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.

Mass extinctions are defined by extinction rates significantly above background levels and have had substantial consequences for the evolution of life. Geographically selective extinctions, subsequent originations and species redistributions may have changed global biogeographical structure, but quantification of this change is lacking. In order to assess quantitatively the biogeographical impact of mass extinctions, we outline time-traceable bioregions for benthic marine species across the Phanerozoic using a compositional network. Mass extinction events are visually recognizable in the geographical depiction of bioregions. The end-Permian extinction stands out with a severe reduction of provinciality. Time series of biogeographical turnover represent a novel aspect of the analysis of mass extinctions, confirming concentration of changes in the geographical distribution of benthic marine life.

Geologically rapid climate change is anticipated to increase extinction risk nonuniformly across the Earth's surface. Tropical species may be more vulnerable than temperate species to current climate warming because of high tropical climate velocities and reduced seawater oxygen levels. To test whether rapid warming indeed preferentially increased the extinction risk of tropical fossil taxa, we combine a robust statistical assessment of latitudinal extinction selectivity (LES) with the dominant views on climate change occurring at ancient extinction crises. Using a global data set of marine fossil occurrences, we assess extinction rates for tropical and temperate genera, applying log ratios to assess effect size and Akaike weights for model support. Among the classical “big five” mass extinction episodes, the end-Permian mass extinction exhibits temperate preference of extinctions, whereas the Late Devonian and end-Triassic selectively hit tropical genera. Simple links between the inferred direction of climate change and LES are idiosyncratic, both during crisis and background intervals. More complex models, including sampling patterns and changes in the latitudinal distribution of continental shelf area, show tropical LES to be generally associated with raised tropical heat and temperate LES with global cold temperatures. With implications for the future, our paper demonstrates the consistency of high tropical temperatures, habitat loss, and the capacity of both to interact in generating geographic patterns in extinctions.

Similar environmental driving forces can produce similarity among geographically distant ecosystems. Coastal oceanic upwelling, for example, has been associated with elevated biomass and abundance patterns of certain functional groups, e.g., corticated macroalgae. In the upwelling system of Northern Chile, we examined measures of intertidal macrobenthic composition, structure and trophic ecology across eighteen shores varying in their proximity to two coastal upwelling centres, in a hierarchical sampling design (spatial scales of >1 and >10 km). The influence of coastal upwelling on intertidal communities was confirmed by the stable isotope values (δ13C and δ15N) of consumers, including a dominant suspension feeder, grazers, and their putative resources of POM, epilithic biofilm, and macroalgae. We highlight the utility of muscle δ15N from the suspension feeding mussel, Perumytilus purpuratus, as a proxy for upwelling, supported by satellite data and previous studies. Where possible, we used corrections for broader-scale trends, spatial autocorrelation, ontogenetic dietary shifts and spatial baseline isotopic variation prior to analysis. Our results showed macroalgal assemblage composition, and benthic consumer assemblage structure, varied significantly with the intertidal influence of coastal upwelling, especially contrasting bays and coastal headlands. Coastal topography also separated differences in consumer resource use. This suggested that coastal upwelling, itself driven by coastline topography, influences intertidal communities by advecting nearshore phytoplankton populations offshore and cooling coastal water temperatures. We recommend the isotopic values of benthic organisms, specifically long-lived suspension feeders, as in situ alternatives to offshore measurements of upwelling influence.

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