Phylogenetic bracketing is a method of inference used in biological sciences. It is to infer the likelihood of unknown traits in organisms based on their position in a phylogenetic tree. One of the main applications of phylogenetic bracketing is on extinct animals, known only from fossils. The method is often used for understanding traits that do not fossilize well, such as soft tissue anatomy, physiology and behaviour. By considering the closest and second closest well known (usually extant) organisms, traits can be asserted with a fair degree of certainty, though the method is extremely sensitive to problems from convergent evolution.
While the method has its greatest value when extant species are used for bracketing, the method itself does not require that both bracketing groups have extant members, nor that the species or group to be bracketed is extinct. The only real requisite is that the two bracketing species/groups be better known, with regard to the trait in question, than the species to be bracketed is.
Extant phylogenetic bracketing (EPB)
Normally, phylogenetic bracketing is done by comparing an extinct animal to its nearest living relatives. For example, Tyrannosaurus, a theropod dinosaur, is bracketed by birds and crocodiles. A feature found in both birds and crocodiles would likely be present in Tyrannosaurus, such as the capability to lay an amniotic egg, whereas a feature both birds and crocodiles lack, such as hair, would probably not be present in Tyrannosaurus. Sometimes this approach is used for the reconstruction of ecological traits as well.
Example of bracketing with one extinct and one extant group
Assuming that the Kryptobaatar and Tachyglossidae spurs are homologous, they were a feature of their tribosphenidan last common ancestor, so we can tentatively conclude that they were present among the Early Cretaceous Eobaataridae—its descendants—as well.
Example of bracketing with only extinct groups
A fragmentary fossil with a known phylogeny can be compared to more complete fossil specimen to give an idea about general build and habit. The body of labyrinthodonts can usually be interfered to be broad and squat with a sideways compressed tail, although only the skull has been known for many taxa, based on the shape of more well-known labyrinthodont finds.
Types of inference
There are three types of inferences that can be drawn based on phylogeny. 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.
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