Integrative and Comparative Biology
Integrative and Comparative Biology, volume 53, number 3, pp. 503–511
doi:10.1093/icb/ict008
Society for Integrative and Comparative Biology
SYMPOSIUM
Novel Scenarios of Early Animal Evolution—Is It Time to Rewrite
Textbooks?
Martin Dohrmann* and Gert Wörheide1,†,‡,§
*Meiborssen 12, 37647 Vahlbruch, Germany; †Department of Earth and Environmental Sciences, Palaeontology &
Geobiology, Ludwig-Maximilians-Universität München, 80333 München, Germany; ‡GeoBio-Center, LudwigMaximilians-Universität München, 80333 München, Germany; §Bayerische Staatssammlung für Paläontologie und
Geologie, 80333 München, Germany
From the symposium ‘‘Assembling the Poriferan Tree of Life’’ presented at the annual meeting of the Society for
Integrative and Comparative Biology, January 3–7, 2013 at San Francisco, California.
1
E-mail: [email protected]
Synopsis Understanding how important phenotypic, developmental, and genomic features of animals originated and
evolved is essential for many fields of biological research, but such understanding depends on robust hypotheses about
the phylogenetic interrelationships of the higher taxa to which the studied species belong. Molecular approaches to
phylogenetics have proven able to revolutionize our knowledge of organismal evolution. However, with respect to the
deepest splits in the metazoan Tree of Life—the relationships between Bilateria and the four non-bilaterian phyla
(Porifera, Placozoa, Ctenophora, and Cnidaria)—no consensus has been reached yet, since a number of different,
often contradictory, hypotheses with sometimes spectacular implications have been proposed in recent years. Here, we
review the recent literature on the topic and contrast it with more classical perceptions based on analyses of morphological characters. We conclude that the time is not yet ripe to rewrite zoological textbooks and advocate a conservative
approach when it comes to developing scenarios of the early evolution of animals.
Introduction
Molecular phylogenetics and, more recently, its largescale version, phylogenomics (Delsuc et al. 2005;
Philippe et al. 2005), have led to numerous novel
hypotheses about the evolutionary relationships
among major groups of animals (Metazoa). In some
cases, this has revolutionized our understanding of the
evolution of these lineages, leading to reconsiderations
of how certain morphological, developmental, and genomic traits originated and were modified in deep
time. For example, in the higher-level phylogeny of
bilateral, triploblastic animals (Bilateria), the long-held
view that segmented worms (Annelida) are the closest
living relatives of arthropods (the Articulata hypothesis, based on the shared presence of segmentation in
these two groups), was shattered by molecular phylogenetic studies initiated in the 1990s (e.g., Adoutte
et al. 2000). These studies surprisingly found annelids
to be nested within a large clade of animals that
includes
molluscs
and
other
taxa
(the
Lophotrochozoa), whereas Arthropoda formed a
clade (the Ecdysozoa) with roundworms (Nematoda)
and other mostly unsegmented animals. While first
met with skepticism, the division of protostomial bilaterians into Lophotrochozoa and Ecdysozoa, with its
profound implications for understanding the evolution of segmentation and other characters, has subsequently gained so much corroboration that it is now
generally-accepted, basic textbook
knowledge.
Through the enormous efforts put into deciphering
the deep phylogeny of Bilateria by using molecular
approaches, a rather stable backbone has now been
achieved (Edgecombe et al. 2011) and is providing
an invaluable scaffold on which the evolution of important traits can be reconstructed.
In order to understand, however, the early evolution of animals, from their origin until the emergence of the Bilateria, we must investigate the
Advanced Access publication March 28, 2013
ß The Author 2013. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved.
For permissions please email: [email protected].
504
phylogenetic relationships of the non-bilaterian
(‘‘basal,’’ or better ‘‘early-branching’’) metazoans.
These comprise the Porifera (sponges), Cnidaria
(corals, jellyfish, and their kin), Ctenophora (comb
jellies), and the enigmatic, monospecific (but see
Voigt et al. 2004; Guidi et al. 2011) Placozoa
(Trichoplax adhaerens). A robust hypothesis of the
interrelationships of these groups to each other and
to the Bilateria is a prerequisite for understanding
the evolution of important metazoan traits such as
nervous systems, muscles, epithelia, developmental
mechanisms, reproductive and feeding ecology, as
well as the interpretation of genomic structure and
content. Recently, several, often contradictory, phylogenies based mostly on molecular data have been
published, and quickly led some authors to propose
novel, sometimes revolutionary, scenarios about early
metazoan evolution. Here, we review the current
state of affairs in early-branching metazoan phylogenetics and ask the question: is there enough solid
evidence to rewrite textbooks dealing with animal
evolution?
Deep metazoan phylogeny: the current
state of affairs
Based on ‘‘manual’’ cladistic analyses (Hennig 1966)
of morphological and cytological characters, Ax
(1996) proposed a systematization of the five major
animal lineages (Porifera, Placozoa, Cnidaria,
Ctenophora, and Bilateria), which we first outline
here to contrast it with more recent results from
molecular phylogenetic studies. According to this
system (Fig. 1), Porifera is monophyletic and forms
the sister-group to the remaining Metazoa, which are
grouped together as Epitheliozoa.
Features interpreted as derived characters (apomorphies) in support of the monophyly of sponges
include a biphasic life cycle with planktonic larvae
and sessile adults, and the unique body plan and
Fig. 1 Phylogenetic relationships of the major groups of animals
(Metazoa) based on analysis of morphological and cytological
characters. After Ax (1996).
M. Dohrmann and G. Wörheide
mode of filter feeding of the adult, with a system
of water-conducting canals (aquiferous system) and
a mesohyl sandwiched between an outer layer of
pinacocytes and an inner layer of choanocytes
(the flagellated feeding cells that generate the water
current). Note that Ax (1996) neither regarded the
choanocytes as homologous to the flagellated cells of
Choanoflagellata, a unicellular or colonial group of
eukaryotes now hypothesized to be the sister-group
of Metazoa (e.g., Carr et al. 2008; King et al. 2008),
nor did he regard the outer and inner layers of
sponges (pinacoderm and choanoderm) as homologous to true epithelia (but see Leys and Riesgo 2012
for a more liberal view).
True epithelia were defined as cell layers held
together by belt desmosomes (zonulae adhaerentes)
that constitute the main and defining apomorphy of
Epitheliozoa. Another character listed by Ax (1996) in
support of Epitheliozoa are gland cells producing enzymes used in extracellular digestion. Epitheliozoa is
divided into Placozoa and Eumetazoa. Since placozoans apparently lack extracellular matrix (ECM), which
is present both in Porifera and Eumetazoa and was
interpreted as an autapomorphy of Metazoa,
Ax (1996) regarded this lack as a secondary loss.
Eumetazoa is supported as a monophyletic group
by the shared presence in Cnidaria, Ctenophora, and
Bilateria of gap junctions between neighboring cells,
ectoderm and entoderm (interpreted as homologous
to the dorsal and ventral epithelia of Placozoa), sensory cells, nerve cells, and muscle cells. Note, however, that recently the possibility of independent
evolution of muscle cells in the three eumetazoan
lineages has been suggested by Dayraud et al.
(2012) and Steinmetz et al. (2012).
Contrary to the classical view that Cnidaria
and Ctenophora are closely allied (forming the
Coelenterata), Ax (1996) placed Ctenophora as the
sister-group of Bilateria, interpreting the presence of
an acrosome and perforatorium in the sperm cells of
these two groups as a synapomorphy and uniting
them under the name Acrosomata. A second character he listed in support of Acrosomata is the presence
of true muscle cells, as opposed to the epithelial
muscle cells found in Cnidaria. However, acrosomes
have since also been found in sponge spermatocytes
(Riesgo and Maldonado 2009), and true muscle cells
might have evolved independently in ctenophores
and bilaterians (Dayraud et al. 2012), which casts
doubt on the usefulness of these characters in determining the sister-group of Ctenophora.
Whereas the monophyly of Placozoa, Cnidaria,
Ctenophora, and Bilateria has never seriously been
questioned by molecular phylogenetic studies, this
Scenarios of early animal evolution
is not the case for Porifera. Furthermore, a number
of different hypotheses for the relative phylogenetic
positions of the non-bilaterian lineages have been
proposed, based on the analysis of molecular data.
Following we summarize these results, one taxon at a
time, and discuss some of the implications of the
proposed hypotheses for the early evolution of
animals.
Porifera
Given the strong morphological evidence for sponge
monophyly, it came as a surprise that the first
molecular phylogenetic studies sampling multiple
lineages of sponges could not corroborate this hypothesis. Virtually all these studies (but see
Dohrmann et al. 2008) from the early 1990s to the
late 2000s reconstructed sponges as paraphyletic
(reviewed by Erpenbeck and Wörheide 2007;
Wörheide et al. 2012), with calcareous sponges
(Calcarea) and/or Homoscleromorpha—a small
taxon now considered as a fourth extant class of
Porifera (Gazave et al. 2012)—being more closely
related to eumetazoans (or epitheliozoans in studies
including Trichoplax) than to the two remaining
major lineages of sponges, the demosponges
(Demospongiae) and glass sponges (Hexactinellida),
which usually were grouped together at the very base
of the metazoan tree. However, these studies, which
were based on a single or a few markers—most commonly ribosomal RNA genes (rDNA)—never demonstrated sponge paraphyly with significant statistical
support and/or did not sample representatives of all
relevant taxa (reviewed by Wörheide et al. 2012).
Despite this, sponge paraphyly rapidly became the
accepted working hypothesis in large parts of the
scientific community (e.g., Pennisi 2003; Halanych
2004; Minelli 2009) and is even shown in the metazoan Tree of Life at public display in the American
Museum of Natural History in New York. This is
probably because it is a very tempting hypothesis
with far-reaching implications for the early evolution
of animals: if sponges were indeed a paraphyletic
‘‘grade’’ at the base of the metazoan tree, then the
unique body plan previously interpreted as apomorphic for Porifera must have already characterized
the last common ancestor of Metazoa, meaning that
the first animal was a bona-fide sponge and all
higher animals (i.e., Epitheliozoa, including humans)
are nothing but derived sponges.
Following the earlier studies, mostly based on
rDNA, another line of evidence stemmed from a
set of seven nuclear housekeeping proteins (NHP7
hereafter) originally established by Peterson et al.
505
(2004). The first NHP7 analysis including multiple
sponge lineages and using character-based, probabilistic reconstruction methods showed strong support
for sponge paraphyly, with Homoscleromorpha (represented by a single species) being the sister-group of
Eumetazoa (Cnidaria þ Bilateria; Placozoa and Ctenophora were not sampled), and Calcarea being
sister to that clade (Sperling et al. 2007). The inferred
position of Homoscleromorpha led the authors to
include them in Epitheliozoa because sponges of
this group possess tissue layers resembling true epithelia. Note, however, that genuine belt desmosomes—the defining feature of true epithelia sensu
Ax (1996)—seem to be absent from any group of
sponges (Leys and Riesgo 2012). The study by
Sperling et al. (2007) attracted quite some attention,
and inspired some authors to develop elaborate
novel scenarios of the early evolution of animals;
for example, Nielsen (2008) hypothesized that the
ancestor of Eumetazoa evolved from a progenetic
homoscleromorph larva (see also Nielsen 2011).
However, in a follow-up study (Sperling et al.
2009) with increased taxonomic sampling (including
more demosponges and calcareans, another homoscleromorph, and also Hexactinellida and Placozoa),
statistical support for this topology became insignificant under the evolutionary models identified as
best-fitting for NHP7, although ‘‘phylogenetic
signal-dissection’’ analyses showed a general tendency of this dataset toward favoring paraphyly of
sponges (Sperling et al. 2009). Finally, sponge paraphyly was also recovered from a dataset consisting of
NHP7 supplemented with rDNA sequences (Erwin
et al. 2011), although in this study a clade of Homoscleromorpha þ Calcarea formed the sister-group to
Epitheliozoa. Curiously, Hexactinellida was excluded
from that analysis for undisclosed reasons.
Large-scale phylogenomic datasets drawn from expressed sequence tag and whole-genome sequencing
projects now appear most promising for reconstructing the deepest splits in the animal Tree of Life, because they have the potential for considerably
reducing stochastic errors associated with the analysis
of single or few genes or proteins (Delsuc et al.
2005). The first phylogenomic study—based on 128
nuclear-encoded proteins—that explicitly tried to resolve the relationships among the five major metazoan groups (Philippe et al. 2009) strongly recovered
Porifera as monophyletic and sister to Placozoa þ
Eumetazoa, consistent with the system of Ax
(1996). Subsequently, monophyletic Porifera as
sister-group to Epitheliozoa was also recovered—
albeit with somewhat weaker statistical support—
by Pick et al. (2010), who included additional
506
non-bilaterian species in an independent phylogenomic dataset (150 proteins) originally established
by Dunn et al. (2008). Most recently, Nosenko
et al. (2013) assembled a novel phylogenomic data
matrix of 122 nuclear-encoded proteins and investigated the phylogenetic signal present in different partitions of this dataset. These authors found that
different partitions supported strongly conflicting
phylogenetic hypotheses about deep metazoan phylogeny. Their study showed that monophyly of
Porifera was mostly supported by slowly evolving
proteins involved in translation, whereas the phylogenetic signal in support of the paraphyly scenario
mainly came from non-translational proteins that
showed a comparatively higher level of substitutional
saturation. Thus, the authors concluded that sponge
paraphyly might be a reconstruction artifact caused
by oversaturated sequences.
Curiously, Sperling et al. (2009) came to the opposite conclusion, claiming that the signal for sponge
monophyly in their much smaller NHP7 dataset was
caused by oversaturated positions and thus likely to
be artifactual. However—although more data alone
are not enough to increase the accuracy of phylogenetic inference (Jeffroy et al. 2006; Philippe et al.
2011)—the final answer about the phylogenetic
status of Porifera is unlikely to come from datasets
containing only a few genes or proteins, and for the
time being, it seems most reasonable to assume that
sponges are monophyletic when trying to reconstruct
early metazoan evolution (see also discussion by
Wörheide et al. 2012 and Nosenko et al. 2013).
Placozoa
With only four different cell types, Trichoplax adhaerens can rightfully be regarded as the simplest of all
free-living extant animals (e.g., Schierwater 2005). It
is thus tempting to speculate that it represents the
earliest offshoot of the metazoan Tree of Life, i.e., the
sister-group to all remaining animals. In particular,
its lack of ECM, which is present in all other metazoans, could be interpreted as a primary absence—
ECM would then be a synapomorphy of Porifera and
Eumetazoa. Under this scenario, epithelia with belt
desmosomes and extracellular digestion by ventrally
located gland cells would have been secondarily lost
in sponges, which could be explained by the evolution of their derived sessile, filter-feeding mode of
life. Comparison of mitochondrial (mt) genomes
provides another line of evidence consistent with
an earliest-branching position of placozoans—their
mt genomes are much larger and more complex
than those of other metazoans (including sponges),
M. Dohrmann and G. Wörheide
appearing intermediate between those of unicellular
eukaryotes and non-placozoan animals (Dellaporta
et al. 2006; Signorovitch et al. 2007). However, phylogenetic analyses of molecular sequences tell a different story.
A number of early molecular phylogenetic studies
based on rDNA (reviewed by Ender and Schierwater
2003) suggested a position of Placozoa within
Cnidaria, a hypothesis that is hard to support by
morphological characters and has subsequently been
dismissed (Ender and Schierwater 2003). da Silva
et al. (2007) analyzed the complete large and small
subunit rDNA of a number of early-branching metazoans and bilaterians and found ambiguous support
for Placozoa as the sister-group of Cnidaria and/or
Bilateria (also see Collins 1998). These authors
concluded that rDNA is not informative enough to
resolve early-branching animal relationships and suggested that genomic approaches might be required to
address this issue. Subsequently, a number of multigene and phylogenomic studies, including sequences
from Trichoplax, were published and strongly suggested a sister-group relationship of Placozoa to
Eumetazoa (Srivastava et al. 2008, 2010; Philippe
et al. 2009; Sperling et al. 2009; Erwin et al. 2011),
consistent with the Epitheliozoa hypothesis (Ax
1996). However, Ctenophora was not included in
most of these studies (except Philippe et al. 2009),
thereby preventing a true test of the phylogenetic
placement of Placozoa. Philippe et al. (2009) could
confirm the monophyly of Eumetazoa (Cnidaria þ
Ctenophora þ Bilateria) and Epitheliozoa (Placozoa
þ Eumetazoa), but Pick et al. (2010), while also recovering Epitheliozoa, found Trichoplax as sister to
Bilateria to the exclusion of Cnidaria and Ctenophora, thus rejecting the monophyly of Eumetazoa
sensu Ax (1996). Non-monophyletic Eumetazoa was
also proposed by Ryan et al. (2010), who found that
ParaHox genes are absent from the genomes of Porifera and Ctenophora, and might thus be a synapomorphy of Placozoa, Cnidaria, and Bilateria.
Nosenko et al. (2013) confirmed the result of
Philippe et al. (2009) from the analysis of their combined data matrix, but recovered a Placozoa þ Porifera clade as sister to Eumetazoa from the more
slowly evolving translational protein partition; however, this relationship was not statistically wellsupported.
Recently, Osigus et al. (2013) raised doubts about
the ability of molecular sequence data (‘‘quantity
data’’ in their parlance) to ever resolve the phylogenetic position of Placozoa, instead opting for analysis
of ‘‘quality data,’’ i.e., organismal and molecular
morphology, patterns of gene order, and the like.
Scenarios of early animal evolution
However, it remains to be demonstrated whether
studies not recovering Placozoa as the earliest-branching animal lineage were seriously flawed by methodological artifacts. Thus, for the time being, and
although no unequivocal support has been achieved
for either hypothesis, it seems likely that placozoans
are closely related to Eumetazoa, or at least to
Cnidaria þ Bilateria, depending on the phylogenetic
position of Ctenophora. If true, this would suggest
secondary loss of ECM in Placozoa (as proposed by
Ax 1996) and, more interestingly, a secondary
increase in size and complexity of mt genomes in
this phylum (see Burger et al. 2009) or, alternatively,
convergent reduction of the mt genome in Porifera
and Eumetazoa.
Cnidaria
A number of multi-gene and phylogenomic analyses
that did not include Ctenophora found a sistergroup relationship of Cnidaria to Bilateria
(Srivastava et al. 2008, 2010; Sperling et al. 2009;
Erwin et al. 2011). Among those studies that included data from ctenophores, Dunn et al. (2008)
found a statistically unsupported Cnidaria þ
Porifera clade, which vanished in follow-up studies
of this dataset by Hejnol et al. (2009) and Pick et al.
(2010), who recovered Cnidaria as sister to Bilateria
and sister to Placozoa þ Bilateria, respectively. In
contrast, Philippe et al. (2009) found strong support
for a Cnidaria þ Ctenophora clade as the sister-group
to Bilateria, thus reviving the classical Coelenterata
concept (Hyman 1940). This hypothesis was subsequently corroborated by Nosenko et al. (2013) from
analyses of their combined dataset and the translational protein partition, although these authors recovered
the
alternative
Cnidaria þ Bilateria
relationship from analysis of their more saturated
non-translational protein partition.
In summary, a bilaterian ‘‘affinity’’ of Cnidaria
finds strong support from molecular evidence, i.e.,
if Ctenophora and Placozoa are ignored (e.g. Boero
et al. 2007) a Cnidaria þ Bilateria clade (¼ Planulozoa) is consistently recovered (but see section
‘‘Diploblasta?’’). Of course the picture is more complicated, and reconstructing the evolution of
‘‘planulozoan’’ characters (see Wallberg et al. 2004;
Boero et al. 2007) will crucially depend on determining the exact phylogenetic positions of Ctenophora
and Placozoa.
Ctenophora
Although some early rDNA studies had found an
affinity of comb jellies with sponges, these results
507
were quickly dismissed (reviewed by Wallberg et al.
2004), and the inclusion of ctenophores within
Epitheliozoa has—until recently—never seriously
been doubted. Then, in a landmark phylogenomic
study aimed at resolving deep bilaterian relationships, Dunn et al. (2008; see also Hejnol et al.
2009) surprisingly recovered Ctenophora as the
sister-group to all remaining Metazoa. Although the
authors explicitly stated that this result should be
taken with caution until it could be corroborated
by more evidence—especially an increased taxon
sampling at the base of the metazoan tree (see also
DeSalle and Schierwater 2008)—the ‘‘Ctenophorafirst’’ hypothesis has attracted enormous attention
in the scientific community. As with the paraphyly
of sponges (see above), this can be explained by the
far-reaching implications it would have for our understanding of the early evolution of animals: if true,
all the complex characters previously thought to be
apomorphic for Eumetazoa (such as nervous systems) and Epitheliozoa (true epithelia and digestional gland cells) would have evolved convergently
in Ctenophora and the other non-poriferan animal
groups, or alternatively, they would be ancestral
metazoan characters that have been secondarily lost
in sponges and (for the eumetazoan characters)
placozoans.
However, it was demonstrated shortly after its original publication (Dunn et al. 2008) that the
‘‘Ctenophora-first’’ topology resulted from methodological artifacts caused by insufficient sampling of
non-bilaterian taxa and inadequate outgroup choice
(Pick et al. 2010; see also Philippe et al. 2011). Pick
et al. (2010) instead found Ctenophora as the sistergroup to a Cnidaria þ Placozoa þ Bilateria clade,
which, although contradicting the Eumetazoa hypothesis, is consistent with Epitheliozoa sensu Ax (1996).
Furthermore, in a phylogenomic study specifically designed to resolve deep metazoan phylogeny, Philippe
et al. (2009; see also Nosenko et al. 2013) found
strong support for Coelenterata, i.e., Ctenophora
being the sister-group of Cnidaria. Despite this, the
‘‘Ctenophora-first’’ hypothesis continues to be seriously considered by many authors and has even
found its way into a recent updated ‘‘evo-Linnaean
classification’’ of animal phyla (Zhang 2011).
We here argue that no convincing evidence to
exclude Ctenophora from Epitheliozoa has been presented thus far, because topologies in which ctenophores branch off first from the metazoan tree are
very likely to be artifactual (Pick et al. 2010; Philippe
et al. 2011; Nosenko et al. 2013). Certainly, the
highly anticipated publication of comprehensive
analyses of ctenophoran nuclear genomes will shed
508
more light on this issue (see e.g., Byrum 2012;
Maxmen 2013; Pennisi 2013), but it can be expected
that these genomes are highly unusual, as has already
been shown for ctenophoran mt genomes (Pett et al.
2011; Kohn et al. 2012). Thus, one should be careful
to avoid circular reasoning by interpreting genomic
features such as lack of certain genes (e.g., those
coding for the microRNA processing machinery)
(Maxwell et al. 2012) as ancestral characters in support of the pre-conceived ‘‘Ctenophora-first’’ hypothesis—comb jellies appear anatomically highly
derived, so this is likely to be true for their genomes
as well.
For the time being, two main hypotheses about
the phylogenetic placement of Ctenophora can be
considered: (1) as the sister-group to the remaining
Epitheliozoa (Pick et al. 2010), consistent with the
‘‘ParaHoxozoa’’ hypothesis (Ryan et al. 2010) and
(2) as sister-group to Cnidaria (Philippe et al.
2009), consistent with the Eumetazoa and
Coelenterata hypotheses. From a comparative morphological perspective, the first hypothesis appears
highly unparsimonious because it implies that all
the characters interpreted as apomorphies of
Eumetazoa (e.g., gap junctions and nerve cells)
were secondarily lost in Placozoa; in contrast, the
second hypothesis would only require loss of
ParaHox genes in Ctenophora. On the other hand,
a sister-group relationship of Ctenophora and
Cnidaria, although consistent with more classical
views, is also hard to explain on morphological
grounds; a medusa stage in the life cycle and an
overall ‘‘jellyness’’ (i.e., mesogloea) are hardly interpretable as synapomorphies of these two phyla, given
that phylogenetic analyses suggest them to be rather
derived characters within Cnidaria (Ax 1996; Collins
et al. 2006; Park et al. 2012; Kayal et al. 2013), i.e.,
convergent evolution of these similarities seems more
likely. Since ctenophores (along with placozoans)
appear to be the most problematic group in recent
phylogenomic analyses (probably due to elevated
substitution rates), more in-depth comparative analyses of morphology, cytology, development, and genomes of the four epitheliozoan lineages are required
to robustly resolve their relationships.
Diploblasta?
In the previous sections, we have only discussed hypotheses of deep metazoan phylogeny in which
Bilateria is nested within a paraphyletic grade of diploblastic animals, i.e., in which some diploblastic lineages are more closely related to Bilateria than to
other diploblastic lineages. However, an alternative
M. Dohrmann and G. Wörheide
scenario has also been proposed—the Diploblasta hypothesis, according to which the non-bilaterian phyla
form a monophyletic group that is the sister-group
of Bilateria (Triploblasta). Such a topology was first
recovered from phylogenetic analyses of whole mitochondrial protein complements (Dellaporta et al.
2006; see also Wang and Lavrov 2007), and showed
Trichoplax as the sister-group to the remaining sampled diploblasts (Porifera þ Cnidaria). However,
Burger et al. (2009) demonstrated, by massively increasing the taxonomic sampling of mt genomes,
that these data do not provide enough phylogenetic
signal to resolve the relationships among the major
animal lineages. Nonetheless, the ‘‘Diploblasta-withPlacozoa-first’’ topology (this time also including
Ctenophora as the sister-group of Cnidaria) was
also recovered in a much-discussed study based
on a combined dataset of nuclear and mitochondrial genes and a few morphological characters
(Schierwater et al. 2009a). Schierwater et al. (2009a)
claimed to have deciphered the true phylogenetic
relationships among the five major metazoan
groups and promoted their result as a revolution
leading to a reconsideration of current textbook
knowledge about the early evolution of animals
(see also Blackstone 2009; Schierwater et al. 2009b;
Schierwater and Kamm 2010).
Of course, the implications of the Diploblasta hypothesis are enormous: if true, all the complex characters shared by Coelenterata and Bilateria (i.e.,
characters previously interpreted as apomorphies of
Eumetazoa) must have evolved convergently in these
two groups, or alternatively they were present in the
last common ancestor of Metazoa and have subsequently been lost twice, in Placozoa and Porifera.
Viewed from a different angle, however, the Diploblasta hypothesis is extremely unparsimonious, for
exactly the same reasons. Plus, we can think of no
character that would convincingly be interpretable as
a synapomorphy of Placozoa, Porifera, and Coelenterata. Finally, it has been shown that the analysis of
Schierwater et al. (2009a) was flawed by methodological shortcomings and contaminations, and that
their favored topology is actually not supported by
the underlying data (Philippe et al. 2011). We conclude that the Diploblasta hypothesis currently lacks
sufficient evidence to be seriously considered in
attempts to derive scenarios of the early evolution
of animals.
Conclusions
Understanding the early evolution of animals crucially hinges on an accurate reconstruction of the
509
Scenarios of early animal evolution
Fig. 2 Consensus view of phylogenetic relationships of the major
metazoan lineages based on recent phylogenomic studies.
phylogenetic relationships between Porifera, Placozoa, Cnidaria, Ctenophora, and Bilateria. This is
because different hypotheses about their interrelationships imply different scenarios about how important phenotypic, developmental, and genotypic traits
seen in extant animal species, including humans and
major model organisms used in biomedical research
and other areas, have originated and evolved over
hundreds of million years of Earth’s history. In the
past 20 years or so, molecular approaches have revolutionized the field of phylogenetics, often leading
to surprising new insights into animal evolution that
had profound implications for other areas of biology.
So where are we now with respect to our knowledge
about the deepest splits in the metazoan Tree of Life?
Is it time to rewrite textbooks yet?
Our answer is: ‘‘no.’’ Although a number of novel
phylogenetic hypotheses have been proposed that,
taken at face value, suggest that more traditional
views about metazoan evolution were awfully
wrong, most of these results could not stand up to
scrutiny. In fact, many molecular phylogenetic studies corroborated previous hypotheses based on comparative analyses of morphological data, and where
they could not, more questions were raised than
were answered, leading to a less resolved picture of
deep metazoan phylogeny (Fig. 2) that calls for
additional research. Phylogenomics certainly has a
great potential, but increased taxon sampling and
better methods are needed in future studies
(Philippe et al. 2011; Telford and Copley 2011).
Furthermore, analysis of molecular sequence data
might not be enough to address these issues, so integrative approaches, including in-depth analyses of
morphology, cytology, development, and genome architecture, are particularly promising. Other lines of
research, such as comparison of microRNA (miRNA)
distributions (Sperling and Peterson 2009) and analyses of rare genomic changes (reviewed by Rokas and
Holland 2000), e.g., insertion–deletion events
(indels) or near-intron positions thus far were
unable to robustly resolve deep metazoan phylogeny
(Belinky et al. 2010; Lehmann et al. 2013; Robinson
et al. 2013). However, with the increasing availability
of fully-sequenced non-bilaterian nuclear genomes,
future developments in these fields could also provide valuable contributions.
We suggest that, until the positions of the four
non-bilaterian animal lineages in the metazoan tree,
especially Ctenophora and Placozoa, are robustly resolved by phylogenomics and other integrative
approaches, it would be wise to stick to solid evidence—however little that may be—instead of hastily
proposing novel (and often far-reaching) scenarios of
animal evolution with every tree that gets published.
Acknowledgments
We thank the two anonymous reviewers and editor
H. Heatwole for critical comments and suggestions
for improvement of this article. Support for this
issue was provided by the American Microscopical
Society and the Society for Integrative and
Comparative Biology, including the Division of
Phylogenetics and Comparative Biology and the
Division of Invertebrate Zoology.
Funding
M.D. received no particular funding for this work.
Research in the Wörheide laboratory was supported
from 2006 to 2012 by funding from the German
Research Foundation (DFG) through their Priority
Program SPP1174 ‘‘Deep Metazoan Phylogeny’’
(Project Wo896/6).
References
Adoutte A, Balavoine G, Lartillot N, Lespinet O,
Prud’homme B, de Rosa R. 2000. The new animal phylogeny: reliability and implications. Proc Natl Acad Sci USA
97:4453–6.
Ax P. 1996. Multicellular animals: a new approach to the
phylogenetic order in nature, Vol. 1. Berlin (Germany):
Springer.
510
Belinky F, Cohen O, Huchon D. 2010. Large-scale parsimony
analysis of metazoan indels in protein-coding genes. Mol
Biol Evol 27:441–51.
Blackstone NW. 2009. A new look at some old animals. PLoS
Biol 7:e1000007.
Boero F, Schierwater B, Piraino S. 2007. Cnidarian milestones
in metazoan evolution. Integr Comp Biol 47:693–700.
Burger G, Yan Y, Javadi P, Lang BF. 2009. Group I-intron
trans-splicing and mRNA editing in the mitochondria of
placozoan animals. Trends Genet 25:381–6.
Byrum CA. 2012. A gathering of minds: expanding understanding of the origins of biological diversity and the evolution of developmental mechanisms. EvoDevo 3:5.
Carr M, Leadbeater BSC, Hassan R, Nelson M, Baldauf SL.
2008. Molecular phylogeny of choanoflagellates, the sister
group to Metazoa. Proc Natl Acad Sci USA 105:16641–6.
Collins AG. 1998. Evaluating multiple alternative hypotheses
for the origin of Bilateria: an analysis of 18S rRNA molecular evidence. Proc Natl Acad Sci USA 95:15458–63.
Collins AG, Schuchert P, Marques AC, Jankowski T,
Medina M, Schierwater B. 2006. Medusozoan phylogeny
and character evolution clarified by new large and small
subunit rDNA data and an assessment of the utility of
phylogenetic mixture models. Syst Biol 55:97–115.
da Silva FB, Muschner VC, Bonatto L. 2007. Phylogenetic
position of Placozoa based on large subunit (LSU) and
small subunit (SSU) rRNA genes. Genet Mol Biol
30:127–32.
Dayraud C, Alié A, Jager M, Chang P, Le Guyader H,
Manuel M, Quéinnec E. 2012. Independent specialisation
of myosin II paralogues in muscle vs. non-muscle functions
during early animal evolution: a ctenophore perspective.
BMC Evol Biol 12:107.
Dellaporta SL, Xu A, Sagasser S, Jakob W, Moreno MA,
Buss LW, Schierwater B. 2006. Mitochondrial genome of
Trichoplax adhaerens supports Placozoa as the basal lower
metazoan phylum. Proc Natl Acad Sci USA 103:8751–6.
Delsuc F, Brinkmann H, Philippe H. 2005. Phylogenomics
and the reconstruction of the tree of life. Nat Rev Genet
6:361–75.
DeSalle R, Schierwater B. 2008. An even ‘‘newer’’ animal phylogeny. BioEssays 30:1043–7.
Dohrmann M, Janussen D, Reitner J, Collins AG,
Wörheide G. 2008. Phylogeny and evolution of glass
sponges (Porifera, Hexactinellida). Syst Biol 57:388–405.
Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE,
Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD,
et al. 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745–9.
Edgecombe GD, Giribet G, Dunn CW, Hejnol A,
Kristensen RM, Neves RC, Rouse GW, Worsaae K,
Sørensen MV. 2011. Higher-level metazoan relationships:
recent progress and remaining questions. Org Divers Evol
11:151–72.
Ender A, Schierwater B. 2003. Placozoa are not derived cnidarians: evidence from molecular morphology. Mol Biol
Evol 20:130–4.
Erpenbeck D, Wörheide G. 2007. On the molecular phylogeny
of sponges (Porifera). Zootaxa 1668:107–26.
Erwin DH, Laflamme M, Tweedt SM, Sperling EA, Pisani D,
Peterson KJ. 2011. The Cambrian conundrum: early
M. Dohrmann and G. Wörheide
divergence and later ecological success in the early history
of animals. Science 334:1091–7.
Gazave E, Lapébie P, Ereskovsky AV, Vacelet J, Renard E,
Cárdenas P, Borchiellini C. 2012. No longer Demospongiae:
Homoscleromorpha formal nomination as a fourth class of
Porifera. Hydrobiologia 687:3–10.
Guidi L, Eitel M, Cesarini E, Schierwater B, Balsamo M. 2011.
Ultrastructural analyses support different morphological
lineages in the phylum Placozoa Grell, 1971. J Morphol
272:371–8.
Halanych KM. 2004. The new view of animal phylogeny.
Annu Rev Ecol Evol Syst 35:229–56.
Hejnol A, Obst M, Stamatakis A, Ott M, Rouse GW,
Edgecombe GD, Martinez P, Bagunà J, Bailly X,
Jondelius U, et al. 2009. Assessing the root of bilaterian
animals with scalable phylogenomic methods. Proc R Soc
B 276:4261–70.
Hennig W. 1966. Phylogenetic systematics. Urbana (IL):
University of Illinois Press.
Hyman LH. 1940. The invertebrates. New York (NY):
McGraw-Hill.
Jeffroy O, Brinkmann H, Delsuc F, Philippe H. 2006. Phylogenomics: the beginning of incongruence? Trends Genet
22:225–31.
Kayal E, Roure B, Philippe H, Collins AG, Lavrov DV. 2013.
Cnidarian phylogenetic relationships as revealed by mitogenomics. BMC Evol Biol 13:5.
King N, Westbrook MJ, Young SL, Kuo A, Abedin M,
Chapman J, Fairclough S, Hellsten U, Isogai Y, Letunic I,
et al. 2008. The genome of the choanoflagellate Monosiga
brevicollis and the origin of metazoans. Nature 451:783–8.
Kohn AB, Citarella MR, Kocot KM, Bobkova YV,
Halanych KM, Moroz LL. 2012. Rapid evolution of the
compact and unusual mitochondrial genome in the ctenophore, Pleurobrachia bachei. Mol Phylogenet Evol 63:203–7.
Lehmann J, Stadler PF, Krauss V. 2013. Near intron pairs and
the metazoan tree. Mol Phylogenet Evol 66: 811–23.
Leys SP, Riesgo A. 2012. Epithelia, an evolutionary novelty of
metazoans. J Exp Zool (Mol Dev Evol) 318:438–47.
Maxmen A. 2013. Genome reveals comb jellies’ ancient origin.
Nature News 2013 Jan 8. (http://www.nature.com/news/genome–reveals-comb-jellies-ancient-origin-1.12176).
Maxwell EK, Ryan JF, Schnitzler CE, Browne WE,
Baxevanis AD. 2012. MicroRNAs and essential components
of the microRNA processing machinery are not encoded in
the genome of the ctenophore Mnemiopsis leidyi. BMC
Genomics 13:714.
Minelli A. 2009. Perspectives in animal phylogeny and evolution. New York (NY): Oxford University Press.
Nielsen C. 2008. Six major steps in animal evolution: are we
derived sponge larvae? Evol Dev 10:241–57.
Nielsen C. 2011. Animal evolution: interrelationships of the
living phyla. 3rd ed. Oxford: Oxford University Press.
Nosenko T, Schreiber F, Adamska M, Adamski M, Eitel M,
Hammel J, Maldonado M, Müller WEG, Nickel M,
Schierwater B, et al. 2013. Deep metazoan phylogeny:
when different genes tell different stories. Mol Phylogenet
Evol 67:223–33.
Osigus H-J, Eitel M, Schierwater B. 2013. Chasing the urmetazoon: striking a blow for quality data? Mol Phylogenet
Evol 66:551–7.
Scenarios of early animal evolution
Park E, Hwang D-S, Lee JS, Sog J-I, Seo T-K, Won Y-J. 2012.
Estimation of divergence times in cnidarian evolution based
on mitochondrial protein-coding genes and the fossil
record. Mol Phylogenet Evol 62:329–45.
Pennisi E. 2003. Drafting a tree. Science 300:1694–5.
Pennisi E. 2013. Nervous system may have evolved twice.
Science 339:391.
Peterson KJ, Lyons JB, Nowak KS, Takacs CM, Wargo MJ,
McPeek MA. 2004. Estimating metazoan divergence times
with a molecular clock. Proc Natl Acad Sci USA 101:6536–41.
Pett W, Ryan JF, Pang K, Mullikin JC, Martindale MQ,
Baxevanis AD, Lavrov DV. 2011. Extreme mitochondrial
evolution in the ctenophore Mnemiopsis leidyi: insight
from mtDNA and the nuclear genome. Mitochondrial
DNA 22:130–42.
Philippe H, Brinkmann H, Lavrov DV, Littlewood DTJ,
Manuel M, Wörheide G, Baurain D. 2011. Resolving difficult phylogenetic questions: why more sequences are not
enough. PLoS Biol 9:e1000602.
Philippe H, Delsuc F, Brinkmann H, Lartillot N. 2005.
Phylogenomics. Annu Rev Ecol Evol Syst 36:541–62.
Philippe H, Derelle R, Lopez P, Pick K, Borchiellini C, BouryEsnault N, Vacelet J, Renard E, Houliston E, Quéinnec E,
et al. 2009. Phylogenomics revives traditional views on deep
animal relationships. Curr Biol 19:706–12.
Pick KS, Philippe H, Schreiber F, Erpenbeck D, Jackson DJ,
Wrede P, Wiens M, Alié A, Morgenstern B, Manuel M, et al.
2010. Improved phylogenomic taxon sampling noticeably affects non-bilaterian relationships. Mol Biol Evol 27:1983–7.
Riesgo A, Maldonado M. 2009. An unexpectedly sophisticated,
V-shaped spermatozoon in Demospongiae (Porifera): reproductive and evolutionary implications. Biol J Linn Soc
97:413–26.
Robinson JM, Sperling EA, Bergum B, Adamski M,
Nichols SA, Adamska M, Peterson KJ. 2013. The identification of microRNAs in calcisponges: independent evolution of microRNAs in basal metazoans. J Exp Zool (Mol
Dev Evol) 320:84–93.
Rokas A, Holland PWH. 2000. Rare genomic changes as a
tool for phylogenetics. Trends Ecol Evol 15:454–9.
Ryan JF, Pang K, NISC Comparative Sequencing Program,
Mullikin JC, Martindale MQ, Baxevanis AD. 2010. The
homeodomain complement of the ctenophore Mnemiopsis
leidyi suggests that Ctenophora and Porifera diverged prior
to the ParaHoxozoa. EvoDevo 1:9.
Schierwater B. 2005. My favorite animal, Trichoplax adhaerens. BioEssays 27:1294–302.
Schierwater B, Eitel M, Jakob W, Osigus H-J, Hadrys H,
Dellaporta SL, Kolokotronis S-O, DeSalle R. 2009a.
Concatenated analysis sheds light on early metazoan evolution and fuels a modern ‘‘Urmetazoon’’ hypothesis. PLoS
Biol 7:e1000020.
Schierwater B, Kolokotronis S-O, Eitel M, DeSalle R. 2009b.
The diploblast-Bilateria sister hypothesis. Parallel evolution
511
of a nervous system may have been a simple step. Commun
Integr Biol 2:403–5.
Schierwater B, Kamm K. 2010. The early evolution of Hox
genes: a battle of belief? Adv Exp Med Biol 689:81–90.
Signorovitch AY, Buss LW, Dellaporta S. 2007. Comparative
genomics of large mitochondria in placozoans. PLoS Genet
3:e13.
Sperling EA, Peterson KJ. 2009. MicroRNAs and metazoan
phylogeny: big trees from little genes. In: Telford MJ,
Littlewood DTJ, editors. Animal evolution: genomes, fossils,
and trees. Oxford: Oxford University Press. p. 157–70.
Sperling EA, Peterson KJ, Pisani D. 2009. Phylogenetic-signal
dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa. Mol
Biol Evol 26:2261–74.
Sperling EA, Pisani D, Peterson KJ. 2007. Poriferan paraphyly
and its implications for Precambrian paleobiology. Geol
Soc Lond Spec Pub 286:355–68.
Srivastava M, Begovic E, Chapman J, Putnam NH,
Hellsten U, Kawashima T, Kuo A, Mitros T, Salamov A,
Carpenter ML, et al. 2008. The Trichoplax genome and the
nature of placozoans. Nature 454:955–60.
Srivastava M, Simakov O, Chapman J, Fahey B,
Gauthier MEA, Mitros T, Richards GS, Conaco C,
Dacre M, Hellsten U, et al. 2010. The Amphimedon queenslandica genome and the evolution of animal complexity.
Nature 466:720–6.
Steinmetz PRH, Kraus JEM, Larroux C, Hammel JU, AmonHassenzahl A, Houliston E, Wörheide G, Nickel M,
Degnan BM, Technau U. 2012. Independent evolution of
striated muscles in cnidarians and bilaterians. Nature
487:231–4.
Telford MJ, Copley RR. 2011. Improving animal phylogenies
with genomic data. Trends Genet 27:86–195.
Voigt O, Collins AG, Pearse VB, Pearse JS, Ender A,
Hadrys H, Schierwater B. 2004. Placozoa—no longer a
phylum of one. Curr Biol 14:R944–5.
Wallberg A, Thollesson M, Farris JS, Jondelius U. 2004. The
phylogenetic position of the comb jellies (Ctenophora) and
the importance of taxonomic sampling. Cladistics
20:558–78.
Wang X, Lavrov DV. 2007. Mitochondrial genome of the
homoscleromorph Oscarella carmela (Porifera, Demospongiae) reveals unexpected complexity in the common
ancestor of sponges and other animals. Mol Biol Evol
24:363–73.
Wörheide G, Dohrmann M, Erpenbeck D, Larroux C,
Maldonado M, Voigt O, Borchiellini C, Lavrov DV. 2012.
Deep phylogeny and evolution of sponges (Phylum
Porifera). Adv Mar Biol 61:1–78.
Zhang Z-Q. 2011. Animal biodiversity: an introduction to
higher-level classification and taxonomic richness. Zootaxa
3148:7–12.