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 journalArticlepeer-review

    33 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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