A semi-variance approach to visualising phylogenetic autocorrelation

Comparing traits across species has been a hallmark of biological research for centuries. While interspecific comparisons can be highly informative, phylogenetic inertia can bias estimates if not properly accounted for in comparative analyses. In response, researchers typically treat phylogenetic inertia as a form of autocorrelation that can be detected, modelled and corrected for. Despite the range of methods available for quantifying the strength of phylogenetic autocorrelation, no tools exist for visualising these autocorrelation structures. Here we derive variogram methods suitable for phylogenetic data, and show how they can be used to straightforwardly visualise phylogenetic autocorrelation. We then demonstrate their utility for three empirical examples: sexual size dimorphism (SSD) in the Musteloidea, maximum per capita rate of population growth, r, in the Carnivora, and brain size in the Artiodactyla. When modelling musteloid SSD, the empirical variogram showed a tendency for the variance in SSD to stabilise over time, a characteristic feature of Ornstein-Uhlenbeck (OU) evolution. In agreement with this visual assessment, model selection identified the OU model as the best fit to the data. In contrast, the infinitely diffusive Brownian motion (BM) model did not capture the asymptotic behaviour of the variogram and was less supported than the OU model. Phylogenetic variograms proved equally useful in understanding why an OU model was selected when modelling r in the Carnivora, and why BM was the selected evolutionary model for brain size in the Artiodactyla. Because the variograms of the various evolutionary processes each have different theoretical profiles, comparing fitted semi-variance functions against empirical semi-variograms can serve as a useful diagnostic tool, allowing researchers to understand why any given evolutionary model might be selected over another, which features are well captured by a model, and which are not. This allows for fitted models to be compared against the empirical variogram, facilitating model identification prior to subsequent analyses. We therefore recommend that any phylogenetic analysis include a nonparametric estimate of the autocorrelation structure of the data that can be visualised. The methods developed in this work are openly available in the new R package ctpm.