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

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Authors Ádám T. Kocsis, Carl J. Reddin, John Alroy, Wolfgang Kiessling
Journal/Conference Name Methods in Ecology and Evolution
Paper Category , ,
Paper 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.
Date of publication 2019
Code Programming Language R

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