Phylogenetic comparative methods (PCMs) use information on the evolutionary relationships of organisms (phylogenetic trees) to compare species (Harvey and Pagel, 1991). The most common applications are to test for correlated evolutionary changes in two or more traits, or to determine whether a trait contains a phylogenetic signal (the tendency for related species to resemble each other ). However, several methods are available to relate particular phenotypic traits to variation in rates of speciation and/or extinction, including attempts to identify evolutionary key innovations. 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 (see list below). 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, maximum likelihood or Bayesian 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 (see below).
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.
The comparative method is also used heavily in linguistics.
Read more about Phylogenetic Comparative Methods: Applications, Phylogenetically Independent Contrasts, Phylogenetically Informed Monte Carlo Computer Simulations, Related Quotations, See Also
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