MotivationThe BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community‐led open‐source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.Main types of variables includedThe database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.Spatial location and grainBioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).Time period and grainBioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.Major taxa and level of measurementBioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.Software format.csv and .SQL.

Abstract.On

Humans have elevated global extinction rates and thus lowered global scale species richness. However, there is no a priori reason to expect that losses of global species richness should always, or even often, trickle down to losses of species richness at regional and local scales, even though this relationship is often assumed. Here, we show that scale can modulate our estimates of species richness change through time in the face of anthropogenic pressures, but not in a unidirectional way. Instead, the magnitude of species richness change through time can increase, decrease, reverse, or be unimodal across spatial scales. Using several case studies, we show different forms of scale‐dependent richness change through time in the face of anthropogenic pressures. For example, Central American corals show a homogenization pattern, where small scale richness is largely unchanged through time, while larger scale richness change is highly negative. Alternatively, birds in North America showed a differentiation effect, where species richness was again largely unchanged through time at small scales, but was more positive at larger scales. Finally, we collated data from a heterogeneous set of studies of different taxa measured through time from sites ranging from small plots to entire continents, and found highly variable patterns that nevertheless imply complex scale‐dependence in several taxa. In summary, understanding how biodiversity is changing in the Anthropocene requires an explicit recognition of the influence of spatial scale, and we conclude with some recommendations for how to better incorporate scale into our estimates of change.

Climate change and other anthropogenic drivers of biodiversity change are unequally distributed across the world. Overlap in the distributions of different drivers have important implications for biodiversity change attribution and the potential for interactive effects. However, the spatial relationships among different drivers and whether they differ between the terrestrial and marine realm has yet to be examined. We compiled global gridded datasets on climate change, land‐use, resource exploitation, pollution, alien species potential and human population density. We used multivariate statistics to examine the spatial relationships among the drivers and to characterize the typical combinations of drivers experienced by different regions of the world. We found stronger positive correlations among drivers in the terrestrial than in the marine realm, leading to areas with high intensities of multiple drivers on land. Climate change tended to be negatively correlated with other drivers in the terrestrial realm (e.g. in the tundra and boreal forest with high climate change but low human use and pollution), whereas the opposite was true in the marine realm (e.g. in the Indo‐Pacific with high climate change and high fishing). We show that different regions of the world can be defined by Anthropogenic Threat Complexes (ATCs), distinguished by different sets of drivers with varying intensities. We identify 11 ATCs that can be used to test hypotheses about patterns of biodiversity and ecosystem change, especially about the joint effects of multiple drivers. Our global analysis highlights the broad conservation priorities needed to mitigate the impacts of anthropogenic change, with different priorities emerging on land and in the ocean, and in different parts of the world.

The modern biodiversity crisis reflects global extinctions and local introductions. Human activities have dramatically altered rates and scales of processes that regulate biodiversity at local scales. Reconciling the threat of global biodiversity loss with recent evidence of stability at fine spatial scales is a major challenge and requires a nuanced approach to biodiversity change that integrates ecological understanding. With a new dataset of 471 diversity time series spanning from 1962 to 2015 from marine coastal ecosystems, we tested (1) whether biodiversity changed at local scales in recent decades, and (2) whether we can ignore ecological context (e.g., proximate human impacts, trophic level, spatial scale) and still make informative inferences regarding local change. We detected a predominant signal of increasing species richness in coastal systems since 1962 in our dataset, though net species loss was associated with localized effects of anthropogenic impacts. Our geographically extensive dataset is unlikely to be a random sample of marine coastal habitats; impacted sites (3% of our time series) were underrepresented relative to their global presence. These local-scale patterns do not contradict the prospect of accelerating global extinctions but are consistent with local species loss in areas with direct human impacts and increases in diversity due to invasions and range expansions in lower impact areas. Attempts to detect and understand local biodiversity trends are incomplete without information on local human activities and ecological context.

Human activities have led to widespread ecological decline; however, the severity of degradation is spatially heterogeneous due to some locations resisting, escaping, or rebounding from disturbances. We developed a framework for identifying oases within coral reef regions using long‐term monitoring data. We calculated standardised estimates of coral cover (z‐scores) to distinguish sites that deviated positively from regional means. We also used the coefficient of variation (CV) of coral cover to quantify how oases varied temporally, and to distinguish among types of oases. We estimated “coral calcification capacity” (CCC), a measure of the coral community's ability to produce calcium carbonate structures and tested for an association between this metric and z‐scores of coral cover. We illustrated our z‐score approach within a modelling framework by extracting z‐scores and CVs from simulated data based on four generalized trajectories of coral cover. We then applied the approach to time‐series data from long‐term reef monitoring programmes in four focal regions in the Pacific (the main Hawaiian Islands and Mo'orea, French Polynesia) and western Atlantic (the Florida Keys and St. John, US Virgin Islands). Among the 123 sites analysed, 38 had positive z‐scores for median coral cover and were categorised as oases. Synthesis and applications. Our framework provides ecosystem managers with a valuable tool for conservation by identifying “oases” within degraded areas. By evaluating trajectories of change in state (e.g., coral cover) among oases, our approach may help in identifying the mechanisms responsible for spatial variability in ecosystem condition. Increased mechanistic understanding can guide whether management of a particular location should emphasise protection, mitigation or restoration. Analysis of the empirical data suggest that the majority of our coral reef oases originated by either escaping or resisting disturbances, although some sites showed a high capacity for recovery, while others were candidates for restoration. Finally, our measure of reef condition (i.e., median z‐scores of coral cover) correlated positively with coral calcification capacity suggesting that our approach identified oases that are also exceptional for one critical component of ecological function.

Sea Grant. She studies dynamics of marine systems and how we can manage ecosystems for long term sustainability. This work was completed as a postdoctoral researcher at Stanford University's Hopkins Marine Station. 2 Fiorenza Micheli is a Professor at Hopkins Marine Station of Stanford University and a Senior Fellow at Stanford's Woods Institute for the Environment. Her research focuses on the ecology and conservation of coastal marine ecosystems. 3 Laura Airoldi is a marine ecologist at the University of Bologna She studies what factors facilitate the recovery and restoration of damaged marine ecosystems. 4 Charles Boch is a postdoctoral fellow at the Monterey Bay Aquarium Research Institute. He studies biological response to global and local environmental drivers. 5 Giulio De Leo is a Professor at Hopkins Marine Station of Stanford University and a Senior Fellow at Stanford's Woods Institute for the Environment. He studies theoretical ecology focused on disease ecology, marine conservation, and public health. 6 Robin Elahi is an ecologist at Hopkins Marine Station of Stanford University. He studies the drivers of biodiversity change in marine ecosystems. 7 Francesco Ferretti is a quantitative and computational marine ecologist at Hopkins Marine Station of Stanford University. He studies ecosystem baselines and the effect of human impact on marine ecosystems.

Anthropogenic environmental change has increased coral reef disturbance regimes in recent decades, altering the structure and function of many coral reefs globally. In this study, we used coral community survey data collected from 1996 to 2015 to evaluate reef-scale coral calcification capacity (CCC) dynamics with respect to recorded pulse disturbances for 121 reef sites in the Main Hawaiian Islands and Mo'orea (French Polynesia) in the Pacific and the Florida Keys Reef Tract and St. John (U.S. Virgin Islands) in the western Atlantic. CCC remained relatively high in the Main Hawaiian Islands in the absence of recorded widespread disturbances; declined and subsequently recovered in Mo'orea following a crown-ofthorns sea star outbreak, coral bleaching, and major cyclone; decreased and remained low following coral bleaching in the Florida Keys Reef Tract; and decreased following coral bleaching and disease in St. John. Individual coral taxa have variable calcification rates and susceptibility to disturbances because of their differing life-history strategies. As a result, temporal changes in CCC in this study were driven by shifts in both overall coral cover and coral community composition. Analysis of our results considering coral lifehistory strategies showed that weedy corals generally increased their contributions to CCC over time while the contribution of competitive corals decreased. Shifts in contributions by stress-tolerant and generalist corals to CCC were more variable across regions. The increasing frequency and intensity of disturbances under 21st century global change therefore has the potential to drive lower and more variable CCC because of the increasing dominance of weedy and some stress-tolerant corals.