Phylogenetic Comparative Methods

Phylogenetic comparative methods (PCMs) use information on the evolutionary relationships of organisms (phylogenetic trees) to analyze the origin and maintenance of biodiversity. Biodiversity is most commonly discussed in terms of the number of species, but it can also be phrased in terms of the amount of "morphospace" that a given set of species occupies (see also Cambrian explosion). PCMs focus more on the latter. Although most studies that employ PCMs focus on extant organisms, the methods can also be applied to extinct taxa and can incorporate information from the fossil record.
Owing to their computational requirements, they are usually implemented by computer programs . PCMs can be viewed as part of evolutionary biology, systematics, phylogenetics, bioinformatics or even statistics, as most methods involve statistical procedures and principles for estimation of various parameters and drawing inferences about evolutionary processes.
What distinguishes PCMs from most traditional approaches in systematics and phylogenetics is that they typically do not attempt to infer the phylogenetic relationships of the species under study. Rather, they use an independent estimate of the phylogenetic tree (topology plus branch lengths) that is derived from a separate phylogenetic analysis, such as comparative DNA sequences that have been analyzed by maximum parsimony or maximum likelihood methods. PCMs are consumers of phylogenetic trees, not primary producers of them. Accordingly, the list of phylogenetics software shows little overlap with the programs for PCMs .
Comparison of species to elucidate aspects of biology has a long history. Charles Darwin relied on such comparisons as a major source of evidence when writing The Origin of Species. Many other fields of biology use interspecific comparison as well, including behavioral ecology, ethology, ecophysiology, comparative physiology, evolutionary physiology, functional morphology, comparative biomechanics, and the study of sexual selection.