A Cautionary Note on "A Cautionary Note on the Use of Ornstein Uhlenbeck Models in Macroevolutionary Studies".

Models based on the Ornstein-Uhlenbeck process have become standard for the comparative study of adaptation. Cooper et al. (2016) have cast doubt on this practice by claiming statistical problems with fitting Ornstein-Uhlenbeck models to comparative data. Specifically, they claim that statistical tests of Brownian motion may have too high Type I error rates and that such error rates are exacerbated by measurement error. In this note, we argue that these results have little relevance to the estimation of adaptation with Ornstein-Uhlenbeck models for three reasons. First, we point out that Cooper et al. (2016) did not consider the detection of distinct optima (e.g. for different environments), and therefore did not evaluate the standard test for adaptation. Second, we show that consideration of parameter estimates, and not just statistical significance, will usually lead to correct inferences about evolutionary dynamics. Third, we show that bias due to measurement error can be corrected for by standard methods. We conclude that Cooper et al. (2016) have not identified any statistical problems specific to Ornstein-Uhlenbeck models, and that their cautions against their use in comparative analyses are unfounded and misleading. [adaptation, Ornstein-Uhlenbeck model, phylogenetic comparative method.].

Rapidly changing speciation and extinction rates can be inferred in spite of nonidentifiability.

The birth-death model is commonly used to infer speciation and extinction rates by fitting the model to phylogenetic trees with exclusively extant taxa. Recently, it was demonstrated that speciation and extinction rates are not identifiable if the rates are allowed to vary freely over time. The group of birth-death models that have the same likelihood is called a congruence class, and there is no statistical evidence to favor one model over the other. This issue has led researchers to question if and what patterns can reliably be inferred from phylogenies of only extant taxa and whether time-variable birth-death models should be fitted at all. We explore the congruence class in the context of several empirical phylogenies as well as hypothetical scenarios. For these empirical phylogenies, we assume that we inferred the true congruence class. Thus, our conclusions apply to any empirical phylogeny for which we robustly inferred the true congruence class. When we summarize shared patterns in the congruence class, we show that strong directional trends in speciation and extinction rates are shared among most models. Therefore, we conclude that the inference of strong directional trends is robust. Conversely, estimates of constant rates or gentle slopes are not robust and must be treated with caution. Interestingly, the space of valid speciation rates is narrower and more limited in contrast to extinction rates, which are less constrained. These results provide further evidence and insights that speciation rates can be estimated more reliably than extinction rates.

Both Diet and Sociality Affect Primate Brain-Size Evolution.

Increased brain size in humans and other primates is hypothesized to confer cognitive benefits but brings costs associated with growing and maintaining energetically expensive neural tissue. Previous studies have argued that changes in either diet or levels of sociality led to shifts in brain size, but results were equivocal. Here we test these hypotheses using phylogenetic comparative methods designed to jointly account for and estimate the effects of adaptation and phylogeny. Using the largest current sample of primate brain and body sizes with observation error, complemented by newly compiled diet and sociality data, we show that both diet and sociality have influenced the evolution of brain size. Shifting from simple to more complex levels of sociality resulted in relatively larger brains, while shifting to a more folivorous diet led to relatively smaller brains. While our results support the role of sociality, they modify a range of ecological hypotheses centered on the importance of frugivory, and instead indicate that digestive costs associated with increased folivory may have resulted in relatively smaller brains. [adaptation; allometry; bayou; evolutionary trend; energetic constraints; phylogenetic comparative methods; primate brain size; Slouch; social-brain hypothesis.].