DOI: 10.5061/dryad.j2r64
title: Data from: A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera

description: Phylogenies are usually dated by calibrating interior nodes against the
 fossil record. This relies on indirect methods that, in the worst case,
 misrepresent the fossil information. Here, we contrast such node dating
 with an approach that includes fossils along with the extant taxa in a
 Bayesian total-evidence analysis. As a test case, we focus on the early
 radiation of the Hymenoptera, mostly documented by poorly preserved
 impression fossils that are difficult to place phylogenetically.
 Specifically, we compare node dating using nine calibration points derived
 from the fossil record with total-evidence dating based on 343
 morphological characters scored for 45 fossil (4–20% complete) and 68
 extant taxa. In both cases we use molecular data from seven markers (about
 5 kb) for the extant taxa. Because it is difficult to model speciation,
 extinction, sampling, and fossil preservation realistically, we develop a
 simple uniform prior for clock trees with fossils, and we use relaxed
 clock models to accommodate rate variation across the tree. Despite
 considerable uncertainty in the placement of most fossils, we find that
 they contribute significantly to the estimation of divergence times in the
 total-evidence analysis. In particular, the posterior distributions on
 divergence times are less sensitive to prior assumptions and tend to be
 more precise than in node dating. The total-evidence analysis also shows
 that four of the seven Hymenoptera calibration points used in node dating
 are likely to be based on erroneous or doubtful assumptions about the
 fossil placement. With respect to the early radiation of Hymenoptera, our
 results suggest that the crown group dates back to the Carboniferous,
 approximately 309 Ma (95% interval: 291–347 Ma), and diversified into
 major extant lineages much earlier than previously thought, well before
 the Triassic.
description: Appendix-1_MorphoCharacterDescriptionsAppendix 1. Morphological character descriptions.MrBayes_Commands_NewMrBayes commands needed to run the analyses described in the paper.MrBayes_Commands.nexR-Scripts_PriorFitting-RelaxedClockModels_NewR scripts used to find appropriate relaxed-clock prior parameters.R-Scripts_PriorFitting-RelaxedClockModels.rSupplementary Figure 1. Morphological versus molecular branch lengthsFigure showing the molecules-only and morphology-only trees, as well as the correlation between morphological and molecular branch lengths.Supplementary-Figure-1_Morphological-versus-molecular-BranchLengths.epsSupplementary Figure 2. Effect of removing the least complete fossilsSupplementary Figure 2. Divergence time estimates from total-evidence analyses based on all data (45 fossils; tree and 95% highest posterior density (HPD) interval bars in red) or only the fossils with more than 10% of the 343 morphological characters scored (31 fossils; green bars). While the topology is the same and the median age estimates are similar, the HPD intervals are in general wider when the most poorly preserved fossils are excluded.Supplementary-Figure-2_DatedTree-ErrorBars.eps