Phylogeny
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The phylogeny (evolutionary "family tree") of molluscs is a controversial subject. In addition to the debates about whether Kimberella and any of the "halwaxiids" were molluscs or closely related to molluscs, debates arise about the relationships between the classes of living molluscs. In fact, some groups traditionally classified as molluscs may have to be redefined as distinct but related.
Molluscs are generally regarded members of the Lophotrochozoa, a group defined by having trochophore larvae and, in the case of living Lophophorata, a feeding structure called a lophophore. The other members of the Lophotrochozoa are the annelid worms and seven marine phyla. The diagram on the right summarizes a phylogeny presented in 2007.
Because the relationships between the members of the family tree are uncertain, it is difficult to identify the features inherited from the last common ancestor of all molluscs. For example, it is uncertain whether the ancestral mollusc was metameric (composed of repeating units)—if it was, that would suggest an origin from an annelid-like worm. Scientists disagree about this: Giribet and colleagues concluded, in 2006, the repetition of gills and of the foot's retractor muscles were later developments, while in 2007, Sigwart concluded the ancestral mollusc was metameric, and it had a foot used for creeping and a "shell" that was mineralized. In one particular branch of the family tree, the shell of conchiferans is thought to have evolved from the spicules (small spines) of aplacophorans; but this is difficult to reconcile with the embryological origins of spicules.
The molluscan shell appears to have originated from a mucus coating, which eventually stiffened into a cuticle. This would have been impermeable and thus forced the development of more sophisticated respiratory apparatus in the form of gills. Eventually, the cuticle would have become mineralized, using the same genetic machinery (engrailed) as most other bilaterian skeletons. The first mollusc shell almost certainly was reinforced with the mineral aragonite.
The evolutionary relationships 'within' the molluscs are also debated, and the diagrams below show two widely supported reconstructions:
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Morphological analyses tend to recover a conchiferan clade that receives less support from molecular analyses, although these results also lead to unexpected paraphylies, for instance scattering the bivalves throughout all other mollusc groups.
However, an analysis in 2009 using both morphological and molecular phylogenetics comparisons concluded the molluscs are not monophyletic; in particular, Scaphopoda and Bivalvia are both separate, monophyletic lineages unrelated to the remaining molluscan classes; the traditional phylum Mollusca is polyphyletic, and it can only be made monophyletic if scaphopods and bivalves are excluded. A 2010 analysis managed to recover the traditional conchiferan and aculiferan groups, but similarly concluded the molluscs are not monophyletic, this time suggesting the solenogastres are more closely related to the nonmolluscan taxa used as an outgroup than to other molluscs. Current molecular data are insufficient to constrain the molluscan phylogeny, and since the methods used to determine the confidence in clades are prone to overestimation, it is risky to place too much emphasis even on the areas of which different studies agree. Rather than eliminating unlikely relationships, the latest studies add new permutations of internal molluscan relationships, even bringing the conchiferan hypothesis into question.