cdysozoans and other lophotrochozoans. In addition, 11 genes shared only with non-bilaterians were identified, illustrating the ubiquity of gene loss.
The significance of cnidarians for understanding the urbilaterian gene complement
Although the genome of a choanoflagellate (thought to be the closest living relatives of the animals)  showed us that some 'animal-specific' genes came earlier in evolution, many other genes really are unique to metazoans, and these include components of several signaling pathways (such as the Wnt, transforming growth factor β and nuclear hormone receptor pathways). When the genomes of bilaterians are compared with those (admittedly, as yet few) available for 'lower' (non-bilaterian) animals, one fact that clearly stands out is that a quantitative leap in terms of signaling molecule complexity preceded the emergence of the Cnidaria (the phylum that includes hydras, sea anemones, corals and jellyfish). Whereas most or all of the animal-specific signaling systems seem to be present in the genomes of Porifera (sponges) and Placozoa (placozoans; very simple animals with only three or four distinct cell types), they are much less highly elaborated than in cnidarians or bilaterians. For example, whereas the sea anemone Nematostella has 12 Wnts, most of which are recognizable as homologs of specific Wnt types known from bilaterians , the sponge Amphimedon and the placozoan Trichoplax each have only three Wnts that are not easily assignable. In addition, these lower animals seem to have much less well developed arsenals of signaling molecule antagonists. The situation with respect to transcription factors is a little less clear cut but, for example, the homeobox gene complement of Nematostella is much more bilaterian-like than are those of sponges and placozoans . In summary, cnidarians seem to be particularly important in terms of under standing the urbilaterian gene repertoire.
Have lophotrochozoans lost fewer genes?
There is a widespread perception that ecdysozoans have lost more of the ancestral 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