Types of Inference
There are three types of inferences that can be drawn based on phyolgeny. The above example, concluding that Tyrannosaurus could lay amniotic eggs, is the standard type, and is called a type I inference. A type II inference is made where one of the extant relatives has the trait and the other does not. In the case of the Tyrannosaurus, a type II inference could be to conclude that it had feathers (like a bird). This is less certain, and depends on at what stage feathers evolved. From phylogeny alone, it is equally possible Tyrannosaurus had scutes (like a crocodile). In contrast, concluding that Tyrannosaurus had hair would be a type III inference, and considered unlikely. Type III inferences are only warranted if there is some positive evidence that the extinct creature possessed the trait.
Read more about this topic: Phylogenetic Bracketing
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