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.

Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity

“…To identify the genes that correlate with species longevity, the phylogenetic generalized least‐squares approach was employed to adjust for the evolutionary relationship (Felsenstein, 1985; Freckleton, Harvey & Pagel, 2002; Grafen, 1989; Martins & Garland, 1991). Regression was performed between expression values and male median lifespan (“ML”), different models of trait evolution were tested, and the best‐fit model was then selected based on maximal likelihood (Table S3).…”

The evolution of sex roles in birds is related to adult sex ratio

“…We used Phylogenetic Generalized Least Squares (PGLS) with maximum likelihood to find the best fitting l 17,18 . For most analyses, we used a supertree of shorebirds 36 , from which we pruned species with missing data, and following a recent molecular phylogenetic study, we separated C. nivosus from C. alexandrinus 37 (Supplementary Fig.…”

“…We carried out a comprehensive search in primary publications, reference books and online resources for data on ASR, social mating system and parental care, with special attention to species that have been reported to exhibit sex-role reversal. We tested whether ASR predicts mating systems and parental care using Phylogenetic Generalized Least Squares 17,18 . Although data on ASR from wild populations are difficult to obtain 19 , the information now available for shorebirds permits tests of the theoretical predictions using statistically robust sample sizes.…”

Sex‐biased breeding dispersal is predicted by social environment in birds

“…We used phylogenetic least‐squares (PGLS) analysis to investigate relationships between sex‐specific natal and breeding dispersal as well as predictors related to sexual selection and social environment as specified by the hypotheses (Freckleton, Harvey, & Pagel, 2002; Martins & Hansen, 1997; Pagel, 1999). This approach allows controlling for the nonindependence among species by incorporating a variance–covariance matrix that represents their phylogenetic relationships.…”

“…This approach allows controlling for the nonindependence among species by incorporating a variance–covariance matrix that represents their phylogenetic relationships. In all analyses, we set the phylogenetic signal (λ) to the maximum‐likelihood value (Freckleton et al., 2002). To test phylogenetic signal in the sign of sex‐biased dispersal, we retrieved the values of λ from PGLS models and performed D ‐statistics, a further measure of the strength of phylogenetic signal, presented in Appendix S5.…”