Originally, we had a neat little diagram here with links to the literature for the phylogenetic position of each taxon. This fastidious arrangement degenerated into swirling chaos when we had several changes of heart while writing a number of the individual sponge essays. Ultimately, we hit on a completely different phylogeny which satisfies us, but would probably be dismissed as pathological by more knowledgeable folks. Consequently, most of the citations had to be dropped from the cladogram.
At the tail end of our research we discovered that at least a few others may be sympathetic with some of our more radical rearrangements. If so, we look forward to being vindicated eventually. We remain optimistic since, as with other primates with keyboards, the laws of probability require that we will sometimes get one right. Although, having just finished de Waal's Our Inner Ape, we have the unsettling suspicion that certain apes might resolve the phylogeny faster than ourselves.
The story that emerged begins on the calcite "reefs" created by mineralizing bacteria in the Neoproterozoic. We discuss how small protoanimals took up residence in bacterial thrombolites and eventually adapted to mimic the form of these structures. In fact, this may have happened more than once, if archaeocyaths, Cloudina, and Namacalathus are all unrelated. In any case, the outcome of that process was a generally "thrombolitic" structure: a cup-like, sessile, calcareous organism with internal septae and a sponge-like way of sucking water in from external pores and shooting exhalant water from a central osculum. All three lineages also begin with an essentially single-walled body plan. All, even Namacalathus, tend to become double-walled at some point above the base. Archaeocyaths show a similar tendency in an evolutionary sense, with increasing development of the inner wall and elaboration of tabulae and septae into a regular set of box-like chambers between the walls.
It turns out that stromatoporoids may well have developed in the same fashion, as discussed by Hladil (2007). In fact, it isn't all that easy to tell juvenile specimens of some stromatoporoids from archaeocyaths, or even a Namacalathus. However, other stromatoporoids responded to a unique set of ecological pressures in the Furongian and Ordovician, by becoming flat and massive. This trend was both slow and progressive, so we can be relatively certain that it represented a true evolutionary trend. We discuss some of the reasons why this may have occurred.
Other sponges retained the "cyath" body plan, but found a new, and less mineral-intensive, way to support it -- by using spicules. Note that most Paleozoic sponges had quite regular body plans, all derived from the cyath system of external pores, an "intervallum" with living cells, and a wide central space with open osculum. See, for example, the various Paleozoic sponges discussed in connection with hexactinellids and demosponges. We outline some of the key biochemistry and molecular biology which unite the synthesis of calcareous and siliceous spicules, and unite both with the chemistry of the massive calcareous skeletons formed by stromatoporoids and archaeocyaths, in general agreement with the hypothesis of Botting & Butterfield (2005). Eventually, these spicules removed the necessity for maintaining a regular body plan of any type.
Homoscleromorphs are key players because they seem to share synapomorphies with eumetazoans. However, some studies based on molecular sequence data (e.g. Sperling et al., 2006) have united Homoscleromorpha with Calcarea, rather than Demospongiae. We explain why this arrangement is unworkable. The single morphological character that supposedly united calcareans with homoscleromorphs, the cross-striated ciliary rootlet, is plesiomorphic "primitive") and known from any number of eukaryotes. Very recently, a cross-striated ciliary rootlet has also been identified in a demosponge. Riesgo, Taylor et al. (2007). Thus, this character cannot support a clade of Calcarea + Homoscleromorpha + Eumetazoa. Conversely, the characters which tend to unite homoscleromorphs with non-sponge animals are all traceable to developments in the demosponges (and generally not in Calcarea): for example the key collagen types, various aspects of embryology (see also here), and fatty acid structure.
Thus, when we'd walked this road as far as we could, we arrived at a phylogeny very different from the one we had in mind when we set out. In a general way, the whole phylogeny can be interpreted as a series of different strategies for physical support -- clearly the first and most obvious problem for multicellular organisms. After the choanoflagellate-like ancestral forms evolved the basic machinery for adhesion, metazoans adapted to take advantage of pre-existing physical supports. It seems likely that thrombolites were merely the most succesful of many structures adopted as templates. These bacterial structures provided a transition mechanism and medium through which the early metazoans could easily develop the cyath body plan.
However, the thrombolitic structure is workable only in environments which favor microbialites in the first place. Thus, selection would favor sponges which could either (a) out-mineralize the cyanobacteria on their home ground, or (b) adopt a lifestyle which would allow the sponge to live elsewhere. Stromatoporoids perfected the first approach, while the spiculate sponges tried the second. As argued by Botting & Butterfield, the evolution of spicules probably involved a host of different molecular strategies, with the crystalline calcareous spicule and amorphous silicate spicule representing only the two most succesful systems. Both strategies eventually permitted sponges to abandon the cyath body plan, although traces remained in the structure and development of the stromatoporoids, as well as the regular morphology of early spiculate sponges.
Collagen is used in the assembly of all spicules. At some point on the demosponge stem lineage, sponges evolved spongin from this starting point. Spongin proteins could be used, without mineralization, to supplement spicules. The homoscleromorphs diverged at this point, evolving a long-chain Type IV collagen which aggregated to form basement membranes, allowing a further reduction or (in many cases) elimination of the spicule-generating mechanism. The basement membrane, in turn, permitted the evolution of novel kinds of cell-cell interactions
Ultimately, at least one lineage evolved to derive physical support from the interactions between cells as much as the basement membrane in which the cells were embedded. The stability of cell-cell connections in a basement membrane also permitted the evolution of more specialized tissues. However, this step required regular symmetry in the adult. The maintenance of numerous specialized tissues is most easily accomplished if the tissues have predictable geometrical relations to each other and to the medium. Similarly, the balance between numerous specialized tissues can only be maintained through long-range structural interactions (mediated, e.g., through neurons and contractile fibrils). Long-range interactions, in turn, require long-range order -- a precondition met most easily through symmetry, and perhaps acquired by building on the symmetrical morphology of the homoscleromorph cinctoblastula embryo, with its large central cavity.
Thus, the Eumetazoa evolved as a natural and straightforward consequence of a series of evolutionary changes favoring structural stability under differing conditions. With some relatively arbitrary additions (Chancelloriidae) and speculations (Namacalathus), the whole gemisch looks like this:
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