Phylogenetic Analysis and Comparative Data: A Test and Review of Evidence

Abstract

The question is often raised whether it is statistically necessary to control for phylogenetic associations in comparative studies. To investigate this question, we explore the use of a measure of phylogenetic correlation, lambda, introduced by Pagel (1999), that normally varies between 0 (phylogenetic independence) and 1 (species' traits covary in direct proportion to their shared evolutionary history). Simulations show lambda to be a statistically powerful index for measuring whether data exhibit phylogenetic dependence or not and whether it has low rates of Type I error. Moreover, lambda is robust to incomplete phylogenetic information, which demonstrates that even partial information on phylogeny will improve the accuracy of phylogenetic analyses. To assess whether traits generally show phylogenetic associations, we present a quantitative review of 26 published phylogenetic comparative data sets. The data sets include 103 traits and were chosen from the ecological literature in which debate about the need for phylogenetic correction has been most acute. Eighty-eight percent of data sets contained at least one character that displayed significant phylogenetic dependence, and 60% of characters overall (pooled across studies) showed significant evidence of phylogenetic association. In 16% of tests, phylogenetic correlation could be neither supported nor rejected. However, most of these equivocal results were found in small phylogenies and probably reflect a lack of power. We suggest that the parameter lambda be routinely estimated when analyzing comparative data, since it can also be used simultaneously to adjust the phylogenetic correction in a manner that is optimal for the data set, and we present an example of how this may be done.

Serum antioxidant levels in wild birds vary in relation to diet, season, life history strategy, and species

“…There has been considerable debate about when phylogenetic correction is important and which method to use (e.g., Freckleton et al 2002), but the lack of strong phylogenetic eVect we see here suggests that phylogenetic control is not a crucial issue for this study (see Results, Table 1). The phylogeny used was the same as for Cohen et al (2008a); methods of construction can be found there, and the phylogeny is available in supplementary material as shown in Newick format (S1).…”

Exceptional avian herbivores: multiple transitions toward herbivory in the bird order Anseriformes and its correlation with body mass

“…While PGLS allows for the fitting of several different evolutionary models while performing the regression, these models explain phylogenetic signal in the residuals (the fit of the tree to the regression) and do not relate directly to the test of whether the variables are significantly correlated (Freckleton et al. 2002; Revell 2010). …”

Urbanized birds have superior establishment success in novel environments

“…To control for the phylogenetic relationship among the sampled species, we used phylogenetic generalized least square regression (PGLS) models as implemented in the R statistical environment, using the libraries ape, MASS and mvtnorm and the function pglm3.3.r (see Díaz et al 2013 for a similar approach). After testing whether the phylogenetic scaling parameter lambda (λ) differs from 0 (phylogenetic independence; Freckleton et al 2002), we calculated the phylogenetically corrected correlation between the variables of interest after adjusting for phylogenetic effects through the estimated λ (see Díaz et al 2013 for a similar approach and the R script).…”