Ammonite

The ammonite is a standalone fossil in the introduced in  that appears in all subsequent games to date.

In
After donating the fossil in, its plaque in the museum will read:

"Ammonites were sea creatures with shells ranging from a few inches to a few feet in diameter. However, theories speculate that giant varieties existed as well, with shells six feet in diameter. Oddly, the ammonite is a closer relative to the squid or octopus than to the chambered nautilus."

In
Alfonso and Yū manage to dig up an ammonite fossil in during the summertime. Later, they, along with Ai, Margie, and Rosie, go into a cave to hunt for more ammonite fossils. After going through a waterfall, they stumble upon a mountain of ammonite fossils. Later in the wintertime, when searching for the Gulliver's spaceship part, Yū and the others see the same mountain of ammonite fossils.

Real-world information
Ammonites were a group of cephalopods which lived from the Devonian to the Cretaceous period. Despite their appearance, they are more closely related to the coleoids (shell-less cephalopods like squids, cuttlefish, and octopuses) than nautiluses (which have shells). They were extremely abundant during the Mesozoic - with some species used as index fossils to mark the beginnings of geologic stages - and remain the most common fossils on beaches. They went extinct at the same time as the non-avian dinosaurs.