A it is
Fossils of a whale that beached on an African shore more than a million years ago and was subsequently butchered by homonids
have been recovered by paleontologists.
The red part is 2 restrictive clauses introduced by relative pronoun "that" and linked by conjunction "and". Pronoun reference has been explained by Hjort already but this is how sentence structure looks like. The black part is the independent clause which now looks like:
Fossils of a whale have been recovered by paleontologists.
"have been" is proper because it is the "fossils" which have been
recovered, not the "whale"