becomes 1
119 in both bases the curves in both cases the curves
129 with affinities to schmoos with affinities to shmoos
152 Gascuel (1997) Gascuel (1997b)
157 it will certainly rise linearly it will certainly not rise linearly
170 Gascuel (1997) Gascuel (1997a)
174 Gascuel, Desper, and Denis Gascuel, Bryant, and Denis
178 more then four more than four
178 Dil+Dij Dil+Djk
179 (in equation 12.7)    max min
179 should not be the largest should be the smallest
188 (in Table 12.2) The numbers 10 in the bottom three rows should be 5.
226 only between amino acids can be reached only between amino acids that can be reached
236 more defensible that it proved more defensible than it proved
241 high rates of change has high rates of change have
250 (in caption of Fig. 16.1) series of 13 independent     series of 11 independent
269 states will be spend states will spend
269 as as it will with a as they will with a
269 and site being variable and the site being variable
310 that can takes values that can take values
313 have been used give a good approximation have been
318 (in the Figure) quantities T should be R
327 noted, in Chapter 16 that noted in Chapter 16 that
328 for each these simulated data sets for each of these simulated data sets
337 we would back get our original data we would get back our original data
340 0.68066 of the time 0.680905 of the time
344 have randomly assigned rate each have a randomly assigned rate
348 (the one-tailed 95% point (the two-tailed 95% point
349 even greater when consider even greater when we consider
351 that lead to that led to
352 with more then R3 replicates with more than R3 replicates
355 we find ABCEDF we find ABCDEF
371 Data sets generated Data sets are generated
386 seven degrees of freedom six degrees of freedom
388 Then number of equations The number of equations
395 tree has the same topology as Figure 23.2 tree has the same topology as Figure 23.1
396 The tree has the same topology as Figure 23.1. (delete the sentence)
395 ith character in the jth population jth character in the ith population
402-403 The values of all n characters
in population 1 are on top.
Below them are the values for all n
characters in population 2, and so on.
The values for all n populations
of character 1 are on top.
Below them are the values for all n
populations of character 2, and so on.
403 an p × p array a p × p array
403 (in Figure 23.34) V(n) V(p)
403 (in equation 23.36) (mean vector 0 should be) (a vector μ Kronecker-product with the identity matrix I)
403 an (n-1)p × (n-1)p matrix an (n-1)p × np matrix
410 Gegenbaur Gegenbauer
418 2N times the variance of change N times the
418 2N times the variance of change N times the variance of change
425 It seem that there is It seems that there is
430 reversion to state 1 reversion to state 0
435 1.11666 1.1666
436 1.11666 1.1666
463 (in equation 26.13) The first occurrence of mlj should instead be mjl
463 (in equation 26.14) The third occurrence of kji should instead be kli
471 two occurrences of ki should both be kli
472 n-1, n-2, ..., 2 lineages n, n-1, ..., 2 lineages
512 in its immediate ancestors in its immediate descendants
512 shows three unrooted trees shows two unrooted trees
514 all possible number of loci all possible numbers of loci
521 placement of their root. the two trees placement of their roots, the two trees
559 test hypothesis about evolution test hypotheses about evolution
563 tips in the tree, or N-bar its mean tips in the tree, or N-bar, its mean
563 compared it to a the probabilities compared it to the probabilities
576 lowermost ancestor is used lowermost descendant is used
568 (in equation 33.6)    ..., tn    ..., tn-1
588 one calls function traverse or Traverse one calls function postorder or Traverse
604 (Edwards 1971 reference) The likelihood for
multinomial proportions under stereographic
projection. Biometrics 28: 618-620
Distance between populations on the basis of
gene frequencies. Biometrics 27: 873-881.
611 (the two listings for Gascuel, 1997) the first should be 1997a, the second 1997b
613 (in Griffiths and Tavaré 1994 reference)
Philosophical Transactions of the
Royal Society of London, series B
Philosophical Transactions: Biological Sciences
(Actually, I'm confused. The journal seems to have been
known by both names in that period! Which is official?)
614 (Reference to Hein, J. 1989), title should be: A new method that simultaneously aligns and
reconstructs ancestral sequences for any number of
homologous sequences, when the phylogeny is given.
616 (Reference to Hudson, R. 1983 in Evolution) This reference needs to start on its own
(negatively indented) line.
626 (Reference to Nielsen, R. 2002) volume number needs to be in boldface type
633 (Reference to Sankoff, Morel,
and Cedergren, 1973)
volume number needs to be in boldface type
638 Swofford, D. L. and D. R. Maddison Swofford, D. L. and W. P. Maddison
639 (Thompson 1972 reference) Distance
between populations on the basis of
gene frequencies. Biometrics 27: 873-881.
The likelihood for multinomial proportions
under stereographic projection.
Biometrics 28: 618-620
658 indexing of Ronquist, 2000 (should have been on page 659
among the other Ronquist page numbers)

Typos in the second printing

The following typographical errors are found in the first and second printings. They are corrected in the third printing.

Corrections in book text, figures, or index
page phrase (or location): should be:
  2 Figure 1.4 shows the single reconstruction Figure 1.4 shows the two reconstructions
  2 (in Figure 1.1) Raise label Delta to be level with the others
 33 In Table 3.5, many of the lines for even
numbers of species were computed incorrectly
The corrected lines are (showing
only the ones that have changed):
308.913 x 10113.294 x 107
40    1.377 x 1017    1.385 x 1011
 35 now [(n-1)-1][(n-2)-1]/2 = now [n-1][(n-1)-1]/2 =
102 they arive at they arrive at
113 as long as q < 1/2, p > 0, and q > 0 as long as q < 1/2, and either p > 0 or q > 0
123 carried our by a computer carried out by a computer
134 prefer not to assume either reversibility prefer not to assume either irreversibility
155 (in equation 11.14)   D   d
155 (in equation 11.15)   D   d
156 of length t of time t
156 of length dt each of time dt each
161 is then the average of the distances is then half the average of the distances
161 is the average of the distances is half the average of the distances
172 the neighbor-Joining methods the neighbor-joining methods
177 see the papers by Gascuel see the paper by Gascuel
200 (in equation 13.4)         Qn2(1/2 Q)n2
203 (In numerator of second line of equation 13.11) the epsilon should be the same style
as the one in the denominator
213 all the bases frequencies all the base frequencies
221 Rzhetsky, 1995, Tillier, and Collins, 1998 Rzhetsky, 1995; Tillier and Collins, 1998
229 Pagel (1995) Pagel (1994)
245 (in equation 15.28)   max min
261 amounts of diveregence amounts of divergence
279 each entry in the this vector each entry in this vector
294 Figure 18.2 should have its upper-right circle open to the path that comes in from its lower left.
332 the the confidence limits the confidence limits
355 if we could Type I if we count Type I
382 the triple of species a, b, and c the triple of species c, d, and e
410 the Ornstein-Uhlenbeck process
(which will be described later in this chapter)
the Ornstein-Uhlenbeck process
(which will be described in the next chapter)
418 (in equation 24.6)   Var[g-bar]   Var[Δ g-bar]
430 (in equation 24.18)  The last integral should be from -infinity to 0.
438 x1-x2 multiplied by x'1-x'2 multiplied by
491 they give is no way they give no way
500 Wang and Jiang (1994 Wang and Jiang (1993)
532 (in Figure 30.8)   {BC | ADEFG}    0.2    0.2    {BC | ADEFG}    0.2    0.3
532 (in equation 30.1)
 | 0 - 0.2 |  +  | 0.4 - 0.3 |  +   | 0.3 - 0 |  +  | 0.1 - 0 | 
         +  | 0.05 - 0.2 |  +  | 0.2 - 0.1 | = 0.95
   | 0 - 0.2 |  +  | 0.4 - 0.3 |  +  | 0.2 - 0.3 |  +  | 0.3 - 0 |
        +  | 0.1 - 0 |  +  | 0.05 - 0.2 |  +  | 0.2 - 0.1 | = 1.05
532 (in equation 30.2)
 (0 - 0.2)2  +  (0.4 - 0.3)2  +   (0.3 - 0)2  +  (0.1 - 0)2 
    +  (0.05 - 0.2)2  +  (0.2 - 0.1)2 = 0.1825
   (0 - 0.2)2  +  (0.4 - 0.3)2  +  (0.2 - 0.3)2  +  (0.3 - 0)2
   +  (0.1 - 0)2  +  (0.05 - 0.2)2  +  (0.2 - 0.1)2 = 0.1925
563 tree in Figure 33.1 this is 7/72 tree in Figure 33.1 this is 14/72
578 will attached be three or more subtrees will be three or more subtrees attached
581 the branches leading to D and B the branches leading to D and E
586 composed to records composed of records
587 in turns of itself in terms of itself
591 <clade length=0.6>  
   <clade length=0.102><name>A</name>
   <clade length=0.23><name>B</name>
  <clade length=0.4><name>C</name></clade>
<clade length="0.6">
   <clade length="0.102"><name>A</name></clade>
   <clade length="0.23"><name>B</name></clade>
  <clade length="0.4"><name>C</name></clade>
593 The URL given for TNT is outdated It should instead be:
615 (in Hendy and Penny 1982 reference)    60: 133-142. 59: 277-290.

Typos in the first printing

The first printing contains the above errors plus these:

Corrections of page numbers in Table of Contents entries
page in entry: page number should be:
vTree shapes, p. 28p. 29
viGenetic algorithms, p. 44p. 45
viTree space, p. 48p. 50
viNP-hardness, p. 57p. 59
viiNonsuccessive algorithms, p. 84 p. 85
viiObserved fractions of the patterns, p. 110p. 111
viiCamin-Sokal and parsimony, p. 128p. 129
viiiHypothetico-deductive, p. 138p. 139
viiiLogical parsimony?, p. 140p. 141
viiiThe Jukes-Cantor model - an example, p. 155p. 156
ixCodon-based models, p. 225p. 226
xiBayesian methods for phylogenies, p. 289p. 291
xiFlat priors and doubts about them, p. 301p. 302
xiTesting assertions about parameters, p. 311p. 312
xiiParsimony-based methods, p. 322p. 323
xiiTests for three species with a clock, p. 329p. 330
xiiIndependence of characters, p. 342p. 343
xiiPermutation tests, p. 358p. 359
xiiThe SH test, p. 369p. 370
xiiiSymmetry invariants, p. 374p. 375
xiiiFinding all invariants empirically, p. 387p. 388
xiiiThe REML approach, p. 400p. 401
xiiiUsing approximate Brownian motion, p. 411p. 412
xivSelection for an optimum, p. 420p. 421
xvFu's method, p. 484p. 485
xvMethods of inferring the species phylogeny, p. 490p. 491
xvParsimony method, p. 497p. 498
xvReconciled trees, p. 509p. 510
xviStrict consensus, p. 521p. 522
xviThe symmetric difference, p. 528p. 529
xviStratocladistics, p. 549p. 550
xviiIndex, p. 644p. 645

Corrections in book text, figures, or index
page phrase (or location): should be:
xiii 23 Brownian motion and
     gene frequencies
23 Brownian motion and gene frequencies
13 only A or G are possible only A or C are possible
15 In Figure 2.2, the fourth tip
has:    infinity, infinity, infinity, 0
should be:    0, infinity, infinity, infinity
15 these total to 2.5 these total to 4.5
16 Wheeler and Nixon (1990)Wheeler and Nixon (1994)
23   (2n-3)!
2n-1 (n-1)!
2n-2 (n-2)!
24rise to a rooted bifurcating treesrise to rooted bifurcating trees
29 Edwards and Cavalli-Sforza Cavalli-Sforza and Edwards
30 (in Table caption):    Edwards and Cavalli-Sforza Cavalli-Sforza and Edwards
35 connected with of genes connected with coalescent trees of genes
36 program and want to know program and wants to know
38because they sieze the firstbecause they seize the first
42 (in figure caption)   separates B and C separates G and C
44 304 288
62 (which requires 3 changes) (which requires 5 changes)
63 (in Figure 5.4)   bottommost node has number 3 should be 5
66there are not two states that both occurthere are not two or more states that occur
69reconstruction of states at interior nodes isreconstructions of states at interior nodes are
73any one of them are presentany one of them is present
75 (in middle row of equation 7.1)   xl ≤ xr    xl ≤ x ≤ xr
79 (in figure caption) which shows that that shows which
88 (in Table 8.2) the table should be transposed so that
the 01 combination is the one missing
92 Table 1.1 Table 8.1
92 {Alpha, Delta, Gamma} {Alpha, Gamma, Delta}
94 if there is missing data if there are missing data
99 index i in product
in equation 9.3
index should be j
102 pioneering attempts pioneering attempt
103 branch that applies to all characters character that applies to all branches
105 so do the number of parameters so does the number of parameters
105 this connected between this connection between
In equation 9.12, the expression is not correct. The product over branches
should not be there at all. The top and middle cases also need an extra factor of
1/2. The assertions below the expression are still correct, however!
112 and has presumable been and has presumably been
112 (in Equation 9.16)     P1100 P0011
112 1100, but there is also the pattern 0011 0011, but there is also the pattern 1100
115 that there is probability there is probability
117 as only parallel changes as parallel changes
142 Sober chooses former Sober chooses the former
143 when the data is randomized when the data are randomized
144 regard the experiment as repeatibleregard the experiment as repeatable
150 Equation 11.4 Before the big left parenthesis there
should be a term of xij,k
151(in equations 11.8 and 11.9)      D    d
152(in equations 11.11 and 11.12)   D    d
15211.10 (or 11.7)XTX (or XT W X)
15211.12 (or 11.9)11.9 (or 11.12)
161 indexclusteringclustering clustering
163 The two distance matrices
on this page are identical,
when they should not be.
The first should have no boldfacing, boxes
or asterisks. It should be placed after
"branch length" in line 3. The second
should be placed after "borders of the table".
169 indexclusteringclustered clustered
173 extent to which the data departs extent to which the data depart
180 it could still be fairly slow it could still be fairly fast
181 likelihood methods infer from this data likelihood methods infer from these data
183 is discussed is their paper is discussed in their paper
186 this data with a parsimony method these data with a parsimony method
191 for the finding it for finding it
191and, if they are compatible finds and, if they are compatible, finds
191 the same as the any the same as any
(equation 13.2)   -------
204 pii in line 11 the pi should be the Greek letter π instead
204 first ni in equation 13.12 mi
204many C's at one end a branchmany Cs at one end of a branch
204and many T's at the otherand many Ts at the other
204the C's were in the ancestorthe Cs were in the ancestor
204the T's in the descendantthe Ts in the descendant
206 eigenvectors lambdai and eigenvalues eigenvalues lambdai and eigenvectors
206 (in lower-right corner of first matrix
in equation 13.18)     πA
207 to give Table 13.5 to give Table 13.4
208 as in Table 13.5 as in Table 13.4
210 such as Table 13.5 such as Table 13.4
213 approximate,du approximate,
(in equation 13.34)   
215 remarkable level remarkably level
215 power of 1.0 power of 2.0
215 wij = 1/Dij wij = 1/Dij2
217 xα-1e-x/β rα-1e-r/β
220 A's, B's and C's As, Bs and Cs
220 such as exp(-brt) such as exp(-bt)
220 E[e-brt] Er[e-brt]
220 difference between
sequences (horizontal axis)
difference between
sequences (vertical axis)
225 is contributed by assignments contributed by the assignments
226 (CGT, CGC) (AGC, AGT)
232 (in equation 15.3)  max[0,l-k] max[0,k-l]
232 The Kimura 2-parameter does this The Kimura 2-parameter model does this
233 factor of 64 factor of 16
233 2 x 108 3 x 105
238 (equation 15.22)
[1 -
F  =  ------------------------
    F = -------
238 we can use numerical methods to iterate
Q in equation (15.22) until the expected
fraction of restriction fragments equals
the observed fraction F,
we can note that equation (15.22)
is a quadratic equation in Q and
solve it for Q,
241 concerned with of genes concerned with coalescent trees of genes
242 (in equation 15.26, twice)   k=-infinity k=0
244 it does has some robustness it does have some robustness
245 (in equation 15.28)
   μ   t  √(2 π)
√(μ t) √(2 π)
Prob(D | H1)
(in equation 16.3)   -----------------
Prob(D | H2)
   Prob(H1 | D)
Prob(H2 | D)
250 Thus is does not show Thus it does not show
253 in equation 16.11 in equation 16.10
253 Equation 16.11 can be Equation 16.10 can be
256 (at end of equation 16.17) add these factors:  L6(i)(y) L8(i)(z)
256 (at end of equation 16.19) add these factors:  L6(i)(y) L8(i)(z)
257 [figure caption] around nodes 6 and 8 around branch 7
257-258 all occurences of node 6
or branch length t6
... should be node 7 or
branch length t7
259 In equation 16.11 that would In equation 16.10 that would
263 (in equation 16.28)   rij, rij+1, ..., rim    rij
264 in equation 16.29, before the summation sign add a factor    Prob(D(j) | T, rij)
265 sometimes too more flexibility sometimes more flexibility
268C0  G0G0  C0
269Using Gu's model,Using a similar model,
271number of character patters number of character patterns
273showed a particular interesting showed a particularly interesting
276 H3 = H2H2 H3 = H1H2
277branch in common.branch in common, their path
lengths add to these sums.
279r1+r2+r3+r4 Noter1+r2+r3+r4. Note
280(equation 17.12)    q   g
280(equation 17.13)    q   g
283are denoted by qi   gi
283(equation 17.15)    qi   gi
284those that have nonzero qithose that have nonzero gi
284minimizing C in equation 17.15minimizing Γ2 in equation 17.15
289Now some data is examined.Now some data are examined.
289less influence with 22 tossesless influence with 44 tosses
289data is half as probable as it isdata are half as probable as they are
291Gomberg (1966)Gomberg (1968)
293drawn will be less that Rdrawn will be less than R
300followed by (Yang and
Rannala, 1997) by
also be followed (Yang and
Rannala, 1997) by
309-310the symbol for the vector theta should be boldface throughout
310 we look this up on we look this up in
312 (in legend of Figure 19.1)    hightest likelihood highest likelihood
314 Thus we can find Thus, if we can find
315 branch lengths of evolutionary rates branch lengths or evolutionary rates
316penalize it by subtracting twice penalize it by adding twice
319one tree on that we seeone tree on which we see
328whether a two data setswhether two data sets
330the closest fit to this datathe closest fit to these data
332equal numbers changes in interiorequal numbers of changes in interior
333 (in equation 19.19)
   Prob(n1, n2, n3 | p1, q1)
Prob(n1, n2, n3 | p1, q1)
   Prob(n1, n2, n3 | p1, q1)
Prob(n1, n2, n3 | p2, q2)
333   p1 = q1 = 1/3   p2 = q2 = 1/3
333 alternative values of p2 alternative values of p1
340 between the delete-1/e jackknife and
the delete-1/e jackknife
between the delete-1/e jackknife
and the bootstrap
In Figure 20.4, the central curve is too dark,
and the rightmost curve has its left part too dark
350triple bootsraptriple bootstrap
356rather that distance between rather than distance between
364 their parsimony or likelihood
or likelihood scores
their parsimony or likelihood scores
364 PHYLIP (Should be in regular Palatino font)
365 Heading "An example" Should be a section head:
Roman font, bold face
375 2415 2,415
375 62,741 (shift it half a digit to the right)
376 equal numbers of A's, C's, G's, and T's equal numbers of As, Cs, Gs, and Ts
381(in equation 22.17, first line)  Pxyyx  Pxyxz
(terms in equation 22.17 have also been
arranged in a more logical order)
393Gomberg (1966)Gomberg (1968)
393 (in equation 23.4)
   σ2 v122 v112 v7
  σ2 v122 v11
      +σ2v102 v7
394 v4 in Figure 23.1 the v should be italic font
395 species 1 by xi1 species 1 by x1i
395 species 2 by xi2 species 2 by x2i
397 (in equation 23.15)
σi-2p exp( - 
2 σi2
σi-2 ) exp( - 
σi2( v1+v2 )
398 (in equation 23.16)
-2p  ln(σi) - 
p ln(v1v2) - 
2 σi2
( v1+v2 )
 ln(σi) - 
p ln(v1v2) - 
σi2( v1+v2 )
402 (in equation 23.33)    x     x   (boldfaced)
(in equation 23.60)     yij2
417 frac1N 1/N
418 VA/(2N) VA/N
418 (in equation 24.6)     (2NVM)/(2N) = VM (2NVM)/N = 2VM
418 N times the variance of change 2N times the variance of change
424 1973b 1973a
435 (in equation 25.1)    Y2 = y2/square root(0.75)Y2 = y2/square root(0.975)
439 (in equation 25.2)    AT + EI TA + IE
439 matrix, EI matrix, IE
440 (in equation 25.3)   Iμ, A⊗T + EI 1μ, TA + IE
457have any number lineages have any number of lineages
461 of equation 26.9 of equation 26.10
4663 x 2 / 106 = 0.0000063 x 2 /(4 x 106) = 0.0000015
4664 x 3 / 106 = 0.0000124 x 3 / (4 x 106) = 0.000003
467 ancestry of below ancestry below
471 were one were once
(In equation 27.7)      --------
  -  --------
475 Prob(G | Θ0)
at start of line in middle of page
Prob(G | Θ)
(in equation 27.22)    
482 Heading "MCMC for a variety
of coalescent models"
Should be a section heading:
Roman font, bold face
486the data was representedthe data were represented
488the copies from B and C arethe copies from A and C are
488than either is to the copy from Athan either is to the copy from B
494 the N - i would actually the Ni would actually
498 (in Figure caption):    are shown by by the hash marks are shown by the hash marks
499 an alignment of of position an alignment of position
501all the G's on the same sideall the Gs on the same side
501the sequence in the two parts of the treethe sequences in the two parts of the tree
504Two T's are inserted to its right.Two Ts are inserted to its right
504Two T's are deleted.Two Ts are deleted.
504T's in the middle of the sequenceTs in the middle of the sequence.
507adjacent A's are deletedadjacent As are deleted
507turn out to be A's,turn out to be As,
525Heading: "A dismaying result"Should be a subsection heading:
Italic font and not boldfaced
531 based on NNI's based on NNIs
532 ranch lengths branch lengths
544 parasite species of a species parasite species or a species
in Figure 32.1, for each large ellipse the
leftmost small ellipse within it is too dark
557 (in Figure 32.6)
e dv
4Ne τ
4Ne τ
e dv
557 exp[ exp[-
561 probability that then urn probability that the urn
578 subtrees of size 5, 7, and 1 subtrees of size 8, 4, and 1
578 these are species A-E, F-L, and Mthese are species A-H, I-L, and M
578 angles 2.4166, 3.33833, and 0.24166 angles 3.8666, 1.9333, and 0.48332
578 Thus the five-species subtree has a branch length 10 Thus the eight-species subtree has a branch length 13
578 one with four species and one with one one with five species and one with three
578 for the five-species subtree for the eight-species subtree
578 branch of length 10 branch of length 13
578 Thus the five-species subtree Thus the eight-species subtree
578 starts with an angle of 2.4166 radians starts with an angle of 3.8666 radians
578 moves out a distance 10 moves out a distance 13
578 with four and one species with five and three species
578 2.4166 radian sector 3.8666 radian sector
578 branch of length 10 branch of length 13
578 one of 1.9333 and the other of 0.48332 one of 2.4166 and the other of 1.4500
578 lengths 3 and 21 lengths 10 and 13
dashed curves in Figure 34.6 need to
connect more accurately with dashed lines
612Gomberg, D. 1966.Gomberg, D. 1968.
619Kishino, H., T. Miyata andKishino, H., T. Miyata, and
621(in Lande 1976 reference) 31: 442-446.30: 314-334.
623(in reference for Lundy, 1985)  198  .   198.
627 (in Nielsen et al. 1998 reference):    maximumlikelihoodmaximum-likelihood
630 Purvis and Garland reference It is out of alphabetical order.
It should follow Purdom et al.
641 (add reference after Wakeley 1998:) Wald, A. 1949. Note on the consistency of
the maximum likelihood estimate. Annals
of Mathematical Statistics
20: 595-601.
644 posledobatel'nostyam. (in Russian) posledovatel'nostyam (in Russian).
645 (after Angielczyk entry) Antonov, 631
646 Bousquet, 325 Bousquet, 325, 622
648 Cucumel, 191, 527 Cucumel, 191, 527, 621
651 Hannenhalli, 516, 614 Hannenhalli, 516, 597, 614
654 Landrum, 95 Landrum, 95, 605
655 Margoliash, 131, 132, 134, 148, 222 Margoliash, 131, 132, 134, 148, 222, 609
655 Markowitz, 217, 268 Markowitz, 217, 268, 609
655 Meacham, 92, 95, 530, 578, 590, 624 Meacham, 92, 95, 530, 578, 590, 591, 605,
660 Schoenberg, xx, 51 Schoenberg, xx, 40, 51
660 (after Solovyov entry) Soules, 597
663 Wald, 269-272 Wald, 269-272, 641
664 Zharkikh, 65, 66, 120, 213, 346, 349, 351,
                631, 644
Zharkikh, 65, 66, 120, 213, 346, 349, 351,
                622, 631, 644

These typos are corrected in the second printing.


I'd appreciate being told of any other typos that are discovered.
There will be a chance to correct them at the next reprinting.

Thanks for pointing out some of these to:
Brian Anton       Gangolf Jobb       Andrew Roger
David Bryant Russ Lande Eric Rynes
Jose Clemente Dennis Lavrov Dave Schruth
James Cotton Erick Matsen Nikolaus Schueler
Alexei Drummond Peter Midford Kelly Smith
Casey Dunn Shlomo Moran Michael Sorenson
Steve Evans Peter Morcos John Trueman
Walter Fitch Anders Gorm Pedersen Jiaye Yu
Alex Griffing Markus Riester Jie Zha
Simon Ho

I am particularly grateful to John Trueman, Simon Ho, Peter Morcos, and Nik Schueler, who reported many of these typos.

What got left out?

Of course the book omits all work after early August, 2003. But some earlier works were not discussed that should have been. Particularly egregious omissions include:

What is incorrect?

As for incorrect arguments, there will be those who say most of the book is incorrect. Obviously I don't agree. The arguments I made that may be wrong are:

What about a second edition?

There has been thre further printing, and there will be additional reprintings as necessary, with correction of typos. I don't think there is ever likely to be a full second edition. Work on phylogenies is growing rapidly, and the second edition would have to be twice the size. Aside from whether people would buy or read such a massive tome, there is the issue of who has the energy to write it. I don't. Follow-up books probably either will have to be more narrowly focussed on particular subfields, or will skim more lightly through the literature, citing much less of it.

It is possible that a Revised Edition might be produced, correcting the above errors, adding a smallish amount of material to bring the coverage more up to date, while compensating for the extra length by dropping coverage of some of the more obscure methods. We're thinking about this.

Downloads page

Those interested in downloading the data sets and trees that were used for the examples in the book should look at the web page here.


A list of reviews of the book that have appeared, and some reactions to them, will be found here.

Joe Felsenstein