Testing for Phylogenetic Signal in Comparative Data: Behavioral Traits Are More Labile

Abstract

Abstract. The primary rationale for the use of phylogenetically based statistical methods is that phylogenetic signal, the tendency for related species to resemble each other, is ubiquitous. Whether this assertion is true for a given trait in a given lineage is an empirical question, but general tools for detecting and quantifying phylogenetic signal are inadequately developed. We present new methods for continuous-valued characters that can be implemented with either phylogenetically independent contrasts or generalized least-squares models. First, a simple randomization procedure allows one to test the null hypothesis of no pattern of similarity among relatives. The test demonstrates correct Type I error rate at a nominal ␣ ϭ 0.05 and good power (0.8) for simulated datasets with 20 or more species. Second, we derive a descriptive statistic, K, which allows valid comparisons of the amount of phylogenetic signal across traits and trees. Third, we provide two biologically motivated branch-length transformations, one based on the OrnsteinUhlenbeck (OU) model of stabilizing selection, the other based on a new model in which character evolution can accelerate or decelerate (ACDC) in rate (e.g., as may occur during or after an adaptive radiation). Maximum likelihood estimation of the OU (d) and ACDC (g) parameters can serve as tests for phylogenetic signal because an estimate of d or g near zero implies that a phylogeny with little hierarchical structure (a star) offers a good fit to the data. Transformations that improve the fit of a tree to comparative data will increase power to detect phylogenetic signal and may also be preferable for further comparative analyses, such as of correlated character evolution. Application of the methods to data from the literature revealed that, for trees with 20 or more species, 92% of traits exhibited significant phylogenetic signal (randomization test), including behavioral and ecological ones that are thought to be relatively evolutionarily malleable (e.g., highly adaptive) and/or subject to relatively strong environmental (nongenetic) effects or high levels of measurement error. Irrespective of sample size, most traits (but not body size, on average) showed less signal than expected given the topology, branch lengths, and a Brownian motion model of evolution (i.e., K was less than one), which may be attributed to adaptation and/or measurement error in the broad sense (including errors in estimates of phenotypes, branch lengths, and topology). Analysis of variance of log K for all 121 traits (from 35 trees) indicated that behavioral traits exhibit lower signal than body size, morphological, life-history, or physiological traits. In addition, physiological traits (corrected for body size) showed less signal than did body size itself. For trees with 20 or more species, the estimated OU (25% of traits) and/or ACDC (40%) transformation parameter differed significantly from both zero and unity, indicating that a hierarchical tree with less (or occasionally more) structure than the ori...

Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity

“…To examine the evolutionary models at the individual gene level, phylogenetic signals were measured using two metrics, Pagel's λ (Pagel, 1999) and Blomberg's K (Blomberg, Garland & Ives, 2003). These metrics are usually high for genes that follow BM model, but can be weakened by processes such as stabilizing selection.…”

Incorporating evolutionary insights to improve ecotoxicology for freshwater species

“…Blomberg K values can be >1, signaling a similarity in traits among closely related species that is greater than expected by Brownian motion evolution. Values <1 indicate less similarity among closely related species than expected by the null model of evolution, as seen in our K of 0.23 for the full 55‐species tree (Blomberg et al., 2003; Garland, Bennett, & Rezende, 2005). …”

“…The variability in association between evolutionary relationship and chloride toxicity across different groupings within our dataset is somewhat surprising because phylogenetic signal is expected to be common (Blomberg et al., 2003). In a synthesis of published trees, Blomberg et al.…”

“…The resulting tree was paired with species level chloride LC50s to investigate phylogenetic signal of chloride toxicity. Phylogenetic signal describes a pattern where the value of a given trait is more similarly distributed among closely related taxa than predicted by chance (Blomberg, Garland, & Ives, 2003). In other words, a phylogenetic signal would indicate that closely related species are similar in their sensitivity to chloride.…”

“…We used the package “phytools” v. 0.6 (Zhang, Pei, & Mi, 2012) to evaluate the potential phylogenetic signal of chloride toxicity. Signal was inferred using both Pagel's lambda, a parameter that scales the correlation between species (Pagel, 1999), and Blomberg's K, a metric consisting of the ratio of phylogenetic dependence explained by a given tree to that expected by a null model of trait evolution (Blomberg et al., 2003). A random walk Brownian motion process is used as the null evolutionary model for both metrics.…”