The r package divDyn for quantifying diversity dynamics using fossil sampling data

Ádám T. Kocsis*, Carl J. Reddin, John Alroy, Wolfgang Kiessling

*Corresponding author for this work

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Unbiased time series of diversity dynamics are vital for quantifying the grand history of life. Applications include identifying ancient mass extinctions and inferring both biotic and abiotic controls on diversification rates. We introduce divDyn, a new r package that facilitates the calculation of taxonomic richness, extinction and origination rates from time-binned fossil data. State-of-the-art counting protocols, and sampling standardization functions permit the reconstruction of biologically meaningful time series. Additional functions permit the partitioning of turnover rates by environmental affinity. Using divDyn, we display Phanerozoic-scale diversity dynamics of marine invertebrates. With the help of the core function and standard subsampling options, we revisit the hypothesis of declining taxonomic rates over time, mass extinctions and equilibrial diversity dynamics and assess their methodological dependency. Our results suggest that rates declined only over the early Phanerozoic, only three mass extinctions stand out clearly, and evidence of equilibrial dynamics is dependent on the used methods. The modular and fast implementation of published methods ensures traceability, reproducibility and comparability of future studies.

Original languageEnglish
Pages (from-to)735-743
Number of pages9
JournalMethods in Ecology and Evolution
Volume10
Issue number5
Early online date31 Jan 2019
DOIs
Publication statusPublished - May 2019

Keywords

  • diversity dynamics
  • extinction
  • fossil record
  • origination
  • Palaeobiology Database
  • subsampling

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