stylistic:tone, information:extraction
Family tree

It is difficult to reconstruct the early stages in the evolutionary "family tree" of animals using only morphology (their shapes and structures), because the large differences between Porifera (sponges), Cnidaria plus Ctenophora (comb jellies), Placozoa and Bilateria (all the more complex animals) make comparisons difficult. Hence reconstructions now rely largely or entirely on molecular phylogenetics, which groups organisms according to similarities and differences in their biochemistry, usually in their DNA or RNA.

It is now generally thought that the Calcarea (sponges with calcium carbonate spicules) are more closely related to Cnidaria, Ctenophora (comb jellies) and Bilateria (all the more complex animals) than they are to the other groups of sponges. In 1866 it was proposed that Cnidaria and Ctenophora were more closely related to each other than to Bilateria and formed a group called Coelenterata ("hollow guts"), because Cnidaria and Ctenophora both rely on the flow of water in and out of a single cavity for feeding, excretion and respiration. In 1881, it was proposed that Ctenophora and Bilateria were more closely related to each other, since they shared features that Cnidaria lack, for example muscles in the middle layer (mesoglea in Ctenophora, mesoderm in Bilateria). However more recent analyses indicate that these similarities are rather vague, and the current view, based on molecular phylogenetics, is that Cnidaria and Bilateria are more closely related to each other than either is to Ctenophora. This grouping of Cnidaria and Bilateria has been labelled " Planulozoa " because it suggests that the earliest Bilateria were similar to the planula larvae of Cnidaria.

Within the Cnidaria, the Anthozoa (sea anemones and corals) are regarded as the sister-group of the rest, which suggests that the earliest cnidarians were sessile polyps with no medusa stage. However, it is unclear how the other groups acquired the medusa stage, since Hydrozoa form medusae by budding from the side of the polyp while the other Medusozoa do so by splitting them off from the tip of the polyp. The traditional grouping of Scyphozoa included the Staurozoa, but morphology and molecular phylogenetics indicate that Staurozoa are more closely related to Cubozoa (box jellies) than to other "Scyphozoa". Similarities in the double body walls of Staurozoa and the extinct Conulariida suggest that they are closely related.

However, in 2005 Katja Seipel and Volker Schmid suggested that cnidarians and ctenophores are simplified descendants of triploblastic animals, since ctenophores and the medusa stage of some cnidarians have striated muscle, which in bilaterians arises from the mesoderm. They did not commit themselves on whether bilaterians evolved from early cnidarians or from the hypothesized triploblastic ancestors of cnidarians.

In molecular phylogenetics analyses from 2005 onwards, important groups of developmental genes show the same variety in cnidarians as in chordates. In fact cnidarians, and especially anthozoans (sea anemones and corals), retain some genes that are present in bacteria, protists, plants and fungi but not in bilaterians.

The mitochondrial genome in the medusozoan cnidarians, unlike those in other animals, is linear with fragmented genes. The reason for this difference is unknown.