Distributions of extinction times from fossil ages and tree topologies: the example of mid-Permian synapsid extinctions.

Gilles Didier,Michel Laurin

doi:10.7717/peerj.12577

Abstract

Given a phylogenetic tree that includes only extinct, or a mix of extinct and extant taxa, where at least some fossil data are available, we present a method to compute the distribution of the extinction time of a given set of taxa under the Fossilized-Birth-Death model. Our approach differs from the previous ones in that it takes into account (i) the possibility that the taxa or the clade considered may diversify before going extinct and (ii) the whole phylogenetic tree to estimate extinction times, whilst previous methods do not consider the diversification process and deal with each branch independently. Because of this, our method can estimate extinction times of lineages represented by a single fossil, provided that they belong to a clade that includes other fossil occurrences. We assess and compare our new approach with a standard previous one using simulated data. Results show that our method provides more accurate confidence intervals. This new approach is applied to the study of the extinction time of three Permo-Carboniferous synapsid taxa (Ophiacodontidae, Edaphosauridae, and Sphenacodontidae) that are thought to have disappeared toward the end of the Cisuralian (early Permian), or possibly shortly thereafter. The timing of extinctions of these three taxa and of their component lineages supports the idea that the biological crisis in the late Kungurian/early Roadian consisted of a progressive decline in biodiversity throughout the Kungurian.

Highlights

Reconstructing the history of the diversification of life on Earth has long been one of the main goals of evolutionary biology
Because it is computed independently on each extinct taxon, the level of precision provided by the previous methods depends on the number of fossils present on each terminal branch. This point can be a major issue for datasets where the fossil recovery is low. This limitation does not apply to the method we propose, in which the extinction-time distribution of taxa with a single fossil on their terminal branch can be determined, if this branch belongs to a clade with a sufficient number of fossils
Methods to estimates extinction times which are presented below all return a confidence upper bound of the extinction date at a given order (95% is the usual choice), i.e., the time t which is such that the probability for the extinction date to be anterior to t is equal to the order required

Summary

Introduction

Reconstructing the history of the diversification of life on Earth has long been one of the main goals of evolutionary biology. It even documents spectacular changes in the rates of cladogenesis (evolutionary divergence of a lineage that splits into two lineages, a process that we here equate with speciation), anagenesis, and extinction, which occurred more or less frequently in the history of life These were often caused by environmental changes, some of which may have resulted from intense volcanism (Wignall et al, 2009), impacts of large meteorites (Basu et al, 2003; Tabor et al, 2020), a combination of both (Arens and West, 2008), or transgressions, regressions (Hallam, 1989), or glaciations, among others.

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