Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria)

Abstract

Dated phylogenies of fossil taxa allow palaeobiologists to estimate the timing of major divergences and placement of extinct lineages, and to test macroevolutionary hypotheses. Recently developed Bayesian 'tip-dating' methods simultaneously infer and date the branching relationships among fossil taxa, and infer putative ancestral relationships. Using a previously published dataset for extinct theropod dinosaurs, we contrast the dated relationships inferred by several tip-dating approaches and evaluate potential downstream effects on phylogenetic comparative methods. We also compare tip-dating analyses to maximum-parsimony trees time-scaled via alternative a posteriori approaches including via the probabilistic cal3 method. Among tip-dating analyses, we find opposing but strongly supported relationships, despite similarity in inferred ancestors. Overall, tip-dating methods infer divergence dates often millions (or tens of millions) of years older than the earliest stratigraphic appearance of that clade. Model-comparison analyses of the pattern of body-size evolution found that the support for evolutionary mode can vary across and between tree samples from cal3 and tip-dating approaches. These differences suggest that model and software choice in dating analyses can have a substantial impact on the dated phylogenies obtained and broader evolutionary inferences.

Keywords: divergence dates; phylogenetic comparative methods; theropods; tip-dating.

Figure 1.

Age estimates for four nested theropod clades, across five different approaches for obtaining a dated phylogeny using the Xu et al. [1] dataset. Plotted boxes represent the first quantile, the median and the third quantile, respectively. From left to right, the approaches used are minimum node age dating and cal3, both applied to a sample of 100 randomly selected maximum-parsimony topologies, and three tip-dating approaches, the noSA and SA with BEAST2, and SA with MrBayes. The four clades examined (ordered left-to-right for each approach) are the root node (essentially, the Avetheropoda) and three clades with ‘branch-based’ definitions: the Coelurosauria (all taxa more closely related to modern birds than Sinraptor and Allosaurus), the Maniraptora (…than Ornithomimus) and the Avialae (…than Troodon or Deinonychus). (Online version in colour.)

Figure 2.

The fit of models of body-size evolution across different sets of trees, each from a different approach for obtaining dated phylogenies. The right-most set is trees with edge lengths constrained to a minimum length of 1 myr; for all others, see caption for figure 1. Models are fit to a single dated tree, with Akaike weights for each model, for that tree (which sum to 1), figured as a bar along with other trees from that sample, as a block of 100 stacked barplots with borders removed. The barplots for each sample are reordered relative to their support for Brownian motion (BM), versus Ornstein–Uhlenbeck (OU) and early burst (EB). (Online version in colour.)