New genes or ancient genes?
From Trends in Genetics
The resulting data set… implies that much of the genetic complexity commonly assumed to have arisen much later in animal evolution is actually ancestral. The most surprising implication of these analyses, however, is that anthozoans have retained a substantial number of genes not previously known in the animal kingdom. Two possibilities remain to explain the presence of these genes in the anthozoan genomes:
(i) lateral gene transfer (LGT); or
(ii) conservation of ancient genes that have been lost from those animals for which complete sequences are available.
Although we cannot rule out LGT in all cases, we favor the latter explanation for most of these matches…
In many respects, the complexity of the anthozoan gene set does not differ substantially from that of vertebrates and frequently exceeds that of the model invertebrates Drosophila and Caenorhabditis… One possible interpretation of the counterintuitive genetic complexity of cnidarians could be that they are actually highly derived deuterostomes. However, this interpretation is strongly contradicted by a large body of phylogenetic data, which indicates that cnidarians are a monophyletic group basal within the Eumetazoa and forming the sister group to the Bilateria….
Four general conclusions emerge from this work. First, a link between morphological complexity and gene number is illusory. Second, the common ancestor of cnidarians and ‘higher’ animals (the Ureumetazoa) was surprisingly complex at the genetic level. Third, a small percentage of genes in the two anthozoans represents preserved ancient genes that were present in the common ancestor but have been lost in the ‘higher’ animals so far examined… Finally, gene loss has had a major role in animal evolution, and has been particularly extensive in the ecdysozoan model organisms… The remarkable genetic complexity of anthozoan cnidarians implies that most of the qualitative genetic differences between animals and other eukaryotes are ancestral…