Paleontology investigates past life through fossils and their geological context. It combines anatomy, ecology, evolution and evidence about burial and preservation to infer what extinct organisms were like and how life changed.
The connection between evidence and history is the central challenge. A fossil may preserve a tooth but lose its surrounding soft tissues; absence of a visible character need not mean the living organism lacked it. Taphonomy therefore informs both reconstruction of individual organisms and interpretation of the fossil record.
Experiments following carcass decay test that inference directly: anatomically selective loss can remove derived characters and produce stemward slippage in a phylogenetics analysis.[ref]
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