Unravelling the complexities of biotic homogenization and heterogenization in the British avifauna

Biotic homogenization is a process whereby species assemblages become more similar through time. The standard way of identifying the process of biotic homogenization is to look for decreases in spatial beta-diversity. However, using a single assemblage-level metric to assess homogenization can mask important changes in the occupancy patterns of individual species. Here, we analysed changes in the spatial beta-diversity patterns (i.e. biotic heterogenization or homogenization) of British bird assemblages within 30 km × 30 km regions between two periods (1988-1991 and 2008-2011). We partitioned the change in spatial beta-diversity into extirpation and colonization-resultant change (i.e. change in spatial beta-diversity within each region resulting from both extirpation and colonization). We used measures of abiotic change in combination with Bayesian modelling to disentangle the drivers of biotic heterogenization and homogenization. We detected both heterogenization and homogenization across the two time periods and three measures of diversity (taxonomic, phylogenetic, and functional). In addition, both extirpation and colonization contributed to the observed changes, with heterogenization mainly driven by extirpation and homogenization by colonization. These assemblage-level changes were primarily due to shifting occupancy patterns of generalist species. Compared to habitat generalists, habitat specialists had significantly (i) higher average contributions to colonization-resultant change (indicating heterogenization within a region due to colonization) and (ii) lower average contributions to extirpation-resultant change (indicating homogenization from extirpation). Generalists showed the opposite pattern. Increased extirpation-resultant homogenization within regions was associated with increased urban land cover and decreased habitat diversity, precipitation, and temperature. Changes in extirpation-resultant heterogenization and colonization-resultant heterogenization were associated with differences in elevation between regions and changes in temperature and land cover. Many of the 'winners' (i.e. species that increased in occupancy) were species that had benefitted from conservation action (e.g. buzzard (Buteo buteo)). The 'losers' (i.e. those that decreased in occupancy) consisted primarily of previously common species, such as cuckoo (Cuculus canorus). Our results show that focusing purely on changes in spatial beta-diversity over time may obscure important information about how changes in the occupancy patterns of individual species contribute to homogenization and heterogenization.

Atmospheric nitrogen deposition is related to plant biodiversity loss at multiple spatial scales

Due to various human activities, including intensive agriculture, traffic, and the burning of fossil fuels, in many parts of the world, current levels of reactive nitrogen emissions strongly exceed pre-industrial levels. Previous studies have shown that the atmospheric deposition of these excess nitrogen compounds onto semi-natural terrestrial environments has negative consequences for plant diversity. However, these previous studies mostly investigated biodiversity loss at local spatial scales, that is, at the scales of plots of typically a few square meters. Whether increased atmospheric nitrogen deposition also affects plant diversity at larger spatial scales remains unknown. Here, using grassland plant community data collected in 765 plots, across 153 different sites and 9 countries in northwestern Europe, we investigate whether relationships between atmospheric nitrogen deposition and plant biodiversity are scale-dependent. We found that high levels of atmospheric nitrogen deposition were associated with low levels of plant species richness at the plot scale but also at the scale of sites and regions. The presence of 39% of plant species was negatively associated with increasing levels of nitrogen deposition at large (site) scales, while only 1.5% of the species became more common with increasing nitrogen deposition, indicating that large-scale biodiversity changes were mostly driven by "loser" species, while "winner" species profiting from high N deposition were rare. Some of the "loser" species whose site presence was negatively associated with atmospheric nitrogen deposition are listed as "threatened" in at least some EU member states, suggesting that nitrogen deposition may be a key contributor to their threat status. Hence, reductions in reactive nitrogen emissions will likely benefit plant diversity not only at local but also at larger spatial scales.

Biodiversity in changing environments: An external-driver internal-topology framework to guide intervention

Accompanying the climate crisis is the more enigmatic biodiversity crisis. Rapid reorganization of biodiversity due to global environmental change has defied prediction and tested the basic tenets of conservation and restoration. Conceptual and practical innovation is needed to support decision making in the face of these unprecedented shifts. Critical questions include: How can we generalize biodiversity change at the community level? When are systems able to reorganize and maintain integrity, and when does abiotic change result in collapse or restructuring? How does this understanding provide a template to guide when and how to intervene in conservation and restoration? To this end, we frame changes in community organization as the modulation of external abiotic drivers on the internal topology of species interactions, using plant-plant interactions in terrestrial communities as a starting point. We then explore how this framing can help translate available data on species abundance and trait distributions to corresponding decisions in management. Given the expectation that community response and reorganization are highly complex, the external-driver internal-topology (EDIT) framework offers a way to capture general patterns of biodiversity that can help guide resilience and adaptation in changing environments.

Dispersal-diversity feedbacks and their consequences for macroecological patterns

Dispersal is a key process in ecology and evolution. While the effects of dispersal on diversity are broadly acknowledged, our understanding of the influence of diversity on dispersal remains limited. This arises from the dynamic, context-dependent, nonlinear and ubiquitous nature of dispersal. Diversity outcomes, such as competition, mutualism, parasitism and trophic interactions can feed back on dispersal, thereby influencing biodiversity patterns at several spatio-temporal scales. Here, we shed light on the dispersal-diversity causal links by discussing how dispersal-diversity ecological and evolutionary feedbacks can impact macroecological patterns. We highlight the importance of dispersal-diversity feedbacks for advancing our understanding of macro-eco-evolutionary patterns and their challenges, such as establishing a unified framework for dispersal terminology and methodologies across various disciplines and scales. This article is part of the theme issue 'Diversity-dependence of dispersal: interspecific interactions determine spatial dynamics'.

Species Richness Net Primary Productivity and the Water Balance Problem

Species energy theory suggests that, because of limitations on reproduction efficiency, a minimum density of plant individuals per viable species exists and that this minimum correlates the total number of plant individuals N with the number of species S. The simplest assumption is that the mean energy input per individual plant is independent of the number of individuals, making N, and thus S as well, proportional to the total energy input into the system. The primary energy input to a plant-dominated ecosystem is estimated as its Net Primary Productivity (NPP). Thus, species energy theory draws a direct correspondence from NPP to S. Although investigations have verified a strong connection between S and NPP, strong influences of other factors, such as topography, ecological processes such as competition, and historical contingencies, are also at play. The lack of a simple model of NPP expressed in terms of the principal climate variables, precipitation P, and potential evapotranspiration, PET, introduces unnecessary uncertainty to the understanding of species richness across scales. Recent research combines percolation theory with the principle of ecological optimality to derive an expression for NPP(P, PET). Consistent with assuming S is proportional to NPP, we show here that the new expression for NPP(P, PET) predicts the number of plant species S in an ecosystem as a function of P and PET. As already demonstrated elsewhere, the results are consistent with some additional variation due to non-climatic inputs. We suggest that it may be easier to infer specific deviations from species energy predictions with increased accuracy and generality of the prediction of NPP(P, PET).

Synthesis reveals approximately balanced biotic differentiation and homogenization

It is commonly thought that the biodiversity crisis includes widespread declines in the spatial variation of species composition, called biotic homogenization. Using a typology relating homogenization and differentiation to local and regional diversity changes, we synthesize patterns across 461 metacommunities surveyed for 10 to 91 years, and 64 species checklists (13 to 500+ years). Across all datasets, we found that no change was the most common outcome, but with many instances of homogenization and differentiation. A weak homogenizing trend of a 0.3% increase in species shared among communities/year on average was driven by increased numbers of widespread (high occupancy) species and strongly associated with checklist data that have longer durations and large spatial scales. At smaller spatial and temporal scales, we show that homogenization and differentiation can be driven by changes in the number and spatial distributions of both rare and common species. The multiscale perspective introduced here can help identify scale-dependent drivers underpinning biotic differentiation and homogenization.

Functional consequences of animal community changes in managed grasslands: An application of the CAFE approach

In the midst of an ongoing biodiversity crisis, much research has focused on species losses and their impacts on ecosystem functioning. The functional consequences (ecosystem response) of shifts in communities are shaped not only by changes in species richness, but also by compositional shifts that result from species losses and gains. Species differ in their contribution to ecosystem functioning, so species identity underlies the consequences of species losses and gains on ecosystem functions. Such research is critical to better predict the impact of disturbances on communities and ecosystems. We used the "Community Assembly and the Functioning of Ecosystems" (CAFE) approach, a modification of the Price equation to understand the functional consequences and relative effects of richness and composition changes in small nonvolant mammal and dung beetle communities as a result of two common disturbances in North American prairie restorations, prescribed fire and the reintroduction of large grazing mammals. Previous research in this system has shown dung beetles are critically important decomposers, while small mammals modulate much energy in prairie food webs. We found that dung beetle communities were more responsive to bison reintroduction and prescribed fires than small nonvolant mammals. Dung beetle richness increased after bison reintroduction, with higher dung beetle community biomass resulting from changes in remaining species (context-dependent component) rather than species turnover (richness components); prescribed fire caused a minor increase in dung beetle biomass for the same reason. For small mammals, bison reintroduction reduced energy transfer through the loss of species, while prescribed fire had little impact on either small mammal richness or energy transfer. The CAFE approach demonstrates how bison reintroduction controls small nonvolant mammal communities by increasing prairie food web complexity, and increases dung beetle populations with possible benefits for soil health through dung mineralization and soil bioturbation. Prescribed fires, however, have little effect on small mammals and dung beetles, suggesting a resilience to fire. These findings illustrate the key role of re-establishing historical disturbance regimes when restoring endangered prairie ecosystems and their ecological function.

Deep learning with citizen science data enables estimation of species diversity and composition at continental extents

Effective solutions to conserve biodiversity require accurate community- and species-level information at relevant, actionable scales and across entire species' distributions. However, data and methodological constraints have limited our ability to provide such information in robust ways. Herein we employ a Deep-Reasoning Network implementation of the Deep Multivariate Probit Model (DMVP-DRNets), an end-to-end deep neural network framework, to exploit large observational and environmental data sets together and estimate landscape-scale species diversity and composition at continental extents. We present results from a novel year-round analysis of North American avifauna using data from over nine million eBird checklists and 72 environmental covariates. We highlight the utility of our information by identifying critical areas of high species diversity for a single group of conservation concern, the North American wood warblers, while capturing spatiotemporal variation in species' environmental associations and interspecific interactions. In so doing, we demonstrate the type of accurate, high-resolution information on biodiversity that deep learning approaches such as DMVP-DRNets can provide and that is needed to inform ecological research and conservation decision-making at multiple scales.

Bowler D, Hof C. Global change impacts on bird biodiversity in South Asia: potential effects of future land-use and climate change on avian species richness in Pakistan

Evaluating the impact of future changes in land-use and climate on species communities, especially species richness, is one of the most important challenges of current research in ecology and conservation. The impact of environmental changes on species richness depends on its sensitivity (i.e., how strongly a given level of change influences the ecological community) and its exposure (i.e., the amount of change that occurs). To examine the sensitivity, exposure, and potential impact of future environmental conditions on bird communities, we compiled data on bird species richness for Pakistan-a neglected region in macro- or country-scale studies. Since bird species richness strongly varies across seasons due to the seasonal occurrence of migratory species in winter, we compared both wintering (migratory plus resident species) and breeding (resident species only) bird richness. We found breeding and wintering species richness to be sensitive to temperature, precipitation and rainfed cropland by being positively related to these factors. Exposure varied regionally, with projected temperature changes being most profound in northern regions while the strongest projected precipitation changes occurred in central and southern regions. The projected impact of future environmental change were highly heterogeneous across the country and differed between the wintering and breeding communities. Overall, the most negatively impacted region was projected to be the Khyber Pakhtunkha province in the North of Pakistan, due to reductions in precipitation and rainfed cropland, resulting in a projected negative impact, especially on wintering species richness. By highlighting the regional and seasonal bird communities most at risk, our findings provide useful information for policy makers to help devise new policies for mitigating negative impacts of future environmental changes on birds within Pakistan.

Marine heatwaves are not a dominant driver of change in demersal fishes

Marine heatwaves have been linked to negative ecological effects in recent decades1,2. If marine heatwaves regularly induce community reorganization and biomass collapses in fishes, the consequences could be catastrophic for ecosystems, fisheries and human communities3,4. However, the extent to which marine heatwaves have negative impacts on fish biomass or community composition, or even whether their effects can be distinguished from natural and sampling variability, remains unclear. We investigated the effects of 248 sea-bottom heatwaves from 1993 to 2019 on marine fishes by analysing 82,322 hauls (samples) from long-term scientific surveys of continental shelf ecosystems in North America and Europe spanning the subtropics to the Arctic. Here we show that the effects of marine heatwaves on fish biomass were often minimal and could not be distinguished from natural and sampling variability. Furthermore, marine heatwaves were not consistently associated with tropicalization (gain of warm-affiliated species) or deborealization (loss of cold-affiliated species) in these ecosystems. Although steep declines in biomass occasionally occurred after marine heatwaves, these were the exception, not the rule. Against the highly variable backdrop of ocean ecosystems, marine heatwaves have not driven biomass change or community turnover in fish communities that support many of the world's largest and most productive fisheries.

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5,6,7 vast areas of the tropics remain understudied.8,9,10,11 In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepresented in biodiversity databases.13,14,15 To worsen this situation, human-induced modifications16,17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%-18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost.

Avian Diversity Responds Unimodally to Natural Landcover: Implications for Conservation Management

Predicting species' ecological responses to landcovers within landscapes could guide conservation practices. Current modelling efforts derived from classic species-area relationships almost always predict richness monotonically increasing as the proportion of landcovers increases. Yet evidence to explain hump-shaped richness-landcover patterns is lacking. We tested predictions related to hypothesised drivers of peaked relationships between richness and proportion of natural landcover. We estimated richness from breeding bird atlases at different spatial scales (25 to 900 km2) in New York State and Southern Ontario. We modelled richness to gradients of natural landcover, temperature, and landcover heterogeneity. We controlled models for sampling effort and regional size of the species pool. Species richness peaks as a function of the proportion of natural landcover consistently across spatial scales and geographic regions sharing similar biogeographic characteristics. Temperature plays a role, but peaked relationships are not entirely due to climate-landcover collinearities. Heterogeneity weakly explains richness variance in the models. Increased amounts of natural landcover promote species richness to a limit in landscapes with relatively little (<30%) natural cover. Higher amounts of natural cover and a certain amount of human-modified landcovers can provide habitats for species that prefer open habitats. Much of the variation in richness among landscapes must be related to variables other than natural versus human-dominated landcovers.

A framework for the detection and attribution of biodiversity change

The causes of biodiversity change are of great scientific interest and central to policy efforts aimed at meeting biodiversity targets. Changes in species diversity and high rates of compositional turnover have been reported worldwide. In many cases, trends in biodiversity are detected, but these trends are rarely causally attributed to possible drivers. A formal framework and guidelines for the detection and attribution of biodiversity change is needed. We propose an inferential framework to guide detection and attribution analyses, which identifies five steps-causal modelling, observation, estimation, detection and attribution-for robust attribution. This workflow provides evidence of biodiversity change in relation to hypothesized impacts of multiple potential drivers and can eliminate putative drivers from contention. The framework encourages a formal and reproducible statement of confidence about the role of drivers after robust methods for trend detection and attribution have been deployed. Confidence in trend attribution requires that data and analyses used in all steps of the framework follow best practices reducing uncertainty at each step. We illustrate these steps with examples. This framework could strengthen the bridge between biodiversity science and policy and support effective actions to halt biodiversity loss and the impacts this has on ecosystems. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.

Looking back on biodiversity change: lessons for the road ahead

Estimating biodiversity change across the planet in the context of widespread human modification is a critical challenge. Here, we review how biodiversity has changed in recent decades across scales and taxonomic groups, focusing on four diversity metrics: species richness, temporal turnover, spatial beta-diversity and abundance. At local scales, change across all metrics includes many examples of both increases and declines and tends to be centred around zero, but with higher prevalence of declining trends in beta-diversity (increasing similarity in composition across space or biotic homogenization) and abundance. The exception to this pattern is temporal turnover, with changes in species composition through time observed in most local assemblages. Less is known about change at regional scales, although several studies suggest that increases in richness are more prevalent than declines. Change at the global scale is the hardest to estimate accurately, but most studies suggest extinction rates are probably outpacing speciation rates, although both are elevated. Recognizing this variability is essential to accurately portray how biodiversity change is unfolding, and highlights how much remains unknown about the magnitude and direction of multiple biodiversity metrics at different scales. Reducing these blind spots is essential to allow appropriate management actions to be deployed. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.

Theory and application of an improved species richness estimator

Species richness is an essential biodiversity variable indicative of ecosystem states and rates of invasion, speciation and extinction both contemporarily and in fossil records. However, limited sampling effort and spatial aggregation of organisms mean that biodiversity surveys rarely observe every species in the survey area. Here we present a non-parametric, asymptotic and bias-minimized richness estimator, Ω by modelling how spatial abundance characteristics affect observation of species richness. Improved asymptotic estimators are critical when both absolute richness and difference detection are important. We conduct simulation tests and applied Ω to a tree census and a seaweed survey. Ω consistently outperforms other estimators in balancing bias, precision and difference detection accuracy. However, small difference detection is poor with any asymptotic estimator. An R-package, Richness, performs the proposed richness estimations along with other asymptotic estimators and bootstrapped precisions. Our results explain how natural and observer-induced variations affect species observation, how these factors can be used to correct observed richness using the estimator Ω on a variety of data, and why further improvements are critical for biodiversity assessments. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.

Biodiversity time series are biased towards increasing species richness in changing environments

The discrepancy between global loss and local constant species richness has led to debates over data quality, systematic biases in monitoring programmes and the adequacy of species richness to capture changes in biodiversity. We show that, more fundamentally, null expectations of stable richness can be wrong, despite independent yet equal colonization and extinction. We analysed fish and bird time series and found an overall richness increase. This increase reflects a systematic bias towards an earlier detection of colonizations than extinctions. To understand how much this bias influences richness trends, we simulated time series using a neutral model controlling for equilibrium richness and temporal autocorrelation (that is, no trend expected). These simulated time series showed significant changes in richness, highlighting the effect of temporal autocorrelation on the expected baseline for species richness changes. The finite nature of time series, the long persistence of declining populations and the potential strong dispersal limitation probably lead to richness changes when changing conditions promote compositional turnover. Temporal analyses of richness should incorporate this bias by considering appropriate neutral baselines for richness changes. Absence of richness trends over time, as previously reported, can actually reflect a negative deviation from the positive biodiversity trend expected by default.

Flora of Northeast Asia

As a component of the MAP project, the study of the flora in Northeast Asia (comprising Japan, South Korea, North Korea, Northeast China, and Mongolia) convincingly underscores the indispensability of precise and comprehensive diversity data for flora research. Due to variations in the description of flora across different countries in Northeast Asia, it is essential to update our understanding of the region's overall flora using the latest high-quality diversity data. This study employed the most recently published authoritative data from various countries to conduct a statistical analysis of 225 families, 1782 genera, and 10,514 native vascular species and infraspecific taxa in Northeast Asia. Furthermore, species distribution data were incorporated to delineate three gradients in the overall distribution pattern of plant diversity in Northeast Asia. Specifically, Japan (excluding Hokkaido) emerged as the most prolific hotspot for species, followed by the Korean Peninsula and the coastal areas of Northeast China as the second richest hotspots. Conversely, Hokkaido, inland Northeast China, and Mongolia constituted species barren spots. The formation of the diversity gradients is primarily attributed to the effects of latitude and continental gradients, with altitude and topographic factors within the gradients modulating the distribution of species.

Who is reporting non-native species and how? A cross-expert assessment of practices and drivers of non-native biodiversity reporting in species regional listing

Each year, hundreds of scientific works with species' geographical data are published. However, these data can be challenging to identify, collect, and integrate into analytical workflows due to differences in reporting structures, storage formats, and the omission or inconsistency of relevant information and terminology. These difficulties tend to be aggravated for non-native species, given varying attitudes toward non-native species reporting and the existence of an additional layer of invasion-related terminology. Thus, our objective is to identify the current practices and drivers of the geographical reporting of non-native species in the scientific literature. We conducted an online survey targeting authors of species regional checklists-a widely published source of biogeographical data-where we asked about reporting habits and perceptions regarding non-native taxa. The responses and the relationships between response variables and predictors were analyzed using descriptive statistics and ordinal logistic regression models. With a response rate of 22.4% (n = 113), we found that nearly half of respondents (45.5%) do not always report non-native taxa, and of those who report, many (44.7%) do not always differentiate them from native taxa. Close to half of respondents (46.4%) also view the terminology of biological invasions as an obstacle to the reporting of non-native taxa. The ways in which checklist information is provided are varied, but mainly correspond to descriptive text and embedded tables with non-native species (when given) mentioned alongside native species. Only 13.4% of respondents mention to always provide the data in automation-friendly formats or its publication in biodiversity data repositories. Data on the distribution of non-native species are essential for monitoring global biodiversity change and preventing biological invasions. Despite its importance our results show an urgent need to improve the frequency, accessibility, and consistency of publication of these data.

Tipping points and interactive effects of chronic human disturbance and acute heat stress on coral diversity

Multiple anthropogenic stressors co-occur ubiquitously in natural ecosystems. However, multiple stressor studies often produce conflicting results, potentially because the nature and direction of stressor interactions depends upon the strength of the underlying stressors. Here, we first examine how coral α- and β-diversities vary across sites spanning a gradient of chronic local anthropogenic stress before and after a prolonged marine heatwave. Developing a multiple stressor framework that encompasses non-discrete stressors, we then examine interactions between the continuous and discrete stressors. We provide evidence of additive effects, antagonistic interactions (with heatwave-driven turnover in coral community composition diminishing as the continuous stressor increased), and tipping points (at which the response of coral Hill-richness to stressors changed from additive to near synergistic). We show that community-level responses to multiple stressors can vary, and even change qualitatively, with stressor intensity, underscoring the importance of examining complex, but realistic continuous stressors to understand stressor interactions and their ecological impacts.

Latitudinal patterns of forest ecosystem stability across spatial scales as affected by biodiversity and environmental heterogeneity

Our planet is facing a variety of serious threats from climate change that are unfolding unevenly across the globe. Uncovering the spatial patterns of ecosystem stability is important for predicting the responses of ecological processes and biodiversity patterns to climate change. However, the understanding of the latitudinal pattern of ecosystem stability across scales and of the underlying ecological drivers is still very limited. Accordingly, this study examines the latitudinal patterns of ecosystem stability at the local and regional spatial scale using a natural assembly of forest metacommunities that are distributed over a large temperate forest region, considering a range of potential environmental drivers. We found that the stability of regional communities (regional stability) and asynchronous dynamics among local communities (spatial asynchrony) both decreased with increasing latitude, whereas the stability of local communities (local stability) did not. We tested a series of hypotheses that potentially drive the spatial patterns of ecosystem stability, and found that although the ecological drivers of biodiversity, climatic history, resource conditions, climatic stability, and environmental heterogeneity varied with latitude, latitudinal patterns of ecosystem stability at multiple scales were affected by biodiversity and environmental heterogeneity. In particular, α diversity is positively associated with local stability, while β diversity is positively associated with spatial asynchrony, although both relationships are weak. Our study provides the first evidence that latitudinal patterns of the temporal stability of naturally assembled forest metacommunities across scales are driven by biodiversity and environmental heterogeneity. Our findings suggest that the preservation of plant biodiversity within and between forest communities and the maintenance of heterogeneous landscapes can be crucial to buffer forest ecosystems at higher latitudes from the faster and more intense negative impacts of climate change in the future.

Regional occupancy increases for widespread species but decreases for narrowly distributed species in metacommunity time series

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.

Dispersal capacity underlies scale-dependent changes in species richness patterns under human disturbance

Changes in the species richness of (meta-)communities emerge from changes in the relative species abundance distribution (SAD), the total density of individuals, and the amount of spatial aggregation of individuals from the same species. Yet, how human disturbance affects these underlying diversity components at different spatial scales and how this interacts with important species traits, like dispersal capacity, remain poorly understood. Using data of carabid beetle communities along a highly replicated urbanization gradient, we reveal that species richness in urban sites was reduced due to a decline in individual density as well as changes in the SAD at both small and large spatial scales. Changes in these components of species richness were linked to differential responses of groups of species that differ in dispersal capacity. The individual density effect on species richness was due to a drastic 90% reduction of low-dispersal individuals in more urban sites. Conversely, the decrease in species richness due to changes in the SAD at large (i.e., loss of species from the regional pool) and small (i.e., decreased evenness) spatial scales were driven by species with intermediate and high dispersal ability, respectively. These patterns coincide with the expected responses of these dispersal-type assemblages toward human disturbance, namely, (i) loss of low-dispersal species by local extinction processes, (ii) loss of higher-dispersal species from the regional species pool due to decreased habitat diversity, and (iii) dominance of a few highly dispersive species resulting in a decreased evenness. Our results demonstrate that dispersal capacity plays an essential role in determining scale-dependent changes in species richness patterns. Incorporating this information improves our mechanistic insight into how environmental change affects species diversity at different spatial scales, allowing us to better forecast how human disturbance will drive local and regional changes in biodiversity patterns.

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.

Universal beta-diversity-functioning relationships are neither observed nor expected

Widespread evidence shows that local species richness (α-diversity) loss hampers the biomass production and stability of ecosystems. β-Diversity, namely the variation of species compositions among different ecological communities, represents another important biodiversity component, but studies on how it drives ecosystem functioning show mixed results. We argue that to better understand the importance of β-diversity we need to consider it across contexts. We focus on three scenarios that cause gradients in β-diversity: changes in (i) abiotic heterogeneity, (ii) habitat isolation, and (iii) species pool richness. We show that across these scenarios we should not expect universally positive relationships between β-diversity, production, and ecosystem stability. Nevertheless, predictable relationships between β-diversity and ecosystem functioning do exist in specific contexts, and can reconcile seemingly contrasting empirical relationships.

Macrosystem community change in lake phytoplankton and its implications for diversity and function

Aim

We use lake phytoplankton community data to quantify the spatio-temporal and scale-dependent impacts of eutrophication, land-use and climate change on species niches and community assembly processes while accounting for species traits and phylogenetic constraints.

Location

Finland.

Time period

1977-2017.

Major taxa

Phytoplankton.

Methods

We use hierarchical modelling of species communities (HMSC) to model metacommunity trajectories at 853 lakes over four decades of environmental change, including a hierarchical spatial structure to account for scale-dependent processes. Using a "region of common profile" approach, we evaluate compositional changes of species communities and trait profiles and investigate their temporal development.

Results

We demonstrate the emergence of novel and widespread community composition clusters in previously more compositionally homogeneous communities, with cluster-specific community trait profiles, indicating functional differences. A strong phylogenetic signal of species responses to the environment implies similar responses among closely related taxa. Community cluster-specific species prevalence indicates lower taxonomic dispersion within the current dominant clusters compared with the historically dominant cluster and an overall higher prevalence of smaller species sizes within communities. Our findings denote profound spatio-temporal structuring of species co-occurrence patterns and highlight functional differences of lake phytoplankton communities.

Main conclusions

Diverging community trajectories have led to a nationwide reshuffling of lake phytoplankton communities. At regional and national scales, lakes are not single entities but metacommunity hubs in an interconnected waterscape. The assembly mechanisms of phytoplankton communities are strongly structured by spatio-temporal dynamics, which have led to novel community types, but only a minor part of this reshuffling could be linked to temporal environmental change.

Factors at multiple scales drive parasite community structure

Understanding how ecological communities are assembled remains a key goal of ecosystem ecology. Because communities are hierarchical, factors acting at multiple scales can contribute to patterns of community structure. Parasites provide a natural system to explore this idea, as they exist as discrete communities within host individuals, which are themselves part of a community and metacommunity. We aimed to understand the relative contribution of multi-scale drivers in parasite community assembly and assess how patterns at one level may mask those occurring at another. Specifically, we wanted to disentangle patterns caused by passive sampling from those determined by ecological drivers, and how these vary with scale. We applied a Markov Random Fields model and assessed measures of β-diversity and nestedness for 420 replicate parasite infracommunities (parasite assemblages in host individuals) across two freshwater mussel host species, three sites and two time periods, comparing our results to simulations from four different ecologically relevant null models. We showed that β-diversity between sites (explaining 25% of variation in parasite distribution) and host species (41%) is greater than expected, and β-diversity between individual hosts is smaller than expected, even after accounting for parasite prevalence and characteristics of host individuals. Furthermore, parasite communities were significantly less nested than expected once parasite prevalence and host characteristics were both accounted for, but more nested than expected otherwise, suggesting a degree of modularity at the within-host level that is masked if underlying host and parasite characteristics are not taken into account. The Markov Random Fields model provided evidence for possible competitive within-host parasite interactions, providing a mechanism for the observed infracommunity modularity. An integrative approach that examines factors at multiple scales is necessary to understand the composition of ecological communities. Furthermore, patterns at one level can alter the interpretation of ecologically important drivers at another if variation at higher scales is not accounted for.

Biotic homogenization and differentiation of plant communities in tropical and subtropical forests

Anthropogenic impacts on biodiversity can lead to biotic homogenization (BH) and biotic differentiation (BD). BH is a process of increasing similarity in community composition (including taxonomic, functional, and phylogenetic components), whereas BD is a process of decreasing similarity over space and time. Here, we conducted a systematic review of BH and BD in plant communities in tropical and subtropical forests to identify trends and knowledge gaps. Our bibliometric search in the Web of Science returned 1989 papers, of which 151 matched our criteria and were included in the analysis. The Neotropical region had the largest number of articles, and Brazil was the most represented country with 92 studies. Regarding the type of change, homogenization was more frequent than differentiation (noted in 69.6% of publications). The taxonomic diversity component was measured more often than functional and phylogenetic diversity components. Most studies (75.6%) assessed homogenization and differentiation based on a single observation in time; as opposed to few studies that monitored plant community over multiple years. Forest fragmentation was cited as the main determinant of homogenization and differentiation processes (57.2% of articles). Our results highlight the importance of evaluating community composition over time and more than taxonomic components (i.e., functional and phylogenetic) to advance understanding of homogenization and differentiation. Both processes were scale dependent and not mutually exclusive. As such, future research should consider differentiation as a potential transition phase to homogenization and that potential differences in both processes may depend on the spatial and temporal scale adopted. Understanding the complexity and causes of homogenization and differentiation is essential for biodiversity conservation in a world increasingly affected by anthropogenic disturbances.

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.

Species Richness, Density, Activity, and Composition of Ground-dwelling Ants in the Humid Forest Zone of Southern Cameroon: Role of Vegetation Cover and Abiotic Factors

The destruction of natural habitats is among the major factors responsible for the decrease in species diversity and distribution. This study focused on the effect of vegetation and its interaction with the season on ant species richness, density, activity, and composition in the three dominant habitats - forest, fallow, and mixed crop field - prevailing in southern Cameroon. Ants were sampled using two sampling techniques -pitfall trap and quadrat - in fallows, forest, and mixed crop fields from May 2007 to April 2008. Average ant species richness did not differ between fallow and forest, but the number of species in both habitats was higher compared with mixed-crop field. Species richness was also higher during the short dry season compared with other seasons. Species density was higher in mixed-crop field and in the long dry season. Species activity was similar in the three habitats, but it was higher during the long-wet season. Species richness, activity, and density were lower at low altitude. Vegetation and season affected the composition of ant species, but not the interaction between the two factors. The highest dissimilarity index was observed between mixed crop-field and forest while between seasons, it was between the short-wet and the long dry season. These results suggest that vegetation cover and abiotic factors interact to determine the distribution, density, activity, and composition of ant species. Identifying key drivers among environmental factors could help to understand the response of species to the variation of those factors in the context of climate change.

Global patterns of vascular plant alpha diversity

Global patterns of regional (gamma) plant diversity are relatively well known, but whether these patterns hold for local communities, and the dependence on spatial grain, remain controversial. Using data on 170,272 georeferenced local plant assemblages, we created global maps of alpha diversity (local species richness) for vascular plants at three different spatial grains, for forests and non-forests. We show that alpha diversity is consistently high across grains in some regions (for example, Andean-Amazonian foothills), but regional 'scaling anomalies' (deviations from the positive correlation) exist elsewhere, particularly in Eurasian temperate forests with disproportionally higher fine-grained richness and many African tropical forests with disproportionally higher coarse-grained richness. The influence of different climatic, topographic and biogeographical variables on alpha diversity also varies across grains. Our multi-grain maps return a nuanced understanding of vascular plant biodiversity patterns that complements classic maps of biodiversity hotspots and will improve predictions of global change effects on biodiversity.

Lower alpha, higher beta, and similar gamma diversity of saproxylic beetles in unmanaged compared to managed Norway spruce stands

Strong anthropogenic pressures on global forests necessitate that managed forests be evaluated as habitat for biodiversity. The complex pattern of habitat types created in forestry systems is ideal for analyses through the theoretical framework of alpha (local), gamma (total) and beta (compositional) diversity. Here I use saproxylic beetles, a species-rich threatened group, to compare four Norway spruce-dominated habitats representative of the boreal forest landscape of northern Europe: unmanaged semi-natural stands, nature reserves, unthinned middle-aged production stands and commercially thinned production stands. The beetles (in total 38 085 individuals of 312 species), including red-listed ones and three feeding guilds (wood consumers, fungivores and predators) were studied in 53 stands in central-southern Sweden, in two regions with differing amounts of conservation forest. Alpha diversity of saproxylic, but not red-listed, beetles was higher in the thinned stands than in the semi-natural stands, and did not differ for the other forest types. Beta diversity of saproxylic beetles was higher in unmanaged semi-natural stands than in the other forest types, but species composition did not differ noticeably. Furthermore, red-listed saproxylic beetles had higher gamma diversity in unmanaged semi-natural stands in the region with more conservation forest, but not in the one with less such forest. The local factors dead wood volume and dead wood diversity did not influence alpha diversity of beetles, but increasing canopy openness had a minor negative influence on saproxylic and red-listed beetles. While the local scale (alpha diversity) indicates the potential for managed forests to house many saproxylic beetle species associated with spruce forests in this boreal landscape, the larger scales (beta and gamma diversity) indicate the value of unmanaged forests for the conservation of the entire saproxylic beetle fauna. These results show the importance of analyses at multiple levels of diversity (alpha, beta, gamma) for identifying patterns relevant to conservation.

Loss of phylogenetic diversity under landscape change

Habitat alteration and destruction are primary drivers of biodiversity loss. However, the evolutionary dimensions of biodiversity loss remain largely unexplored in many systems. For example, little is known about how habitat alteration/loss can lead to phylogenetic deconstruction of ecological assemblages at the local level. That is, while species loss is evident, are some lineages favored over others? Using a long-term dataset of a globally, ecologically important guild of invertebrate consumers, stream leaf "shredders," we created a phylogenetic tree of the taxa in the regional species pool, calculated mean phylogenetic distinctiveness for >1000 communities spanning >10 year period, and related species richness, phylogenetic diversity, and distinctiveness to watershed-scale impervious cover. Using a combination of changepoint and compositional analyses, we learned that increasing impervious cover produced marked reductions in all three measures of diversity. These results aid in understanding both phylogenetic diversity and mean assemblage phylogenetic distinctiveness. Our findings indicate that, not only are species lost when there is an increase in watershed urbanization, as other studies have demonstrated, but that those lost are members of more distinct lineages relative to the community as a whole..

Large herbivores trigger spatiotemporal changes in forest plant diversity

Large herbivores can exert top-down control on terrestrial plant communities, but the magnitude, direction, and scale-dependency of their impacts remain equivocal, especially in temperate and boreal forests, where multiple disturbances often interact. Using a unique, long-term and replicated landscape experiment, we assessed the influence of a high density of white-tailed deer (Odocoileus virginianus) on the spatiotemporal dynamics of diversity, composition, and successional trajectories of understorey plant assemblages in recently logged boreal forests. This experiment provided a rare opportunity to test whether deer herbivory represents a direct filter on plant communities or if it mainly acts to suppress dominant plants which, in turn, release other plant species from strong negative plant-plant interactions. These two hypotheses make different predictions about changes in community composition, alpha and beta diversity in different vegetation layers and at different spatial scales. Our results showed that deer had strong effects on plant community composition and successional trajectories, but the resulting impacts on plant alpha and beta diversity patterns were markedly scale-dependent in both time and space. Responses of tree and non-tree vegetation layers were strongly asymmetric. Deer acted both as a direct filter and as a suppressor of dominant plant species during early forest succession, but the magnitude of both processes was specific to tree and non-tree vegetation layers. Although our data supported the ungulate-driven homogenization hypothesis, compositional shifts and changes of alpha diversity were poor predictors of beta diversity loss. Our findings underscore the importance of long-term studies in revealing non-linear temporal community trends, and they challenge managers to prioritize particular community properties and scales of interest, given contrasting trends of composition, alpha, and beta diversity across spatial scales.

Detecting patterns of vertebrate biodiversity across the multidimensional urban landscape

Explicit characterisation of the complexity of urban landscapes is critical for understanding patterns of biodiversity and for detecting the underlying social and ecological processes that shape them. Urban environments exhibit variable heterogeneity and connectivity, influenced by different historical contingencies, that affect community assembly across scales. The multidimensional nature of urban disturbance and co-occurrence of multiple stressors can cause synergistic effects leading to nonlinear responses in populations and communities. Yet, current research design of urban ecology and evolutionary studies typically relies on simple representation of the parameter space that can be observed. Sampling approaches apply simple urban gradients such as linear transects in space or comparisons of urban sites across the urban mosaic accounting for a few variables. This rarely considers multiple dimensions and scales of biodiversity, and proves to be inadequate to explain observed patterns. We apply a multidimensional approach that integrates distinctive social, ecological and built characteristics of urban landscapes, representing variations along dimensions of heterogeneity, connectivity and historical contingency. Measuring species richness and beta diversity across 100 US metropolitan areas at the city and 1-km scales, we show that distinctive signatures of urban biodiversity can result from interactions between socioecological heterogeneity and connectivity, mediated by historical contingency.

Small-scale drivers on plant and ant diversity in a grassland habitat through a multifaceted approach

Semi-natural grasslands are characterized by high biodiversity and require multifaceted approaches to monitor their biodiversity. Moreover, grasslands comprise a multitude of microhabitats, making the scale of investigation of fundamental importance. Despite their wide distribution, grasslands are highly threatened and are considered of high conservation priority by Directive no. 92/43/EEC. Here, we investigate the effects of small-scale ecological differences between two ecosites present within the EU habitat of Community Interest of semi-natural dry grasslands on calcareous substrates (6210 according to Dir. 92/43/EEC) occurring on a Mediterranean mountain. We measured taxonomic and functional diversity of plant and ant communities, evaluating the differences among the two ecosites, how these differences are influenced by the environment and whether vegetation affects composition of the ant community. Our results show that taxonomic and functional diversity of plant and ant communities are influenced by the environment. While vegetation has no effect on ant communities, we found plant and ant community composition differed across the two ecosites, filtering ant and plant species according to their functional traits, even at a small spatial scale. Our findings imply that small-scale monitoring is needed to effectively conserve priority habitats, especially for those that comprise multiple microhabitats.

Can moderate heavy metal soil contaminations due to cement production influence the surrounding soil bacterial communities?

Events of soil contamination by heavy metals are mostly related to human activities that release these metals into the environment as emissions or effluents. Among the industrial activities related to heavy metal pollution, cement production plants are considered one of the most common sources. In this work we applied the High-throughput sequencing approach called 16 S rDNA metabarcoding to perform the taxonomic characterization of the prokaryotic communities of the soil surrounding three cement plants as well as two areas outside the influence of the cement plants that represented agricultural production environments free of heavy metal contamination (control areas). We applied the environmental genomics approaches known as "structural community metrics" (α- and β-diversity metrics) and "functional community metrics" (PICRUSt2 approach) to verify whether or not the effects of heavy metal contamination in the study area generated impacts on soil bacterial communities. We found that the impact related to the elevation of heavy metal concentration due to the operation of cement plants in the surrounding soil can be considered smooth according to globally recognized indices such as Igeo. However, we identified that both the taxonomic and functional structures of the communities surrounding cement plants were different from those found in the control areas. We consider that our findings contribute significantly to the general understanding of the effects of heavy metals on the soil ecosystem by showing that light contamination can disturb the dynamics of ecosystem services provided by soil, specifically those associated with microbial metabolism.

Biodiversity: Monitoring trends and implications for ecosystem functioning

Systematic, long-term monitoring provides crucial evidence regarding the vulnerability of biodiversity to environmental change. New research shows that trends in taxonomic diversity do not necessarily match trends in functional diversity. Interpreting the implications of different kinds of diversity change for ecosystem functioning remains a key priority.

Grand challenges in biodiversity-ecosystem functioning research in the era of science-policy platforms require explicit consideration of feedbacks

Feedbacks are an essential feature of resilient socio-economic systems, yet the feedbacks between biodiversity, ecosystem services and human wellbeing are not fully accounted for in global policy efforts that consider future scenarios for human activities and their consequences for nature. Failure to integrate feedbacks in our knowledge frameworks exacerbates uncertainty in future projections and potentially prevents us from realizing the full benefits of actions we can take to enhance sustainability. We identify six scientific research challenges that, if addressed, could allow future policy, conservation and monitoring efforts to quantitatively account for ecosystem and societal consequences of biodiversity change. Placing feedbacks prominently in our frameworks would lead to (i) coordinated observation of biodiversity change, ecosystem functions and human actions, (ii) joint experiment and observation programmes, (iii) more effective use of emerging technologies in biodiversity science and policy, and (iv) a more inclusive and integrated global community of biodiversity observers. To meet these challenges, we outline a five-point action plan for collaboration and connection among scientists and policymakers that emphasizes diversity, inclusion and open access. Efforts to protect biodiversity require the best possible scientific understanding of human activities, biodiversity trends, ecosystem functions and—critically—the feedbacks among them.

Complex community responses underpin biodiversity change following invasion

How do invasive species change native biodiversity? One reason why this long-standing question remains challenging to answer could be because the main focus of the invasion literature has been on shifts in species richness (a measure of α-diversity). As the underlying components of community structure—intraspecific aggregation, interspecific density and the species abundance distribution (SAD)—are potentially impacted in different ways during invasion, trends in species richness provide only limited insight into the mechanisms leading to biodiversity change. In addition, these impacts can be manifested in distinct ways at different spatial scales. Here we take advantage of the new Measurement of Biodiversity (MoB) framework to reanalyse data collected in an invasion front in the Brazilian Cerrado biodiversity hotspot. We show that, by using the MoB multi-scale approach, we are able to link reductions in species richness in invaded sites to restructuring in the SAD. This restructuring takes the form of lower evenness in sites invaded by pines relative to sites without pines. Shifts in aggregation also occur. There is a clear signature of spatial scale in biodiversity change linked to the presence of an invasive species. These results demonstrate how the MoB approach can play an important role in helping invasion ecologists, field biologists and conservation managers move towards a more mechanistic approach to detecting and interpreting changes in ecological systems following invasion.