A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera
Top Cited Papers
Open Access
- 26 July 2012
- journal article
- research article
- Published by Oxford University Press (OUP) in Systematic Biology
- Vol. 61 (6), 973-999
- https://doi.org/10.1093/sysbio/sys058
Abstract
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 (∼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, ∼309 Ma (95% interval: 291--347 Ma), and diversified into major extant lineages much earlier than previously thought, well before the Triassic. [Bayesian inference; fossil dating; morphological evolution; relaxed clock; statistical phylogenetics.]Keywords
This publication has 73 references indexed in Scilit:
- Divergence Time Estimation Using Fossils as Terminal Taxa and the Origins of LissamphibiaSystematic Biology, 2011
- Inferring Speciation and Extinction Rates under Different Sampling SchemesMolecular Biology and Evolution, 2011
- Evaluation of Bayesian Models of Substitution Rate Evolution—Parental Guidance versus Mutual IndependenceSystematic Biology, 2011
- Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model SelectionSystematic Biology, 2010
- Sampling-through-time in birth–death treesJournal of Theoretical Biology, 2010
- Combining Phylogenomics and Fossils in Higher-Level Squamate Reptile Phylogeny: Molecular Data Change the Placement of Fossil TaxaSystematic Biology, 2010
- Relaxed Molecular Clocks, the Bias–Variance Trade-off, and the Quality of Phylogenetic InferenceSystematic Biology, 2009
- The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian InferenceSystematic Biology, 2009
- A Site- and Time-Heterogeneous Model of Amino Acid ReplacementMolecular Biology and Evolution, 2008
- The history of early bee diversification based on five genes plus morphologyProceedings of the National Academy of Sciences of the United States of America, 2006