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The r package divDyn for quantifying diversity dynamics using fossil sampling data
Author(s) -
Kocsis Ádám T.,
Reddin Carl J.,
Alroy John,
Kiessling Wolfgang
Publication year - 2019
Publication title -
methods in ecology and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.425
H-Index - 105
ISSN - 2041-210X
DOI - 10.1111/2041-210x.13161
Subject(s) - extinction event , ecology , species richness , extinction (optical mineralogy) , origination , sampling (signal processing) , taxonomic rank , abiotic component , biodiversity , macroecology , biology , paleontology , computer science , taxon , biological dispersal , population , computer network , demography , filter (signal processing) , sociology , computer vision
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.