Exploring the power of Bayesian birth-death skyline models to detect mass extinction events from phylogenies with only extant taxa

The meaning of mass extinctions and what the fossil record tells us about angiosperm survival at K-Pg: a reply to Hagen (2024)

Last year, we published research using phylogenetic comparative methods (PCMs) to reveal no phylogenetic evidence for elevated lineage-level extinction rates in angiosperms across K-Pg (Thompson JB, Ramírez-Barahona S. 2023 No phylogenetic evidence for angiosperm mass extinction at the Cretaceous-Palaeogene (K-Pg) boundary. Biol. Lett. 19, 20230314. (doi:10.1098/rsbl.2023.0314)), results that are in step with the global angiosperm fossil record. In a critique of our paper (Hagen ER. 2024 A critique of Thompson and Ramírez-Barahona (2023) or: how I learned to stop worrying and love the fossil record. EcoEvoRxiv. (doi:10.32942/X2631W)), simulation work is presented to argue we erred in our methodological choices and interpretations, and that we should have deferred to fossil evidence. In our opinion, underlying this critique are poor methodological choices on simulations and philosophical problems surrounding the definition of a mass extinction event, which leads to incorrect interpretations of both the fossil record and PCMs. We further argue that deferring to one source of evidence in favour of the other shuts the door to important evolutionary and philosophical questions.

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 analysed 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.

Convergent Adaptation of True Crabs (Decapoda: Brachyura) to a Gradient of Terrestrial Environments

For much of terrestrial biodiversity, the evolutionary pathways of adaptation from marine ancestors are poorly understood and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7600 species representing a striking diversity of morphology and ecology, including repeated adaptation to non-marine habitats. Here, we reconstruct the evolutionary history of Brachyura using new and published sequences of 10 genes for 344 tips spanning 88 of 109 brachyuran families. Using 36 newly vetted fossil calibrations, we infer that brachyurans most likely diverged in the Triassic, with family-level splits in the late Cretaceous and early Paleogene. By contrast, the root age is underestimated with automated sampling of 328 fossil occurrences explicitly incorporated into the tree prior, suggesting such models are a poor fit under heterogeneous fossil preservation. We apply recently defined trait-by-environment associations to classify a gradient of transitions from marine to terrestrial lifestyles. We estimate that crabs left the marine environment at least 7 and up to 17 times convergently, and returned to the sea from non-marine environments at least twice. Although the most highly terrestrial- and many freshwater-adapted crabs are concentrated in Thoracotremata, Bayesian threshold models of ancestral state reconstruction fail to identify shifts to higher terrestrial grades due to the degree of underlying change required. Lineages throughout our tree inhabit intertidal and marginal marine environments, corroborating the inference that the early stages of terrestrial adaptation have a lower threshold to evolve. Our framework and extensive new fossil and natural history datasets will enable future comparisons of non-marine adaptation at the morphological and molecular level. Crabs provide an important window into the early processes of adaptation to novel environments, and different degrees of evolutionary constraint that might help predict these pathways. [Brachyura; convergent evolution; crustaceans; divergence times; fossil calibration; molecular phylogeny; terrestrialization; threshold model.].

Testing extinction events and temporal shifts in diversification and fossilization rates through the skyline Fossilized Birth-Death (FBD) model: The example of some mid-Permian synapsid extinctions

In the last decade, the Fossilized Birth-Death (FBD) process has yielded interesting clues about the evolution of biodiversity through time. To facilitate such studies, we extend our method to compute the probability density of phylogenetic trees of extant and extinct taxa in which the only temporal information is provided by the fossil ages (i.e. without the divergence times) in order to deal with the piecewise constant FBD process, known as the "skyline FBD", which allows rates to change between pre-defined time intervals, as well as modelling extinction events at the bounds of these intervals. We develop approaches based on this method to assess hypotheses about the diversification process and to answer questions such as "Does a mass extinction occur at this time?" or "Is there a change in the fossilization rate between two given periods?". Our software can also yield Bayesian and maximum-likelihood estimates of the parameters of the skyline FBD model under various constraints. These approaches are applied to a simulated dataset in order to test their ability to answer the questions above. Finally, we study an updated dataset of Permo-Carboniferous synapsids to get additional insights into the dynamics of biodiversity change in three clades (Ophiacodontidae, Edaphosauridae and Sphenacodontidae) in the Pennsylvanian (Late Carboniferous) and Cisuralian (Early Permian), and to assess support for end-Sakmarian (or Artinskian) and end-Cisuralian mass extinction events discussed in previous studies.

On the application, reporting, and sharing of in silico simulations for genetic studies

In silico simulations play an indispensable role in the development and application of statistical models and methods for genetic studies. Simulation tools allow for the evaluation of methods and investigation of models in a controlled manner. With the growing popularity of evolutionary models and simulation‐based statistical methods, genetic simulations have been applied to a wide variety of research disciplines such as population genetics, evolutionary genetics, genetic epidemiology, ecology, and conservation biology. In this review, we surveyed 1409 articles from five journals that publish on major application areas of genetic simulations. We identified 432 papers in which genetic simulations were used and examined the targets and applications of simulation studies and how these simulation methods and simulated data sets are reported and shared. Whereas a large proportion (30%) of the surveyed articles reported the use of genetic simulations, only 28% of these genetic simulation studies used existing simulation software, 2% used existing simulated data sets, and 19% and 12% made source code and simulated data sets publicly available, respectively. Moreover, 15% of articles provided no information on how simulation studies were performed. These findings suggest a need to encourage sharing and reuse of existing simulation software and data sets, as well as providing more information regarding the performance of simulations.

Fossil and phylogenetic analyses reveal recurrent periods of diversification and extinction in dictyopteran insects

Variations of speciation and extinction rates determine the fate of clades through time. Periods of high diversification and extinction (possibly mass-extinction events) can punctuate the evolutionary history of various clades, but they remain loosely defined for many biological groups, especially nonmarine invertebrates like insects. Here, we examine whether the cockroaches, mantises and termites (altogether included in Dictyoptera) have experienced episodic pulses of speciation or extinction and how these pulses may be associated with environmental fluctuations or mass extinctions. We relied on molecular phylogeny and fossil data to shed light on the times and rates at which dictyopterans diversified. The diversification of Dictyoptera has alternated between (i) periods of high diversification in the late Carboniferous, Early-Middle Triassic, Early Cretaceous and middle Palaeogene, and (ii) periods of high extinction rates particularly at the Permian-Triassic boundary, but not necessarily correlated with the major global biodiversity crises as in the mid-Cretaceous. This study advocates the importance of analyzing, when possible, both molecular phylogeny and fossil data to unveil diversification and extinction periods for a given group. The causes and consequences of extinction must be studied beyond mass-extinction events alone to gain a broader understanding of how clades wax and wane.