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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 (et al. 2003 )). 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. The main objective of PCMs is to study the evolution of qualitative and quantitative traits as well as identifying patterns of origination and extinction in phylogenies. Most comparative models assume the phylogenetic tree is known without error in order to estimate parameters of interest. Therefore, PCMs use phylogenies which are already available and do not produce them. Accordingly, the list of phylogenetics software shows little overlap with the programs for PCMs, with the exception to a large series of R packages such as 'ape' and 'geiger' and standalone phylogenetic software such as 'Mesquite' (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. == Applications == PCMs can be used 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 phenotypic (e.g., physiological, morphological) space that a given set of species occupies (see also Cambrian explosion). Phylogenetic comparative methods are commonly applied to such questions as: * What is the slope of an allometric scaling relationship? → ''Example: how does brain mass vary in relation to body mass?'' * Do different clades of organisms differ with respect to some phenotypic trait? → ''Example: do canids have larger hearts than felids?'' * Do groups of species that share a behavioral or ecological feature (e.g., social system, diet) differ in average phenotype? → ''Example: do carnivores have larger home ranges than herbivores?'' * What was the ancestral state of a trait? → ''Example: where did endothermy evolve in the lineage that led to mammals?'' → ''Example: where, when, and why did placentas and viviparity evolve?'' * Does a trait exhibit significant phylogenetic signal in a particular group of organisms? Do certain types of traits tend to "follow phylogeny" more than others? → ''Example: are behavioral traits more labile during evolution?'' * Do species differences in life history traits trade-off, as in the so-called fast-slow continuum? → ''Example: why do small-bodied species have shorter life spans than their larger relatives?'' 抄文引用元・出典: フリー百科事典『 ウィキペディア（Wikipedia）』 ■ウィキペディアで「Phylogenetic comparative methods」の詳細全文を読む スポンサード リンク
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