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F. Marlétaz and Y. Le Parco
The “new view” of animal relationships was further reinforced by the discovery
of molecular signatures derived from the homeodomain of Hox genes (de Rosa et al.
1999). The Hox transcription-factors constitute a multigenic family of about ten paralogous members present in all bilaterians. Those genes are generally tightly clustered in the genome and are expressed in the same order along the body plan of animals as the order of the genes along the chromosome following the so-called colinearity rule (Lemons and McGinnis 2006). The isolation of hox genes from priapulids
and brachiopods by de Rosa et al. (1999) indicated that the posterior hox genes of
ecdysozoans and lophotrochozans are likely to have independent origins, resulting
in the respective Abd-B and Post1/2 classes that may be distinguished by some specific residues (de Rosa et al. 1999). Subsequent data have confirmed the interest of
hox genes as molecular signatures of bilaterian evolution (Balavoine et al. 2002).
4.2.4 The Limits of the “New View”
The “new view” of animal phylogeny durably reshaped our understanding of animal evolution, especially through the reevaluation of the notion of body complexity
(Adoutte et al. 2000). However, these early molecular data failed to convincingly
resolve numerous nodes of the tree: (a) the relationships within the new protostome
clades (Lophotrochozoa and Ecdysozoa) remained extremely elusive, (b) a set of
phyla including chaetognaths, gastrotriches, rotifers, xenoturbellids and acoels were
very difficult to position, often because of their fast evolutionary rates, and (c) the
relationships at the base of the metazoan tree remained virtually unresolved. An
attempt to deal with these issues was made by incorporating data derived from morphological matrices, in addition to the molecular data (Giribet et al. 2000, Peterson
and Eernisse 2001). These “total evidence” studies succeeded in resolving problematic nodes and produced a convincing scheme of animal relationships but they
were extensively criticized for having carelessly recycled previously published data
matrices and thus reproducing their biases and errors (Jenner 2001).
Another approach taken to resolve this problem was the initiation of large-scale
sequencing efforts to identify the least divergent species, but this approach did
not always succeed. For instance, the chaetognaths exhibit very fast evolving SSU
genes, which originally led to them being assigned a basal position among the metazoans (Telford and Holland 1993). However, further characterization of SSU genes
from a large set of species did not lead to the identification of a slower evolving
one (Papillon et al. 2006). Similarly, results suggesting that acoel flatworms had a
basal position among bilaterians were sometimes criticized for possibly being biased
by long-branch attraction (Deutsch 2008, Ruiz-Trillo et al. 1999). Increased taxon
sampling at the base of the metazoan tree, with the addition of cnidarians, poriferans, ctenophores and also the enigmatic placozoans, led to interesting hypotheses
such as sponge paraphyly but no consensus was drawn concerning the respective
relationships of these lineages (Borchiellini et al. 2001, Collins 1998).
F. Marlétaz and Y. Le Parco
The “new view” of animal relationships was further reinforced by the discovery
of molecular signatures derived from the homeodomain of Hox genes (de Rosa et al.
1999). The Hox transcription-factors constitute a multigenic family of about ten paralogous members present in all bilaterians. Those genes are generally tightly clustered in the genome and are expressed in the same order along the body plan of animals as the order of the genes along the chromosome following the so-called colinearity rule (Lemons and McGinnis 2006). The isolation of hox genes from priapulids
and brachiopods by de Rosa et al. (1999) indicated that the posterior hox genes of
ecdysozoans and lophotrochozans are likely to have independent origins, resulting
in the respective Abd-B and Post1/2 classes that may be distinguished by some specific residues (de Rosa et al. 1999). Subsequent data have confirmed the interest of
hox genes as molecular signatures of bilaterian evolution (Balavoine et al. 2002).
4.2.4 The Limits of the “New View”
The “new view” of animal phylogeny durably reshaped our understanding of animal evolution, especially through the reevaluation of the notion of body complexity
(Adoutte et al. 2000). However, these early molecular data failed to convincingly
resolve numerous nodes of the tree: (a) the relationships within the new protostome
clades (Lophotrochozoa and Ecdysozoa) remained extremely elusive, (b) a set of
phyla including chaetognaths, gastrotriches, rotifers, xenoturbellids and acoels were
very difficult to position, often because of their fast evolutionary rates, and (c) the
relationships at the base of the metazoan tree remained virtually unresolved. An
attempt to deal with these issues was made by incorporating data derived from morphological matrices, in addition to the molecular data (Giribet et al. 2000, Peterson
and Eernisse 2001). These “total evidence” studies succeeded in resolving problematic nodes and produced a convincing scheme of animal relationships but they
were extensively criticized for having carelessly recycled previously published data
matrices and thus reproducing their biases and errors (Jenner 2001).
Another approach taken to resolve this problem was the initiation of large-scale
sequencing efforts to identify the least divergent species, but this approach did
not always succeed. For instance, the chaetognaths exhibit very fast evolving SSU
genes, which originally led to them being assigned a basal position among the metazoans (Telford and Holland 1993). However, further characterization of SSU genes
from a large set of species did not lead to the identification of a slower evolving
one (Papillon et al. 2006). Similarly, results suggesting that acoel flatworms had a
basal position among bilaterians were sometimes criticized for possibly being biased
by long-branch attraction (Deutsch 2008, Ruiz-Trillo et al. 1999). Increased taxon
sampling at the base of the metazoan tree, with the addition of cnidarians, poriferans, ctenophores and also the enigmatic placozoans, led to interesting hypotheses
such as sponge paraphyly but no consensus was drawn concerning the respective
relationships of these lineages (Borchiellini et al. 2001, Collins 1998).