DOI: 10.5061/dryad.g7s0hk3
title: Data from: The effect of fossil sampling on the estimation of divergence times with the fossilised birth death process

description: Timescales are of fundamental importance to evolutionary biology as they
 facilitate hypothesis tests of historical evolutionary processes. Through
 the incorporation of fossil occurrence data, the fossilised birth-death
 (FBD) process provides a framework for estimating divergence times using
 more palaeontological data than traditional node calibration approaches
 have allowed. The inclusion of more data can refine evolutionary timescale
 estimates, but for many taxonomic groups it is computationally infeasible
 to include all fossil occurrence data. Here, we utilise both empirical
 data and a simulation framework to identify approaches to subsampling
 fossil occurrence data that result in the most accurate estimates of
 divergence times. To achieve this we assess the performance of the
 FBD-Skyline model when implementing multiple approaches to incorporating
 subsampled fossil occurrences. Our results demonstrate that it is
 necessary to account for all available fossil occurrence data to achieve
 the most accurate estimates of clade age. We show that this can be
 achieved if an empirical Bayes approach to account for fossil sampling
 through time is applied to the FBD process. Random subsampling of
 occurrence data can lead to estimates of clade age that are incompatible
 with fossil evidence if no control over the affinities of fossil
 occurrences is enforced. Our results call into question the accuracy of
 previous divergence time studies incorporating the FBD process that have
 used only a subsample of all available fossil occurrence data.
description: Supplementary Figure
 1Median age estimates and
 95% HPDs obtained to demonstrate the behaviour of the FBD process without
 the subsampling of fossil occurrences. These results demonstrate the
 suitability of the simulation framework employed for subsequent
 analyses.Positive_Control.pdfSupplementary Figure 2Median age estimates and 95% HPDs for Hymenoptera obtained using a range of approaches to constructing a subsample of fossil occurrences and constraining their placement. These approaches consist of: a uniform subsample of occurrences with and without topological constraints, a uniform subsample of occurrences supplemented with the oldest unequivocal members of clades which were then constrained to their respective crown groups, a subsample consisting of only the oldest unequivocal members of clades with and without topological constraints applied to constrain them to their respective crown groups.Supp_Empirical.PDFSupplementary Figure 3The accuracy and precision of estimated node ages obtained from subsamples of 100 replicate fossil occurrence datasets after the addition of the oldest occurrences for each clade to the subsample. These occurrences were then topologically constrained to lineages that descend from the node either 1, 2, or 4 nodes below the direct ancestor of the occurrence. Each point represents the median posterior age estimate of one clade, with grey bars representing the 95% HPD for that node age estimate. When occurrences are placed one node below their direct ancestor an approach in which the rate of fossil sampling is estimated produces the greatest accuracy. When occurrences are placed with reduced accuracy then the accuracy of age estimates when sampling rate is an estimated parameter of the FBD process decreases. Conversely, fixing the rate of fossil sampling or placing an informed prior on this parameter improves the accuracy as fossils are placed with reduced accuracy. For all cases in which fossils occurrences are placed at a node that is lower than their true ancestral fossil the 95% HPDs of age estimates extend to ages that violate the minimum age of the clade, as implied by the complete sample of fossil occurrences.Drop_Results.eps