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On a recent fossil hunting trip, I found a small fossil that an expert identified for me as an ammonite beak. He told me such fossils are not uncommon, but are not normally found with their parent shell due to the decay of the soft tissues holding the beak in place.

I know that under some unusual conditions, (i.e. the Burgess Shale) the soft tissues of animals can be preserved. And a quick google search reveals that there are rare belemnite fossils with their tentacles in place.

However I can find no reference to any ammonite fossils, nor any of the orthocone clades, with soft part preservation.

Shells of similar shape and structure are not unknown in other groups of mollusic (i.e gastropods). So: what characteristics of the shell make taxonomists sure that ammonites and orthocones are cephalopods rather than some other kind of mollusc?

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It really is mostly the siphuncle as @augurar mentioned. The siphuncle is present in modern ammonites, cuttlefish, and Spirula(a deep-sea squid with an internal chambered shell). It links shelled cephalopods neatly with other cephalopods(both extant and extinct) and distinguishes them from other shelled things like snails.

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I am proud that I can answer your very, very good question!

You are right that the soft tissue of ammonites is very, very rare. But along with beaks (I believe you meant aptychi) you can find something with similar function called radula, which is (at least for devonian ammonoids) both in morphology and in number of elements identical to recent coleoids! Ammonites belong to ammonoids and this puts them closer to Coleoids than to Nautiloids. Nautiloids have very, very similar external shell, but with siphuncle going differently and many other details - one would expect them to be closely related.

It is now well known fact that ammonites are ammonoids. And that both ammonoids and coleoids evolved from bactrites.

For more info see: Kröger, B., Vinther, J. & Fuchs, D. (2011): Cephalopod origin and evolution: A congruent picture emerging from fossils, development and molecules. ― Bioessays, 33, 602–613.

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