Figure 2. Example informative divergence time priors estimated with the SNAPE v1.0 software.

These likelihood curves and associated best-fit gamma distributions show some of the variation in prior shape that can be estimated using this method. The y-axis scale is the likelihood (or f for the best-fit gamma distribution) and the x-axis is in millions of years ago (MYA). Note that the scale of discretized likelihood curve and the gamma distribution are not equivalent, and they must be scaled to assist in visualization. A. Estimated prior distribution for the root node in the echinoid data set. Values of the discretized likelihood curve are shown in black, and the best-fit gamma distribution is shown in red. Horizontal lines representing the 95%, 75%, and 50% quantiles of the discretized likelihood curve are labeled on the figure. The quantile values are shown here only for reference when interpreting the simulation results shown in Figure 3. B. Estimated prior distribution for the MRCA of the mammalian order Rodentia. The input data for this prior estimate was assembled by searching the Paleobiology Database (www.pbdb.org) for all Rodentia occurrences (see File S2). This analysis assumed the existence of 400 extant genera in Rodentia. The oldest Rodentia fossil occurrence that met the input data criteria was 55.8 Ma. The vertical line shows the position of the Cretaceous/Paleogene (K/PG) boundary at 65.5 Ma. The analysis was performed once for each of four preservation rates: 0.1  =  black; 0.2  =  blue; 0.3  =  orange; 0.4  =  yellow. The best-fit gamma distribution for the likelihood curve assuming a 0.1 preservation rate is shown in red. This prior for the age of the MRCA of Rodentia was estimated solely for demonstration purposes. The results show how the preservation rate estimate provided by the user can have a large impact on the shape of the prior estimated.