Combining mesocosms with models reveals effects of global warming and ocean acidification on a temperate marine ecosystem

Ocean warming and species exploitation have already caused large-scale reorganization of biological communities across the world. Accurate projections of future biodiversity change require a comprehensive understanding of how entire communities respond to global change. We combined a time-dynamic integrated food web modeling approach (Ecosim) with previous data from community-level mesocosm experiments to determine the independent and combined effects of ocean warming, ocean acidification and fisheries exploitation on a well-managed temperate coastal ecosystem. The mesocosm parameters enabled important physiological and behavioral responses to climate stressors to be projected for trophic levels ranging from primary producers to top predators, including sharks. Through model simulations, we show that under sustainable rates of fisheries exploitation, near-future warming or ocean acidification in isolation could benefit species biomass at higher trophic levels (e.g., mammals, birds, and demersal finfish) in their current climate ranges, with the exception of small pelagic fishes. However, under warming and acidification combined, biomass increases at higher trophic levels will be lower or absent, while in the longer term reduced productivity of prey species is unlikely to support the increased biomass at the top of the food web. We also show that increases in exploitation will suppress any positive effects of human-driven climate change, causing individual species biomass to decrease at higher trophic levels. Nevertheless, total future potential biomass of some fisheries species in temperate areas might remain high, particularly under acidification, because unharvested opportunistic species will likely benefit from decreased competition and show an increase in biomass. Ecological indicators of species composition such as the Shannon diversity index decline under all climate change scenarios, suggesting a trade-off between biomass gain and functional diversity. By coupling parameters from multilevel mesocosm food web experiments with dynamic food web models, we were able to simulate the generative mechanisms that drive complex responses of temperate marine ecosystems to global change. This approach, which blends theory with experimental data, provides new prospects for forecasting climate-driven biodiversity change and its effects on ecosystem processes.

Functional reorganization of North American wintering avifauna

Wintering birds serve as vital climate sentinels, yet they are often overlooked in studies of avian diversity change. Here, we provide a continental-scale characterization of change in multifaceted wintering avifauna and examine the effects of climate change on these dynamics. We reveal a strong functional reorganization of wintering bird communities marked by a north-south gradient in functional diversity change, along with a superimposed mild east-west gradient in trait composition change. Assemblages in the northern United States saw contractions of the functional space and increases in functional evenness and originality, while the southern United States saw smaller contractions of the functional space and stasis in evenness and originality. Shifts in functional diversity were underlined by significant reshuffling in trait composition, particularly pronounced in the western and northern United States. Finally, we find strong contributions of climate change to this functional reorganization, underscoring the importance of wintering birds in tracking climate change impacts on biodiversity.

Degeneration of foundation cushion species induced by ecological constraints can cause massive changes in alpine plant communities

Foundational cushion plants can re-organize community structures and sustain a prominent proportion of alpine biodiversity, but they are sensitive to climate change. The loss of cushion species can have broad consequences for associated biota. The potential plant community changes with the population dynamics of cushion plants remain, however, unclear. Using eight plant communities along a climatic and community successional gradient, we assessed cushion population dynamics, the underlying ecological constraints and hence associated plant community changes in alpine communities dominated by the foundational cushion plant Arenaria polytrichoides. The population dynamics of Arenaria are attributed to ecological constraints at a series of life history stages. Reproductive functions are constrained by increasing associated beneficiary plants; subsequent seedling establishment is constrained by temperature, water and light availability, extreme climate events, and interspecific competition; strong competitive exclusion may accelerate mortality and degeneration of cushion populations. Along with cushion dynamics, species composition, abundance and community structure gradually change. Once cushion plants completely degenerate, previously cushion-dominated communities shift to relatively stable communities that are overwhelmingly dominated by sedges. Climate warming may accelerate the degeneration process of A. polytrichoides. Degeneration of this foundational cushion plant will possibly induce massive changes in alpine plant communities and hence ecosystem functions in alpine ecosystems. The assessment of the population dynamics of foundation species is critical for an effective conservation of alpine biodiversity.

Evaluating plant lineage losses and gains in temperate forest understories: a phylogenetic perspective on climate change and nitrogen deposition

Global change has accelerated local species extinctions and colonizations, often resulting in losses and gains of evolutionary lineages with unique features. Do these losses and gains occur randomly across the phylogeny? We quantified: temporal changes in plant phylogenetic diversity (PD); and the phylogenetic relatedness (PR) of lost and gained species in 2672 semi-permanent vegetation plots in European temperate forest understories resurveyed over an average period of 40 yr. Controlling for differences in species richness, PD increased slightly over time and across plots. Moreover, lost species within plots exhibited a higher degree of PR than gained species. This implies that gained species originated from a more diverse set of evolutionary lineages than lost species. Certain lineages also lost and gained more species than expected by chance, with Ericaceae, Fabaceae, and Orchidaceae experiencing losses and Amaranthaceae, Cyperaceae, and Rosaceae showing gains. Species losses and gains displayed no significant phylogenetic signal in response to changes in macroclimatic conditions and nitrogen deposition. As anthropogenic global change intensifies, temperate forest understories experience losses and gains in specific phylogenetic branches and ecological strategies, while the overall mean PD remains relatively stable.

Population abundance estimates in conservation and biodiversity research

Measuring and tracking biodiversity from local to global scales is challenging due to its multifaceted nature and the range of metrics used to describe spatial and temporal patterns. Abundance can be used to describe how a population changes across space and time, but it can be measured in different ways, with consequences for the interpretation and communication of spatiotemporal patterns. We differentiate between relative and absolute abundance, and discuss the advantages and disadvantages of each for biodiversity monitoring, conservation, and ecological research. We highlight when absolute abundance can be advantageous and should be prioritized in biodiversity monitoring and research, and conclude by providing avenues for future research directions to better assess the necessity of absolute abundance in biodiversity monitoring.

Climate regulation processes are linked to the functional composition of plant communities in European forests, shrublands, and grasslands

Terrestrial ecosystems affect climate by reflecting solar irradiation, evaporative cooling, and carbon sequestration. Yet very little is known about how plant traits affect climate regulation processes (CRPs) in different habitat types. Here, we used linear and random forest models to relate the community-weighted mean and variance values of 19 plant traits (summarized into eight trait axes) to the climate-adjusted proportion of reflected solar irradiation, evapotranspiration, and net primary productivity across 36,630 grid cells at the European extent, classified into 10 types of forest, shrubland, and grassland habitats. We found that these trait axes were more tightly linked to log evapotranspiration (with an average of 6.2% explained variation) and the proportion of reflected solar irradiation (6.1%) than to net primary productivity (4.9%). The highest variation in CRPs was explained in forest and temperate shrubland habitats. Yet, the strength and direction of these relationships were strongly habitat-dependent. We conclude that any spatial upscaling of the effects of plant communities on CRPs must consider the relative contribution of different habitat types.

Ocean climate and hydrodynamics drive decadal shifts in Northeast Atlantic dinoflagellates

The abundance of large marine dinoflagellates has declined in the North Sea since 1958. Although hypotheses have been proposed to explain this diminution (increasing temperature and wind), the mechanisms behind this pattern have thus far remained elusive. In this article, we study the long-term changes in dinoflagellate biomass and biodiversity in relation to hydro-climatic conditions and circulation within the North Atlantic. Our results show that the decline in biomass has paralleled an increase in biodiversity caused by a temperature-induced northward movement of subtropical taxa along the European shelf-edge, and facilitated by changes in oceanic circulation (subpolar gyre contraction). However, major changes in North Atlantic hydrodynamics in the 2010s (subpolar gyre expansion and low-salinity anomaly) stopped this movement, which triggered a biodiversity collapse in the North Sea. Further, North Sea dinoflagellate biomass remained low because of warming. Our results, therefore, reveal that regional climate warming and changes in oceanic circulation strongly influenced shifts in dinoflagellate biomass and biodiversity.

Fast Bayesian inference for large occupancy datasets

In recent years, the study of species' occurrence has benefited from the increased availability of large-scale citizen-science data. While abundance data from standardized monitoring schemes are biased toward well-studied taxa and locations, opportunistic data are available for many taxonomic groups, from a large number of locations and across long timescales. Hence, these data provide opportunities to measure species' changes in occurrence, particularly through the use of occupancy models, which account for imperfect detection. These opportunistic datasets can be substantially large, numbering hundreds of thousands of sites, and hence present a challenge from a computational perspective, especially within a Bayesian framework. In this paper, we develop a unifying framework for Bayesian inference in occupancy models that account for both spatial and temporal autocorrelation. We make use of the Pólya-Gamma scheme, which allows for fast inference, and incorporate spatio-temporal random effects using Gaussian processes (GPs), for which we consider two efficient approximations: subset of regressors and nearest neighbor GPs. We apply our model to data on two UK butterfly species, one common and widespread and one rare, using records from the Butterflies for the New Millennium database, producing occupancy indices spanning 45 years. Our framework can be applied to a wide range of taxa, providing measures of variation in species' occurrence, which are used to assess biodiversity change.

Correlated biodiversity change between plant and insect assemblages resurveyed after 80 years across a dynamic habitat mosaic

Historical data on co-occurring taxa are extremely rare. As such, the extent to which distinct co-occurring taxa experience similar long-term patterns in species richness and compositional change (e.g., when exposed to a changing environment) is not clear. Using data from a diverse ecological community surveyed in the 1930s and resurveyed in the 2010s, we investigated whether local plant and insect assemblages displayed cross-taxon congruence-that is, spatiotemporal correlation in species richness and compositional change-across six co-occurring taxa: vascular plants, non-vascular plants, grasshoppers and crickets (Orthoptera), ants (Hymenoptera: Formicinae), hoverflies (Diptera: Syrphidae), and dragonflies and damselflies (Odonata). All taxa exhibited high levels of turnover across the ca. 80-year time period. Despite minimal observed changes at the level of the whole study system, species richness displayed widespread cross-taxon congruence (i.e., correlated temporal change) across local assemblages within the study system. Hierarchical logistic regression models suggest a role for shared responses to environmental change underlying cross-taxon correlations and highlight stronger correlations between vascular plants and their direct consumers, suggesting a possible role for biotic interactions between these groups. These results provide an illustration of cross-taxon congruence in biodiversity change using data unique in its combination of temporal and taxonomic scope, and highlight the potential for cascading and comparable effects of environmental change (abiotic and biotic) on co-occurring plant and insect communities. However, analyses of historical resurveys based on currently available data come with inherent uncertainties. As such, this study highlights a need for well-designed experiments, and monitoring programs incorporating co-occurring taxa, to determine the underlying mechanisms and prevalence of congruent biodiversity change as anthropogenic environmental change accelerates apace.

Comparing temporal dynamics of compositional reorganization in long-term studies of birds and fish

The composition of ecological assemblages has changed rapidly over the past century. Compositional reorganization rates are high relative to rates of alpha diversity change, creating an urgent need to understand how this compositional reorganization is progressing. We developed a quantitative framework for comparing temporal trajectories of compositional reorganization and applied it to two long-term bird and marine fish datasets. We then evaluated how the number and magnitude of short-term changes relate to overall rates of change. We found varied trajectories of turnover across birds and fish, with linear directional change predominating in birds and non-directional change more common in fish. The number of changes away from the baseline was a more consistent correlate of the overall rate of change than the magnitude of such changes, but large unreversed changes were found in both fish and birds, as were time series with accelerating compositional change. Compositional reorganization is progressing through a complex mix of temporal trajectories, including both threshold-like behaviour and the accumulation of repeated, linear change.

Elevated compositional change in plant assemblages linked to invasion

Alien species are widely linked to biodiversity change, but the extent to which they are associated with the reshaping of ecological communities is not well understood. One possible mechanism is that assemblages where alien species are found exhibit elevated temporal turnover. To test this, we identified assemblages of vascular plants in the BioTIME database for those assemblages in which alien species are either present or absent and used the Jaccard measure to compute compositional dissimilarity between consecutive censuses. We found that, although alien species are typically rare in invaded assemblages, their presence is associated with an increase in the average rate of compositional change. These differences in compositional change between invaded and uninvaded assemblages are not linked to differences in species richness but rather to species replacement (turnover). Rapid compositional restructuring of assemblages is a major contributor to biodiversity change, and as such, our results suggest a role for alien species in bringing this about.

Ongoing over-exploitation and delayed responses to environmental change highlight the urgency for action to promote vertebrate recoveries by 2030

To safeguard nature, we must understand the drivers of biodiversity loss. Time-delayed biodiversity responses to environmental changes (ecological lags) are often absent from models of biodiversity change, despite their well-documented existence. We quantify how lagged responses to climate and land-use change have influenced mammal and bird populations around the world, while incorporating effects of direct exploitation and conservation interventions. Ecological lag duration varies between drivers, vertebrate classes and body size groupings-e.g. lags linked to climate-change impacts are 13 years for small birds, rising to 40 years for larger species. Past warming and land conversion generally combine to predict population declines; however, such conditions are associated with population increases for small mammals. Positive effects of management (>+4% annually for large mammals) and protected areas (>+6% annually for large birds) on population trends contrast with the negative impact of exploitation (<-7% annually for birds), highlighting the need to promote sustainable use. Model projections suggest a future with winners (e.g. large birds) and losers (e.g. medium-sized birds), with current/recent environmental change substantially influencing abundance trends to 2050. Without urgent action, including effective conservation interventions and promoting sustainable use, ambitious targets to stop declines by 2030 may already be slipping out of reach.

The Living Planet Index's ability to capture biodiversity change from uncertain data

The Living Planet Index (LPI) is a crucial tool to track global biodiversity change, but necessarily sacrifices information to summarize thousands of population trends into a single communicable index. Evaluating when and how this information loss affects the LPI's performance is essential to ensure interpretations of the index reflect the truth as reliably as possible. Here, we evaluated the ability of the LPI to accurately and precisely capture trends of population change from uncertain data. We derived a mathematical analysis of uncertainty propagation in the LPI to track how measurement and process uncertainty may bias estimates of population growth rate trends, and to measure the overall uncertainty of the LPI. We demonstrated the propagation of uncertainty using simulated scenarios of declining, stable, or growing populations fluctuating independently, synchronously, or asynchronously, to assess the bias and uncertainty of the LPI in each scenario. We found that measurement and process uncertainty consistently pull the index below the expected true trend. Importantly, variability in the raw data scales up to draw the index further below the expected trend and to amplify its uncertainty, particularly when populations are small. These findings echo suggestions that a more complete assessment of the variability in population change trends, with particular attention to covarying populations, would enrich the LPI's already critical influence on conservation communication and decisions. This article is protected by copyright. All rights reserved.

Abundance trends for river macroinvertebrates vary across taxa, trophic group and river typology

There is mounting evidence that terrestrial arthropods are declining rapidly in many areas of the world. It is unclear whether freshwater invertebrates, which are key providers of ecosystem services, are also declining. We addressed this question by analysing a long-term dataset of macroinvertebrate abundance collected from 2002 to 2019 across 5009 sampling sites in English rivers. Patterns varied markedly across taxonomic groups. Within trophic groups we detected increases in the abundance of carnivores by 19% and herbivores by 14.8%, while we estimated decomposers have declined by 21.7% in abundance since 2002. We also found heterogeneity in trends across rivers belonging to different typologies based on geological dominance and catchment altitude, with organic lowland rivers having generally higher rates of increase in abundance across taxa and trophic groups, with siliceous lowland rivers having the most declines. Our results reveal a complex picture of change in freshwater macroinvertebrate abundance between taxonomic groups, trophic levels and river typologies. Our analysis helps with identifying priority regions for action on potential environmental stressors where we discover macroinvertebrate abundance declines.

Quantifying and linking mechanism scenarios to invasive species impact

Plant species invasion represents one of the major drivers of biodiversity change globally, yet there is confusion about the nature of nonindigenous species (NIS) impact. This confusion stems from differing notions of what constitutes invasive species impact and the scales at which it should be assessed. At local scales, the mechanisms of the impact on local competitors can be classified into four scenarios: (1) minimal impact from NIS inhabiting unique niches; (2) neutral impact spread across the community and proportional to NIS abundance; (3) targeted impact on a small number of competitors with overlapping niches; and (4) pervasive impact that is disproportionate to NIS abundance and caused by modifications that filter out other species. I developed a statistical test to distinguish these four mechanism scenarios based on plant community rank-abundance curves and then created a scale-independent standardized impact score. Using an example long-term dataset with high native plant diversity and an abundance gradient of the invasive vine, Vincetoxicum rossicum, I show that the impact resulted in either targeted or pervasive extirpations. Regardless of whether the NIS impact is neutral, targeted, or pervasive, the net outcome will be the homogenization of ecosystems and reduced biodiversity at larger scales, perhaps reducing ecosystem resilience. The framework and statistical evaluation of impact presented in this paper provide researchers and managers with an objective approach to quantifying NIS impact and prioritizing species for further management actions.

Observed and dark diversity dynamics over millennial time scales: fast life-history traits linked to expansion lags of plants in northern Europe

Global change drivers (e.g. climate and land use) affect the species and functional traits observed in a local site but also its dark diversity-the set of species and traits locally suitable but absent. Dark diversity links regional and local scales and, over time, reveals taxa under expansion lags by depicting the potential biodiversity that remains suitable but is absent locally. Since global change effects on biodiversity are both spatially and temporally scale dependent, examining long-term temporal dynamics in observed and dark diversity would be relevant to assessing and foreseeing biodiversity change. Here, we used sedimentary pollen data to examine how both taxonomic and functional observed and dark diversity changed over the past 14 500 years in northern Europe. We found that taxonomic and functional observed and dark diversity increased over time, especially after the Late Glacial and during the Late Holocene. However, dark diversity dynamics revealed expansion lags related to species' functional characteristics (dispersal limitation and stress intolerance) and an extensive functional redundancy when compared to taxa in observed diversity. We highlight that assessing observed and dark diversity dynamics is a promising tool to examine biodiversity change across spatial scales, its possible causes, and functional consequences.

Warming shifts soil microbial communities and tropical tree seedling mortality

Plant-soil feedback (PSF), regulated by both mycorrhizae and soil-borne pathogens, is a primary mechanism maintaining high tree species diversity in the tropics. But how warming actually affects PSF is not well understood. We conducted a field warming experiment to test PSF on seedling mortality of two tree species: a rhizobia-associated tree (Ormosia semicastrata, Fabaceae) suffering from host-specific soil-borne pathogens and an ectomycorrhizal fungi-associated tree (Cyclobalanopsis patelliormis, Fagaceae) with low susceptibility to soil-borne pathogens. Soil fungi from the warming versus control seedling plots were identified by molecular sequencing. Results showed that the elevated temperature lowered seedling mortality of O. semicastrata, but had no effect on C. patelliormis seedlings. This indicates that warming weakened the negative PSF on O. semicastrata, presumably due to the observed decrease of the relative abundance of plant-pathogenic fungi and increase of ectomycorrhizal fungi but did not affect the PSF on C. patelliormis. The differential warming effects on seedling mortality of species with different microbial associations afford an example showcasing how the change in soil-borne microbes in response to global warming would in turn, through PSF, alters tropical tree species composition and diversity. This study helps shed mechanistic light on the debate of biodiversity change as driven by climate change.

Directional turnover towards larger-ranged plants over time and across habitats

Species turnover is ubiquitous. However, it remains unknown whether certain types of species are consistently gained or lost across different habitats. Here, we analysed the trajectories of 1827 plant species over time intervals of up to 78 years at 141 sites across mountain summits, forests, and lowland grasslands in Europe. We found, albeit with relatively small effect sizes, displacements of smaller- by larger-ranged species across habitats. Communities shifted in parallel towards more nutrient-demanding species, with species from nutrient-rich habitats having larger ranges. Because these species are typically strong competitors, declines of smaller-ranged species could reflect not only abiotic drivers of global change, but also biotic pressure from increased competition. The ubiquitous component of turnover based on species range size we found here may partially reconcile findings of no net loss in local diversity with global species loss, and link community-scale turnover to macroecological processes such as biotic homogenisation.

Network motifs involving both competition and facilitation predict biodiversity in alpine plant communities

Biological diversity depends on multiple, cooccurring ecological interactions. However, most studies focus on one interaction type at a time, leaving community ecologists unsure of how positive and negative associations among species combine to influence biodiversity patterns. Using surveys of plant populations in alpine communities worldwide, we explore patterns of positive and negative associations among triads of species (modules) and their relationship to local biodiversity. Three modules, each incorporating both positive and negative associations, were overrepresented, thus acting as "network motifs." Furthermore, the overrepresentation of these network motifs is positively linked to species diversity globally. A theoretical model illustrates that these network motifs, based on competition between facilitated species or facilitation between inferior competitors, increase local persistence. Our findings suggest that the interplay of competition and facilitation is crucial for maintaining biodiversity.

The multidimensionality of soil macroecology

The recent past has seen a tremendous surge in soil macroecological studies and new insights into the global drivers of one-quarter of the biodiversity of the Earth. Building on these important developments, a recent paper in Global Ecology and Biogeography outlined promising methods and approaches to advance soil macroecology. Among other recommendations, White and colleagues introduced the concept of a spatial three-dimensionality in soil macroecology by considering the different spheres of influence and scales, as soil organism size ranges vary from bacteria to macro- and megafauna. Here, we extend this concept by discussing three additional dimensions (biological, physical, and societal) that are crucial to steer soil macroecology from pattern description towards better mechanistic understanding. In our view, these are the requirements to establish it as a predictive science that can inform policy about relevant nature and management conservation actions. We highlight the need to explore temporal dynamics of soil biodiversity and functions across multiple temporal scales, integrating different facets of biodiversity (i.e., variability in body size, life-history traits, species identities, and groups of taxa) and their relationships to multiple ecosystem functions, in addition to the feedback effects between humans and soil biodiversity. We also argue that future research needs to consider effective soil conservation policy and management in combination with higher awareness of the contributions of soil-based nature's contributions to people. To verify causal relationships, soil macroecology should be paired with local and globally distributed experiments. The present paper expands the multidimensional perspective on soil macroecology to guide future research contents and funding. We recommend considering these multiple dimensions in projected global soil biodiversity monitoring initiatives.

An experimental approach to assessing the impact of ecosystem engineers on biodiversity and ecosystem functions

Plants acting as ecosystem engineers create habitats and facilitate biodiversity maintenance within plant communities. Furthermore, biodiversity research has demonstrated that plant diversity enhances the productivity and functioning of ecosystems. However, these two fields of research developed in parallel and independent from one another, with the consequence that little is known about the role of ecosystem engineers in the relationship between biodiversity and ecosystem functioning across trophic levels. Here, we present an experimental framework to study this relationship. We combine facilitation by plants acting as ecosystem engineers with plant-insect interaction analysis and variance partitioning of biodiversity effects. We present a case-study experiment in which facilitation by a cushion-plant species and a dwarf-shrub species as ecosystem engineers increases positive effects of plant functional diversity (ecosystem engineers and associated plants) on ecosystem functioning (flower visitation rate). The experiment, conducted in the field during a single alpine flowering season, included the following treatments: (1) removal of plant species associated with ecosystem engineers, (2) exclusion (covering) of ecosystem engineer flowers, and (3) control, i.e., natural patches of ecosystem engineers and associated plant species. We found both positive and negative associational effects between plants depending on ecosystem engineer identity, indicating both pollination facilitation and interference. In both cases, patches supported by ecosystem engineers increased phylogenetic and functional diversity of flower visitors. Furthermore, complementarity effects between engineers and associated plants were positive for flower visitation rates. Our study reveals that plant facilitation can enhance the strength of biodiversity-ecosystem functioning relationships, with complementarity between plants for attracting more and diverse flower visitors being the likely driver. A potential mechanism is that synergy and complementarity between engineers and associated plants increase attractiveness for shared visitors and widen pollination niches. In synthesis, facilitation among plants can scale up to a full network, supporting ecosystem functioning both directly via microhabitat amelioration and indirectly via diversity effects.

A multiscale framework for disentangling the roles of evenness, density, and aggregation on diversity gradients

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.

Widespread decline in Central European plant diversity across six decades

Based on plant occurrence data covering all parts of Germany, we investigated changes in the distribution of 2136 plant species between 1960 and 2017. We analyzed 29 million occurrence records over an area of ~350,000 km2 on a 5 × 5 km grid using temporal and spatiotemporal models and accounting for sampling bias. Since the 1960s, more than 70% of investigated plant species showed declines in nationwide occurrence. Archaeophytes (species introduced before 1492) most strongly declined but also native plant species experienced severe declines. In contrast, neophytes (species introduced after 1492) increased in their nationwide occurrence but not homogeneously throughout the country. Our analysis suggests that the strongest declines in native species already happened in the 1960s-1980s, a time frame in which often few data exist. Increases in neophytic species were strongest in the 1990s and 2010s. Overall, the increase in neophytes did not compensate for the loss of other species, resulting in a decrease in mean grid cell species richness of -1.9% per decade. The decline in plant biodiversity is a widespread phenomenon occurring in different habitats and geographic regions. It is likely that this decline has major repercussions on ecosystem functioning and overall biodiversity, potentially with cascading effects across trophic levels. The approach used in this study is transferable to other large-scale trend analyses using heterogeneous occurrence data.

Recent increases in assemblage rarity are linked to increasing local immigration

As pressures on biodiversity increase, a better understanding of how assemblages are responding is needed. Because rare species, defined here as those that have locally low abundances, make up a high proportion of assemblage species lists, understanding how the number of rare species within assemblages is changing will help elucidate patterns of recent biodiversity change. Here, we show that the number of rare species within assemblages is increasing, on average, across systems. This increase could arise in two ways: species already present in the assemblage decreasing in abundance but with no increase in extinctions, or additional species entering the assemblage in low numbers associated with an increase in immigration. The positive relationship between change in rarity and change in species richness provides evidence for the second explanation, i.e. higher net immigration than extinction among the rare species. These measurable changes in the structure of assemblages in the recent past underline the need to use multiple biodiversity metrics to understand biodiversity change.

Temporal lags in observed and dark diversity in the Anthropocene

Understanding biodiversity changes in the Anthropocene (e.g. due to climate and land-use change) is an urgent ecological issue. This important task is challenging because global change effects and species responses are dependent on the spatial scales considered. Furthermore, responses are often not immediate. However, both scale and time delay issues can be tackled when, at each study site, we consider dynamics in both observed and dark diversity. Dark diversity includes those species in the region that can potentially establish and thrive in the local sites' conditions but are currently locally absent. Effectively, dark diversity connects biodiversity at the study site to the regional scales and defines the site-specific species pool (observed and dark diversity together). With dark diversity, it is possible to decompose species gains and losses into two space-related components: one associated with local dynamics (species moving from observed to dark diversity and vice versa) and another related to gains and losses of site-specific species pool (species moving to and from the pool after regional immigration, regional extinction or change in local ecological conditions). Extinction debt and immigration credit are useful to understand dynamics in observed diversity, but delays might happen in species pool changes as well. In this opinion piece we suggest that considering both observed and dark diversity and their temporal dynamics provides a deeper understanding of biodiversity changes. Considering both observed and dark diversity creates opportunities to improve conservation by allowing to identify species that are likely to go regionally extinct as well as foreseeing which of the species that newly arrive to the region are more likely to colonize local sites. Finally, by considering temporal lags and species gains and losses in observed and dark diversity, we combine phenomena at both spatial and temporal scales, providing a novel tool to examine biodiversity change in the Anthropocene.

Positive correlations in species functional contributions drive the response of multifunctionality to biodiversity loss

Changes in biodiversity can severely affect ecosystem functioning, but the impacts of species loss on an ecosystem's ability to sustain multiple functions remain unclear. When considering individual functions, the impacts of biodiversity loss depend on correlations between species functional contributions and their extinction probabilities. When considering multiple functions, the impacts of biodiversity loss depend on correlations between species contributions to individual functions. However, how correlations between extinction probabilities and functional contributions determine the impact of biodiversity loss on multifunctionality (MF) is not well understood. Here, we use biodiversity loss simulations to examine the influence of correlations among multiple functions and extinction probabilities on the diversity-MF relationship. In contrast with random extinction, we find that the response of MF to biodiversity loss is influenced by the absence of positive correlations between species functional contributions, rather than by negative correlations. Communities with a high number of pairwise positive correlations in functional contributions achieve higher levels of MF, but are also less resilient to extinction. This work implies that understanding how species extinction probabilities correlate with their contribution to MF can help identify the degree to which MF will change with ongoing biodiversity loss and target conservation efforts to maximize MF resiliency.

Extinction debt in local habitats: quantifying the roles of random drift, immigration and emigration

We developed a time-dependent stochastic neutral model for predicting diverse temporal trajectories of biodiversity change in response to ecological disturbance (i.e. habitat destruction) and dispersal dynamic (i.e. emigration and immigration). The model is general and predicts how transition behaviours of extinction may accumulate according to a different combination of random drift, immigration rate, emigration rate and the degree of habitat destruction. We show that immigration, emigration, the areal size of the destroyed habitat and initial species abundance distribution (SAD) can impact the total biodiversity loss in an intact local area. Among these, the SAD plays the most deterministic role, as it directly determines the initial species richness in the local target area. By contrast, immigration was found to slow down total biodiversity loss and can drive the emergence of species credits (i.e. a gain of species) over time. However, the emigration process would increase the extinction risk of species and accelerate biodiversity loss. Finally but notably, we found that a shift in the emigration rate after a habitat destruction event may be a new mechanism to generate species credits.

Increases in local richness (α-diversity) following invasion are offset by biotic homogenization in a biodiversity hotspot

The world's ecosystems are experiencing unparalleled rates of biodiversity change, with invasive species implicated as one of the drivers that restructure local assemblages. Here we focus on the processes leading to biodiversity change in a biodiversity hotspot, the Brazilian Cerrado. The null expectation that invasion leads to increase in local species richness is supported by our investigation of the grass layer in two key habitats (campo sujo and campo úmido). Our analysis uncovered a linear relationship between total richness and invasive richness at the plot level. However, because the invasive species-even though few in number-are widespread, their contribution to local richness (α-diversity) is offset by their homogenizing influence on composition (β-diversity). We thus identify a mechanism that can help explain the paradox that species richness is not declining in many local assemblages, yet compositional change is exceeding the predictions of ecological theory. As such, our results emphasize the importance of quantifying both α-diversity and β-diversity in assessments of biodiversity change in the contemporary world.

Ecosystem responses to exotic earthworm invasion in northern North American forests

Earth is experiencing a substantial loss of biodiversity at the global scale, while both species gains and losses are occurring at local and regional scales. The influence of these nonrandom changes in species distributions could profoundly affect the functioning of ecosystems and the essential services that they provide. However, few experimental tests have been conducted examining the influence of species invasions on ecosystem functioning. Even fewer have been conducted using invasive ecosystem engineers, which can have disproportionately strong influence on native ecosystems relative to their own biomass. The invasion of exotic earthworms is a prime example of an ecosystem engineer that is influencing many ecosystems around the world. In particular, European earthworm invasions of northern North American forests cause simultaneous species gains and losses with significant consequences for essential ecosystem processes like nutrient cycling and crucial services to humanity like soil erosion control and carbon sequestration. Exotic earthworms are expected to select for specific traits in communities of soil microorganisms (fast-growing bacteria species), soil fauna (promoting the bacterial energy channel), and plants (graminoids) through direct and indirect effects. This will accelerate some ecosystem processes and decelerate others, fundamentally altering how invaded forests function. This project aims to investigate ecosystem responses of northern North American forests to earthworm invasion. Using a novel, synthetic combination of field observations, field experiments, lab experiments, and meta-analyses, the proposed work will be the first systematic examination of earthworm effects on (1) plant communities and (2) soil food webs and processes. Further, (3) effects of a changing climate (warming and reduced summer precipitation) on earthworm performance will be investigated in a unique field experiment designed to predict the future spread and consequences of earthworm invasion in North America. By assessing the soil chemical and physical properties as well as the taxonomic (e.g., by the latest next-generation sequencing techniques) and functional composition of plant, soil microbial and animal communities and the processes they drive in four forests, work packages I-III take complementary approaches to derive a comprehensive and generalizable picture of how ecosystems change in response to earthworm invasion. Finally, in work package IV meta-analyses will be used to integrate the information from work packages I-III and existing literature to investigate if earthworms cause invasion waves, invasion meltdowns, habitat homogenization, and ecosystem state shifts. Global data will be synthesized to test if the relative magnitude of effects differs from place to place depending on the functional dissimilarity between native soil fauna and exotic earthworms. Moving from local to global scale, the present proposal examines the influence of earthworm invasions on biodiversity-ecosystem functioning relationships from an aboveground-belowground perspective in natural settings. This approach is highly innovative as it utilizes the invasion by exotic earthworms as an exciting model system that links invasion biology with trait-based community ecology, global change research, and ecosystem ecology, pioneering a new generation of biodiversity-ecosystem functioning research.

Improving estimates of environmental change using multilevel regression models of Ellenberg indicator values

Ellenberg indicator values (EIVs) are a widely used metric in plant ecology comprising a semi-quantitative description of species' ecological requirements. Typically, point estimates of mean EIV scores are compared over space or time to infer differences in the environmental conditions structuring plant communities-particularly in resurvey studies where no historical environmental data are available. However, the use of point estimates as a basis for inference does not take into account variance among species EIVs within sampled plots and gives equal weighting to means calculated from plots with differing numbers of species. Traditional methods are also vulnerable to inaccurate estimates where only incomplete species lists are available.We present a set of multilevel (hierarchical) models-fitted with and without group-level predictors (e.g., habitat type)-to improve precision and accuracy of plot mean EIV scores and to provide more reliable inference on changing environmental conditions over spatial and temporal gradients in resurvey studies. We compare multilevel model performance to GLMMs fitted to point estimates of mean EIVs. We also test the reliability of this method to improve inferences with incomplete species lists in some or all sample plots. Hierarchical modeling led to more accurate and precise estimates of plot-level differences in mean EIV scores between time-periods, particularly for datasets with incomplete records of species occurrence. Furthermore, hierarchical models revealed directional environmental change within ecological habitat types, which less precise estimates from GLMMs of raw mean EIVs were inadequate to detect. The ability to compute separate residual variance and adjusted R 2 parameters for plot mean EIVs and temporal differences in plot mean EIVs in multilevel models also allowed us to uncover a prominent role of hydrological differences as a driver of community compositional change in our case study, which traditional use of EIVs would fail to reveal. Assessing environmental change underlying ecological communities is a vital issue in the face of accelerating anthropogenic change. We have demonstrated that multilevel modeling of EIVs allows for a nuanced estimation of such from plant assemblage data changes at local scales and beyond, leading to a better understanding of temporal dynamics of ecosystems. Further, the ability of these methods to perform well with missing data should increase the total set of historical data which can be used to this end.

Global environmental change effects on plant community composition trajectories depend upon management legacies

The contemporary state of functional traits and species richness in plant communities depends on legacy effects of past disturbances. Whether temporal responses of community properties to current environmental changes are altered by such legacies is, however, unknown. We expect global environmental changes to interact with land-use legacies given different community trajectories initiated by prior management, and subsequent responses to altered resources and conditions. We tested this expectation for species richness and functional traits using 1814 survey-resurvey plot pairs of understorey communities from 40 European temperate forest datasets, syntheses of management transitions since the year 1800, and a trait database. We also examined how plant community indicators of resources and conditions changed in response to management legacies and environmental change. Community trajectories were clearly influenced by interactions between management legacies from over 200 years ago and environmental change. Importantly, higher rates of nitrogen deposition led to increased species richness and plant height in forests managed less intensively in 1800 (i.e., high forests), and to decreases in forests with a more intensive historical management in 1800 (i.e., coppiced forests). There was evidence that these declines in community variables in formerly coppiced forests were ameliorated by increased rates of temperature change between surveys. Responses were generally apparent regardless of sites' contemporary management classifications, although sometimes the management transition itself, rather than historic or contemporary management types, better explained understorey responses. Main effects of environmental change were rare, although higher rates of precipitation change increased plant height, accompanied by increases in fertility indicator values. Analysis of indicator values suggested the importance of directly characterising resources and conditions to better understand legacy and environmental change effects. Accounting for legacies of past disturbance can reconcile contradictory literature results and appears crucial to anticipating future responses to global environmental change.

Increasing and declining native species in urban remnant grasslands respond differently to nitrogen addition and disturbance

BACKGROUND AND AIMS

Atmospheric nitrogen deposition and natural fire regime suppression are key drivers of vegetation change in urbanizing grasslands. Some species thrive under these conditions, while others face local extinction. In the natural grasslands that surround Melbourne, Australia, biotic homogenization has occurred with intensifying urbanization. Some native species have become rarer (decreaser species) across the landscape, while others have become more widespread (increaser species). This study experimentally examined the response of increaser and decreaser plant species to nitrogen addition/depletion, and examined the presence/absence of annual disturbance to the vegetation.

METHODS

Decreaser and increaser species were planted into 60 field plots established in an urban Melbourne grassland and examined over 2 years. Annual removal of above-ground biomass occurred in half the plots to simulate biomass removal via fire, with the remaining plots undisturbed. Soil nitrogen was depleted in one-third of plots, one-third received no nitrogen treatment and one-third were fertilized with nitrogen. Increaser plant species were predicted to persist in the absence of disturbance, and thrive when fertilized. In contrast, high mortality was predicted for decreaser species in the absence of disturbance, with fertilization providing no advantage.

KEY RESULTS

Seedling mortality for increaser and decreaser species was unrelated to the treatments. The mortality of decreaser species was high (69 %), and the mortality of increaser species low (20 %). However, seedling growth was related to the treatments. The total biomass of decreaser species was highest in annually disturbed plots, with growth suppressed in undisturbed plots. In contrast, the total biomass of increaser species was unrelated to the disturbance regime, but responded positively to nitrogen enrichment.

CONCLUSIONS

The results provide evidence that by affecting plant growth, declines in biomass removal and atmospheric nitrogen deposition could be key drivers of biotic homogenization in urban grasslands.

Divergent biodiversity change within ecosystems

The Earth's ecosystems are under unprecedented pressure, yet the nature of contemporary biodiversity change is not well understood. Growing evidence that community size is regulated highlights the need for improved understanding of community dynamics. As stability in community size could be underpinned by marked temporal turnover, a key question is the extent to which changes in both biodiversity dimensions (temporal α- and temporal β-diversity) covary within and among the assemblages that comprise natural communities. Here, we draw on a multiassemblage dataset (encompassing vertebrates, invertebrates, and unicellular plants) from a tropical freshwater ecosystem and employ a cyclic shift randomization to assess whether any directional change in temporal α-diversity and temporal β-diversity exceeds baseline levels. In the majority of cases, α-diversity remains stable over the 5-y time frame of our analysis, with little evidence for systematic change at the community level. In contrast, temporal β-diversity changes are more prevalent, and the two diversity dimensions are decoupled at both the within- and among-assemblage level. Consequently, a pressing research challenge is to establish how turnover supports regulation and when elevated temporal β-diversity jeopardizes community integrity.

Invasive earthworms erode soil biodiversity: A meta-analysis

Biological invasions pose a serious threat to biodiversity and ecosystem functioning across ecosystems. Invasions by ecosystem engineers, in particular, have been shown to have dramatic effects in recipient ecosystems. For instance, invasion by earthworms, a below-ground invertebrate ecosystem engineer, in previously earthworm-free ecosystems alters the physico-chemical characteristics of the soil. Studies have shown that such alterations in the soil can have far-reaching impacts on soil organisms, which form a major portion of terrestrial biodiversity. Here, we present the first quantitative synthesis of earthworm invasion effects on soil micro-organisms and soil invertebrates based on 430 observations from 30 independent studies. Our meta-analysis shows a significant decline of the diversity and density of soil invertebrates in response to earthworm invasion with anecic and endogeic earthworms causing the strongest effects. Earthworm invasion effects on soil micro-organisms were context-dependent, such as depending on functional group richness of invasive earthworms and soil depth. Microbial biomass and diversity increased in mineral soil layers, with a weak negative effect in organic soil layers, indicating that the mixing of soil layers by earthworms (bioturbation) may homogenize microbial communities across soil layers. Our meta-analysis provides a compelling evidence for negative effects of a common invasive below-ground ecosystem engineer on below-ground biodiversity of recipient ecosystems, which could potentially alter the ecosystem functions and services linked to soil biota.

Contrasting changes in the abundance and diversity of North American bird assemblages from 1971 to 2010

Although it is generally recognized that global biodiversity is declining, few studies have examined long-term changes in multiple biodiversity dimensions simultaneously. In this study, we quantified and compared temporal changes in the abundance, taxonomic diversity, functional diversity, and phylogenetic diversity of bird assemblages, using roadside monitoring data of the North American Breeding Bird Survey from 1971 to 2010. We calculated 12 abundance and diversity metrics based on 5-year average abundances of 519 species for each of 768 monitoring routes. We did this for all bird species together as well as for four subgroups based on breeding habitat affinity (grassland, woodland, wetland, and shrubland breeders). The majority of the biodiversity metrics increased or remained constant over the study period, whereas the overall abundance of birds showed a pronounced decrease, primarily driven by declines of the most abundant species. These results highlight how stable or even increasing metrics of taxonomic, functional, or phylogenetic diversity may occur in parallel with substantial losses of individuals. We further found that patterns of change differed among the species subgroups, with both abundance and diversity increasing for woodland birds and decreasing for grassland breeders. The contrasting changes between abundance and diversity and among the breeding habitat groups underscore the relevance of a multifaceted approach to measuring biodiversity change. Our findings further stress the importance of monitoring the overall abundance of individuals in addition to metrics of taxonomic, functional, or phylogenetic diversity, thus confirming the importance of population abundance as an essential biodiversity variable.

Counting the cost of overfishing on sharks and rays

Over half of all shark and ray species are at risk of extinction or at least heading that way.

Extinction risk and conservation of the world's sharks and rays

The rapid expansion of human activities threatens ocean-wide biodiversity. Numerous marine animal populations have declined, yet it remains unclear whether these trends are symptomatic of a chronic accumulation of global marine extinction risk. We present the first systematic analysis of threat for a globally distributed lineage of 1,041 chondrichthyan fishes-sharks, rays, and chimaeras. We estimate that one-quarter are threatened according to IUCN Red List criteria due to overfishing (targeted and incidental). Large-bodied, shallow-water species are at greatest risk and five out of the seven most threatened families are rays. Overall chondrichthyan extinction risk is substantially higher than for most other vertebrates, and only one-third of species are considered safe. Population depletion has occurred throughout the world's ice-free waters, but is particularly prevalent in the Indo-Pacific Biodiversity Triangle and Mediterranean Sea. Improved management of fisheries and trade is urgently needed to avoid extinctions and promote population recovery. DOI: http://dx.doi.org/10.7554/eLife.00590.001.

Extinction risk and conservation of the world's sharks and rays

The rapid expansion of human activities threatens ocean-wide biodiversity. Numerous marine animal populations have declined, yet it remains unclear whether these trends are symptomatic of a chronic accumulation of global marine extinction risk. We present the first systematic analysis of threat for a globally distributed lineage of 1,041 chondrichthyan fishes—sharks, rays, and chimaeras. We estimate that one-quarter are threatened according to IUCN Red List criteria due to overfishing (targeted and incidental). Large-bodied, shallow-water species are at greatest risk and five out of the seven most threatened families are rays. Overall chondrichthyan extinction risk is substantially higher than for most other vertebrates, and only one-third of species are considered safe. Population depletion has occurred throughout the world’s ice-free waters, but is particularly prevalent in the Indo-Pacific Biodiversity Triangle and Mediterranean Sea. Improved management of fisheries and trade is urgently needed to avoid extinctions and promote population recovery.

DOI:http://dx.doi.org/10.7554/eLife.00590.001

Ocean ecosystems are under pressure from overfishing, climate change, habitat destruction and pollution. These pressures have led to documented declines of some fishes in some places, such as those living in coral reefs and on the high seas. However, it is not clear whether these population declines are isolated one-off examples or, instead, if they are sufficiently widespread to risk the extinction of large numbers of species.

Most fishes have a skeleton that is made of bone, but sharks and rays have a skeleton that is made of cartilage. A total of 1,041 species has such a skeleton and they are collectively known as the Chondrichthyes. To find out how well these fish are faring, Dulvy et al. worked with more than 300 scientists around the world to assess the conservation status of all 1,041 species.

Based on this, Dulvy et al. estimate that one in four of these species are threatened with extinction, mainly as a result of overfishing. Moreover, just 389 species (37.4% of the total) are considered to be safe, which is the lowest fraction of safe species among all vertebrate groups studied to date.

The largest sharks and rays are in the most peril, especially those living in shallow waters that are accessible to fisheries. A particular problem is the ‘fin trade’: the fins of sharks and shark-like rays are a delicacy in some Asian countries, and more than half of the chondrichthyans that enter the fin trade are under threat. Whether targeted or caught by boats fishing for other species, sharks and rays are used to supply a market that is largely unmonitored and unregulated. Habitat degradation and loss also pose considerable threats, particularly for freshwater sharks and rays.

Dulvy et al. identified three main hotspots where the biodiversity of sharks and rays was particularly seriously threatened—the Indo-Pacific Biodiversity Triangle, Red Sea, and the Mediterranean Sea—and argue that national and international action is needed to protect them from overfishing.

DOI:http://dx.doi.org/10.7554/eLife.00590.002