 on the annelid P. dumerilii, which shows that this organism is closer to vertebrates than to ecdysozoans in intron structure and retention, and in protein coding sequence similarity (see, for example, ). The only lophotrochozoans with sequenced and analyzed genomes, Schistosoma mansoni and S. japonicum, are both parasitic platyhelminths, which, consistent with other parasites, have undergone extensive gene loss and divergence. Thus, they can hardly be considered representative of phyla consisting mostly of free-living forms. There are bound to be derived lophotrochozoans, just as there are derived ecdysozoans and derived deuterostomes.
So, although this limited sample of two annelids  is consistent with greater gene loss in Ecdysozoa than in Lophotrochozoa, it is still very early days, and it would be premature to yet draw general conclusions. We await with interest the analysis and publication of more lophotrochozoan genomes, particularly those of free-living flatworms, mollusks, and some of the smaller phyla, such as bryozoans, nemertines and brachiopods.
Any gene can go
One surprising implication of comparative genomics is that no gene is indispensable; every animal seems to have lost hundreds of what one might have assumed were 'core requirement' genes. For example, Wyder et al.  report that 40% of ancient orthologous genes were lost in a least one of the ten animals included in their analysis (five insects and five vertebrates). One example of loss of a core gene is the case of the Toll receptor in Hydra magnipapillata.
Whereas Nematostella and other members of the basal cnidarian class Anthozoa have a canonical Toll receptor, Hydra (which is a member of the more derived class Hydrozoa) has lost this gene . Hydra seems to have undergone non-orthologous gene replacement, Toll receptor function being fulfilled by two unrelated proteins . Evolution sometimes dispenses with whole pathways, for instance the entire DNA methylation system in the case of dipterans (flies and mosquitoes).
Inferring the ancestral complement - was Urbilateria a monster?
All animals have lost genes, but it does not follow that Urbilateria was a monster in terms of gene content. Bilaterian animals typically have around 20,000 genes (range 11,500 to 28,000;Meloidogyne to Tetraodon), but a substantial fraction of these are taxonomically restricted at some level. Many of these taxonomically restricted genes are paralogs or highly diverged members of large gene families, generated by duplication events that have occurred at all levels. On the basis of the currently available data, the core bilaterian gene set probably contained fewer than 10,000 genes, the caveat being that the available data are rather limited. Taxonomic gaps need to be plugged, and more data for non-bilaterians in particular will be critical in revealing the genomic makings of Urbilateria. Far too few whole-genome sequences are yet available for firm estimates to be made, but it is clear that there is no need to invoke monsters - either hopeful or hopeless.
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