Fig. 4

Density tree contrasting divergence times under distinct clock and tree models (single morphological clock). Each tree represents the maximum compatibility tree and median divergence times obtained from each model combination. The greatest disparity of divergence time variation given model choice is observed on nodes closer to the root. Sampling for ancestors (blue) yields much older age estimates for the root and most other nodes compared to not sampling for ancestors, regardless of the clock model. When not sampling for ancestors, the uncorrelated clock model (red) results in relatively older divergence times compared to the best fit autocorrelated clock model (green) in nodes closer to the root, but slightly younger on nodes closer to the tips. The SFBD tree model (purple) further reduces divergence times compared to the simpler FBD tree model when using the best fit autocorrelated clock model. Orange bars indicate range between maximum and minimum divergence times for each model combination and orange circles represent the midpoint between these respective maximum and minimum divergence times. Div, diversity sampling with fossils as tips or ancestors; FBD, fossilized birth-death tree model with constant perimeter rates across time; IGR, independent gamma rates uncorrelated clock model; NoSA diversity, diversity sampling with fossils as tips only; SFBD(s)2 l, skyline FBD tree model with one rate shift point for the relative fossilization parameter; TK02, continuous autocorrelated clock model