Phylogenetic uncertainty
We acknowledged phylogenetic uncertainty throughout our analyses, which result in high overlap of parameter estimates (Figs. 2-4, S8-S10). Upham et al. (2019) reported that building their rodent phylogeny was especially challenging due to missing genetic data and topological uncertainty producing polytomies. These uncertainties were further propagated across our estimates of tip-based metrics. Thus, our inference of traits was based on the collective evidence provided by the phylogenies of Upham et al. 2019.
Results suggest two major implications of phylogenetic uncertainty. The first is the error possible when estimating the average value of the tip-based metrics. For example, consider the density plot in the middle of Figure 3 where we have two peaks of stasis time. If you choose calculating tip-based metrics using only one phylogeny it is very likely that you would have an estimate of either ~2 or ~3 ma, but would err by at least ~1 ma. The second implication is the error we can make when estimating the effect size of variables. Again, considering the density plot in the middle of Figure 3, at ~2 ma of stasis time the assemblages from the Atlantic Rainforest have higher stasis time than assemblages located outside Atlantic Rainforest. However, no difference between these regions can be found at ~3 ma. By propagating uncertainty in our estimates, we infer that the more likely value of average stasis time is ~2.3 ma (inset gray boxplot, Fig. 3), and the more likely effect of Atlantic Rainforest ecoregions is a positive deviation from average aST (inset black boxplot, Fig. 3). Therefore, it is highly desirable that, when available, we use a set of phylogenies rather than only one to test hypothesis about the evolution of ecological traits (Rangel et al. 2015).