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F. Marlétaz and Y. Le Parco
4.5.2 Chaetognaths Fit into the Bilaterian Tree
The phylogenomic approach has made it possible to more accurately determine
the phylogenetic position of some groups that have represented longstanding problems. Chaetognaths have been puzzling for many years because their body plan
exhibits several protostome features whereas their early development is typically
deuterostomian, with enterocoelic formation of the coelom (Ball and Miller 2006).
EST sequencing enabled phylogenomic analyses, which revealed that chaetognaths
neither cluster within the ecdysozoans nor the lophotrochozoans and that they are
probably a sister group of all the other protostomes (Marlétaz et al. 2008, Marlétaz
et al. 2006). Their inclusion in protostomes had previously been supported by the
analysis of their mitochondrial genome (Papillon et al. 2004). Alternative studies
based on another chaetognath species also supported protostome affinities but rather
argued for a basal position in lophotrochozoans (Matus et al. 2006) or alternatively,
an unresolved position among protostomes (Dunn et al. 2008). Nevertheless, the
basal branching of chaetognaths among protostomes was further supported by the
recovery of an unusual molecular signature in chaetognath ESTs: the guanidinoacetate N-methyltransferase (GMT) gene was retrieved in all lineages predating the
radiation of protostomes but in no current protostome group, which suggests that this
gene was probably lost after the split of chaetognaths from protostomes (Marlétaz
et al. 2008, Marlétaz et al. 2006). Despite alternative claims that chaetognaths should
branch closer to lophotrochozoans, several studies independently support their position as a branching sister-group to the protostomes (Lartillot and Philippe 2008,
Philippe et al. 2007). This peculiar phylogenetic position has two major implications. On one hand, this indicates that deuterostome-like embryology and especially
enterocoelous formation of the coelom may be ancestral among bilaterians, a view
which is reminiscent of the archecoelomate theory (Remane 1963) (Fig. 4.2). On the
other hand, this constitutes the first clear contradiction of the “new view” of animal
phylogeny since this phylum escapes the lophotrochozoan/ecdysozoan dichotomy
(Adoutte et al. 2000).
4.5.3 Acoel Flatworms, Basal or Not?
Phylogenomics has also shed some light on the phylogenetic position of acoel flatworms, another highly debated topic since they were originally proposed to be the
most basal bilaterian on the base of SSU analysis (Ruiz-Trillo et al. 1999). This
phylogenetic position would suggest that the body organization of these triploblastic acoelomate flatworms could be reminiscent of those of bilaterian ancestor.
Meanwhile, the status of acoels as an intermediate taxon has been extensively
debated because their very fast evolutionary rates make long branch attraction artifacts possible (Deutsch 2008). Recently, a phylogenomic assessment of the position
of acoels reached the conclusion that they are not platyhelminthes (Philippe et al.
2007). Their exclusion from protostomes is also supported by the occurrence of a
F. Marlétaz and Y. Le Parco
4.5.2 Chaetognaths Fit into the Bilaterian Tree
The phylogenomic approach has made it possible to more accurately determine
the phylogenetic position of some groups that have represented longstanding problems. Chaetognaths have been puzzling for many years because their body plan
exhibits several protostome features whereas their early development is typically
deuterostomian, with enterocoelic formation of the coelom (Ball and Miller 2006).
EST sequencing enabled phylogenomic analyses, which revealed that chaetognaths
neither cluster within the ecdysozoans nor the lophotrochozoans and that they are
probably a sister group of all the other protostomes (Marlétaz et al. 2008, Marlétaz
et al. 2006). Their inclusion in protostomes had previously been supported by the
analysis of their mitochondrial genome (Papillon et al. 2004). Alternative studies
based on another chaetognath species also supported protostome affinities but rather
argued for a basal position in lophotrochozoans (Matus et al. 2006) or alternatively,
an unresolved position among protostomes (Dunn et al. 2008). Nevertheless, the
basal branching of chaetognaths among protostomes was further supported by the
recovery of an unusual molecular signature in chaetognath ESTs: the guanidinoacetate N-methyltransferase (GMT) gene was retrieved in all lineages predating the
radiation of protostomes but in no current protostome group, which suggests that this
gene was probably lost after the split of chaetognaths from protostomes (Marlétaz
et al. 2008, Marlétaz et al. 2006). Despite alternative claims that chaetognaths should
branch closer to lophotrochozoans, several studies independently support their position as a branching sister-group to the protostomes (Lartillot and Philippe 2008,
Philippe et al. 2007). This peculiar phylogenetic position has two major implications. On one hand, this indicates that deuterostome-like embryology and especially
enterocoelous formation of the coelom may be ancestral among bilaterians, a view
which is reminiscent of the archecoelomate theory (Remane 1963) (Fig. 4.2). On the
other hand, this constitutes the first clear contradiction of the “new view” of animal
phylogeny since this phylum escapes the lophotrochozoan/ecdysozoan dichotomy
(Adoutte et al. 2000).
4.5.3 Acoel Flatworms, Basal or Not?
Phylogenomics has also shed some light on the phylogenetic position of acoel flatworms, another highly debated topic since they were originally proposed to be the
most basal bilaterian on the base of SSU analysis (Ruiz-Trillo et al. 1999). This
phylogenetic position would suggest that the body organization of these triploblastic acoelomate flatworms could be reminiscent of those of bilaterian ancestor.
Meanwhile, the status of acoels as an intermediate taxon has been extensively
debated because their very fast evolutionary rates make long branch attraction artifacts possible (Deutsch 2008). Recently, a phylogenomic assessment of the position
of acoels reached the conclusion that they are not platyhelminthes (Philippe et al.
2007). Their exclusion from protostomes is also supported by the occurrence of a