DOI: 10.5061/dryad.02v6wwq6d
title: Data and code for: Diversity-dependent diversification in the history of marine animals

description: By comparing detrended estimates of diversity (taxonomic richness) and
 rates of origination, extinction, and net diversification, I show that, at
 the global scale over the course of the Phanerozoic Eon, rates of
 diversification and origination are negatively correlated with diversity.
 By contrast, extinction rates are only weakly correlated with diversity
 for the most part. These results hold for both genus- and species-level
 data and for many alternative analytical protocols. The asymmetry between
 extinction on the one hand and origination and net diversification, on the
 other hand, supports a model whereby extinction is largely driven by
 abiotic perturbations, with subsequent origination filling the void left
 by depleted diversity. Diversity-dependence is somewhat weaker, but still
 evident, if the initial Ordovician radiation or rebounds from major mass
 extinctions are omitted from analysis; thus, diversity-dependence is
 influenced, but not dominated, by these special intervals of Earth
 history. In the transition from Paleozoic to post-Paleozoic time,
 diversity-dependence of origination weakens while that of extinction
 strengthens; however, diversity-dependence of net diversification barely
 changes in strength. Despite nuances, individual clades largely yield
 results consistent with those for the aggregate data on all animals. On
 the whole, diversity-dependent diversification appears to be a pervasive
 factor in the macroevolution of marine animal life.
description: Data and code for "Diversity-dependent diversification in
 the history of marine animals" (American Naturalist).
 Author: Michael Foote The main goal of the
 study is to test for negative diversity-dependence of origination,
 extinction, and net diversification rates. Data are
 derived from the Paleobiology Database (paleodb.org). Author is
 responsible for data collation and code. Methods are
 described in the main text of the paper and in the R code file.
   FILES 1. TimeScale.csv
 gives a list of time intervals used in this study. These are mainly
 international stages, with some epochs and sub-epochs. It is based
 primarily on Gradstein et al. 2012 (The Geologic Time Scale 2012,
 Elsevier, Amsterdam) and Ogg et al. 2016 (A Concise Geologic Time Scale
 2016, Elsevier, Amsterdam), cross-referenced with stratigraphic
 information associated with collections in the Paleobiology Database
 (paleodb.org). 2. Occurrences.genus-level.csv: Number
 of collections in which each genus is present in each time interval. Data
 source is the Paleobiology Database (paleodb.org). 3.
 Occurrences.genus-level.low-latitude.csv: Number of collections in which
 each genus is present in each time interval, including only collections
 with paleolatitude less than 30 degrees. Collections without paleolatitude
 information are excluded. 4.
 Occurrences.genus-level.high-latitude.csv: Number of collections in which
 each genus is present in each time interval, including only collections
 with paleolatitude greater than or equal to 30 degrees. Collections
 without paleolatitude information are excluded. 5.
 Occurrences.species-level.csv: Number of collections in which each species
 is present in each time interval. 6. R-Code.R: Code
 used to analyze data.
description: Software required is R. No extra packages need to be loaded.