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Global biodiversity assessments have highlighted land-use change as a key driver of biodiversity change. However, there is little empirical evidence of how habitat transformations such as forest loss and gain are reshaping biodiversity over time. We quantified how change in forest cover has influenced temporal shifts in populations and ecological assemblages from 6090 globally distributed time series across six taxonomic groups. We found that local-scale increases and decreases in abundance, species richness, and temporal species replacement (turnover) were intensified by as much as 48% after forest loss. Temporal lags in population- and assemblage-level shifts after forest loss extended up to 50 years and increased with species’ generation time. Our findings that forest loss catalyzes population and biodiversity change emphasize the complex biotic consequences of land-use change.

While human activities are known to elicit rapid turnover in species composition through time, the properties of the species that increase or decrease their spatial occupancy underlying this turnover are less clear. Here, we used an extensive dataset of 238 metacommunity time series of multiple taxa spread across the globe to evaluate whether species that are more widespread (large-ranged species) differed in how they changed their site occupancy over the 10–90 years the metacommunities were monitored relative to species that are more narrowly distributed (small-ranged species). We found that on average, large-ranged species tended to increase in occupancy through time, whereas small-ranged species tended to decrease. These relationships were stronger in marine than in terrestrial and freshwater realms. However, in terrestrial regions, the directional changes in occupancy were less extreme in protected areas. Our findings provide evidence for systematic decreases in occupancy of small-ranged species, and that habitat protection could mitigate these losses in the face of environmental change. Whether a species declines under the current biodiversity crisis could partly depend on its range size. Here, the authors use replicated metacommunity data to identify global patterns in the relationship between species’ range size and changes in occupancy through time.

BackgroundDisturbances alter the diversity and composition of microbial communities. Yet a generalized empirical assessment of microbiome responses to disturbance across different environments is needed to understand the factors driving microbiome recovery, and the role of the environment in driving these patterns. Results To this end, we combined null models with Bayesian generalized linear models to examine 86 time series of disturbed mammalian, aquatic, and soil microbiomes up to 50 days following disturbance. Overall, disturbances had the strongest effect on mammalian microbiomes, which lost taxa and later recovered their richness, but not their composition. In contrast, following disturbance, aquatic microbiomes tended away from their pre-disturbance composition over time. Surprisingly, across all environments, we found no evidence of increased compositional dispersion (i.e., variance) following disturbance, in contrast to the expectations of the Anna Karenina Principle. Conclusions This is the first study to systematically compare secondary successional dynamics across disturbed microbiomes, using a consistent temporal scale and modeling approach. Our findings show that the recovery of microbiomes is environment-specific, and helps to reconcile existing, environment-specific research into a unified perspective.

While biodiversity is being reshaped across the globe, extinction risk assessments are lacking for most species, and a major challenge remains in understanding whether global threat status aligns with local population trends. Here, we assess whether population temporal prevalence trends are consistent with a species’ global extinction risk, using over 60,000 populations of 2362 species across 978 marine and terrestrial assemblages (sampled for at least 20 years, mostly from temperate regions). We assign each population to one of five categories of temporal prevalence dynamics, and retrieve each species’ extinction risk from the International Union for Conservation of Nature (IUCN) Red List. Fewer than 10% of local populations show consistent increasing or decreasing prevalence over time, with most exhibiting random patterns of temporal change, especially marine populations. Overall, higher extinction risk is associated with a higher frequency of decreasing local prevalence, and vice-versa for increasing prevalence, against a backdrop of complex links between extinction risk and local temporal dynamics. Our results suggest that directional changes in species local prevalence could be harbingers of future changes in global threat status, and highlight how leveraging assemblage monitoring data can aid conservation efforts and extinction assessments. Most species lack extinction risk assessments. This study shows decreasing local prevalence within assemblages correlates with extinction risk, with complex links between extinction risk and local temporal dynamics, highlighting the value of assemblage monitoring.

Disentangling the drivers of diversity gradients can be challenging. The Measurement of Biodiversity (MoB) framework decomposes scale-dependent changes in species diversity into three components of community structure: species abundance distribution (SAD), total community abundance, and within-species spatial aggregation. Here we extend MoB from categorical treatment comparisons to quantify variation along continuous geographic or environmental gradients. Our approach requires sites along a gradient, each consisting of georeferenced plots of abundance-based species composition data. We demonstrate our method using a case study of ants sampled along an elevational gradient of 28 sites in a mixed deciduous forest of the Great Smoky Mountains National Park, USA. MoB analysis revealed that decreases in ant species richness along the elevational gradient were associated with decreasing evenness and total number of species, which counteracted the modest increase in richness associated with decreasing spatial aggregation along the gradient. Total community abundance had a negligible effect on richness at all but the finest spatial grains, SAD effects increased in importance with sampling effort, and the aggregation effect had the strongest effect at coarser spatial grains. These results do not support the more-individuals hypothesis, but they are consistent with a hypothesis of stronger environmental filtering at coarser spatial grains. Our extension of MoB has the potential to elucidate how components of community structure contribute to changes in diversity along environmental gradients and should be useful for a variety of assemblage-level data collected along gradients.

Marine protected areas (MPAs) are a well‐established conservation practice worldwide, but their effectiveness in protecting or replenishing fish biodiversity remains uneven. Understanding the patterns of this heterogeneity is central to general guidelines for MPA design and can ultimately provide guidance on how to maximize MPA potential. Here, we examine associations between the degree of protection, duration of protection, and protected area size, with fish biodiversity inside of protected areas relative to that of sites nearby, but outside of protected areas. We quantitatively synthesize 116 published estimates of species richness from 72 MPAs and 38 estimates of Shannon entropy from 21 MPAs. We show that species richness is on average 18% (95% CIs: 10%–29%) higher in protected areas than in areas open to fishing; on average, Shannon entropy is 13% (95% CIs: −2% to 31%) higher within protected areas relative to outside. We find no relationship between the degree and duration of protection with the ratio of species richness inside versus outside of protected areas; both fully and partially protected areas contribute to the accumulation of species inside of protected areas, and protected areas of all ages contribute similarly on average to biodiversity conservation. In contrast to our expectations, increasing protected area size was associated with a decreased ratio of species richness sampled at sites inside versus outside of the protected area, possibly due, for example, to insufficient enforcement and/or low compliance. Finally, we discuss why meta‐analyses such as ours that summarize effect sizes of local scale biodiversity responses, that is, those at a single site, can only give a partial answer to the question of whether larger protected areas harbor more species than comparable unprotected areas.

Broad‐scale biodiversity monitoring relies, at least in part, on the efforts of citizen, or community, scientists. To ensure robust inferences from citizen science data, it is important to understand the spatial pattern of sampling effort by citizen scientists and how it deviates from an optimal pattern. Here, we develop a generalized workflow to estimate the optimal distribution of sampling effort for inference of species diversity (e.g., species richness, Shannon diversity, and Simpson's diversity) patterns using the relationship between species diversity and land cover. We used data from the eBird citizen science project that was collected across heterogeneous landscapes in Florida (USA) to illustrate this workflow across different grain sizes. We found that a relatively small number of samples are needed to meet 95% sampling completeness when diversity estimation is focused on dominant species: 43, 64, 96, 123, 172, and 176 for 5 × 5, 10 × 10, 15 × 15, 20 × 20, 25 × 25, and 30 × 30‐km2 grain sizes, respectively. In contrast, three to five times more samples are necessary to infer species diversity when estimation is focused on rare species. However, in both cases, the optimal distribution of effort was spatially heterogeneous, with more effort needed in regions of higher diversity. Our results highlight the potential of citizen science data to make informed comparisons of species diversity in space and time, as well as how sampling effort inherently depends on monitoring goals, such as whether dominant or rare species are targeted. Our general workflow allows for the quantification of sampling effort needed to estimate species diversity with citizen science data and can guide future adaptive sampling by citizen science participants.

Although habitat loss is the predominant factor leading to biodiversity loss in the Anthropocene 1 , 2 , exactly how this loss manifests—and at which scales—remains a central debate 3 – 6 . The ‘passive sampling’ hypothesis suggests that species are lost in proportion to their abundance and distribution in the natural habitat 7 , 8 , whereas the ‘ecosystem decay’ hypothesis suggests that ecological processes change in smaller and more-isolated habitats such that more species are lost than would have been expected simply through loss of habitat alone 9 , 10 . Generalizable tests of these hypotheses have been limited by heterogeneous sampling designs and a narrow focus on estimates of species richness that are strongly dependent on scale. Here we analyse 123 studies of assemblage-level abundances of focal taxa taken from multiple habitat fragments of varying size to evaluate the influence of passive sampling and ecosystem decay on biodiversity loss. We found overall support for the ecosystem decay hypothesis. Across all studies, ecosystems and taxa, biodiversity estimates from smaller habitat fragments—when controlled for sampling effort—contain fewer individuals, fewer species and less-even communities than expected from a sample of larger fragments. However, the diversity loss due to ecosystem decay in some studies (for example, those in which habitat loss took place more than 100 years ago) was less than expected from the overall pattern, as a result of compositional turnover by species that were not originally present in the intact habitats. We conclude that the incorporation of non-passive effects of habitat loss on biodiversity change will improve biodiversity scenarios under future land use, and planning for habitat protection and restoration. Analysis of 123 studies of assemblage-level abundances of focal taxa from fragmented habitats finds that increasing fragmentation has a disproportionately large effect on biodiversity loss, supporting the ecosystem decay hypothesis.

Ecological stability is a vital component of natural ecosystems that can inform effective conservation and ecosystem management. Furthermore, there is increasing interest in making comparisons of stability values across sites, systems and taxonomic groups, often using comparative synthetic approaches, such as meta‐analysis. However, these synthetic approaches often compare/contrast systems where measures of stability mean very different things to the taxa involved. Here, we present results from theoretical models and empirical data to illustrate how differences in growth rates among taxa influence four widely used metrics of ecological stability of species abundances responding to pulse perturbations: resilience, recovery, resistance and temporal stability. We refer to these classic growth‐rate‐dependent metrics as ‘realised’ stability. We show that realised resilience and realised temporal stability vary as a function of organisms' growth rates; realised recovery depends on the relation between growth rate and sampling duration; and realised resistance depends on the relation between growth rate and sampling interval. To account for these influences, we introduce metrics intended to be more independent of growth rates, which we refer to as ‘intrinsic’ stability. Intrinsic stability can be used to summarise the overall effects of a disturbance, separately from internal recovery processes – thereby allowing more general comparisons of disturbances across organisms and contexts. We argue that joint consideration of both realised and intrinsic stability is important for future comparative studies. We present results from theoretical models and empirical data to illustrate how differences in growth rates among taxa influence four widely used metrics of ecological stability of species abundances responding to pulse perturbations: resilience, recovery, resistance and temporal stability. To account for these influences on growth rate, we introduce ‘intrinsic’ stability metrics. Intrinsic stability can be used to summarise the overall effects of a disturbance, separately from internal recovery processes – thereby allowing more general comparisons of disturbances across organisms and contexts.

Human activities are fundamentally altering biodiversity. Projections of declines at the global scale are contrasted by highly variable trends at local scales, suggesting that biodiversity change may be spatially structured. Here, we examined spatial variation in species richness and composition change using more than 50,000 biodiversity time series from 239 studies and found clear geographic variation in biodiversity change. Rapid compositional change is prevalent, with marine biomes exceeding and terrestrial biomes trailing the overall trend. Assemblage richness is not changing on average, although locations exhibiting increasing and decreasing trends of up to about 20% per year were found in some marine studies. At local scales, widespread compositional reorganization is most often decoupled from richness change, and biodiversity change is strongest and most variable in the oceans.