DOI: 10.5061/dryad.b8gtht79t
title: Impacts of speciation and extinction measured by an evolutionary decay clock

description: The hypothesis that destructive mass extinctions enable creative
 evolutionary radiations (creative destruction) is central to classic
 concepts of macroevolution[1,2]. However, the relative impacts of
 extinction and radiation on the co-occurrence of species have not been
 directly quantitatively compared across the Phanerozoic eon. Here we apply
 machine learning to generate a spatial embedding (multidimensional
 ordination) of the temporal co-occurrence structure of the Phanerozoic
 fossil record, covering 1,273,254 occurrences in the Paleobiology Database
 for 171,231 embedded species. This facilitates simultaneous comparison of
 macroevolutionary disruptions, using measures independent of secular
 diversity trends. Among the 5% most significant periods of disruption, we
 identify the ‘big five’ mass extinction events[2], seven additional mass
 extinctions, two combined mass extinction–radiation events and 15 mass
 radiations. In contrast to narratives that emphasize post-extinction
 radiations[1,3], we find that the proportionally most comparable mass
 radiations and extinctions (such as the Cambrian explosion and the
 end-Permian mass extinction) are typically decoupled in time, refuting any
 direct causal relationship between them. Moreover, in addition to
 extinctions[4], evolutionary radiations themselves cause evolutionary
 decay (modelled co-occurrence probability and shared fraction of species
 between times approaching zero), a concept that we describe as destructive
 creation. A direct test of the time to over-threshold macroevolutionary
 decay[4] (shared fraction of species between two times ≤ 0.1), counted by
 the decay clock, reveals saw-toothed fluctuations around a Phanerozoic
 mean of 18.6 million years. As the Quaternary period began at a
 below-average decay-clock time of 11 million years, modern extinctions
 further increase life’s decay-clock debt.
description: Data accompanying Hoyal Cuthill et al 2020, Nature, DOI
 10.1038/s41586-020-3003-4, including the occurrence numbers for the source
 datasets used in the study (downloaded from the Paleobiology Database
 at https://paleobiodb.org) and custom data generated in the study.
description: In use of provided custom data please cite the associated paper
 (Hoyal Cuthill et al 2020, Impacts of speciation and extinction measured
 by an evolutionary decay clock. Nature, DOI:
 10.1038/s41586-020-3003-4). ReadMe<br> For Dryad
 dataset https://doi.org/10.5061/dryad.b8gtht79t<br> Hoyal Cuthill et
 al Nature DOI 10.1038/s41586-020-3003-4 Files and usage
 notes: fossil_embeddings.txt<br> Spatial
 embedding of fossil species produced in the associated publication (Hoyal
 Cuthill et al, Nature).<br> This file can be opened with a text
 editor or read in by the Supplementary Computer code of the associated
 publication (Hoyal Cuthill et al, Nature).<br> Rows correspond to
 fossil species, columns correspond to axes of the multidimensional spatial
 embedding, values give locations of species on these axes.
 fossil_time_embeddings.th<br> This file is a PyTorch state
 dictionary object, recording machine learning parameter values from the
 analysis of the associated publication (Hoyal Cuthill et al,
 Nature).<br> This file can be opened with a CUDA enabled PyTorch
 instance. For example see instructions for handling PyTorch state
 dictionary files at:<br>
 https://pytorch.org/tutorials/beginner/saving_loading_models.html OccNs_pbdb_data_1lineheader.csv<br> This is a comma separated values file containing the occurrence numbers of the Paleobiology Database download of the complete dataset used in the associated publication (Hoyal Cuthill et al, Nature). Corresponding full raw data can be downloaded from https://paleobiodb.org/ using the following data download url:<br> http://paleobiodb.org/data1.2/occs/list.csv?datainfo&rowcount&taxon_reso=genus&max_ma=1000&min_ma=0&show=class,coords,env OccNs_pbdb_data19_03_20_species_lineheader.csv<br> This is a comma separated values file containing the occurrence numbers of the Paleobiology Database download of the taxonomically screened dataset used in the associated publication (Hoyal Cuthill et al, Nature).<br> Corresponding full raw data can be downloaded from https://paleobiodb.org/ using the following data download url:<br> http://paleobiodb.org/data1.2/occs/list.csv?datainfo&rowcount&taxon_reso=species&max_ma=1000&min_ma=0&show=class,acconly,coords,paleoloc,env,acconly stimes.txt<br> This is a text file containing time range mid points for analysed fossil species as described further in the Supplementary Computer code of the associated publication (Hoyal Cuthill et al, Nature).