Phylogenetic comparative methods

Phylogenetic comparative methods (PCMs) use information on the historical relationships of lineages (phylogenies) to test evolutionary hypotheses.

[3] Although most studies that employ PCMs focus on extant organisms, many methods can also be applied to extinct taxa and can incorporate information from the fossil record.

[5] Typically the tree that is used in conjunction with PCMs has been estimated independently (see computational phylogenetics) such that both the relationships between lineages and the length of branches separating them is assumed to be known.

And because they can be used to explicitly model evolutionary processes occurring over very long time periods, they can provide insight into macroevolutionary questions, once the exclusive domain of paleontology.

The value at the root is equivalent to that obtained from the "squared-change parsimony" algorithm and is also the maximum likelihood estimate under Brownian motion.

The method is a special case of generalized least squares (GLS) and as such the PGLS estimator is also unbiased, consistent, efficient, and asymptotically normal.

[15][16][17] Martins and Garland[18] proposed in 1991 that one way to account for phylogenetic relations when conducting statistical analyses was to use computer simulations to create many data sets that are consistent with the null hypothesis under test (e.g., no correlation between two traits, no difference between two ecologically defined groups of species) but that mimic evolution along the relevant phylogenetic tree.

Home range areas of 49 species of mammals in relation to their body size . Larger-bodied species tend to have larger home ranges, but at any given body size members of the order Carnivora ( carnivores and omnivores ) tend to have larger home ranges than ungulates (all of which are herbivores ). Whether this difference is considered statistically significant depends on what type of analysis is applied [ 7 ]
Testes mass of various species of Primates in relation to their body size and mating system. Larger-bodied species tend to have larger testes, but at any given body size species in which females tend to mate with multiple males have males with larger testes.
The standardized contrasts are used in conventional statistical procedures, with the constraint that all regressions , correlations , analysis of covariance , etc., must pass through the origin.
Data for a continuous-valued trait can be simulated in such a way that taxa at the tips of a hypothetical phylogenetic tree will exhibit phylogenetic signal, i.e., closely related species will tend to resemble each other.