Analyzing Disparity and Rates of Morphological Evolution with Model-Based Phylogenetic Comparative Methods.

Thomas F Hansen,Geir H Bolstad,Masahito Tsuboi,Simon Ho

doi:10.1093/sysbio/syab079

Thomas F Hansen, Geir H Bolstad + Show 2 more

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https://doi.org/10.1093/sysbio/syab079

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Abstract

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.[Baldwin effect; beak shape; behavioral drive; bird; brain size; disparity; phylogenetic comparative method; rate of evolution.]

Highlights

While substantial progress may have to wait for a more mature quantitative theory of macroevolutionary change, it is important to move beyond mere description toward testing hypotheses about factors influencing rates of evolution
We illustrate the models with an analysis of rates of evolution in bird beaks based on data from Cooney et al (2017) and Chira et al (2018). We relate these rates to measures of absolute and relative brain sizes, revisiting the classical analyses of Wyles et al (1983) to test whether evolution is speeded up by increased behavioral flexibility due to a Baldwin effect (e.g., Baldwin 1896; Popper 1972; Wilson 1985)
We model the species trait vector as y = ymacro +ymicro, where ymacro is the result of a macroevolutionary process (e.g., Brownian motion) unfolding on the phylogeny and ymicro is a microevolutionary deviation, independent of the macroevolutionary process, but with a variance that may depend on the predictor variable as ymicro ∼ N 0,aI+diag bx, (9)

Summary

METHODS

To analyze these models we will use the standard framework of phylogenetic generalized least squares (e.g., Martins and Hansen 1997). For relative brain mass, which is on an interval scale type, the Brownian-motions-based Model 1 is the natural choice Fitting this model to the beak-shape variables shows little effect (Fig. 3). We used a Brownianmotion-based mixed model to predict the states of the shape variables at the tips of the phylogeny and used the squared deviance of the observed states from these predicted states as response variables in the regression This model makes no assumptions about the evolution or distribution of the predictor variables, which can be transformed and fitted on any scale that is deemed biologically reasonable. For the recent-evolution model, the effects of body mass were similar to those of brain mass (Supplementary Fig. S3)

DISCUSSION

CALCULATION OF MOMENTS

Findings

CONSTRUCTING THE REGRESSION MATRICES