Phylogenetic bracketing

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 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.KryptobaatarCimolomyidaeEobaataridaeOrnithorhynchus (platypus)Tachyglossidae (echidnas) 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 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. There are three levels of inference, with each higher level indicating less confidence for the inference. Level 1 — The inference of a character that leaves a bony signature on the skeleton in both members of the extant sister groups. Example: Saying that Tyrannosaurus rex had an eyeball is a level 1 inference because both extant members of the groups encompassing Tyrannosaurus rex have eyeballs, and eyeball sockets (orbital excavations) in the skull, the homology of which is well established, and the fossils of Tyrannosaurus rex skulls have similar morphology. Level 2 — The inference of a character that leaves a signature on the skeleton of only one of the extant sister groups. For example, saying that Tyrannosaurus rex had air sacs running through its skeleton is a level 2 inference as birds are the only extant sister group to Tyrannosaurus rex to show such air sacs. However the underlying pneumatic fossae, air sacs, in the bones of extant birds are remarkably similar to the cavities seen in the fossil vertebrae of Tyrannosaurus rex. The high degree of similarity between the pneumatic fossae in Tyrannosaurus rex and extant birds makes this a fairly strong inference, yet not as strong as a level 1 inference. Level 3 — The inference of a character that leaves a bony signature on the skeleton but is not present in either extant sister group to the taxon in question. For example, saying that ceratopsian dinosaurs such as Triceratops horridus had horns in life would be a level 3 inference. Neither extant crocodylians, nor extant birds have horns today, but the osteological evidence for horns in ceratopsians is without question. Thus a level 3 inference receives no support from the extant phylogenetic bracket, but can still be used with confidence based on the merits of the fossil data itself. The Extant Phylogenetic Bracket can be used to infer the presence of soft tissues even when those tissues do not interact with the skeleton. As before, there are three different levels of inference. These levels are designated as prime levels. They descend in confidence as they move up a level. Level 1′ — The inference of a character that is shared by both extant sister groups, but does not leave behind a bony signature. For example, saying that Tyrannosaurus rex had a four-chambered heart would be a level 1′ inference as both extant sister groups (Crocodylia and Aves) have four-chambered hearts, but this trait does not leave behind any bony evidence.