DOI: 10.5061/dryad.44j0zpcn8
title: A critique of Thompson and Ramírez-Barahona (2023) or: how I learned to stop worrying and love the fossil record

description: 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.
description: 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.
description: # Data and code for: A critique of Thompson and Ramírez-Barahona (2023)
 or: how I learned to stop worrying and love the fossil record [Access this
 dataset on Dryad](doi.org/10.5061/dryad.44j0zpcn8) This dataset contains
 two software files, both written in R, used to conduct the analyses for
 the publication. The first, critique_kpg_paper.R, takes one data file as
 an input: raw_smithandbrown.tre.txt, the seed plant phylogeny published by
 Smith and Brown (2018). With help from functions provided by several free,
 open-source R packages, this file particularly contains analyses of which
 models of evolution best fit the Smith and Brown tree. This was done
 following the methodology of Thompson and Ramírez-Barahona (2023). The
 second software file, kpg_simulations.R, simulates trees of similar size
 and age to the Smith and Brown phylogeny to examine whether the results
 described in Thompson and Ramírez-Barahona (2023) might be due to Type II
 error. It conducts similar model-fitting tests as written in
 critique_kpg_paper.R on trees for which the true generating parameters are
 known. ## Description of the data and file structure
 raw_smithandbrown.tre.txt is the only input data file in this repository,
 and it is only input for critique_kpg_paper.R. It is a file containing a
 phylogeny of seed plants. All R code files can be run line-by-line in an
 integrated development environment like RStudio. One warning is that some
 of the analyses contained in kpg_simulations.R are computationally
 expensive, particularly when generating multiple very large simulated
 phylogenies, and they can take several hours to complete. The repository
 contains several supplemental figures for analyses described in the text,
 as well as the five simulated phylogenies described in the text. ##
 Sharing/Access information The data contained in this repository can also
 be accessed on GitHub (link in the Related Works section). The tree
 published by Smith and Brown (2018) was derived from GitHub (specifically
 "GBMB.tre") linked in the Related Works section. ##
 Code/Software To run the two code files, you will need the following
 packages (the versions with which analyses were conducted are also
 listed): 1. ape (version 5.6.2) 2. TESS (version 2.1.2) 3. diversitree
 (version 0.9.16) 4. geiger (version 2.0.10) 5. TreeSim (version 2.4) 6.
 paleotree (version 3.4.5) 7. dplyr (version 1.1.3) 8. TreeTools (version
 1.9.1) 9. phytools (version 1.2.0)