Quantifying Phylogenetically Structured Environmental Variation

Abstract

Comparative analysis methods control for the variation linked to phylogeny before attempting to correlate the remaining variation of a trait to present-day conditions (i.e., ecology and/or environment). A portion of the phylogenetic variation of the trait may be related to ecology, however; this portion is called "phylogenetic niche conservatism." We propose a method of variation partitioning that allows users to quantify this portion of the variation, called the "phylogenetically structured environmental variation." The new method is applied to published data to study, in a phylogenetic framework, the link between body mass and population density in 79 species of mammals. The results suggest that an important part of the variation of mammal body mass is related to the common influence of phylogeny and population density.

Determination of Mitochondrial Genetic Diversity in Mammals

“…Supra-order average levels of diversity are also significantly different from each other, Euarchontoglire species being more diverse than Laurasiatheria. Similarly, we calculated the phylogenetic autocorrelation using Moran's I statistic (Gittleman and Kot 1990) and the phylogenetic inertia using PVR (Diniz-Filho et al 1998;Desdevises et al 2003). Genetic diversity had a highly significant autocorrelation (I ¼ À0.01943, P-value , 0.0001) and the PVR method indicated a strong phylogenetic inertia on this variable (r 2 ¼ 0.319, P-value , 0.0001, after 10,000 random permutations).…”

“…First, we used the residuals of the nested-hierarchical ANOVA for reanalyzing the effects of ecological and life-history traits. Second, we employed the phylogenetic eigenvector regression (PVR) method to correct for phylogenetic inertia (Diniz-Filho et al 1998;Desdevises et al 2003). This method can be applied to both continuous and discrete variables.…”

“…The method starts by performing a principal coordinate analysis on a matrix of between-species patristic distances (implemented in ADE4-R package, Chessel et al 2004). Following Desdevises et al (2003), all the principal coordinates that were significantly correlated to the dependent variable were selected. Traits under analysis were then regressed on the retained eigenvectors.…”

“…The estimated values express phylogenetic trends in the data, and residuals express independent evolution of each species. The proportion of genetic diversity variance explained exclusively by the ecological and life-history variables was quantified using multiple linear regressions, and its significance was assessed by using a regular parametric F-test (the permutation test used by Desdevises et al 2003 gave similar results). Finally, the contrast method (Felsenstein 1985) was also used on continuous variables, yielding qualitatively equivalent results (not shown).…”

A Comment on Phylogenetic Correction

“…Westoby et al (1995b) said that comparative methods can be used to test the null hypothesis that the correlation between traits is due to phylogeny. Desdevises et al (2003) viewed phylogeny as a confounding variable whose effects must be removed. Beauchamp and Fernandez-Juricic (2004) and many others said that comparative methods are able to partial out the effect of common ancestry or to remove trait variation that is correlated with phylogeny.…”