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 For an explanation of mtDNA phylogenies, and an interminable diatribe about their weaknesses, see Insectivora. We've been railing against the use of mtDNA phylogenies almost as long as people have been doing them. As it turns out, we were mostly correct (although not always for the right reasons). This is rare enough that we've made the most of the opportunity -- perhaps our last chance to kick this particular dead horse.
 But not all. Schütze et al. (1999) note that choanodermal cells of Calcarea lack the distinctive collar of choanoflagellates, and that many details of sponge ultrastructure differ from those of these probable poriferan ancestors.
 We, of course, take issue with this point because we regard spicule formation as closely related in all sponge taxa, as discussed earlier. In fact, we assert elsewhere that spicules were developed exactly once. However, we tend to agree that chancelloriids are indeed sponges, largely for the other reasons cited by Sperling et al. (2006).
 Oscarella is actually aspiculate. The Homoscleromorpha in general have silicate spicules.
 The UCMP site cites to Reitner J (1990), Polyphyletic origin of the "Sphinctozoans" in K Rutzler (ed.), New Perspectives in Sponge Biology, Proceedings of the Third International Conference on the Biology of Sponges (Woods Hole). Smithsonian Institution Press, pp. 33-42. However, we have not read this paper.
 Grotzinger et al. cite to Grant SWF (1990), Shell structure and distribution of Cloudina, a potential index fossil for the terminal Proterozoic. Am. J. Sci. 290A: 261–294 as their basic text on Cloudina.
 We expect this statement to become obsolete very quickly.
 Archaeolynthus could also assume a growth pattern of branching, tube-like structures, somewhat like Figures A and B.
 From the First Phillipic of Demosthenes, directed against Phillip of Macedon in 351 B.C. (Middle Holocene of Europe).
 "Each PCR product was sequenced from a minimum of two clones [so they stopped after two if the sequences agreed?]; when contradictions in the sequences of several clones could not be resolved [how would one resolve them?], the corresponding positions were coded according to the UPIAC code. The two strands were sequenced for the main part of the sequence length, with special attention ["main part"? What is non-"special attention"?] to the D2 domain where strong secondary structures of the molecule cause compressions in the sequence migration [how do they know it's restricted to D2?]." Chombard et al. (1997: 361). What this might mean is: "We had some troubling problems with inconsistency, and ran out of time/funding, but we think the errors were not too significant." Quite possibly, that conclusion is correct. On the other hand, it isn't the sort of painstacking accuracy we might expect with the improved methods available today -- nor the kind of thing on which we should rely for mapping fundamental branches in the phylogeny of the Metazoa.
 As do certain nucleariid amoebae (Patterson, 1999), also thought to be on or around the metazoan stem. However, this may well be a convergent specialization. For the moment, we will ignore the nucleariids.
 It is interesting, if probably irrelevant, that some demosponge larvae, which lack a cross-striated ciliary rootlet, also have a ciliary "foot" which does appear to have cross-striations. Maldonado et al. (2003).
 Prof. Leys has expressed the view that the "plugged pores" of hexactinellids are not at all like Fungi. We think she's probably correct on this, but opinions vary.
 We discuss three of these features (basement membrane, flagellum, and embryonic development) in much more detail in connection with the Demospongiae. As discussed in that section, and in the section on Homoscleromorpha, none of these characters support a supposed clade composed of Calcarea + Homoscleromorpha + Eumetazoa, various papers to the contrary notwithstanding.
 One bizarre phylogenetic possibility raised by this similarity is that spicules evolved as a by-product of embryogenesis. Demoponge embryos frequently have spicules and, oddly enough, those spicules may be shed at metamorphosis. Maldonado et al. (1997). Sponges are also usually viviparous. Thus, we might imagine a Cloudina-like form, with internally growing embryos. Some embryos are released as young (and later shed their "baby spicules"), while others are retained to transdifferentiate into internal supports. This is pure speculation. But, in sponges, nearly anything is possible; and this would account for two sponge peculiarities at once.
 It's a bit hard to put any particular date on Prof. Claude Lévi. His first publication was in 1951. He retired from the MNHN (Paris) in about 2000, but we understand that he is still consulted on particularly difficult taxonomic calls.
 Oddly, this concern for contamination has never been addressed in the published sponge sequence phylogenies. Perhaps it is of less concern in such cases, for some reason.
 Briefly, (1) these polyketides look as if they may be derivatives of Δ5,9unsaturated fatty acids. These are better dealt with on their own terms and are discussed below. 2) Some members of this family are branched, which is rare among animals, but more common in bacterial metabolites. (3) The creation of peroxy derivatives is not only unusual, particularly for animals, but means that the resulting substance is probably quite unstable -- a bad thing when one is looking for potential presence/absence characters. For what it may be worth, our suspicion is that peroxypolyketides are an incidental by-product of the reaction of sponge enzymes evolved for the metabolism of Δ5,9unsaturated fatty acids with improper substrates, perhaps derived from fungi or dietary bacteria.
 (1) Reproductive biology reminds us of all the incredibly tedious stuff that bored us into catatonia during high school biology. (2) Characters of reproductive biology are wildly variable, seldom carry much long-range phylogenetic signal, and virtually never fossilize. (3) The subject requires a clear understanding of endocrinology and population genetics, both of which we lack because of item #1. 4) Finally, and perhaps most significantly, the subject requires a vocabulary which causes content censor programs to go into cardiac arrest and, conversely, attracts attention to the site from various types we like to avoid.