Diversification dynamics estimation
To investigate if diversification rates varied through time we used a series of likelihood-based diversification models in the R package RPANDA (Morlon et al., 2016). One of the models implemented in RPANDA estimates the likelihood that speciation and extinction are constant or variable through time. Accordingly, we tested a combination of models in which we allowed speciation and extinction to be either constant or variable following a linear or an exponential model (see Table 1 for model specification and results for details on linear models). We compared the models using AIC.
In addition to the RPANDA time dependent diversification analyses, we used alternative methods to support the estimation of diversification rates for the tribe. Overall, we estimated diversification rates using the Constant-Rates test (CRT; Pybus and Harvey, 2000), Magallón and Sanderson’s estimator (Magallon and Sanderson, 2001), and Bayesian Analysis of Macroevolutionary Mixtures (BAMM; Rabosky, 2014) and MEDUSA (Alfaro et al., 2009), and visualized the results with a lineage through time plot (LTT). See detail about these diversification analyses in the Appendix.