Phylogeny

Abstract

A phylogeny is a pattern of historical evolutionary relationship among species and higher level taxa that is often presented as a tree diagram, or phylogenetic tree. The term phylogenetics is often applied to the study of such relationships. Historically, phylogenetic trees were often produced by indirect methods and were not reproducible. Classifications often had little if any direct relationship to phylogeny. Modern phylogenetics utilizes cladistic methods to construct phylogenetic trees based directly on morphological and molecular data. For those who distinguish cladistics from phylogenetics, cladistics refers only to the methods by which the branching patterns are generated (e.g., parsimony or maximum likelihood) while phylogenetics refers to the interpretation of such diagrams as historical patterns. This is a useful distinction, since cladistic methods are neutral to the type of data and the resulting interpretations, and could be applied to nonphylogenetic problems (e.g., recovering or imposing hierarchic structure within any system of objects with shared variation). Phylogenies are analogous to genealogies on the scale of species and higher level taxa (e.g., genera and families). Phylogenies are usually presented as treelike branching diagrams, in which taxa that are on the same branch are thought to be more closely related to each other than taxa that occur on different branches. Interpreting such diagrams as historical patterns requires a basic understanding of hierarchy, and phylogenetic trees are often incorrectly assumed to support particular historical suppositions (e.g., one modern taxon is “primitive”) that are not indicated by the results. Phylogenetic trees are increasingly useful in a broad array of biological studies as a basis for experimental design as well as the framework on which to generalize results. Additional uses of phylogenetic information include measures of phylogenetic diversity, which can be used in making conservation and habitat preservation decisions.