Analyzing disparity and rates of morphological evolution with model-based phylogenetic comparative methods

Understanding variation in rates of evolution and morphological disparity is a goal of macroevolutionary research. In a phylogenetic comparative methods framework, we present three explicit models for linking the rate of evolution of a trait to the state of another evolving trait. This allows testing hypotheses about causal influences on rates of phenotypic evolution with phylogenetic comparative data. We develop a statistical framework for fitting the models with generalized least-squares regression, and use this to discuss issues and limitations in the study of rates of evolution more generally. We show that the power to detect effects on rates of evolution is low in that even strong causal effects are unlikely to explain more than a few percent of observed variance in disparity. We illustrate the models and issues by testing if rates of beak-shape evolution in birds are influenced by brain size, as may be predicted from a Baldwin effect in which presumptively more behaviorally flexible large-brained species generate more novel selection on themselves leading to higher rates of evolution. From an analysis of morphometric data for 645 species we find evidence that both macro- and microevolution of the beak are faster in birds with larger brains, but with the caveat that there are no consistent effects of relative brain size.

Methods
The dataset archived here are predominantly taken from published sources. References are as follows.

Brain mass: Tsuboi et al. 2018 Nat Ecol Evol 2: 1492-1500., Fristoe et al. 2017 Nat Ecol Evol 1: 1706-1715.

Body mass: Tsuboi et al. 2018 Nat Ecol Evol 2: 1492-1500., Fristoe et al. 2017 Nat Ecol Evol 1: 1706-1715.

Standard error of log brain mass: Estimated from within-species variance and a method described in our aerticle. 

Standard error of log body mass: Estimated from within-species variance and a method described in our aerticle. 

Relative brain size: Estimated from generalized least squares regression of log(brain mass) against log(body mass) including the presented 645 species and phylogeny using SLOUCH as described in our article.

Beak shape: Chira et al. 2018. Ecology Letters 21: 1505-1514., Cooney et al. 2017. Nature 542: 344-347.

Phylogeny: Jetz et al. 2014. Curr. Biol. 24: 919-930.