Blackwell Science, LtdOxford, UKBIJBiological Journal of the Linnean Society0024-4066The Linnean Society of London, 2003?

2003
80••
99106
Original Article

SPECIATIONAL CHANGE IN RATITE EVOLUTION

J. CUBO

Biological Journal of the Linnean Society, 2003, 80, 99–106. With 3 figures

Evidence for speciational change in the evolution of

ratites (Aves: Palaeognathae)
JORGE CUBO*
UMR CNRS 8570, Université Paris 6/7-2, Pl Jussieu, Case 7077, 75005 Paris, France

Received 20 September 2002; accepted for publication 11 February 2003

To perform a comparative analysis of character associations framed in a phylogenetic context (e.g. independent con-
trasts), a model of character evolution must be assumed. According to phyletic gradualism, morphological change
accumulates gradually over time within lineages, and speciation events do not have a major role. Under speciational
models, morphological change is assumed to occur during or just after cladogenesis in both daughter species, and the
resulting morphologies do not change over long periods of time (stasis), until the next cladogenetic event. A novel
method is presented for comparing these models of character evolution that uses permutational multiple phyloge-
netic regressions. The addition of divergence times to well-corroborated phylogenetic trees and the utilization of the
method developed in this paper allows the estimation of relative frequency of gradual change and speciational
change from living organisms. This method is applied to a dataset from ratites with the conclusion that, for a range
of morphological features, change tends to have been speciational rather than gradual. © 2003 The Linnean Society
of London, Biological Journal of the Linnean Society, 2003, 80, 99–106.

ADDITIONAL KEYWORDS: heterochrony – independent contrasts – phyletic gradualism – phylogenetic

comparative method – punctuational change.

INTRODUCTION affect the rate of change (Gould & Eldredge, 1993;

Mooers, Vamosi & Schluter, 1999). If we assume the
To perform a comparative analysis of character asso- gradual model of evolution, our comparative method
ciations framed in a phylogenetic context (e.g. inde- should consider branch lengths between speciation
pendent contrasts), a model of character evolution events in terms of either geological time or genetic
must be assumed (Harvey & Pagel, 1991; Harvey & change (assuming a clock model). According to the spe-
Purvis, 1991; Garland, Harvey & Ives, 1992; Pagel, ciational model, changes occur at the time of specia-
1999). In fact, 12 years ago, Harvey & Purvis (1991) tion in both daughter species and the resulting
and Martins & Garland (1991) showed that the result morphologies do not change over long periods of time
of a comparative analysis strongly depends on the (stasis), until the next cladogenetic event (Rohlf et al.,
model of evolution that has been assumed. However, 1990). (Note that under the punctuational model,
most comparative studies do not determine an appro- changes occur at the time of speciation but only in a
priate model of evolution for character change prior to single daughter species, Rohlf et al., 1990.) Under the
choosing the comparative method to be used. The speciational model, morphological change between
approach presented here allows a comparison of the specified times is proportional to the number of speci-
relative efficacy of phyletic gradualism vs. speciational ation events that have occurred (Mooers et al., 1999).
models prior to choosing the comparative method. If the speciational model of character evolution is
Under phyletic gradualism, geological time is an assumed, our comparative method should assume
appropriate predictor of the amount of morphological equal branch lengths between speciation events. Here
change that has occurred, and speciation does not I present a novel method for comparing these models
of character evolution that uses permutational multi-
ple phylogenetic regressions (Legendre, Lapointe &
*E-mail: cubo@ccr.jussieu.fr Casgrain, 1994; Böhning-Gaese & Oberrath, 1999). I

© 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 80, 99–106 99
100 J. CUBO
apply this method to a dataset from ratites and con-
clude that, for a range of morphological features,
change tends to have been speciational rather than
gradual.
MATERIAL
I measured total length and diaphyseal diameter of
stylopodial bones (humerus and femur) and zeugopo-
dial bones (ulna, radius and tibiotarsus) to the nearest
0.01 mm using a digital caliper in a sample of nine
species of ratites. The number of specimens for each
species is given in parentheses: Rhea americana (Lin-
naeus, 1758) (3), Rhea pennata (d’Orbigny, 1834) (3),
Struthio camelus Linnaeus, 1758 (3), Dromaius novae-
hollandiae (Latham, 1790) (2), Casuarius casuarius
(Linnaeus, 1758) (2), Casuarius bennetti Gould, 1857
(1), Casuarius unappendiculatus Blyth, 1860 (2),
Apteryx australis Shaw, 1813 (3) and Apteryx owenii
Gould, 1847 (1). Following Cubo et al. (2002), dimen-
sionless shape variables were computed to be com-
pared between species: for each bone, the ratio
diaphyseal diameter/total length was calculated. In
addition, the ratio wing length/leg ratio was also cal-
culated (limb length was measured as stylopodial
length + zeugopodial length). Mean values of these
ratios for each species were used, assuming no sam-
pling error because of small sample sizes.
DEVELOPMENT OF THE METHOD
I used multiple regression and the Mantel permuta-
tion test to compare the gradual and the speciational
models of character evolution for ratite birds. Distance
matrices of size 9 ¥ 9 were constructed (nine species,
36 comparisons). The dependent matrices (Y 1, Y2,…Y6)
contain the morphological dissimilarity (regarding the
different ratios described above) for each pair of spe-
cies. The independent matrices (X i) contain the phylo-
genetic distances for each pair of species. These
distances were quantified under assumptions of the
gradual model (XGr) and the speciational model
(XSpeciat) of evolution. In all cases, I used the topology
of the phylogenetic tree of extant ratites published by
Cooper et al. (2001) and by Haddrath & Baker (2001)
(Figs 1A,2A,3A).
Under the gradual model of evolution, phylogenetic
distances were measured as divergence times. For
each comparison, the distance between the two species
being compared was computed as the geological time
since their last common ancestor. Both molecular clock
data (van Tuinen & Hedges, 2001) and the fossil
record (Cracraft, 2001) agree that the split between
Palaeognathae (ratites and tinamous) and Neo-
gnathae (all other modern birds) occurred prior to the
Cretaceous–Tertiary extinction event. Within ratites,
© 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 80, 99–106
estimations of divergence times between the different
clades found by two recent molecular studies are
slightly different (Cooper et al., 2001; Haddrath &
Baker, 2001). I used divergence times found by Cooper
et al. (2001) (Fig. 1A) to construct matrix X Gr-1 and
divergence times found by Haddrath & Baker (2001)
(Fig. 2A) to construct matrix X Gr-2. In general, no diver-
gence times are available for within-genus compari-
sons (Casuarius, Apteryx, Rhea). In these cases, the
first occurrence in the fossil record of each one of these
genera (the geological age of the oldest fossil of each
genus, Unwin, 1993) was tentatively used as the date
of divergence between the different species of each
genus (Figs 1A,2A).
The following method to quantify the phylogenetic
distances under the speciational model of evolution
(matrix XSpeciat) was used. For each comparison, the
phylogenetic distance was measured as the number of
speciation events that separates each pair of extant
species being compared since their last common ances-
tor (Fig. 3a). In the cases of unresolved trichotomies
(three species of Casuarius and three species of
Apteryx), according to Lemen & Freeman (1989), the
number of nodes between a species and the last com-
mon ancestor for that trichotomy was calculated as
the average of all possible arrangements; that is, 1.67.
Ideally, under the speciational model of evolution, all
speciation events of ratite evolution should be incor-
porated, including those leading to extinct species.
However, the total number of extinct species of a clade
cannot be quantified. In order to minimize this prob-
lem, I used a ‘complete tree’ (Mooers, 1995) that con-
tains at least N - 1 of the total known extant species of
the in-group (in the case of ratites, N = 10), a neces-
sary requirement for a valid test of the speciational
model (Mooers et al., 1999).
The goal of the present analysis was to determine
in ratites which model of character change (gradual
or speciational) best describes the evolution of the mor-
phological features in question. For this, I used
permutational multiple phylogenetic regressions
(Legendre et al., 1994; Böhning-Gaese & Oberrath,
1999). I computed multiple regression between the
dependent morphological-dissimilarity matrices
(Yi) and the independent phylogenetic-distance
matrices XGr-1 and XSpeciat. Similarly, the dependent
morphological-dissimilarity matrices (Y i) were
regressed on the independent phylogenetic-distance
matrices XGr-2 and XSpeciat. Figures 1B, 2B and 3B show
scatter plots of the dependent matrix containing the
morphological dissimilarity in humerus shape for each
pair of species vs. the independent matrices containing
phylogenetic distances for each pair of species calcu-
lated under assumptions of the gradual and the
speciational models of evolution. I was interested in
considering in multiple regression only the
 SPECIATIONAL CHANGE IN RATITE EVOLUTION 101

Figure 1. (A) Phylogenetic relationships among extant ratites (modified from Cooper et al., 2001). Branch lengths have
been scaled proportional to divergence times (taken from Cooper et al., 2001; with the exception of within-genus divergence
times that were estimated as the first occurrence in the fossil record of each one of these genera, Unwin, 1993). Under
the gradual model of evolution, for each comparison, the phylogenetic distance between the two species being compared
was computed as the geological time since their last common ancestor. (B) Scatter-plot of the dependent matrix containing
the morphological dissimilarity in humerus shape for each pair of species vs. the independent matrix containing phyloge-
netic distances for each pair of species calculated under assumptions of the gradual model of evolution by using divergence
dates of Fig. 1A.

independent-matrix variables (corresponding to the
gradual and the speciational models of evolution) that
contribute significantly to the explanation of each
dependent-matrix variable (the morphological-dissim-
ilarity matrices). For this, I used a forward-selection
procedure (Legendre et al., 1994). At each step, the
independent-matrix variable whose multiple regres-
sion equation provides the most significant R2 coeffi-
cient is selected, provided that both this probability
and the probability of the corresponding partial stan-
dardized regression coefficient P(b) are smaller than or
equal to the predetermined Bonferroni-corrected P-to-
enter value (P = 0.05). The significance of statistics of
the multiple regression equation ( R2 and partial stan-
dardized regression coefficients, bi) could not be tested
in the parametric way because the values of the matrix
variables corresponding to the morphological differ-
ences (simple distance matrices) are not independent
from each other and the independence of the observa-
tions is a fundamental condition of parametric testing
(Legendre et al., 1994). In these cases, significance of
model statistics should be tested through permuta-
tional tests (Harvey & Pagel, 1991). I used the Mantel
permutation test: the model and its statistics were

© 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 80, 99–106
102 J. CUBO

Figure 2. (A) Phylogenetic relationships among extant ratites (modified from Haddrath & Baker, 2001). Branch lengths
have been scaled proportional to divergence times (taken from Haddrath & Baker, 2001; with the exception of some within-
genus divergence times, Casuarius, Apteryx, that were estimated as the first occurrence in the fossil record of each one of
these genera, Unwin, 1993). Under the gradual model of evolution, for each comparison, the phylogenetic distance between
the two species being compared was computed as the geological time since their last common ancestor. (B) Scatter-plot of
the dependent matrix containing the morphological dissimilarity in humerus shape for each pair of species vs. the
independent matrix containing phylogenetic distances for each pair of species calculated under assumptions of the gradual
model of evolution by using divergence dates of Fig. 2A.

recomputed by repeatedly randomizing the values of
the matrices corresponding to the morphological dif-
ferences to obtain null distributions against which to
test the significance of the statistics of the actual
regression (Legendre et al., 1994). The matrix vari-
ables containing the morphological differences were
randomly permuted 999 times, the independent-
matrix variables with the phylogenetic distances (cor-
responding to the gradual and speciational models of
evolution) were held constant, and the statistics of the
regression model were repeatedly computed. The sig-
nificance of the actual statistics was tested by compar-
ing them with the distribution of values obtained from
permutations (Legendre et al., 1994).
RESULTS
Table 1 shows results of the multiple regression
through a forward-selection procedure between the
dependent morphological-dissimilarity matrices (Y i)
and (i) the independent phylogenetic-distance matri-
ces XGr-1 and XSpeciat, and (ii) the independent
phylogenetic-distance matrices X Gr-2 and XSpeciat.
Results obtained by using divergence times taken

© 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 80, 99–106
 SPECIATIONAL CHANGE IN RATITE EVOLUTION 103

Figure 3. (A) Phylogenetic relationships among extant ratites (modified from Cooper et al., 2001 and Haddrath & Baker,
2001). Under the speciational model of evolution, for each comparison, the phylogenetic distance was measured as the
number of speciation events that separates each pair of extant species being compared since their last common ancestor.
In the cases of unresolved trichotomies (Casuarius, Apteryx), according to Lemen & Freeman (1989), the number of nodes
between a species and the last common ancestor for that trichotomy was calculated as the average of all possible
arrangements, that is, 1.67. (B) Scatter-plot of the dependent matrix containing the morphological dissimilarity in humerus
shape for each pair of species vs. the independent matrix containing phylogenetic distances for each pair of species
calculated under assumptions of the speciational model of evolution represented in Fig. 3A.

from Cooper et al. (2001) (XGr-1, Fig. 1A) are very sim-
ilar to those obtained by using divergence times taken
from Haddrath & Baker (2001) (XGr-2, Fig. 2A).
Regarding wing bones, the phylogenetic-distance
matrix constructed assuming a speciational model of
evolution (XSpeciat) was the only independent variable
that significantly explained morphological differences
in humerus shape, ulna shape, radius shape and the
ratio wing length/leg length. In most cases (Table 1),
XSpeciat (speciational model) was the only selected inde-
pendent variable at the predetermined Bonferroni-
corrected P-to-enter value P = 0.05. In a few cases (see
Table 1), both the speciational and the gradual model
were selected at P = 0.05. In these cases, I repeated the
multiple regression through a forward-selection pro-
cedure by using a predetermined Bonferroni-corrected
P-to-enter value P = 0.01. Again, XSpeciat (speciational
model) was the only independent variable that signif-
icantly explained morphological differences. Regard-
ing leg bones, neither the gradual model nor the
speciational model explain morphological differences
in femur shape and tibiotarsus shape.
DISCUSSION
Different approaches have been used to test for grad-
ual vs. speciational models of character evolution from
living organisms. Avise (1977) performed a test by

© 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 80, 99–106
104 J. CUBO

Table 1. Selection through multiple regression of an optimal subset of independent phylogenetic-distance matrices (X i,
constructed assuming the gradual and the speciational models of evolution) to explain the dependent morphological-
dissimilarity matrices (Yi) in ratites. Abbreviations: b, standard partial regression coefficients; DR2, increment in multiple
regression coefficient produced when a new variable is added to the regression model; XGr-1, gradual model, divergence
times were taken from Cooper et al. (2001); XGr-2, gradual model, divergence times were taken from Haddrath & Baker
(2001); XSpeciat, speciational model; Y1 = wing length/leg length; Y2 = humerus shape; Y3 = ulna shape; Y4 = radius shape;
Y5 = femur shape; Y6 = tibiotarsus shape; *, independent variable selected to be added to the model; #, predetermined
Bonferroni-corrected P-to-enter value = 0.01 (P = 0.05 in all other cases). Note that P-to-enter value in step 2 is half of
P-to-enter value in step 1

Step 1 Step 2

bi P(b) DR2 P(R2) bi P(b) DR2 P(R2)

Y1
XGr-1 0.747 0.002 0.558 0.002 0.433 0.047 0.063 0.001
XSpeciat* 0.738 0.001* 0.545 0.001*
XGr-2 0.640 0.002 0.409 0.002 0.142 0.302 0.007 0.001
XSpeciat* 0.738 0.001* 0.545 0.001*
Y2
#XGr-1 0.496 0.015 0.264 0.015 -0.359 0.013 0.043 0.001
#XSpeciat* 0.754 0.001* 0.569 0.001*
XGr-2 0.531 0.003 0.282 0.003 -0.191 0.126 0.013 0.001
XSpeciat* 0.754 0.001* 0.569 0.001*
Y3
XGr-1 0.347 0.043 0.120 0.043 -0.515 0.052 0.088 0.001
XSpeciat* 0.635 0.002* 0.403 0.002*
XGr-2 0.328 0.048 0.108 0.048 -0.486 0.041 0.086 0.001
XSpeciat* 0.635 0.002* 0.403 0.002*
Y4
XGr-1 0.376 0.039 0.142 0.039 -0.484 0.040 0.078 0.001
XSpeciat* 0.659 0.001* 0.434 0.001*
#XGr-2 0.349 0.043 0.122 0.043 -0.480 0.022 0.084 0.001
#XSpeciat* 0.659 0.001* 0.434 0.001*
Y5
XGr-1 0.307 0.046 0.094 0.066
XSpeciat -0.062 0.385 0.004 0.711
#XGr-2 0.371 0.016 0.137 0.016
#XSpeciat -0.062 0.385 0.004 0.711
Y6
XGr-1 0.063 0.339 0.004 0.723
XSpeciat 0.016 0.413 0.0003 0.932
XGr-2 0.154 0.194 0.024 0.397
XSpeciat 0.016 0.413 0.0003 0.932

comparing genetic differences in a speciose and a dep-
auperate group of fishes, assuming these groups have
similar geological ages. Mayden (1986) has criticized
this method on the basis that the assumption of equal
antiquity was not justified and this author suggested
the use of cladistic methods to overcome this problem
(as sister clades have, necessarily, the same geological
age). Mindell, Sites & Graur (1989) and Lemen &
Freeman (1989) have used cladistic methods which
are based on character polarization and the compari-
son of primitive and derived character states. This
approach is useful to analyse discrete characters,
where ancestral states are estimated through out-
group comparison by using parsimony. For con-
tinuous characters, ancestral states are estimated in
part or whole from daughter taxa by assuming a

© 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 80, 99–106
 SPECIATIONAL CHANGE IN RATITE EVOLUTION
set of assumptions (Brownian motion, maximum
parsimony, . . . ). In this last case, ancestral states are
not independent from character states of daughter
taxa and comparisons between ancestors and descen-
dants are not valid (Harvey & Purvis, 1991). The char-
acters analysed in this paper, bone shape and the ratio
wing length/leg length, vary continuously across spe-
cies. Therefore, the method developed here avoids the
estimation of ancestral states to test the gradual and
the speciational models of character evolution. Other
methods have been proposed to test these models that
also avoid the estimation of ancestral states for con-
tinuous traits (Pagel, 1997, 1999; Mooers et al., 1999).
While these last methods perform estimation of evo-
lutionary parameters by using a maximum likelihood
approach (Pagel, 1997, 1999; Mooers et al., 1999), the
method developed in this paper (based on permuta-
tional multiple phylogenetic regressions) is not con-
strained to the estimation of such parameters.
Table 1 shows that, for a range of morphological fea-
tures of ratites, change tends to have been specia-
tional rather than gradual. The speciational model
significantly explains morphological variation of
humerus shape, ulna shape, radius shape, as well as
the variation of the ratio wing length/leg length.
Morphological change is assumed to occur during or
just after cladogenesis in both daughter species, and
the resulting morphologies do not change over long
periods of time (stasis), until the next cladogenetic
event (Rohlf et al., 1990). Consequently, comparative
analyses of character associations framed in a phylo-
genetic context (e.g. independent contrasts) in ratites
should assume equal branch lengths between specia-
tion events. Regarding leg bones (femur and tibiotar-
sus), the rate of character change would have been
rapid enough to erase phylogenetic effects. In fact, the
speciational and the gradual models of change are not
mutually exclusive. As quoted above, in a few cases
(see Table 1), both the speciational and the gradual
models were selected at a predetermined Bonferroni-
corrected P-to-enter value P = 0.05, although the
speciational model was the only selected variable at a
predetermined Bonferroni-corrected P-to-enter value
P = 0.01.
We can wonder about the proximal factors (Cubo
et al., 2000; Cubo, 2000) underlying the similar pat-
terns of character evolution in the different wing
bones of ratites. Ratite wing bones are under-
developed and this has been interpreted by Cubo &
Arthur (2000) as a case of paedomorphosis (the reten-
tion of ancestral juvenile character states in adult
stages of descendants, Gould, 1977). Considering that
the development of forelimbs is delayed relative to the
development of hindlimbs in birds (Carrier & Leon,
1990), either the truncation or the retardation of
somatic development (heterochrony) is likely to pro-
© 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 80, 99–106
105
duce reduction of the size of all wing bones by
correlated development (Cubo & Arthur, 2000). Het-
erochronic changes can be instantaneous in terms of
geological time (Gould, 1977) and they are likely to
produce patterns of speciational character evolution.
Ratite wing bones do not play a function in locomotion,
they do not undergo adaptation linked to flight, and
this would have contributed to preserve the pattern of
speciational character evolution generated by hetero-
chronic changes.
ACKNOWLEDGEMENTS
I thank Paul Harvey (University of Oxford) and
Jacques Castanet and Emmanuel de Margerie (Pierre
& Marie Curie University, Paris) for a critical reading
of a preliminary version of this manuscript. I also
thank Philippe Casgrain (University of Montreal) for
useful comments on statistical methods and two anon-
ymous reviewers for comments on the submitted ver-
sion of the manuscript.
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