DOI: 10.5061/dryad.7kh57t5
title: Data from: The impact of fossil stratigraphic ranges on tip‐calibration, and the accuracy and precision of divergence time estimates

description: The molecular clock provides the only viable means of establishing
 realistic evolutionary timescales but it remains unclear how best to
 calibrate divergence time analyses. Calibrations can be applied to the
 tips and/or to the nodes of a phylogeny. Tip‐calibration is an attractive
 approach since it allows fossil species to be included alongside extant
 relatives in molecular clock analyses. However, most fossil species are
 known from multiple stratigraphical horizons and it remains unclear how
 such age ranges should be interpreted to codify tip‐calibrations. We use
 simulations and empirical data to explore the impact on precision and
 accuracy of different approaches to informing tip‐calibrations. In
 particular, we focus on the effect of using tip‐calibrations defined using
 the oldest vs youngest stratigraphic occurrences, the full stratigraphical
 range, as well as confidence intervals on these data points. The results
 of our simulations show that using different calibration approaches leads
 to different divergence‐time estimates and demonstrate that concentrating
 tip‐calibrations near the root of the dated phylogeny improves both
 precision and accuracy of estimated divergence times. Finally, our results
 indicate that the highest levels of accuracy and precision are achieved
 when fossil tips are calibrated based on the fossil occurrence from which
 the morphological data were derived. These trends were corroborated by
 analysis of an empirical dataset for Ursidae. Overall, we conclude that
 tip‐dating analyses should, in particular, employ tip calibrations close
 to the root of the tree and they should be calibrated based on the age of
 the fossil used to inform the morphological data used in Total Evidence
 Dating.
description: Data from 'The
 impact of fossil stratigraphic ranges on tip-calibration, and the accuracy
 and precision of divergence time estimates'This data package is
 composed of three components: 1. Appendices: appendices 1-5 which are
 supplementary figures and tables 2. R scripts: R scripts 1-4 used for our
 different simulation strategies:
 "1_Data_simulation_tree1_stem__Mk_MaxFoss_v2" This R script
 allows you to generate the 100 replicates simulation Nexus files for tree
 1 (fossils in the stem group) using the parameters described in the
 article. "2_Data_simulation_tree2_crown_Mk_MaxFoss_v2" This R
 script allows you to generate the 100 replicates simulation Nexus files
 for tree 2 (fossils in the crown group) using the parameters described in
 the article. "3_Extract_ages_simulation_results" This R script
 allows to extract from the .p and .t files of MrBayes all the ages of the
 nodes from the posterior of 100 replicates in the tree for each
 calibration approach. It results in 5 .csv files. It can be used for both
 trees (1 stem and 2 crown) "4_Extract_ages_empirical_Ursidae"
 This R script allows to extract all the node ages from the the .p and .t
 files of MrBayes 3. Bear Molecular Clock analyses: composed of five
 folders with each calibration approach called "Maximum",
 "Minimum", "Minimum-maximum",
 "Min-max_95CI_max" and "Min-max_95CI_min". Inside
 these folders you have the nexus files necessary to run the empirical
 analyses in MrBayes and the output files after running the
 analyses.Püschel_et_al_Supplementary.zip