Abstract
Through phylogenetic modelling, we previously presented strong support for diversification decline in the three major subclades of dinosaurs (Sakamoto et al. 2016 Proc. Natl Acad. Sci. USA 113, 5036–5040. (doi:10.1073/pnas.1521478113)). Recently, our support for this model has been criticized (Bonsor et al. 2020 R. Soc. Open Sci. 7, 201195. (doi:10.1098/rsos.201195)). Here, we highlight that these criticisms seem to largely stem from a misunderstanding of our study: contrary to Bonsor et al.'s claims, our model accounts for heterogeneity in diversification dynamics, was selected based on deviance information criterion (DIC) scores (not parameter significance), and intercepts were estimated to account for uncertainties in the root age of the phylogenetic tree. We also demonstrate that their new analyses are not comparable to our models: they fit simple, Dinosauria-wide models as a direct comparison to our group-wise models, and their additional trees are subclades that are limited in taxonomic coverage and temporal span, i.e. severely affected by incomplete sampling. We further present results of new analyses on larger, better-sampled trees (N = 961) of dinosaurs, showing support for the time-quadratic model. Disagreements in how we interpret modelled diversification dynamics are to be expected, but criticisms should be based on sound logic and understanding of the model under discussion.
Highlights
Bonsor et al [1] criticized our selection of a model of diversification in dinosaurs that supported a long-term decline in the rate at which speciation events accumulated across the dinosaur tree of life through time [2]
We previously presented strong support for diversification decline in the three major subclades of dinosaurs
We highlight that these criticisms seem to largely stem from a misunderstanding of our study: contrary to Bonsor et al.’s claims, our model accounts for heterogeneity in diversification dynamics, was selected based on deviance information criterion (DIC) scores, and intercepts were estimated to account for uncertainties in the root age of the phylogenetic tree. We demonstrate that their new analyses are not comparable to our models: they fit simple, Dinosauria-wide models as a direct comparison to our group-wise models, and their additional trees are subclades that are limited in taxonomic coverage and temporal span, i.e. severely affected by incomplete sampling
Summary
Bonsor et al [1] criticized our selection of a model of diversification in dinosaurs that supported a long-term decline in the rate at which speciation events accumulated across the dinosaur tree of life through time (time-quadratic model) [2]. Bonsor et al criticize us for basing our selection of the time-quadratic model on parameter significance instead of DIC scores. We used parameter significance to determine whether certain grouping parametrization was more informative over another, namely in how the slopes and intercepts were modelled for the hadrosauriforms and ceratopsids (see SI from [2]) This approach does not apply to the selection of the time-quadratic model over the timesquare root model. Bonsor et al fitted and compared the three models (Models A–C) in nine additional trees as well as the three trees we analysed in our 2016 paper [1,2] Their results show ambiguity in model selection based on DIC, with the time-quadratic model rarely being selected, even in the reanalyses of our three trees. Their results show ambiguity in model selection based on DIC, with the time-quadratic model rarely being selected, even in the reanalyses of our three trees. 4 there are largely two problems with their analyses: (i) they equate the Dinosauria-wide model with the 5-group model and refute the latter through reanalyses of the former; and (ii) their nine additional trees are substantially smaller with severely limited taxonomic coverage and are, not comparable to our trees and subclades therein
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