Geoscientists generally start with the assumption of material realism, that everything happens by natural causes. The fossils are interpreted under the paradigm of Neo Darwinian evolution. The simplest fossils are regarded as the oldest regardless of the strata in which the fossils are found. The more complex fossils are always considered to be younger.
The birds for example are thought to be descended from dinosaurs. This is based on fossils of birds thought to be more primitive that modern birds even though the most primitive birds are found in strata though to be younger than more complex birds.
Most geoscientists depend on theory of descent with modification as a framework for interpreting the fossil record.