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Aim Biodiversity responses to changing environmental forcing on species are often characterized by considerable time-lags (= relaxation times). Although changes to the occurrence and abundance of species likely have cascading effects (e.g. on species of other trophic levels, genes, community structure and ecosystem processes), current concepts addressing lagged biodiversity responses are limited to single drivers affecting a few biodiversity components (e.g. extinction debt in terms of species numbers or population size). Little attention has been paid to the interacting and cumulative nature of time-lag phenomena. Here, we synthesize current knowledge, mechanisms and implications of delayed biodiversity responses and propose a 'cumulative biodiversity lags-framework' which aims to integrate lagged responses of various components of biological organization. Location Global. Results Effects of change in environmental forcing are transmitted along a series of linked cause–effect relationships which act on different biodiversity components (e.g. individuals, populations, species, communities). We show that lagged responses to environmental forcing are caused by different mechanisms (e.g. metapopulation dynamics, dispersal limitation, successional dynamics), which operate sequentially on these intermediary links. Lags manifest themselves on the respective biodiversity component which changes over time; the full relaxation time of a focal system will therefore depend on the aggregate length of different lags. We elucidate key mechanisms and circumstances which are likely to cause cumulative lagged responses, and propose research avenues to improve understanding of cumulative biodiversity lags. Main conclusions The failure to give adequate consideration to widespread cumulative time-lags often masks the full extent of biodiversity changes that have already been triggered. Effects that are particularly relevant for human livelihoods (e.g. changes in the provision of ecosystem services) may emerge with the most pronounced delay. Accordingly, the consideration of appropriate temporal scales should become a key topic in future work at the science–policy interface.

Summary The effects of the present biodiversity crisis have been largely focused on the loss of species. However, a missed component of biodiversity loss that often accompanies or even precedes species disappearance is the extinction of ecological interactions. Here, we propose a novel model that (i) relates the diversity of both species and interactions along a gradient of environmental deterioration and (ii) explores how the rate of loss of ecological functions, and consequently of ecosystem services, can be accelerated or restrained depending on how the rate of species loss covaries with the rate of interactions loss. We find that the loss of species and interactions are decoupled, such that ecological interactions are often lost at a higher rate. This implies that the loss of ecological interactions may occur well before species disappearance, affecting species functionality and ecosystems services at a faster rate than species extinctions. We provide a number of empirical case studies illustrating these points. Our approach emphasizes the importance of focusing on species interactions as the major biodiversity component from which the ‘health’ of ecosystems depends. Lay Summary

Small habitat patches have been historically neglected in conservation, primarily because extinction risk is higher in small patches. Nevertheless, sets of small patches usually harbor more species than one or a few larger patches of equal total area. Resolving this inconsistency is key to policy and practice in biodiversity conservation. Our analysis of 32 datasets (603 patches and 2290 taxa) provides two novel lines of evidence confirming that small patches have disproportionately high value for biodiversity. First, sets of small patches harbor more species than large patches even when considering only species of conservation concern. Second, sets of small patches harbor more species than large patches even when the small patches are very small compared to the large patches. Therefore, higher extinction risk in small than large patches does not decrease the cumulative value of small patches for biodiversity. We contend that acknowledging the conservation value of small patches, even very small patches, will be a necessary step for stemming biodiversity loss in the Anthropocene.

There is increasing awareness that plants and fungi, as natural solutions, can play an important role in tackling ongoing global environmental challenges. We illustrate how understanding current and projected threats to plants and fungi is necessary to manage and mitigate risks, and how building awareness and understanding of gaps and bias in current assessment coverage is essential to prioritize conservation efforts. We highlight the state of the art in conservation science and point to current methods of assessment and future studies needed to mitigate species extinction Societal Impact Statement There is increasing awareness that plants and fungi, as natural solutions, can play an important role in tackling ongoing global environmental challenges. We illustrate how understanding current and projected threats to plants and fungi is necessary to manage and mitigate risks, while building awareness of gaps and bias in current assessment coverage is essential to adequately prioritize conservation efforts. We highlight the state of the art in conservation science and point to current methods of assessment and future studies needed to mitigate species extinction. Summary Plant and fungal biodiversity underpin life on earth and merit careful stewardship in an increasingly uncertain environment. However, gaps and biases in documented extinction risks to plant and fungal species impede effective management. Formal extinction risk assessments help avoid extinctions, through engagement, financial, or legal mechanisms, but most plant and fungal species lack assessments. Available global assessments cover c. 30% of plant species (ThreatSearch). Red List coverage overrepresents woody perennials and useful plants, but underrepresents single‐country endemics. Fungal assessments overrepresent well‐known species and are too few to infer global status or trends. Proportions of assessed vascular plant species considered threatened vary between global assessment datasets: 37% (ThreatSearch), and 44% (International Union for Conservation of Nature Red List of Threatened Species). Our predictions, correcting for several quantifiable biases, suggest that 39% of all vascular plant species are threatened with extinction. However, other biases remain unquantified, and may affect our estimate. Preliminary trend data show plants moving toward extinction. Quantitative estimates based on plant extinction risk assessments may understate likely biodiversity loss: they do not fully capture the impacts of climate change, slow‐acting threats, or clustering of extinction risk, which could amplify loss of evolutionary potential. The importance of extinction risk estimation to support existing and emerging conservation initiatives is likely to grow as threats to biodiversity intensify. This necessitates urgent and strategic expansion of efforts toward comprehensive and ongoing assessment of plant and fungal extinction risk.

Changes in species diversity often result from species losses and gains. The dynamic nature of beta diversity (spatial variation in species composition) that derives from such temporal species turnover, however, has received relatively little attention. Here, we disentangled extinction and colonization components of beta diversity by using the sets of species that went locally extinct and that newly colonized the study sites. We applied this concept of extinction and colonization beta diversity to ground vegetation communities that have been repeatedly surveyed in forests where fire and harvesting were experimentally applied. We first found that fire and harvesting caused no effect on beta diversity 2 yr after the treatments. From this result, we might conclude that they did not alter the ways in which species assemble across space. However, when we analyzed the extinction and colonization beta diversity between pretreatment and 2 yr after the treatments, both measures were found to be significantly lower in burned sites compared to unburned sites (i.e., the groups of excluded and newly colonized species both showed low beta diversity in the burned sites). These results indicate that the fire excluded similar subsets of species across space, making communities become more heterogeneous, but at the same time induced spatially uniform colonization of new species, causing communities to homogenize. Consequently, the effects of these two processes canceled each other out. The relative importance of extinction and colonization components per se also changed temporally after the treatments. Fire and harvesting showed synergetic negative impacts on extinction beta diversity between pre-treatment and 10 yr after the treatments. Overall, analyses using extinction and colonization beta diversity allowed us to detect nonrandom disassembly and reassembly dynamics in ground vegetation communities. Our results suggest that common practices of analyzing beta diversity at one point in time can mask significant variation driven by disturbance. Acknowledging the extinction–colonization dynamics behind beta diversity is essential for understanding the spatiotemporal organization of biodiversity.

Land-use change is a root cause of the extinction crisis, but links between habitat change and biodiversity loss are not fully understood. While there is evidence that habitat loss is an important extinction driver, the relevance of habitat fragmentation remains debated. Moreover, while time delays of biodiversity responses to habitat transformation are well-documented, time-delayed effects have been ignored in the habitat loss versus fragmentation debate. Here, using a hierarchical Bayesian multi-species occupancy framework, we systematically tested for time-delayed responses of bird and mammal communities to habitat loss and to habitat fragmentation. We focused on the Argentine Chaco, where deforestation has been widespread recently. We used an extensive field dataset on birds and mammals, along with a time series of annual woodland maps from 1985 to 2016 covering recent and historical habitat transformations. Contemporary habitat amount explained bird and mammal occupancy better than past habitat amount. However, occupancy was affected more by the past rather than recent fragmentation, indicating a time-delayed response to fragmentation. Considering past landscape patterns is therefore crucial for understanding current biodiversity patterns. Not accounting for land-use history ignores the possibility of extinction debt and can thus obscure impacts of fragmentation, potentially explaining contrasting findings of habitat loss versus fragmentation studies.

Aim Land use is a main driver of biodiversity loss worldwide. However, quantifying its effects on global plant diversity remains a challenge due to the limited availability of data on the distributions of vascular plant species and their responses to land use. Here, we estimated the global extinction threat of land use to vascular plant species based on a novel integration of an ecoregion‐level species‐area model and the relative endemism richness of the ecoregions. Location Global. Methods First, we assessed ecoregion‐level extinction threats using a countryside species–area relationship model based on responses of local plant richness to land use types and intensities and a high‐resolution global land use map. Next, we estimated global species extinction threat by multiplying the relative endemism richness of each ecoregion with the ecoregion‐level extinction threats. Results Our results indicate that 11% of vascular plant species are threatened with global extinction. We found the largest extinction threats in the Neotropic and Palearctic realms, mainly due to cropland of minimal and high intensity, respectively. Main Conclusions Our novel integration of the countryside species–area relationship and the relative endemism richness allows for the identification of hotspots of global extinction threat, as well as the contribution of specific land use types and intensities to this threat. Our findings inform where the development of measures to protect or restore plant diversity globally are most needed.

1. Habitat loss is the primary cause of local extinctions. Yet, there is considerable uncertainty regarding how fast species respond to habitat loss, and how time-delayed responses vary in space. 2. We focused on the Argentine Dry Chaco (c. 32 million ha), a global deforestation hotspot, and tested for time-delayed response of bird and mammal communities to landscape transformation. We quantified the magnitude of extinction debt by modelling contemporary species richness as a function of either contemporary or past (2000 and 1985) landscape patterns. We then used these models to map communities' extinction debt. 3. We found strong evidence for an extinction debt: landscape structure from 2000 explained contemporary species richness of birds and mammals better than contemporary and 1985 landscapes. This suggests time-delayed responses between 10 and 25 years. Extinction debt was especially strong for forest specialists. 4. Projecting our models across the Chaco highlighted areas where future local extinctions due to unpaid extinction debt are likely. Areas recently converted to agriculture had highest extinction debt, regardless of the post-conversion land use. Few local extinctions were predicted in areas with remaining larger forest patches. 5. Synthesis and applications. The evidence for an unpaid extinction debt in the Argentine Dry Chaco provides a substantial window of opportunity for averting local biodiversity losses. However, this window may close rapidly if conservation activities such as habitat restoration are not implemented swiftly. Our extinction debt maps highlight areas where such conservation activities should be implemented.

Predicting the future ecological impact of global change drivers requires understanding how these same drivers have acted in the past to produce the plant populations and communities we see today. Historical ecological data sources have made contributions of central importance to global change biology, but remain outside the toolkit of most ecologists. Here we review the strengths and weaknesses of four unconventional sources of historical ecological data: land survey records, \"legacy\" vegetation data, historical maps and photographs, and herbarium specimens. We discuss recent contributions made using these data sources to understanding the impacts of habitat disturbance and climate change on plant populations and communities, and the duration of extinction—colonization time lags in response to landscape change. Historical data frequently support inferences made using conventional ecological studies (e.g., increases in warm-adapted species as temperature rises), but there are cases when the addition of different data sources leads to different conclusions (e.g., temporal vegetation change not as predicted by chronosequence studies). The explicit combination of historical and contemporary data sources is an especially powerful approach for unraveling long-term consequences of multiple drivers of global change. Despite the limitations of historical data, which include spotty and potentially biased spatial and temporal coverage, they often represent the only means of characterizing ecological phenomena in the past and have proven indispensable for characterizing the nature, magnitude, and generality of global change impacts on plant populations and communities.

The extinction debt, delayed species extinctions following landscape degradation, is a widely discussed concept. But a consensus about the prevalence of extinctions debts is hindered by a multiplicity of methods and a lack of comparisons among habitats. We applied three contrasting species–area relationship methods to test for plant community extinction debts in three habitats which had different degradation histories over the last century: calcareous grassland, heathland and woodland. These methods differ in their data requirements, with the first two using information on past and current habitat area alongside current species richness, whilst the last method also requires data on past species richness. The most data‐intensive, and hence arguably most reliable method, identified extinction debts across all habitats for specialist species, whilst the other methods did not. All methods detected an extinction debt in calcareous grassland, which had undergone the most severe degradation. We conclude that some methods failed to detect an extinction debt, particularly in habitats that have undergone moderate degradation. Data on past species numbers are required for the most reliable method; as such data are rare, extinction debts may be under‐reported.