|Ctenophore (Image: John Wollwerth)|
There are many analogies here to the current understanding of fungal relationships, and relationships within groups of fungi, some of which are pretty confounding. The relationship of the microsporidia to the other fungi is something that's still being worked out for example, as are the relationships among the organisms that used be lumped in to the Zygomycota. For several years, the Glomeromycota (arbuscular mycorrhizal fungi) have come up in phylogenetic trees as a sister group to the Asco- and Basidiomycota line (supporting the hypothesis of a grand fungal radiation diverging with early plants), but on the other hand at least one phylogeny published in the last few years has grouped the Glomeromycota with the Mucoromycota and other core "zygos", supporting the classification that was largely abandoned at least a decade ago (and supporting alternate hypotheses of mycorrhizal evolution).
What to make of all this? Basically that while molecular phylogeny is wonderful and revolutionary, and has really deepened our understanding of the relationships and evolution of organisms, the information content can be as contradictory and unclear as any other method of understanding evolutionary relationships among organisms, and hence can't necessarily be treated as the final word on the matter. And this is why morphological, developmental, and ecological data, in other words, the stuff of old-fashioned natural history, is still critical to understanding evolutionary relationships and much else about the living world.
Addendum: I didn't think to have a look at Jerry Coyne's take on the Ryan, et al. paper until after I'd written the article, but probably should have - his perspective on these kind of discoveries is always valuable, and of course, I defer to his knowledge on anything to do with the subject of evolution, speciation, etc. That said, I'm not sure I entirely agree with him on this. His take is that the quality of molecular phylogenetic work in this paper is the best to date for the deep phylogeny of Metazoa, and that while the implications about evolutionary morphology in animals has some odd implications (notably, that the earliest ancestor living animal groups already had a simple nervous system, possibly some degree of bilateral symmetry, etc) but these should be accepted and studied within the evolutionary framework that this study suggests. I'm less sure given that so many prior studies have supported the idea of Porifera as the earliest metazoan branch, and morphological evidence, notably the strongly choanoflagellate-like collar cells in sponges, lends support to the sponge-like common ancestor hypothesis as well. Also, I've seen papers before that seemed to strongly support some kind of odd relationship between organisms, only to be falsified by the next paper that comes along. I reserve judgement on this matter until, as is bound to happen within a few years, one of these hypotheses becomes settled science.