Syst. Biol. 50(6):848–859, 2001
Molecular Data Indicate the Protostome AfŽnity of Brachiopods
R ENAUD DE R OSA
Centre de Génétique Moléculaire, UPR 9061 CNRS, Bâtiment 26, avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex,
France; E-mail: [email protected]
The phylogenetic afŽnities of brachiopods
have long been a subject of debate. In
this paper, they are treated as a monophyletic group, bearing in mind that, if the
brachiopods are paraphyletic and include
phoronids, the conclusions drawn apply to
phoronids also (Cohen et al., 1998; Cohen,
2000). Brachiopods have been classiŽed as
protostomes, deuterostomes, or an independent or intermediate third lineage of bilateral animals. Still, the classical view of animal phylogeny, based on embryological and
morphological features, places them as sister group to deuterostomes (Hyman, 1940).
More recent phylogenetic analyses have conŽrmed this placement (Eernisse et al., 1992;
Nielsen, 1995; Lüter and Bartholomaeus,
1997). In contrast, molecular phylogenies
have consistently placed brachiopods within
the protostomes (Field et al., 1988). That result has been heavily criticized, but more
careful analysis yielded the same conclusion
(Lake, 1990). More sophisticated ways of analyzing sequence data have helped molecular phylogeny gain more inuence, which
led to a deep rearrangement of the metazoan
tree shown in Figure 1 (Adoutte et al., 1999).
The so-called Lophotrochozoa/Ecdysozoa
hypothesis (Halanych et al., 1995; Aguinaldo
et al., 1997) conŽrms the protostome afŽnity
of brachiopods and places them more precisely in the lophotrochozoan assemblage, together with molluscs, annelids, atworms,
nemerteans, and a few other phyla, to the
exclusion of arthropods and their afŽliates. In the following, the term deuterostomes designates the monophyletic group
of echinoderms, hemichordates, and chordates. Depending on the context—classical
phylogeny or Lophotrochozoa/Ecdysozoa
hypothesis—protostomes exclude or include
brachiopods.
The placement of Brachiopods within
protostomes has been criticized, not only
on the basis of the morphological evidence,
but also by molecular biologists, because
all the trees were obtained from a single
molecule, the small subunit ribosomal RNA
or 18S rRNA, for which the largest sequence
database is available. Moreover, because
the deep branchings between metazoan
phyla are close to the limit of the resolving
power of this molecule (Philippe et al., 1994;
Abouheif et al., 1998), it is important to
test this result. Such a test is most likely to
come from an emerging set of molecular
characters, which originate during large
genome rearrangements. These differ from
primary sequence data in that they are qualitative characters, corresponding to rare or
unique transformation events. Thus far, this
type of character includes rearrangements of
mitochondrial gene order (Boore et al., 1998),
gene duplications and divergence inside
broadly conserved chromosomal arrays
or gene families such as the Hox cluster
848
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Abstract.—Although the phylogenetic position of brachiopods has always been subject to debate,
many authors place them as a sister group to deuterostomes on the basis of morphological and developmental characters. However, molecular phylogeny consistently places them among protostomes.
More precisely, brachiopods are predicted to branch inside the lophotrochozoan assemblage, together
with annelids, molluscs, nemerteans, atworms, and others. That result has been criticized on the
basis of (1) prior knowledge of brachiopod morphology and (2) the known limitation s of molecular
phylogenies. Here I review recent data of molecular origin, particularly those displaying qualitative
properties close to those of morphological characters. The complement of Hox genes present in all
metazoa tested to date has proved to be a powerful tool for broad phylogenetic reconstruction. The
mitochondrial genome also provides qualitative characters, showing discrete events of gene rearrangements. After discussing the data and the way they should be interpreted in the perspective
of several hypotheses for metazoan phylogeny, I conclude that they argue strongly in favor of the
protostome (and lophotrochozoan) afŽnity of the brachiopods. There is therefore a need for a reinterpretation of brachiopod morphological and developmental characters. I also identify some research
axes on brachiopod morphology. [Brachiopod; Hox genes; mitochondrial gene order; phylogeny; rare
genomic changes.]
2001
DE ROS A—EVIDENCE THAT BRACHIOPODS ARE PROTOSTOMES
849
data are available for brachiopods at this
time, and I provide a detailed analysis of
them.
HOX G ENES
(Garcia-Fernandez and Holland, 1994;
Falciani et al., 1996), transposition of mobile
elements inside the genome (Hillis, 1999;
Miyamoto, 1999; Nikaido et al., 1999), and
a few other characteristics (Rokas and
Holland, 2000). Only the Žrst two kinds of
FIGURE 2. A summary of the Hox genes found in bilaterians. Boxes stand for genes. Horizontal lines indicate
chromosomal locations, when known. Vertical white bars delineate orthologous relationships between single genes
or groups of genes. Question marks indicate uncertain orthologies. The nomenclature used in this paper is indicated
at the bottom.
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FIGURE 1. Two highly simpliŽed phylogenies of
metazoans. (a) A traditional phylogeny (simpliŽed from
Hyman, 1940). (b) The Lophotrochozoa/Ecdysozoa hypothesis (Halanych et al., 1995; Aguinaldo et al., 1997).
Hox genes are a set of genes encoding developmental transcriptional regulators that
make up a characteristic DNA-binding motif named the homeodomain. This 60-amino
acid domain is encoded by the homeobox.
Hox genes are not the only homeobox genes,
but the conservation of the Hox homeodomain and a few other parts of the Hox
protein allows their unmistakable identiŽcation (Gehring et al., 1994). Hox genes are
found throughout the whole animal kingdom, including brachiopods (de Rosa et al.,
1999) (Fig. 2). In arthropods and vertebrates,
Hox genes are expressed in a sequential manner along the antero-posterior (A/P) axis of
the animal during development. In phyla
where they have been studied, Hox genes are
usually clustered in a single chromosomal array and are ordered in a way that reects
their spatial and temporal order of expression (Lewis, 1978; Duboule and Dolle, 1989;
Carroll, 1995). I have thus named them according to their expression domain and chromosomal localization as “anterior,” “central,” or “posterior” genes. The elucidation of
orthology relationships between Hox genes
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S YSTEMATIC BIOLOGY
Another group comprises genes that are
too divergent to have easily recognizable orthologs outside of one phylum. These are
the deuterostome posterior genes (P G9–13),
the insect zen and ftz, Branchiostoma oridae AmphiHox2, Caenorhabditis elegans egl-5,
and others. In some cases, chromosomal
mapping data allow identiŽcation of orthologs. They do not provide much phylogenetic information for deep branchings,
but they can be useful for short-range phylogeny. For example, the insect Hox3 orthologs have undergone rapid evolution and
divergence in the dipteran lineage (Falciani
et al., 1996). In that case, and in other instances, the sequence divergence is correlated with the loss of the ancestral Hox expression pattern.
The last group consists of genes that are
conserved enough to be recognized across
several phyla but don’t have obvious orthologs in the whole bilaterian tree. They include genes of the central part of the cluster (PG6-8 in vertebrates, Antp to abd-A in
D. melanogaster) and the posterior genes of
protostomes (Abd-B, Post-1, and Post-2). For
example, the Lox2 gene (identiŽed by its
characteristic residues: lysine at position 21,
leucine at position 34, and serine at position
35 of the homeodomain; see Fig. 3) is found
only in annelids, molluscs, and brachiopods.
Strikingly, all the genes in that group display
similar patterns of phylogenetic distribution:
Some are only found in deuterostomes, some
FIGURE 3. Alignment of central Hox genes and anking sequences. Conserved residues for each group are highlighted. Note the high conservation inside the homeodomain: Only a few residues allow orthology assignment.
The homeodomain and the Ubd-A and Lox5 peptides (Balavoine, 1998) are boxed. Species abbreviations: Pca, Priapulus caudatus; Lsa, Lineus sanguineus; Lan, Lingula anatina; Pvu, Patella vulgata; Hro, Helobdella robusta; Nvi, Nereis
virens; Hme, Hirudo medicinalis. AmphiHox6, 7, and 8 are Branchiostoma oridae genes; Antp, Ubx, and abd-A are D.
melanogaster genes.
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of several phyla has led to the conclusion that
at least seven Hox genes, and probably more,
were present in the last bilaterian ancestor
(de Rosa et al., 1999). After subsequent gene
duplications, gene losses, or both, an average
of 10 Hox genes can be found in almost every bilaterian phylum, except for vertebrates,
which have multiple Hox clusters on different
chromosomes, the result of several duplications of a unique ancestral cluster ( Hart et al.,
1987; Duboule and Dolle, 1989).
Hox genes have proved very useful in phylogenetic inference. Some Hox genes appear
to have recognizable orthologs among only
one phylum or set of phyla. The occurrence of
such cases is often a strong argument in favor
of the monophyly of the considered phyla.
The Žrst example of this use of Hox genes as
phylogenetic markers was to strengthen the
protostome (and lophotrochozoan) afŽnity
of atworms (Balavoine, 1997). To describe
this argument in more details, the Hox genes
are split into three groups according to their
phylogenetic usefulness.
The Žrst group comprises Hox genes that
are too conserved to provide phylogenetic
information. They correspond, with a few
exceptions, to orthologs of the Žve anteriormost Hox genes (represented by paralogy
groups [PG] 1 to 5 in vertebrates and lab to
Scr in Drosophila melanogaster). They are easily identiŽed in all bilaterian phyla by the
presence of characteristic shared residues inside the homeodomain.
VOL. 50
2001
DE ROS A—EVIDENCE THAT BRACHIOPODS ARE PROTOSTOMES
851
only in lophotrochozoans, and some only in
ecdysozoans. This allows one to draw three
distinct sets of Hox genes, each characteristic for one of the three proposed superphyla.
The sets comprise Lox5, Lox2, Lox4, Post-1,
and Post-2 in lophotrochozoans; Antp, Ubx,
abd-A, and Abd-B in ecdysozoans; and PG68 in deuterostomes. Not all the genes of a
given set are found in all species, but at least
some are. Most important, genes from different sets are never mixed. For example,
Lox2 was never found together with abd-A—
perhaps because of undetected orthology relationships (e.g., Lox2 and Lox4 might be orthologous to Ubx and abd-A, respectively). In
this case, the impossibility of solving the relationships among those genes would simply
indicate that a long divergence has blurred
the similarity in the sequences (Fig. 4A). Alternatively, the sequences could have arisen
by independent duplications in the three lineages, which would provide a synapomorphy for each of the three superphyla (Fig. 4B).
Whatever the model, three character states
can be deŽned for the Hox cluster of Bilateria.
Additional information can be found from
the sequences anking the homeodomain.
The Lox2, Lox4, Ubx, and abd-A genes display a highly conserved peptide just next
to the homeodomain, which is named the
Ubd-A peptide. Similarly, the Lox5 genes
possess a conserved peptide (Fig. 3). The
Ubd-A peptide is found only in protostomes, and the Lox5 peptide is restricted to
lophotrochozoans (Balavoine, 1998). The extreme conservation of each of the peptides
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FIGURE 4. Two schematic models for the origin of central Hox genes in bilaterians. (a) Some (or all) of the extant
genes already existed in the ancestor, but sequence divergence has obscured the similarities, preventing recovery
of the orthologous relationships. Thus only three character sets can be distinguished. (b) Only one gene is present
in the ancestor, and independent duplications give rise to the genes present in extant phyla; in this case, the three
groups (lophotrochozoans, ecdysozoans, and deuterostomes) are monophyletic. The two models are extreme and
oversimpliŽed, and the true story is probably an intermediate between the two.
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S YSTEMATIC BIOLOGY
makes it extremely unlikely that they arose
by convergence. The existence of these kinds
of peptides probably indicates that the proteins bearing them interact with a speciŽc cofactor at this site. The gain or loss (depending
on whether the peptides are ancestral or derived features among bilaterians) of one of
the peptides therefore corresponds to a radical change in gene regulation at some stage
of the development. It is a drastic event that
must be very rare or unique.
M ITOCHONDRIAL G ENE O RDER
TABLE 1. Protein and rRNA genes present in animal
mitochondrial genomes and the abbreviations for them
used in the Žgures.
Gene product
Cytochrome oxidase
subunits I, II, III
Cytochrome b apoenzyme
NADH dehydrogenase
subunits 1–6, 4L
ATP synthase subunits 6, 8
rRNA large subunit
rRNA small subunit
Abbreviation used in
Žgures
cox1, cox2, cox3
cob
nad1–6, 4L
atp6, atp8
rnL
rnS
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The mitochondrial DNA is a small, circular, nonnuclear chromosome. It encodes
a part of the proteins used by the mitochondrion, as well as the stable RNAs used
for protein synthesis. Its characteristics are
quite constant in metazoans. It is circular,
»16 kb long, and comprises the same 37
genes, with very few exceptions: 2 for
rRNAs, 22 for tRNAs, and 13 for proteins
(Boore, 1999). Apart from a few taxa (e.g.,
nematodes, gastropods), the gene order is
very conserved and phyla can be connected
by only a few rearrangements. Although
the mechanism for gene rearrangements
is not known, the rearrangement events
are thought to be rare. Mitochondrial gene
arrangements are little prone to convergent
evolution because of the large number of
possible arrangements. They are therefore
a very powerful phylogenetic tool to study
deep branches in the metazoan tree (Boore
and Brown, 1998). Several mitochondrial
genomes have been partially or completely
sequenced; the compiled results can be found
at <http://biology.lsa.umich.edu/»jboore>.
The mitochondrial genomes sequence of
two brachiopods were recently published:
Terebratulina retusa (Stechmann and Schlegel,
1999) and Laqueus rubellus (Noguchi et al.,
2000). Both publications conclude that the
gene order of brachiopods is more closely
related to that of molluscs or annelids than
to chordates. Those results were based on
overall similarity, without inferences of
possible ancestral states. Here I will try
to provide a raw cladistic analysis of the
data.
The gene order of L. rubellus differs strongly from any gene order reported so far. It
has almost no conserved gene segments homologous to those of other species, which
makes the species unsuitable for the analy-
sis. This correlates with other odd properties,
such as small size, great compactness, and
some peculiarities in tRNAs (Noguchi et al.,
2000). Those features are obviously derived,
so I will use the gene order of T. retusa as
a representative for brachiopods, comparing
the gene order of this organism with those
inferred to be primitive for arthropods and
chordates (Boore, 1999) and with the gene order of the mollusc Katharina tunicata (Boore
and Brown, 1994). Because tRNA genes happen to rearrange more often than other genes,
I will focus on protein and rRNA genes (listed
in Table 1).
All the gene orders considered here can
be connected by fewer than four rearrangements steps or six breakpoints (Blanchette
et al., 1999), as shown in Figure 5. Among
the gene arrangements, one is shared by
molluscs and brachiopods: In both of those
phyla, the (cox3-nad3) segment is linked
to the (nad2-: : :-atp6) segment on its 3’
side, but on its 5’ side in chordates and
arthropods. Note that the nad3-nad2 link
is also found in annelids (Boore and
Brown, 1995, 2000). The (cox3-nad3-nad2-: : :atp6) state is thus most probably ancestral
to lophotrochozoans. When comparing the
three possible unrooted tree topologies for
the four taxa—arthropods (A), chordates (C),
K. tunicata (Ktu), and T. retusa (Tre)—the
translocation of (cox3-nad3) from one end
to the other of the (nad2-: : :-atp6) segment
makes the tree ((A, C) (Ktu, Tre)) require one
translocation less than the two other trees, the
classical ((A, Ktu) (C, Tre)) or the unorthodox
((A, Tre) (C, Ktu)). The other translocations
can be interpreted as autapomorphies and do
not inuence the tree topology. The tree obtained by neighbor-joining (Saitou and Nei,
1987), using breakpoint distances (Blanchette
et al., 1999), has the same topology (Fig. 6).
2001
DE ROS A—EVIDENCE THAT BRACHIOPODS ARE PROTOSTOMES
853
D ISCUSS ION
Analysis of Qualitative Molecular Evidence
FIGURE 6. Unrooted neighbor-joining tree obtained
by using breakpoint distances.
The Hox and mitochondrial data can be Žt
only into a single unrooted tree (shown in
Fig. 7A). Any other tree requires additional
convergent steps, which, given the rarity
of the events considered here, is highly unlikely. Of the Žve possible rooted trees, three
(Fig. 7B–D) propose a brachiopod/mollusc
sister grouping, which conŽrms the existence
of lophotrochozoans. The tree in Figure 7B,
which corresponds to the Lophotrochozoa/Ecdysozoa hypothesis, is the only
one that retains protostome monophyly. A
paraphyletic lophotrochozoan assemblage
remains possible, if one assumes that the
lophotrochozoan Hox cluster retained the ancestral state (Fig. 7E, F). In that case, however,
one has to assume a chordate/arthropod
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FIGURE 5. The six pairwise comparisons for the four mitochondrial gene arrangements of Arthropods, Chordates,
Katharina tunicata, and Terebratulina retusa. The gene order maps are arbitrarily started from cox1. A minus before
the name indicates a gene on the opposite DNA strand. One of the minimal sets of rearrangements is proposed
for each comparison. The number of rearrangements needed (and the breakpoint distances [Blanchette et al., 1999]
inside parentheses) are indicated on the left.
854
S YSTEMATIC BIOLOGY
VOL. 50
(or ecdysozoan/deuterostome) sister grouping (also found in Fig. 7D), which, to my
knowledge, has never been proposed.
Although not deŽnitely conclusive, the
data strongly suggest that lophotrochozoans
are a natural group and exclude a close relationship for brachiopods/deuterostomes.
A deŽnitive conŽrmation would require a
rooted tree, which so far has been impossible
to obtain, because the Hox family and mitochondrial gene order in cnidarians, the likely
sister group to bilaterians, differ greatly from
their bilaterian counterparts and are thus far
impossible to connect to one or the other of
the character states described here. Perhaps
this issue could be solved with data from
the ctenophores, but so far such data are not
available. In the meantime, considering the
incoming wealth of independent sequence
data from 18S rRNA (Halanych et al., 1995;
Aguinaldo et al., 1997) and mitochondrial
gene sequences (Stechmann and Schlegel,
1999), together with the qualitative data analyzed here, I consider the Lophotrochozoa/
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FIGURE 7. Hox cluster and mitochondrial character states mapping on phylogenetic trees. (a) Best unrooted tree
according to the data. (b–f) The Žve possible rooted trees. In the rooted trees, solid bars indicate peptide gain; dashed
bars indicate peptide loss. In (b) and (d), arrows indicate alternative possible placements of evolutionary steps.
(b) corresponds to the Lophotrochozoa/Ecdysozoa hypothesis. It is the only one to retain protostome monophyly.
None of the trees is compatible with a chordate/brachiopod sister grouping.
2001
DE ROS A—EVIDENCE THAT BRACHIOPODS ARE PROTOSTOMES
Ecdysozoa hypothesis to be the most probable depiction of bilaterian history.
The Phylogenetic SigniŽcance of Brachiopod
Morphological Features
embryo develops. Given its high contribution to species Žtness and its great variability,
cleavage pattern is not a reliable character for
deep metazoan phylogeny.
Modes of coelom formation.—The classical
split (schizocoelic protostomes vs. enterocoelic deuterostomes and brachiopods) is
also subject to criticism. Brachiopods display
both modes of coelom formation, showing
that this character again is prone to important
variation. Budd and Jensen (2000) argue that
the different modes of coelom formation can
be explained by differences in the timing
of development. The plasticity of the development of body cavities has long been
recognized (Ruppert, 1991), and some have
proposed that the mode of coelom formation is highly correlated with cleavage pattern (Valentine, 1997). What was said above
about cleavage pattern can thus be extended
to coelom formation: It does not appear to
be a character suitable for deep metazoan
classiŽcation.
Protostomy versus deuterostomy.—The fate
of the blastopore and the origin of the mouth
have also been used as characters uniting
brachiopods and deuterostomes. This character is also highly variable and should not
be used for uniting phyla (Nielsen, 1995). Because amphistomy (blastopore giving rise to
mouth and anus by lateral closure) is probably the ancestral state for Bilateria (Arendt
and Nubler-Jung, 1997), deuterostomy (formation of a secondary mouth independent
of the blastopore) would be a derived character. However, deuterostomy unquestionably
is found in protostomes, such as the polychaete Eunice and the gastropod Viviparus
(Anderson, 1973; Arendt and Nubler-Jung,
1997), and therefore is prone to convergence
and cannot be used to link brachiopods and
deuterostomes sensu stricto.
The three examples above illustrate the
danger of reasoning on archetypes (radialcleaving enterocoelous deuterostomes vs.
spiral-cleaving schizocoelous protostomes)
rather than seeing the diversity of characters
among phyla. This practice can lead to overestimation of the conservation of very labile
characters. The three characters mentioned
above are unsuitable to solve the phylogeny
of bilaterians. They might still be useful for
phylogenies at a lower taxonomic level.
Trimery.—Among the other characters proposed to unite brachiopods and deuterostomes are a trimeric coelom and a tentacle
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On the basis of this phylogeny, the need for
a reappraisal of most of the morphological
and embryological characters of brachiopods
is obvious. It is not in the scope of this short
review to make a complete reinterpretation
of the data accumulated over more than a
century. I would like only to point out a
few characters that, in light of the lophotrochozoan afŽnities of brachiopods, must have
been misinterpreted. General morphological and developmental considerations in this
part are mostly taken from classical zoology and development textbooks (Anderson,
1973; Brusca and Brusca, 1990; Meglitsch and
Schram, 1991; Nielsen, 1995; Gilbert, 1997;
Wolpert, 1998).
Egg cleavage patterns.—The question of cleavage patterns has been discussed elsewhere (Valentine, 1997) and can be summarized as follows: Radial cleavage is
most likely ancestral for Bilateria and
therefore cannot be used to unite brachiopods with deuterostomes. The conservation and complexity of the spiral cleavage pattern make it very unlikely to have
arisen several times independently. This pattern is restricted to annelids (sensu lato,
including echiurans and pogonophorans
[McHugh, 1997]), entoprocts, molluscs, nemertines, platyhelminthes, sipunculids, and
a few small phyla, which could be a sister group to the brachiopod/phoronid clade
among lophotrochozoans. Alternatively, if
brachiopods branch inside the spiralian protostomes (Cavalier-Smith, 1998; Giribet et al.,
2000), or if spiral cleavage is ancestral to
protostomes (if the occurrence of a modiŽed spiral cleavage in arthropods [in crustaceans or pycnogonids or both] is a correct
interpretation), then spiral cleavage must
have been lost in brachiopods and other
lineages. Many shifts from spiral or radial
to idiosyncratic cleavages are known (e.g.,
acoel atworms, cephalopods, nematodes,
onychophorans, pogonophorans, and many
arthropod and vertebrate groups), making it
appear that the cleavage pattern is a highly
variable character. That pattern is connected
to the mode of fertilization, the yolkiness of
the egg, and the environment in which the
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S YSTEMATIC BIOLOGY
An upstream collecting system would therefore be a synapomorphy of deuterostomes
and brachiopods. I propose a different interpretation. Because downstream collecting
systems are found only in protostomes, it is
tempting to consider them as blastopore ciliary systems rather than mouth ciliary systems. Additionally, the same kind of compound ciliae are found in the perianal ring
of amphistomous trochophore larvae. In animals that form a secondary mouth, a different
ciliary system must have been recruited. Suppose the competence to form a downstreamcollecting system with compound cilia were
restricted to the edges of the blastopore. The
upstream collecting system would then be
convergently recruited (for example, from locomotory ciliae, to which they are very similar) in animals forming a secondary mouth.
It would thus be very interesting to study
the ciliary bands in unquestioned protostomes that form a secondary mouth. Unfortunately, to my knowledge, neither Viviparus
nor Eunice has Žlter-feeding larvae for testing
this prediction, so this interpretation remains
speculative.
Larval nervous system.—Hay-Schmidt
(2000) has classiŽed the serotonergic nervous
system of larvae into six types. Type 1 is
restricted to cnidarians, types 2 to 4 are
found in spiralians, type 5 is found in
lophophorates and nonchordate deuterostomes, and type 6 is in chordates. Let me
stress that this pattern does not support
a brachiopod/deuterostome relationship
(Fig. 8). Similarly, any character having
the following distribution pattern—state
A in spiralians, state B in deuterostomes
and lophophorates, and other or unknown
states in diploblasts and ecdysozoans—is
not an argument favoring a brachiopod/deuterostome grouping, because B
could be plesiomorphic for bilaterians.
Larval development.—Brachiopods have
many different idiosyncratic larval types.
FIGURE 8. The distribution of larval nervous system
types (Hay-Schmidt, 2000) mapped on two phylogenetic
hypotheses. Both trees require four character changes, so
this character does not favor any one of the hypotheses.
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feeding system connected to the second pair
of coelomic sacs. Concerning the feeding
apparatus, characteristics that would deŽnitely prove the homology of the brachiopod
lophophore with the tentacle feeding system of some hemichordates (pterobranchs)
and echinoderms are not known (Halanych,
1996). Additionally, because hemichordates
and echinoderms are most probably sister
groups (Wada and Satoh, 1994; Halanych,
1995), there is no evidence that a sessile adult
with tentacular feeding apparatus is the ancestral state for deuterostomes. More probably, a sessile adult stage appeared independently in pterobranchs (Cameron et al., 2000)
and urochordates (Swalla et al., 2000). Some
annelids display similar feeding systems
acquired independently. Again, this character seems prone to convergence. The number of coelomic sacs is also a highly variable feature. Cephalochordates have many
pairs of coelomic sacs and some brachiopods
have only two. The number of occurrences
of a repeated structure is not a very strong
character: The ability to replicate a structure
makes modifying the number easy. Annelids
and arthropods, for example, do not always
display the same number of segments. The
number of the different categories of vertebrae is variable among vertebrates. A small
number of coelomic sacs could easily be
reached convergently, by either the splitting
of an original pair of coelomic sacs or the loss
of segments from a segmented ancestor. The
origin of brachiopods from an annelid-like
segmented ancestor has already been proposed, on the basis of a completely different argument (Gutmann et al., 1978). Again,
the phylogeny of Bilateria is not a taxonomic
scale at which this character can be useful.
Larval feeding apparatus.—Larval ciliary
bands used for Žlter-feeding have been used
to unite brachiopods and deuterostomes
(Nielsen, 1987). Protostomes have a downstream collecting system formed of compound cilia, whereas deuterostomes and
brachiopods have an upstream collecting
system formed of single cilia. Although no
Žlter-feeding outgroup exists to prove this,
and although the function of the character
is not well understood, the complexity of an
upstream collecting system causes authors to
consider it a unique derived feature (Nielsen,
1995). In that case, downstream collecting
systems are considered plesiomorphic (but
see Rouse [2000] for a different point of view).
VOL. 50
2001
DE ROS A—EVIDENCE THAT BRACHIOPODS ARE PROTOSTOMES
Conclusion
A whole set of independent molecular
characters, including qualitative data much
less prone to known artifacts than primary
sequence data, point toward making the
Lophotrochozoa/Ecdysozoa hypothesis the
best depiction of bilaterian phylogeny. This
implies that brachiopods are protostomes.
As I have argued here, the characters supposed to unite brachiopods and deuterostomes must have been misinterpreted: Most
of them can be shown to be either plesiomorphic to Bilateria or prone to convergence. A
few morphological and developmental characters do not explicitly support the inclusion
of brachiopods inside protostomes, but no
character overtly conicts with this proposal
either. Brachiopods should therefore be considered protostomes.
ACKNOWLEDGMENTS
Some of the ideas expressed here came to me during lectures or discussions at the 2nd TMR course in
Evolutionary Developmental Biology held in Roscoff in
May–June 2000. I thank here the organizers, the participants, and the funding agencies of the course. I thank
André Adoutte, Guillaume Balavoine, Olivier Lespinet,
Richard Olmstead, and two anonymous reviewers for
helpful discussion and comments on the manuscript.
The work in Gif-sur-Yvette is supported by the Centre
National de la Recherche ScientiŽque and the Universit é
Paris-Sud.
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Received 7 November 2000; accepted 5 February 2001
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