**Divergence Dating Analyses** Our data provided unique challenges for divergence dating. We used the species tree generated in ASTRAL-III from our sequence capture data set to constrain the relationships in a phylogeny constructed from our supermatrix data set containing additional taxa. Because the preservation of the species tree relationships was critical, we could not infer phylogenetic relationships and branch lengths simultaneously using BEAST (ie a typical analysis). We therefore had to generate a starting tree for the BEAST analysis. **Starting Tree:** To use a starting tree in BEAST, 1) the tree must be ultrametric and 2) if node calibrations are used in the analysis, the ultrametric starting tree must not violate the bounds of these calibration points. Therefore, simply making a tree ultrametric in an arbitrary fashion may cause severe problems for the divergence dating analysis. A fast way to overcome this issue is to use the *chronopl* function of *APE* in R to convert a tree properly. We anticipated using four calibration points in the BEAST analysis, and so used these values to create an ultrametric tree with *chronopl* from the RAxML tree created from our supermatrix data (see other analysis folder for these data). The R script (*chronopl_for_BEAST.R*), input tree, and output ultrametric tree are provided in the Tree Conversion folder. The resulting nexus tree file was converted into xml format by arbitrarily importing it into BEAUTI. This format is shown in the Starting Tree folder within the BEAST Analysis folder. **BEAST Analysis:** We performed analyses using a fixed ultrametric starting tree topology by removing relevant operators acting on the tree model (see Calibs2_30M.xml file in the BEAST Analysis folder). To calibrate the analysis, we used four secondary calibration points with normal distributions to constrain the most recent common ancestors (MRCAs) of Afrobatrachia to 80 Ma ± 5 SD, (Hemisotidae + Brevicipitidae) to 50 Ma ± 5 SD, Arthroleptidae to 40 Ma ± 5 SD, and Hyperoliidae to 40 Ma ± 5 SD, based on published age estimates of Afrobatrachian frogs. We used the Yule model of speciation as the tree prior, applied an uncorrelated relaxed lognormal clock, and ran two analyses for 30,000,000 generations sampling every 3,000 generations. Runs were assessed using TRACER v1.5.0 (Rambaut et al. 2013) to examine convergence, and a maximum clade credibility tree with median heights was created from 7,500 trees after discarding a burn-in of 2,500 trees (*Calibs2_30M_con.tre* and *Calibs2_30M_con.newick*). All output files are provided in the BEAST Analysis folder.