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F. Marlétaz and Y. Le Parco
least diverging copy of each selected gene from a pool of species representative of
a monophyletic taxon (Marlétaz et al. 2006). This strategy allowed, for example,
the building of a composite nematode taxon, whose branch is shorter than that of
Trichinella, one of the slowest evolving nematodes.
The strength of the phylogenomic approach has been generally underlined by
its ability to corroborate previous results based on multiple evidences. This suggests
that the phylogenomic approach is a promising tool to address unsolved questions of
animal relationships. However, the phylogenomic approach has also showed itself to
be very sensitive to systematic errors. To set up an accurate analysis, it is thus necessary to carry out a careful examination of the taxonomic sampling, the inference
methods used and the quality of the primary data.
4.5 Toward a Broad Phylogenomic Picture of Metazoan
Relationships
The main limitation of single-gene phylogenies is that they are unable to handle
some diverging taxa in terms of evolutionary rate or sequence composition. Such
taxa are generally considered as problematica when morphological features do not
allow this problem of phylogenetic affinity to be resolved. Among those taxa one
can find what Libbie Hyman called “smaller coelomate groups”, such as chaetognaths (Hyman 1959), and also the huge diversity of aschelminthes, from rotifers
to kinorhynches, whose interpretation is one of the key questions of animal evolution (Jenner 2000). The possibility offered by phylogenomics to more accurately
place these taxa in the metazoan tree has recently prompted a major sequencing
effort, especially using EST methodology. The EST approach involves the sequencing of the extremity of a large set of clones from a cDNA library. The clustering
of these transcript sequences can yield high quality partial transcriptome data. The
lack of one or more markers in a given taxon was demonstrated not to prevent accurate reconstruction of the overall tree (Philippe et al. 2004) and EST collections of
between 3,000 and 10,000 provide a sufficient set of markers to include a new taxon
in a phylogenomic analysis (Marlétaz et al. 2008, Philippe and Telford 2006).
4.5.1 Challenging Well-Established Clades: The Case
of Deuterostomes
Phylogenomics studies have lead to some longstanding phylogenetic hypotheses
being reconsidered. The relationships between deuterostomes were the first to be
challenged when urochordates were proposed to be the sister-group of vertebrates
instead of cephalochordates (Delsuc et al. 2006). This grouping had strong statistical support obtained from the analysis of 146 nuclear genes and several key
new taxa such as lampreys, hagfishes and the appendicularian Oikopleura dioica.
This finding contradicts some well-established synapomorphies joining vertebrates
F. Marlétaz and Y. Le Parco
least diverging copy of each selected gene from a pool of species representative of
a monophyletic taxon (Marlétaz et al. 2006). This strategy allowed, for example,
the building of a composite nematode taxon, whose branch is shorter than that of
Trichinella, one of the slowest evolving nematodes.
The strength of the phylogenomic approach has been generally underlined by
its ability to corroborate previous results based on multiple evidences. This suggests
that the phylogenomic approach is a promising tool to address unsolved questions of
animal relationships. However, the phylogenomic approach has also showed itself to
be very sensitive to systematic errors. To set up an accurate analysis, it is thus necessary to carry out a careful examination of the taxonomic sampling, the inference
methods used and the quality of the primary data.
4.5 Toward a Broad Phylogenomic Picture of Metazoan
Relationships
The main limitation of single-gene phylogenies is that they are unable to handle
some diverging taxa in terms of evolutionary rate or sequence composition. Such
taxa are generally considered as problematica when morphological features do not
allow this problem of phylogenetic affinity to be resolved. Among those taxa one
can find what Libbie Hyman called “smaller coelomate groups”, such as chaetognaths (Hyman 1959), and also the huge diversity of aschelminthes, from rotifers
to kinorhynches, whose interpretation is one of the key questions of animal evolution (Jenner 2000). The possibility offered by phylogenomics to more accurately
place these taxa in the metazoan tree has recently prompted a major sequencing
effort, especially using EST methodology. The EST approach involves the sequencing of the extremity of a large set of clones from a cDNA library. The clustering
of these transcript sequences can yield high quality partial transcriptome data. The
lack of one or more markers in a given taxon was demonstrated not to prevent accurate reconstruction of the overall tree (Philippe et al. 2004) and EST collections of
between 3,000 and 10,000 provide a sufficient set of markers to include a new taxon
in a phylogenomic analysis (Marlétaz et al. 2008, Philippe and Telford 2006).
4.5.1 Challenging Well-Established Clades: The Case
of Deuterostomes
Phylogenomics studies have lead to some longstanding phylogenetic hypotheses
being reconsidered. The relationships between deuterostomes were the first to be
challenged when urochordates were proposed to be the sister-group of vertebrates
instead of cephalochordates (Delsuc et al. 2006). This grouping had strong statistical support obtained from the analysis of 146 nuclear genes and several key
new taxa such as lampreys, hagfishes and the appendicularian Oikopleura dioica.
This finding contradicts some well-established synapomorphies joining vertebrates