A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera

By Fredrik Ronquist, S. Klopfstein, L. Vilhelmsen, Susanne Schulmeister, Debra Murray, A. Rasnitsyn. Systematic Biology, 2012

827 citations recorded by the source corpus.

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.]

Subfields: Ecology, Evolution, Behavior and Systematics

View Paper: https://www.semanticscholar.org/paper/e507d3ed55638d80511c35eda1fc229693701a3e

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology, Evolution, Behavior and Systematics

Citations in the corpus

strap: an R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence (2015, background): “…there have been multiple attempts to reincorporate it, most notably through stratophenetics (Gingerich 1979), stratocladistics (Fischer 1994), stratolikelihood (Huelsenbeck and Rannala 1997, 2000; Wagner 1998, 2000) and, most recently, Bayesian tip dating (Pyron 2011; Ronquist et al. 2012).”
Fast Dating Using Least-Squares Criteria and Algorithms (2015, background): “Moreover, close relationships exist between the calibration-points and dated-tips approaches (Ronquist et al. 2012).”
Evolutionary History of the Hymenoptera. (2017, background): “1] in Figure 1B), with the oldest currently known Hymenoptera fossils being from the Triassic, 224 million years old [8].”
Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration (2014, background): “As sequence data for fossil organisms is rarely available information about fossil locations on the tree obtained by phylogenetic modelling of morphological data [29,45] may become important to enable effective inference.”
Bayesian estimation of fossil phylogenies and the evolution of early to middle Paleozoic crinoids (Echinodermata) (2017, methodology): “…data, especially in paleontology (e.g., Wagner, 1998, 1999; Snively et al., 2004; Pollitt et al., 2005; Clarke andMiddleton, 2008; Pyron, 2011; Ronquist et al., 2012; Slater, 2013, 2015;Wright and Stigall, 2013; Lee et al., 2014; Close et al., 2015; Bapst et al., 2016; Gorscak and O’Connor,…”
FOSSIL CALIBRATIONS FOR THE ARTHROPOD TREE OF LIFE (2016, methodology): “Phylogenetic justification In the total-evidence phylogenetic analysis of Ronquist et al. (2012), T. foveolata was found as a stem group member of the family Xyelidae.”
The peril of dating beetles (2017, background): “For future studies, a more justifiable way to place an interval on the age of the root is to use the age estimates of the recent dating studies of Misof et al. (2014) and Tong et al. (2015) in which the age of the crown Holometabola was found to be ∼345 Ma (CI: ∼320–370 Ma) and ∼370 Ma (CI:∼350–400 ”
The fossilized birth–death process for coherent calibration of divergence-time estimates (2013, methodology): “Moreover, the FBD model allows for inclusion of all available fossils.”