Cladistics

Cladistics 22 (2006) 89–96

www.blackwell-synergy.com

Divergence time estimates for major cephalopod groups: evidence

from multiple genes
Jan Strugnell1,2,3,*, Jennifer Jackson1, Alexei J. Drummond1 and Alan Cooper1
1
Molecular Evolution, Department of Zoology, South Parks Road, Oxford, OX1 3PS, UK; 2School of Biology and Biochemistry, MBC, 97 Lisburn
Road, Queen’s University, Belfast, BT9 7BL, UK; 3British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
Accepted 7 October 2005

Abstract

This is the first study to use both molecular and fossil data to date the divergence of taxa within the coleoid cephalopods (octopus,
squid, cuttlefish). A dataset including sequences from three nuclear and three mitochondrial genes (3415 bp in total) was used to
investigate the evolutionary divergences within the group. Divergence time analyses were performed using the Thorne ⁄ Kishino
method of analysis which allows multiple constraints from the fossil record and permits rates of molecular evolution to vary on
different branches of a phylogenetic tree. The data support a Paleozoic origin of the Orders Vampyromorpha, Octopoda and the
majority of the extant higher level decapodiform taxa. These estimated divergence times are considerably older than paleontological
estimates. The major lineages within the Order Octopoda were estimated to have diverged in the Mesozoic, with a radiation of many
taxa around the Cretaceous ⁄ Cenozoic boundary. Higher level decapodiform phylogenetic relationships appear to have been
obscured due to an ancient diversification of this group.

The Willi Hennig Society 2006.

The fossil record is inevitably an incomplete account
of life that once existed on earth. Due to the nature of
fossilization, organisms that possess hard parts are
better represented in the fossil record than those that are
soft-bodied. As a result, most coleoid cephalopod taxa
rarely fossilize well. The Subclass Coleoidea is divided
into two Superorders: Decapodiformes, currently con-
taining the Orders Teuthoidea (most squids), and
Sepioidea (cuttlefishes, Ram’s Horn, pygmy, bottletail
and bobtail squids) and the Octopodiformes, containing
the Orders Vampyromorpha (vampire ‘‘squid’’) and
Octopoda (octopuses).
Most fossil coleoid cephalopods are known only from
their highly reduced internal shell (gladius [chitinous
and feather shaped] or phragmocone [conical and
chambered]), which is often only partially preserved
and very difficult to classify (Bandel and Leich, 1986;
*Corresponding author: Jan Strugnell, British Antarctic Survey,
High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
E-mail address: jmst@bas.ac.uk
Doyle et al., 1994; Doguzhaeva et al., 1996; Doguzha-
eva, 1999; Vecchione et al., 1999).
Fossilized statoliths (paired, aragonitic stones) found
within the cartilaginous skulls of coleoids provide the
only definite fossil evidence of the Order Teuthoidea
(Clarke and Maddock, 1988).
The lack of preservable hard parts within members of
the Order Octopoda (with the exception of Argonauta
shells) means that only two definite fossil octopod
species have been described, the Cretaceous Paleoctopus
(Woodward, 1896) and the Carboniferous Pohlsepia
(Kluessendorf and Doyle, 2000). The discovery of the
latter pushed the date of the oldest octopod fossil back
100 Ma, illustrating the poor quality of the fossil record.
Evidence of octopod predatory activities is also present
in the fossil record (Bromley, 1993). Bromley (1993)
described octopod drill holes in scallop shells from the
Upper Pliocene.
Recently, molecular studies by Strugnell et al. (2005)
reported the resolution of a number of higher level
relationships within the Coleoidea. These phylogenies

The Willi Hennig Society 2006

90 J. Strugnell et al. / Cladistics 22 (2006) 89–96

can be used in conjunction with known fossil constraints
to estimate the divergence times of coleoid cephalopod
groups.
Traditionally, methods of estimating divergence times
have been based on a molecular clock which assumes
that genes evolve at a constant rate over time (Kimura,
1968). However, this assumption is often violated and
studies have shown that divergence time estimation is
very sensitive to assumptions about evolutionary rates
(Takezaki et al., 1995; Yoder and Yang, 2000). To
circumvent the assumption of a molecular clock both
maximum likelihood (ML) (Kishino and Hasegawa,
1990; Sanderson, 1997; Rambaut and Bromham, 1998;
Yoder and Yang, 2000; Yang and Yoder, 2003) and
Bayesian methodologies (Thorne et al., 1998; Huelsen-
beck et al., 2000; Kishino et al., 2001; Thorne and
Kishino, 2002) have been developed which allow variable
rates among lineages in divergence time estimations.
The aim of this study was to use a Bayesian approach
to estimate the divergence times of coleoid cephalopod
taxa using fossil and molecular data. Thorne and
Kishino’s (2002) method was selected to allow the use
of multiple genes with correlated but different rates.
Materials and methods
Gene and taxon sampling
The dataset contains three nuclear (octopine dehy-
drogenase [ODH], pax-6, rhodopsin) and three mitoch-
ondrial (12S rDNA, 16S rDNA and cytochrome oxidase
I [COI]) genes (together comprising 3415 bp) for 35
coleoid cephalopods including representatives of all
major coleoid cephalopod taxa (Fig. 1).
This dataset was used in the largest phylogenetic
study of coleoid cephalopods to date (Strugnell et al.,
2005). This study showed that the strongest phylogenetic
resolution for the Octopodiformes was obtained from
analyses using all six genes partitioned by gene and
codon. Two topologies were presented for the Decapo-
diformes, one resulting from analysis of nuclear genes
(all three codon positions) partitioned by codon, the
second resulting from only the first and second codon
positions (not partitioned). The current study estimates
divergence times using these three topologies and also
the same partitions used in Strugnell et al. (2005).
To determine the effect of differences between mit-
ochondrial and nuclear genes on dating estimates, the
octopodiform topology was also analyzed using only
nuclear genes.
Branch length estimation
The baseml program in the PAML package (Yang,
1997) was used to obtain estimates of the trans-
ition ⁄ transversion ratio, and the rates for site classes
under the discrete-gamma model of rates among sites
under the F84 model for each partition. These values
were then used to estimate branch lengths using the
estbranches program (Thorne et al., 1998). The Octopo-
diformes were used as the outgroup to investigate
divergence times within the Decapodiformes and vice
versa, as it is well established that these two superorders
are reciprocally monophyletic (Young and Vecchione,
1996; Carlini et al., 2000). To estimate the root of the
Subclass Coleoidea, sequences from the Subclass
Nautiloidea would be required. Unfortunately, nauti-
loid sequences for these genes were not available for this
study as the primers used to sequence the genes
rhodopsin, octopine dehydrogenase and 12S rDNA were
not successful on nautiloid DNA and attempts to
develop primers specific to Nautilus were also unsuc-
cessful. This is likely to be due to a large number of
differences between the DNA sequences of nautiloids
and coleoids in these genes caused by the ancient
diversification of these taxa.
In Strugnell et al. (2005), the third codon positions of
ODH and COI sequences were RY coded to resolve base
composition heterogeneity. Multidivtime is unable to use
RY coded data and so the normal nucleotide data of the
ODH third codon positions were used. COI third
positions were removed from the analyses, as when
not RY coded, these positions were highly saturated
(Strugnell et al., 2005).
Divergence time estimation
The program multidivtime was used to estimate
divergence times (Thorne et al., 1998). Monte Carlo
Markov Chain (MCMC) analyses were run for 1 million
generations and sampled every 100 generations. A burn-
in of 100 000 generations was required to allow Markov
chains to approach stationarity. Convergence of the
MCMC algorithm was monitored by repeating each
analysis at least twice.
Multidivtime requires a value for the mean of the prior
distribution of the time separating the ingroup root from

Fig. 1. Molecular time scale for the orders of coleoid cephalopods based on a mean prior of 400 ± 100 Ma for the coleoid root. (a)
Decapodiformes, three nuclear genes only, all three codon positions partitioned by codon (b) Decapodiformes, three nuclear genes only 1st + 2nd
codon positions only (c) Octopodiformes, three nuclear genes and three mitochondrial genes partitioned by gene and codon (not including 3rd
positions). Numbers on internal nodes (in red) are cross referenced with fossil constraints. The first presence of characteristics of coleoid cephalopods
are indicated with bold arrows. The letters A1 and A2 denote the base of the Suborder Oegopsida.
J. Strugnell et al. / Cladistics 22 (2006) 89–96 91
92 J. Strugnell et al. / Cladistics 22 (2006) 89–96
the present (rttm). A value of 400 Ma was used because
although this value is not accurately known for coleoid
cephalopods the rttm must be between the ages of the
oldest definite Decapodiform or Octopodiform (Pohlse-
pia mazoensis from the Carboniferous, 307 Ma), and
oldest cephalopod (505 Ma) (Benton, 1993). Because of
the uncertainty in determining this prior, a standard
deviation (rttmsd) of 100 million years was chosen. To
determine the sensitivity of our results to this prior, we
also performed a repeat analysis with a prior rttm of
600 Ma. Such a large value was mainly chosen to test out
the effect of this prior, although we believe that it is still
within the realms of possibility.
The prior values of brownmean, brownsd
and the mean (rtrate) and standard deviation
(rtratesd) of the prior distribution for the rate of
molecular evolution at the ingroup root node were
selected using the recommendations within the manual
for using multidivtime (Appendix 1). There was no
reason to expect that each of the partitions would have
an identical expected rate variation over time and thus
common brown was set to 0.
The following fossils were used to provide constraints
on divergence times (node numbers are for cross
referencing with Fig. 1). Where the specific age of a
fossil was not given, the mid-point of the epoch ⁄ age of
the fossil was used as a constraint according to the
geological timescale as determined by the International
Commission on Stratigraphy (ICS):
1. Minimum of 87 Myr for the split between the
Suborders Cirrata and Incirrata (node 1) based on the
fossil of Paleoctopus from the Coniacian, Cretaceous
(Woodward, 1896).
2. Minimum of 29 Myr for the Tremoctopus-Argona-
uta divergence (node 2) based on the Obinautilus pulchra
from the Oligocene (Kobayashi, 1954).
3. Minimum of 162 Myr for the base of the Order
Vampyromorpha (node 3) supported by the discovery of
the vampyromorph, Vampyronassa rhodanica from the
Lower Callovian of the Jurassic (Fischer and Riou, 2002).
4. Minimum of 44 Myr for the origin of Loligo (node 4)
based on loliginid statoliths found from the mid-Eocene
(Clarke and Maddock, 1988).
5. Minimum of 3 Myr for the diversification of the
Family Ommastrephidae (node 5) based on Omma-
strephid statoliths found from the Late Pliocene (Clarke
and Maddock, 1988).
6. Minimum of 44 Myr for the split between the
Families Sepiidae and Spirulidae (node 6) based on the
fossil of Belosaepia from the mid-Eocene (Donovan
pers. comm.).
7. Minimum of 19 Myr for the divergence of the
Family Sepiidae (node 7) (D.T. Donovan, pers. comm.).
Two more phylogenetically controversial fossils were
also used in some analyses to test the effect of the fossils
on various date estimates on the tree.
8. Minimum of 151 Myr for the split between the
Family Ommastrephidae and other oegopsids (node 8)
based on the Upper Jurassic Plesioteuthis (Naef, 1922;
Donovan and Toll, 1988; Doyle et al., 1994). Dono-
van and Toll (1988) argued that Plesioteuthis is an
ancestral ommastrephid due to remarkable similarities
in their gladii. In contrast, Bandel and Leich (1986)
and Engeser and Bandel (1988) argue for a Vampy-
romorpha affinity of Plesioteuthis. They claimed that
the arms of Plesioteuthis were held apart by a web
similar to that of Vampyroteuthis (Bandel and Leich,
1986). The age of the fossil Vampyronassa rhodanica is
older than that of Plesioteuthis, so the date of
Plesioteuthis was not used as a constraint on the
Vampyromorpha.
9. Minimum of 295 Myr for the divergence between
the Spirulidae ⁄ Sepiidae clade and either the Sepiolidae
(node 9) or the Loliginidae (node 9) based on the Late
Carboniferous fossil Shimanskya (Doguzhaeva, 1999).
Investigation of the shell ultrastructure of this fossil led
to its reclassification in the Order Spirulida, due to the
absence of a nacreous layer in the shell. However, the
nacreous layer could have been lost more than once in
the course of evolution, leaving a question over whether
Shimanskya is on the same lineage as the extant
phragmocone-bearing Spirula.
Results
Divergence estimates of decapodiform and octopodiform
taxa
Figure 1 depicts a time scale for the origins of coleoid
cephalopod taxa based on a 400 Ma prior, without the
Shimanskya and Plesioteuthis fossil constraints. A repeat
analysis using different starting states for the Markov
chain was almost identical and gave divergence esti-
mates within one million years.
The mean divergence of almost all of the major lineages
leading to the extant decapodiform taxa are estimated to
have occurred in the Paleozoic in both of the two
decapodiform topologies presented (Fig. 1, Table 1).
The divergence of Spirulidae ⁄ Sepiidae (node 6) is the
one exception, estimated to have occurred in the
Mesozoic for the decapodiform topology using 1st +
2nd codon positions only. The earliest mean divergences
leading to modern lineages are estimated to have occurred
in the Devonian. Interestingly, some diversification with-
in the Suborder Oegopsida (nodes A1 and A2) already
appears to have occurred around the Paleozoic ⁄ Mesozoic
boundary.
Despite the early origin of the sepiid and loliginid
lineages, much of the diversification leading to extant
taxa within these groups appears to have occurred in the
late Mesozoic or early Cenozoic (Fig. 1, Table 1).
 J. Strugnell et al. / Cladistics 22 (2006) 89–96 93

Table 1
Comparison of divergence estimates within the Decapodiformes obtained with different data partitions using a 400 Ma prior. Estimates both with
and without Shimanskya and Plesioteuthis fossil constraints are shown

3 nuclear genes partitioned by codon 3 nuclear genes not partitioned

(all 3 codon positions) (1st +2nd codon positions)

400 Ma rttm prior 400 Ma rttm prior

400 Ma rttm prior (with Shimanskya & Plesioteuthis) 400 Ma rttm prior (with Shimanskya & Plesioteuthis)
Base of Sepiidae 90 (47–154) 108 (67–167) 137 (67–245) 169 (100–272)
Base of Myopsida 155 (87–251) 186 (130–269) 172 (91–300) 210 (127–328)
Base of Sepiolidae 171 (98–272) 205 (148–294) 214 (115–356) 262 (181–383)
Base of Idiosepiidae 262 (154–408) 311 (243–429) 390 (236–596) 463 (355–630)
Base of Spirulidae 260 (154–402) 313 (244–432) 206 (109–345) 254 (171–375)
Base of Oegopsida 338 (205–515) 402 (315–548) 282 (161–454) 344 (251–488)
Decapod root 362 (222–549) 430 (346–581) 390 (236–596) 463 (355–630)

In contrast to the Decapodiformes, the diversification
of most taxa within the Octopodiformes is estimated to
have occurred much more recently (Fig. 1, Table 2). The
mean divergence of Vampyromorpha and the Octopoda
is estimated to have occurred in the upper Paleozoic
(node 3), whilst the origins of the rest of the major
Octopoda lineages is estimated to have begun in the
Mesozoic. The diversification of many of the lineages
leading to extant taxa appears to have occurred just
below the Cretaceous ⁄ Cenozoic boundary.
To ensure that the use of the relatively fast evolving
mitochondrial genes is not making the estimated dates
of divergence younger than would occur when nuclear
genes are used alone, divergence times within the
Octopodiformes are also estimated using nuclear genes
alone. The estimated divergence times within the Oct-
opoda are found to be slightly older (but not signifi-
cantly different) than when only nuclear genes are used
(Table 2), showing that the mtDNA is not biasing the
results downwards.
Shimanskya and Plesioteuthis
The divergence estimates in Fig. 1 show the mean
estimate for the divergence of the lineage leading to
extant Ommastrephidae to be 279 Ma (all three codon
positions) or 171 Ma (1st and 2nd codon positions)
(node 8). Both of these estimates suggest that the fossil
Plesioteuthis 151 Ma could feasibly fall along this
lineage as suggested by Naef (1922); Donovan and Toll
(1988) and Doyle et al. (1994).
Similarly, the estimated divergence times are also
consistent with the fossil Shimanskya, 295 Ma, being
placed on the Spirulidae-Sepiidae lineage (Fig. 1) offer-
ing support to Doguzhaeva (1999) (node 9).
To test the effect that the addition of these two fossils
would have upon the estimation of divergence times
within the Decapodiformes, the analyses were repeated
with the addition of these two fossils.
The results show a notable extension of the mean age
of divergence of each of the nodes (Table 1). However,
the mean estimates are still well within the 95%
confidence intervals of the estimates without Shiman-
skya and Plesioteuthis. (Fig. 1, Table 1).
Effect of the prior?
Increasing the mean of the prior distribution for the
time separating the ingroup root from the present to
600 Ma also notably extends the divergence time

Table 2
Comparison of divergence estimates within the Octopodiformes obtained with different data partitions using a 400 Ma and a 600 Ma prior

all 6 genes partitioned by gene & codon 3 nuclear genes partitioned by gene and codon

400 Ma rttm prior 600 Ma rttm prior 400 Ma rttm prior 600 Ma rttm prior
Base of Octopodinae 79 (50–125) 145 (92–216) 88 (49–147) 148 (89–229)
Base of Pareledone & 67 (43–107) 123 (78–184) 88 (50–146) 149 (92–229)
Vitreledonella ⁄ Japetella
Base of clade containing 100 (66–155) 182 (120–266) 120 (70–196) 201 (127–300)
Octopodidae &
Vitreledonella ⁄ . Japetella
Base of Argonautoidea 105 (67–166) 192 (121–284) 118 (66–196) 198 (118–305)
Base of Incirrata 136 (92–208) 247 (165–353) 176 (106–277) 295 (194–425)
Base of Octopoda 174 (118–262) 315 (215–440) 217 (133–336) 362 (244–512)
Octopod root 252 (175–369) 459 (328–615) 319 (206–476) 532 (382–707)
94 J. Strugnell et al. / Cladistics 22 (2006) 89–96

Table 3
Comparison of divergence estimates within the Decapodiformes obtained with different data partitions using a 600 Ma prior. Estimates both with
and without Shimanskya and Plesioteuthis fossil constraints are shown

3 nuclear genes partitioned by codon 3 nuclear genes not partitioned

(all 3 codon positions) (1st +2nd codon positions)

600 Ma rttm prior 600 Ma rttm prior

600 Ma rttm prior (with Shimanskya & Plesioteuthis) 600 Ma rttm prior (with Shimanskya & Plesioteuthis)
Base of Sepiidae 141 (81–224) 210 (115–343) 207 (109–346) 243 (158–369)
Base of Myopsida 245 (156–358) 262 (150–419) 257 (142–418) 288 (174–437)
Base of Sepiolidae 270 (173–388) 327 (208–491) 321 (194–487) 358 (241–511)
Base of Idiosepiidae 411 (280–573) 596 (435–499) 589 (416–794) 636 (488–821)
Base of Spirulidae 413 (278–575) 316 (196–480) 311 (182–478) 365 (298–504)
Base of Oegopsida 534 (375–728) 433 (291–623) 425 (266–620) 469 (331–645)
Decapod root 573 (407–771) 596 (435–799) 589 (416–794) 636 (488–821)

estimates within the Decapodiformes (Table 3). A prior
of 600 Ma places the root of the Decapodiformes within
Precambrian times and the early divergences within the
group within the Ordovician and Cambrian (Table 3).
Discussion
95% confidence intervals
The large 95% confidence intervals surrounding the
dating estimates in this study are not surprising. Only
eight cephalopod fossils could be used as constraints
with any certainty. Furthermore, no fossils could
provide upper constraints on divergences with any
certainty. It is very difficult to ensure an upper
constraint is placing an accurate boundary on a node.
This is because fossils are unlikely to be direct ancestors
of the taxa in question and are more likely to be sister
taxa (Fortey et al., 2003). The incorrect use of upper
fossil constraints will tend to underestimate the true date
of the divergence, causing evolutionary rates to be
overestimated (Rambaut and Bromham, 1998).
The lack of upper constraints means this analysis is
highly dependent upon the rttm. This is shown when the
analyses were repeated using a 600 Ma prior, and
notably larger mean divergence estimates are obtained.
However, the prior of 400 Ma with a standard deviation
of 100 Ma seems realistic given the oldest Octopodiform
(or Decapodiform) Pohlsepia (307 Ma) (Kluessendorf
and Doyle, 2000) and oldest cephalopod (505 Ma)
(Benton, 1993).
Divergence estimates
The results of the present study suggest a much earlier
origin for each of the major decapodiform and octopo-
diform lineages than previous studies (Naef, 1921–1923;
Donovan, 1977; Engeser and Bandel, 1988; Doyle et al.,
1994; Young et al., 1998) and are the first to suggest a
Paleozoic origin of many of the lineages leading to
extant decapodiform taxa and the divergence of the
Octopoda and Vampyromorpha.
This raises the question of why fossils have not been
discovered in the fossil record during this era? It is well
understood that fossil coleoids, apart from belemnites
and aulacocerids (hard shelled cephalopods) are very
rare in later Paleozoic and Mesozoic rocks (Donovan,
1977). Under the majority of sedimentary conditions
during this era even the relatively hard parts of
coleoids—the gladii and phragmocones—stood little
chance of preservation (Donovan, 1977). Most coleoid
fossils come from a small number of localities and also
originate from a small selection of geological horizons
(mostly Lower Jurassic and upper Cretaceous) (Dono-
van, 1977) where peculiarly favourable preservation
conditions applied.
Previous morphological and molecular studies have
usually found strong support for the monophyly of the
decapodiform taxa, Sepiidae, Loliginidae and Sepioli-
dae; however, they have struggled with resolution at the
suprafamilial level (e.g., Bonnaud et al., 1994, 1997;
Carlini et al., 2000; Strugnell et al., 2005). The present
study suggests that suprafamilial phylogenetic relation-
ships may have become obscured due to the ancient
diversification of these groups, with both morphological
and molecular characters becoming saturated over the
last 300 million years. This also has particular resonance
with the lack of phylogenetic resolution within the
Oegopsida (Young et al., 1998; Carlini et al., 2000).
Such an early diversification may provide some insight
into the high levels of morphological diversity within the
group.
The Paleozoic origin of the major groups of Decapo-
diformes suggested in the present study means that
Plesioteuthis and Shimanskya could feasibly be placed
on the ommastrephid and spirulid lineages, respectively.
Inclusion of these fossils as constraints did not signifi-
cantly change the divergence time estimates, but pushed
mean divergence estimates of the major Decapodiform
lineages back to the Devonian and Silurian, which seems
paleontologically plausible.
 J. Strugnell et al. / Cladistics 22 (2006) 89–96
Cretaceous ⁄ Cenozoic divergence?
Previous studies have argued for a relatively recent
diversification of the Sepiidae & Loliginidae. Khromov
(1998) suggested that the Sepiidae only emerged in the
Old World after the Belosaepiidae became extinct in the
Oligocene.
Doyle et al. (1994) and Engeser (1997) also placed the
origins of the Loliginidae in the Cenozoic, with Young
et al. (1998) suggesting that the lineages leading to
extant loliginids may be a recent innovation, derived
from a stem lineage that separated from other Decapo-
diformes deep in the Mesozoic. Young et al. (1998) also
suggested that considerable cephalopod diversity arose
in the Cenozoic, and that this may coincide with the
extinction of the abundant belemnoids at the Meso-
zoic ⁄ Cenozoic boundary.
The present study largely supports these theories and
estimates that the diversification of the sepiid and
loliginid lineages leading to extant taxa occurred in the
mid- to upper Mesozoic and Cenozoic.
Octopodiform divergence
Previous studies have generally suggested a Creta-
ceous or Jurassic divergence of the Orders Vampyro-
morpha and Octopoda, and a Cenozoic divergence of
the Suborders Incirrata and Cirrata (Naef, 1921–1923;
Donovan, 1977; Engeser and Bandel, 1988; Young
et al., 1998). The present study suggests much older
divergences: a Paleozoic divergence of the Octopoda and
Vampyromorpha (node 3) and a Mesozoic divergence of
the Incirrata and Cirrata (node 1). An older estimated
divergence date using molecular data would be expected
due to the undoubted paucity of the octopodiform fossil
record.
The divergence of most of the incirrate lineages
leading to extant taxa are estimated to have occurred
within a relatively short period between the late Creta-
ceous and Cenozoic. The timing of these divergences
may also correspond to the extinction of the ammonoids
and ⁄ or to the end of the Cretaceous ‘‘oceanic anoxic
event’’ (93 Ma), with mesopelagic depths only habit-
able after this time (Young et al., 1998).
Argonauta origins
The reason why Argonauta is the only shelled
octopodiform is perplexing. Naef (1921–1923) sugges-
ted that ancestral argonauts occupied empty ammo-
noid shells during the late Cretaceous and that the
ancestral argonauts evolved glandular structures on
the arms to repair the ammonoid shells. He suggested
that over time these shells were completely replaced by
‘‘secreted’’ shells which retained the shape of the
original ammonoid shells. Although perhaps a fanciful
95
explanation of how the Argonaut got its shell (see
Hewitt and Westermann, 2003 for a review), the
present study estimates that the Argonautoidea lineage
originated in the Jurassic, with Argonauta and Trem-
octopus diverging in the Cretaceous, thus suggesting
that the ammonoids and ancestral argonauts at least
coexisted.
Acknowledgments
We thanks Desmond Donovan at University College
London for invaluable information on coleoid cephalo-
pod fossils. This work was supported by the Rhodes
Trust and BBSRC grant no. (43 ⁄ G16942).
References
Bandel, K., Leich, H., 1986. Jurassic Vampyromorpha (dibranchiate
cephalopods). Neues Jahrbuch fuer Geologie und Palaeontologie,
Monatshefte, Jahrgang, 1986, 129–148.
Benton, M.J., 1993. The Fossil Record 2. Chapman & Hall, London,
UK.
Bonnaud, L., Boucher-Rodoni, R., Monnerot, M., 1994. Phylogeny of
decapod cephalopods based on partial 16S rDNA nucleotide
sequences. C. R. de l’Acad. Sci., Paris, Sciences de la vie ⁄ Life Sci.
317, 575–580.
Bonnaud, L., Boucher-Rodoni, R., Monnerot, M., 1997. Phylogeny of
cephalopods inferred from mitochondrial DNA sequences. Mol.
Phylogenet. Evol. 7, 44–54.
Bromley, R.G., 1993. Predation habits of octopus past and present and
a new ichnospecies, Oichns ovalis. Bull. Geol. Soc. Denmark. 40,
167–173.
Carlini, D.B., Reece, K.S., Graves, J.E., 2000. Actin gene family
evolution and the phylogeny of coleoid cephalopods (Mollusca:
Cephalopoda). Mol. Biol. Evol. 17, 1353–1370.
Clarke, M.R., Maddock, L., 1988. Statoliths of fossil coleoid cephal-
opods. In: Clarke, M.R., Trueman, E.R. (Eds.), The Mollusca.
Paleontology and Neontology of Cephalopods, Vol. 12. Academic
Press, San Diego, CA.
Doguzhaeva, L.A., Mapes, R.H., Mutvei, H., 1999. A Late
Carboniferous spirulid coleoid from the Southern Mid-continent
(USA). In: Oloriz, F., Rodriguez-Tovar, F.J. (Eds.), Advancing
Research on Living and Fossil Cephalopods. Kluwer Aca-
demic ⁄ Plenum, New York/Boston/Dordrecht/London/Moscow,
pp. 47–57.
Doguzhaeva, L.A., Mapes, R.H., Mutvei, H., 1996. Ultrastructural
comparison of the shell in Carboniferous Bactrites sp. (Russia)
and Bactrites postremus (USA). Paper presented at: Abstracts of
the Fourth International Symposium on Cephalopods – Present
and Past. Grenada, Spain, 14–18 July 1996. Kluwer Academic/
Plenum.
Donovan, D.T., 1977. Evolution of the Dibranchiate Cephalopoda. In:
Nixon, M., Messenger, J.B. (Eds.), The Biology of Cephalopods.
Academic Press, London, UK, pp. 15–46.
Donovan, D.T., Toll, R.B., 1988. The gladius in coleoid (cephalopoda)
evolution. In: Clarke, M.R., Trumena, E.R. (Eds.), The Mollusca,
Paleontology and Neotology of Cephalopods. Academic Press, San
Diego, CA.
Doyle, P., Donovan, D.T., Nixon, M., 1994. Phylogeny and system-
atics of the Coleoidea. Paleontol. Contrib. Univ. Kansas, 5, 398–
420.
96 J. Strugnell et al. / Cladistics 22 (2006) 89–96

Engeser, T., 1997. The fossil Coleoidea page. http://userpagefu-
berlinde/palaeont/fosscolhtml.
Engeser, T., Bandel, K., 1988. Phylogenetic classification of coleoid
cephalopods. In: Wiedman, J., Kullman, J. (Eds.), Cephalopods –
Past and Present. Schweizerbart’sche, Stuttgart, pp. 105–116.
Fischer, J.C., Riou, B., 2002. Vampyronassa rhodanica nov. gen. nov
sp., vampyromorphe (Cephalopoda, Coleoidea) du Callovien
inférieur de la Voulte-sur-Rhône (Ardéche, France). Annales
Paléontologie (Paris), 88, 1–17.
Fortey, R.A., Jackson, J., Strugnell, J., 2003. Phylogenetic fuses and
evolutionary ÔexplosionsÕ: conflicting evidence and critical tests. In:
Donoghue, P.C.J., Smith, M.P. (Eds.), Telling the Evolutionary
Time. Molecular Clocks and the Fossil Record. Taylor & Francis,
London, UK.
Hewitt, R.A., Westermann, G.E.G., 2003. Recurrences of hypotheses
about ammonites and Argonauta. J. Paleontol. 77, 792–795.
Huelsenbeck, J.P., Larget, B., Swofford, D.L., 2000. A compound
Poisson process for relaxing the molecular clock. Genetics, 154,
1879–1892.
Khromov, D.N., 1998. Distribution patterns of Sepiidae. In: Voss,
N.A., Vecchione, M., Toll, R.B., Sweeny, M.J. (Eds.), Systematics
and biogeography of cephalopods. Smithsonian Contributions of
Zoology, USA, pp. 191–206.
Kimura, M., 1968. Evolutionary rate at the molecular level. Nature,
217, 624–626.
Kishino, H., Hasegawa, M., 1990. Converting distance to time:
application to human evolution. Meth Enzymol. 183, 550–570.
Kishino, H., Thorne, J.L., Bruno, W.J., 2001. Performance of a
divergence time estimation method under a probabilistic model of
rate evolution. Mol. Biol. Evol. 18, 352–361.
Kluessendorf, J., Doyle, P., 2000. Pohlsepia mazonensis, an early
ÔoctopusÕ from the Carboniferous of Illinois, USA. Palaeontology,
43, 919–926.
Kobayashi, T., 1954. A new Palaeogene paracenoceratoid from
southern Kyushu in Japan. Jap J. Geol Geogr. 24, 181–184.
Naef, A., 1921–1923. Cephalopoda. Fauna e flora del Golfo di Napoli.
Monograph 35, 917pp. [Translated from German by the Israel
Program for Scientific Translations, Jerusalem, 1972.]
Naef, A., 1922. Die Fossilen Tintenfische. Gustav Fischer, Jena.
Rambaut, A., Bromham, L., 1998. Estimating divergence dates from
molecular sequences. Mol. Biol. Evol. 15, 442–448.
Sanderson, M.J., 1997. A nonparametric approach to estimating
divergence times in the absence of rate constancy. Mol. Biol. Evol.
14, 1218–1231.
Strugnell, J., Norman, M., Jackson, J., Drummond, A.J., Cooper, A.,
2005. Molecular phylogeny of coleoid cephalopods (Mollusca:
Cephalopoda) using a multigene approach; the effect of data
partitioning on resolving phylogenies in a Bayesian framework.
Mol. Phylogenet. Evol. 37, 426–441.
Takezaki, N., Rzhetsky, A., Nei, M., 1995. Phylogenetic test of the
molecular clock and linearized trees. Mol. Biol. Evol. 12, 823–833.
Thorne, J.L., Kishino, H., 2002. Divergence time and evolutionary rate
estimation with multilocus data. Syst. Biol. 51, 689–702.
Thorne, J.L., Kishino, H., Painter, I.S., 1998. Estimating the rate of
evolution of the rate of molecular evolution. Mol. Biol. Evol. 15,
1647–1657.
Vecchione, M., Young, R.E., Donovan, D.T., Rodhouse, P.G., 1999.
Reevaluation of coleoid cephalopod relationships based on modi-
fied arms in the Jurassic coleoid Mastigophora. Lethaia, 32, 113–
118.
Woodward, H., 1896. Calais newboldi from the Lebanon. Q. J. Geol
Soc. London, 52, 229–234.
Yang, Z., 1997. PAML: a program package for phylogenetic analysis
by maximum likelihood. Comput. Appl. Biosci. 13, 555–556
(http://abacus.gene.ucl.ac.uk/software/paml.html ).
Yang, Y.-W., Yoder, A.D., 2003. Comparison of likelihood and
Bayesian methods for estimating divergence times using multiple
loci and calibration points, with application to a radiation of cute-
looking mouse lemur species. Syst. Biol. 52, 705–716.
Yoder, A.D., Yang, Z., 2000. Estimation of primate speciation dates
using local molecular clocks. Mol. Biol. Evol. 17, 1081–1090.
Young, R.E., Vecchione, M., 1996. Analysis of morphology to
determine primary sister taxon relationships within coleoid cephal-
opods. Bull. Am. Malacol. Union, 12, 91–112.
Young, R.E., Vecchione, M., Donovan, D.T., 1998. The evolution of
coleoid cephalopods and their present biodiversity and ecology. S.
Afr. J. Mar. Sci. 20, 393–420.

Appendix 1

Prior values used within the multidivtime analyses

rttm rttmsd rtrate rtratesd brown mean brownsd common brown

Decapodiformes 400 100 0.0002 0.0002 0.004 0.004 0
0
Nuclear genes by codon 600 100 0.0003 0.0003 0.003 0.003 0
(all 3 codon positions)
Decapodiformes 400 100 0.0002 0.0002 0.004 0.004 0
Nuclear genes (1 + 2 codon) 600 100 0.0001 0.0001 0.003 0.003 0
Octopodiformes 400 100 0.0008 0.0008 0.004 0.004 0
All genes by gene and codon 600 100 0.0005 0.0005 0.003 0.003 0
Octopodiformes 400 100 0.0005 0.0005 0.004 0.004 0
Nuclear genes by gene and codon 600 100 0.0003 0.0003 0.003 0.003 0