Phylogenetic bracketing

Phylogenetic bracketing is a method of inference used in biological sciences. It is used 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 organisms, known only from fossils, going all the way back to the last universal common ancestor (LUCA). 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. Extant Phylogenetic Bracketing requires that the species forming the brackets be extant. More general forms of phylogenetic bracketing do not require this and may use a mix of extant and extinct taxa to form the bracket. These more generalized forms of phylogenetic bracketing have the advantage in that they can be applied to a wider array of phylogenetic cases. However, since these forms of bracketing are also more generalized and may rely on inferring traits in extinct animals, they also offer lower explanatory power compared to the EPB. This is a popular form of phylogenetic bracketing first introduced by Witmer in 1995. It works by comparing an extinct taxon 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. The extant phylogenetic bracket approach allows researchers to infer traits in extinct animals with varying levels of confidence. This is referred to as the levels of inference.