cestral gene set than have deuterostomes or lophotrochozoans. This notion has its roots in early comparisons (for example, ) between cnidarians, vertebrates and the model ecdysozoans (fly and nematode worm), which clearly demonstrated that gene loss was much more extensive in Drosophila and Caenorhabditis than in vertebrates. Since that time, genome data have become available for a broader range of species, so to what extent does this generalization still hold? Is it possible (or meaningful) to generalize - have ecdysozoans in general lost more genes than lophotrochozoans or deuterostomes, or do we still have too few whole genome sequences to be able to say?
There are now whole-genome data for over 20 insect species (this includes 12 Drosophila species) and a handful (5) of nematodes. Comparisons between insects and vertebrates (for example, ) indicate that gene loss is largely a function of rates of evolution and divergence times, and does not discriminate between vertebrates or insects. Among insects, Drosophila has a particularly high rate of evolution, whereas the beetle Tribolium and the honeybee Apis have lower rates of evolution and have lost fewer of the ancient genes present in Urbilateria. Although vertebrates in general have lost fewer ancient genes, the chicken is a clear outlier, having lost more genes in the 'universal single-copy orthologs' and 'universal multi-copy orthologs' categories than any of the five insects included in the Wyder et al. analysis . Moreover, whereas the two Caenorhabditis species and the parasitic species Brugia malayi and Meloidogyne hapla all show the 'typical' ecdysozoan pattern of extensive gene loss, a fifth nematode species, Pristionchus pacificus, is not so reduced .
What about lophotrochozoans? Whole genome sequences have been determined for seven genera (eight species; two Schistosoma species), but so far very few large-scale analyses have been published. The idea that the genomes of lophotrochozoans are less derived than those of ecdysozoans comes largely from work 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 com