A critique of Thompson and Ramírez-Barahona (2023) or: how I learned to stop worrying and love the fossil record

A recent study published in Biology Letters by Thompson and Ramírez-Barahona (2023) argued that, according to analyses of diversification on two massive molecular phylogenies comprising thousands of species, there is no evidence that angiosperms (i.e., flowering plants) were affected by the Cretaceous-Paleogene mass extinction. Here I critique these conclusions from both methodological and philosophical perspectives. I demonstrate that the methods used in their study possess statistical limitations that strongly reduce the power to detect a true mass extinction event using data similar to those analyzed by Thompson and Ramírez-Barahona (2023). Additionally, I use their study as a springboard to examine the relationship between phylogenetic and fossil evidence in diversification studies.

Methods
Here I examine the conclusions of Thompson and Ramírez-Barahona (2023) by performing a limited number of tests with TESS and CoMET similar to those found in their paper. All tests involve the phylogeny published by Smith and Brown (2018) and simulated trees of similar sizes.

To test the degree to which TESS and CoMET can accurately identify the generating models of simulated trees, I extracted branching times from the tree and created three simulated trees in TESS to which I could fit the data using the following branching process models: constant birth-death, episodic birth-death, and a birth-death model including a mass extinction. The marginal likelihoods of each model were estimated using stepping-stone sampling in TESS, and the relative support of the models was compared using Bayes factors.

To test the degree to which TESS and CoMET can accurately identify mass extinction events in an analysis like that of Thompson and Ramírez-Barahona (2023), I usedTreeSim (Stadler 2011) to simulate phylogenies of similar size and age to the Smith and Brown phylogeny. I estimated diversification rates using the “tess.analysis” function to test whether a mass extinction would be detected by the CoMET model.