136
F. Marlétaz and Y. Le Parco
4.6 Conclusion: The Future of Animal Phylogeny
This chapter has described the impact of the most recent genome-based studies on
the current view of metazoan relationships with respect to classical schemes based
on morphology and single gene molecular phylogenies (mainly SSU rRNA). The
new field of phylogenomics has been founded in the context of a strong debate
about the status of the Coelomata clade, which finally ended up with the reassessment of the “New View” of animal phylogeny (Adoutte et al. 2000, Dunn et al.
2008). This debate mainly stressed the importance of dealing with extensive taxonomic sampling, even when examining qualitative molecular signatures or genome
level characters. The extension of the phylogenomic approach has rephrased some
longstanding questions in animal phylogeny such as the position of acoel flatworms,
chaetognaths or relationships within the lophotrochozoan clade. It has also brought
some surprising rearrangements, such as the positioning of the tunicates as vertebrate sister group (Delsuc et al. 2005). More surprisingly, the “new view” scheme
was challenged by the branching of some phyla such as acoels or chaetognaths that
do not fit within the ecdysozoan and lophotrochozoan clades. Recently the collection and analysis of a large amount of data from minor groups, described in a
paper by Dunn et al. (2008), showed that that some phyla remain refractory to accurate positioning (Dunn et al. 2008). Several questions concerning metazoan tree
of life thus remain open. For example, the exact relationships at the base of the
metazoan tree remain elusive because of the difficulty of determining the branching order of bilaterians, poriferans, cnidarians and also ctenophores, all of which
are groups that possibly diverge at the base of the metazoan radiation (Dunn et al.
2008). Answering this question would provide important insights into the nature
of the metazoan ancestor: a complex organism that already possessed a mesoderm
and bilateral symmetry, such as a ctenophore, or an organism of lesser complexity such as a sponge larva (Martindale and Henry 1999, Nielsen 2008)? Increased
gene and taxonomic sampling as well as improvements to inference models are
likely to be valuable tools for resolving these issues. Moreover, when the whole
set of employable marker genes will have been exploited by molecular phylogeny,
numerous other features such as gene order and synteny relationships might deserve
further investigation (Philippe et al. 2005a).
The latter example of relationships at the base of metazoans emphasized the
importance of phylogenetics as a means to understand the major evolutionary
transitions of morphological characters. In particular, the power of molecular phylogenetics to ensure the orientation of characters has demonstrated that no general
trends exist in the establishment of morphological complexity. The close association
of nemerteans and annelids as well as that of vertebrates and tunicates has clearly
shown that morphological simplifications have occurred repeatedly during the evolution of metazoans (Delsuc et al. 2005, Dunn et al. 2008). At a deeper evolutionary
scale, the early divergence of ctenophores proposed by Dunn et al. (2008) suggested
that the ancestor of all metazoans was far more complex than expected and that the
morphological simplicity of poriferans could be secondarily derived.
F. Marlétaz and Y. Le Parco
4.6 Conclusion: The Future of Animal Phylogeny
This chapter has described the impact of the most recent genome-based studies on
the current view of metazoan relationships with respect to classical schemes based
on morphology and single gene molecular phylogenies (mainly SSU rRNA). The
new field of phylogenomics has been founded in the context of a strong debate
about the status of the Coelomata clade, which finally ended up with the reassessment of the “New View” of animal phylogeny (Adoutte et al. 2000, Dunn et al.
2008). This debate mainly stressed the importance of dealing with extensive taxonomic sampling, even when examining qualitative molecular signatures or genome
level characters. The extension of the phylogenomic approach has rephrased some
longstanding questions in animal phylogeny such as the position of acoel flatworms,
chaetognaths or relationships within the lophotrochozoan clade. It has also brought
some surprising rearrangements, such as the positioning of the tunicates as vertebrate sister group (Delsuc et al. 2005). More surprisingly, the “new view” scheme
was challenged by the branching of some phyla such as acoels or chaetognaths that
do not fit within the ecdysozoan and lophotrochozoan clades. Recently the collection and analysis of a large amount of data from minor groups, described in a
paper by Dunn et al. (2008), showed that that some phyla remain refractory to accurate positioning (Dunn et al. 2008). Several questions concerning metazoan tree
of life thus remain open. For example, the exact relationships at the base of the
metazoan tree remain elusive because of the difficulty of determining the branching order of bilaterians, poriferans, cnidarians and also ctenophores, all of which
are groups that possibly diverge at the base of the metazoan radiation (Dunn et al.
2008). Answering this question would provide important insights into the nature
of the metazoan ancestor: a complex organism that already possessed a mesoderm
and bilateral symmetry, such as a ctenophore, or an organism of lesser complexity such as a sponge larva (Martindale and Henry 1999, Nielsen 2008)? Increased
gene and taxonomic sampling as well as improvements to inference models are
likely to be valuable tools for resolving these issues. Moreover, when the whole
set of employable marker genes will have been exploited by molecular phylogeny,
numerous other features such as gene order and synteny relationships might deserve
further investigation (Philippe et al. 2005a).
The latter example of relationships at the base of metazoans emphasized the
importance of phylogenetics as a means to understand the major evolutionary
transitions of morphological characters. In particular, the power of molecular phylogenetics to ensure the orientation of characters has demonstrated that no general
trends exist in the establishment of morphological complexity. The close association
of nemerteans and annelids as well as that of vertebrates and tunicates has clearly
shown that morphological simplifications have occurred repeatedly during the evolution of metazoans (Delsuc et al. 2005, Dunn et al. 2008). At a deeper evolutionary
scale, the early divergence of ctenophores proposed by Dunn et al. (2008) suggested
that the ancestor of all metazoans was far more complex than expected and that the
morphological simplicity of poriferans could be secondarily derived.