Literature

Sea anemones, jellyfish and corals are all cnidarians, a phylum that goes back to the Late Precambrian. Geneticists studying this group of organisms have made much use of the starlet sea anemone Nematostella vectensis. Whilst previously reported research has been concerned with specific genetic elements, a new study reports on a comparative analysis of the whole genome. The sea anemone genome has been found to contain about 18,000 protein-coding genes with many of the same gene families that are found in other sequenced animals. This is where the surprises start.
The authors write: "The sea anemone genome is complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes, implying that the genome of the eumetazoan ancestor was similarly complex." Elizabeth Pennisi observes: "This implies that even very ancient genomes were quite complex and contained most of the genes necessary to build today's most sophisticated multicellular creatures." Eugene Koonin of the National Center for Biotechnology Information was interviewed about the research. He said that it is surprising to find such a "high level of genomic complexity in a supposedly primitive animal such as the sea anemone". It implies that the ancestral animal "was already extremely highly complex, at least in terms of its genomic organization and regulatory and signal transduction circuits, if not necessarily morphologically."
The comparative study had some additional surprises. Writing in The Scientist, Melissa Lee Phillips points out: "The study also found that these similarities were absent from fruit fly and nematode genomes, contradicting the widely held belief that organisms become more complex through evolution. The findings suggest that the ancestral animal genome was quite complex, and fly and worm genomes lost some of that intricacy as they evolved."
Some have inferred that the vertebrate genome must therefore be primitive, but this fails to do justice to the observed sophistication. The implication of this research is that we are not tracking an evolution of complexity with time, but we have identified the sudden emergence of complexity in the Precambrian. It is the genetic equivalent of the 'Cambrian explosion'!
A hint of this was published in 2005 in a study of the Wnt gene family, which encodes secreted signalling molecules that control cell fate in animal development and human diseases. "Cnidarians and bilaterians have at least eleven of the twelve known Wnt gene subfamilies in common; [. . .] This unexpectedly complex inventory of Wnt family signalling factors evolved in early multi-cellular animals about 650 million years (Myr) ago, predating the Cambrian explosion by at least 100 Myr."
Researchers have looked for simplicity but have found complexity. They have selected organisms described as primitive and have proved them to be advanced. One evolutionary developmental biologist is quoted as saying: "The work is truly stunning for its deep evolutionary implications". He's right, but not in the sense he intended: when the data is profoundly at variance with evolutionary expectations, it is time to consider whether a new paradigm is needed.

Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization
Nicholas H. Putnam, Mansi Srivastava, Uffe Hellsten, Bill Dirks, Jarrod Chapman, Asaf Salamov, Astrid Terry, Harris Shapiro, Erika Lindquist, Vladimir V. Kapitonov, Jerzy Jurka, Grigory Genikhovich, Igor V. Grigoriev, Susan M. Lucas, Robert E. Steele, John R. Finnerty, Ulrich Technau, Mark Q. Martindale, and Daniel S. Rokhsar
Science, 316, 6 July 2007: 86-94.

Sea anemones are seemingly primitive animals that, along with corals, jellyfish, and hydras, constitute the oldest eumetazoan phylum, the Cnidaria. Here, we report a comparative analysis of the draft genome of an emerging cnidarian model, the starlet sea anemone Nematostella vectensis. The sea anemone genome is complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes, implying that the genome of the eumetazoan ancestor was similarly complex. Nearly one-fifth of the inferred genes of the ancestor are eumetazoan novelties, which are enriched for animal functions like cell signaling, adhesion, and synaptic transmission. Analysis of diverse pathways suggests that these gene "inventions" along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor.

See also:

Pennisi, E., Sea Anemone Provides a New View of Animal Evolution, Science, 316, 6 July 2007: 27.
Melissa Lee Phillips, M.L. Surprises in sea anemone genome, The Scientist, 5th July 2007
Kusserow, A., et al., Unexpected complexity of the Wnt gene family in a sea anemone, Nature 433, 156-160, (13 January 2005)