Joint Species Distribution Modelling (JSDM) is becoming an increasingly popular statistical method for analysing data in community ecology. Hierarchical Modelling of Species Communities (HMSC) is a ...general and flexible framework for fitting JSDMs. HMSC allows the integration of community ecology data with data on environmental covariates, species traits, phylogenetic relationships and the spatio‐temporal context of the study, providing predictive insights into community assembly processes from non‐manipulative observational data of species communities.
The full range of functionality of HMSC has remained restricted to Matlab users only. To make HMSC accessible to the wider community of ecologists, we introduce Hmsc 3.0, a user‐friendly r implementation.
We illustrate the use of the package by applying Hmsc 3.0 to a range of case studies on real and simulated data. The real data consist of bird counts in a spatio‐temporally structured dataset, environmental covariates, species traits and phylogenetic relationships. Vignettes on simulated data involve single‐species models, models of small communities, models of large species communities and models for large spatial data. We demonstrate the estimation of species responses to environmental covariates and how these depend on species traits, as well as the estimation of residual species associations. We demonstrate how to construct and fit models with different types of random effects, how to examine MCMC convergence, how to examine the explanatory and predictive powers of the models, how to assess parameter estimates and how to make predictions. We further demonstrate how Hmsc 3.0 can be applied to normally distributed data, count data and presence–absence data.
The package, along with the extended vignettes, makes JSDM fitting and post‐processing easily accessible to ecologists familiar with r.
Scenario‐based biodiversity modelling is a powerful approach to evaluate how possible future socio‐economic developments may affect biodiversity. Here, we evaluated the changes in terrestrial ...biodiversity intactness, expressed by the mean species abundance (MSA) metric, resulting from three of the shared socio‐economic pathways (SSPs) combined with different levels of climate change (according to representative concentration pathways RCPs): a future oriented towards sustainability (SSP1xRCP2.6), a future determined by a politically divided world (SSP3xRCP6.0) and a future with continued global dependency on fossil fuels (SSP5xRCP8.5). To this end, we first updated the GLOBIO model, which now runs at a spatial resolution of 10 arc‐seconds (~300 m), contains new modules for downscaling land use and for quantifying impacts of hunting in the tropics, and updated modules to quantify impacts of climate change, land use, habitat fragmentation and nitrogen pollution. We then used the updated model to project terrestrial biodiversity intactness from 2015 to 2050 as a function of land use and climate changes corresponding with the selected scenarios. We estimated a global area‐weighted mean MSA of 0.56 for 2015. Biodiversity intactness declined in all three scenarios, yet the decline was smaller in the sustainability scenario (−0.02) than the regional rivalry and fossil‐fuelled development scenarios (−0.06 and −0.05 respectively). We further found considerable variation in projected biodiversity change among different world regions, with large future losses particularly for sub‐Saharan Africa. In some scenario‐region combinations, we projected future biodiversity recovery due to reduced demands for agricultural land, yet this recovery was counteracted by increased impacts of other pressures (notably climate change and road disturbance). Effective measures to halt or reverse the decline of terrestrial biodiversity should not only reduce land demand (e.g. by increasing agricultural productivity and dietary changes) but also focus on reducing or mitigating the impacts of other pressures.
We project the changes in terrestrial biodiversity intactness from 2015 to 2050 corresponding with three of the shared socio‐economic pathways combined with different levels of climate change, using an updated version of the GLOBIO model. Biodiversity intactness declined in all three scenarios, with large losses particularly for sub‐Saharan Africa. Effective measures to halt or reverse the decline of terrestrial biodiversity should not only reduce land demand but also reduce or mitigate the impacts of other pressures.
The current debate on the sustainability of bio-based products questions the environmental benefits of replacing fossil- by bio-resources. Here, we analyze the environmental trade-offs of 98 emerging ...bio-based materials compared to their fossil counterparts, reported in 130 studies. Although greenhouse gas life cycle emissions for emerging bio-based products are on average 45% lower (-52 to -37%; 95% confidence interval), we found a large variation between individual bio-based products with none of them reaching net-zero emissions. Grouped in product categories, reductions in greenhouse gas emissions ranged from 19% (-52 to 35%) for bioadhesives to 73% (-84 to -54%) for biorefinery products. In terms of other environmental impacts, we found evidence for an increase in eutrophication (369%; 163 to 737%), indicating that environmental trade-offs should not be overlooked. Our findings imply that the environmental sustainability of bio-based products should be evaluated on an individual product basis and that more radical product developments are required to reach climate-neutral targets.
While linear infrastructures, such as roads and power lines, are vital to human development, they may also have negative impacts on wildlife populations up to several kilometres into the surrounding ...environment (infrastructure‐effect zones, IEZs). However, species‐specific IEZs are not available for the vast majority of species, hampering global assessments of infrastructure impacts on wildlife. Here, we synthesized 253 studies worldwide to quantify the magnitude and spatial extent of infrastructure impacts on the abundance of 792 vertebrate species. We also identified the extent to which species traits, infrastructure type and habitat modulate IEZs for vertebrate species. Our results reveal contrasting responses across taxa based on the local context and species traits. Carnivorous mammals were generally more abundant in the proximity of infrastructure. In turn, medium‐ to large‐sized non‐carnivorous mammals (>1 kg) were less abundant near infrastructure across habitats, while their smaller counterparts were more abundant close to infrastructure in open habitats. Bird abundance was reduced near infrastructure with larger IEZs for non‐carnivorous than for carnivorous species. Furthermore, birds experienced larger IEZs in closed (carnivores: ≈130 m, non‐carnivores: >1 km) compared to open habitats (carnivores: ≈70 m, non‐carnivores: ≈470 m). Reptiles were more abundant near infrastructure in closed habitats but not in open habitats where abundances were reduced within an IEZ of ≈90 m. Finally, IEZs were relatively small in amphibians (<30 m). These results indicate that infrastructure impact assessments should differentiate IEZs across species and local contexts in order to capture the variety of responses to infrastructure. Our trait‐based synthetic approach can be applied in large‐scale assessments of the impacts of current and future infrastructure developments across multiple species, including those for which infrastructure responses are not known from empirical data.
Linear infrastructures are vital to human development, but they may also have negative impacts on wildlife populations up to several kilometres into the surrounding environment (infrastructure‐effect zones, IEZs). Here, we synthesized 253 studies worldwide to quantify the magnitude and spatial extent of infrastructure impacts on the abundance of 792 vertebrate species. Impacts of infrastructure in mammals were mediated by body size and diet, and depended on the local context (closed vs. open habitat) in mammals, birds and reptiles, yielding IEZs that ranged between 30 and 600 m on average. These differing responses can confound the impact of infrastructure on vertebrate populations when assessments do not account for species traits.
Anthropogenic increases in nitrogen (N) concentrations in the environment are affecting plant diversity and ecosystems worldwide, but relatively little is known about N impacts on terrestrial ...invertebrate communities. Here, we performed an exploratory meta‐analysis of 4365 observations from 126 publications reporting on the richness (number of taxa) or abundance (number of individuals per taxon) of terrestrial arthropods or nematodes in relation to N addition. We found that the response of invertebrates to N enrichment is highly dependent on both species' traits and local climate. The abundance of arthropods with incomplete metamorphosis, including agricultural pest species, increased in response to N enrichment. In contrast, arthropods exhibiting complete or no metamorphosis, including pollinators and detritivores, showed a declining abundance trend with increasing N enrichment, particularly in warmer climates. These contrasting and context‐dependent responses may explain why we detected no overall response of arthropod richness. For nematodes, the abundance response to N enrichment was dependent on mean annual precipitation and varied between feeding guilds. We found a declining trend in abundance with N enrichment in dry areas and an increasing trend in wet areas, with slopes differing between feeding guilds. For example, at mean levels of precipitation, bacterivore abundance showed a positive trend in response to N addition while fungivore abundance declined. We further observed an overall decline in nematode richness with N addition. These N‐induced changes in invertebrate communities could have negative consequences for various ecosystem functions and services, including those contributing to human food production.
a
El aumento de las concentraciones de nitrógeno en el medio ambiente de forma antropogénica está afectando a la diversidad vegetal y a los ecosistemas de todo el mundo, pero aún se sabe relativamente poco sobre su impacto en comunidades de invertebrados terrestres. En este trabajo realizamos modelos meta‐analíticos para explorar el efecto del enriquecimiento de nitrógeno en comunidades de invertebrados terrestres a escala global. Para ello, utilizamos una base de datos proveniente de 4.365 observaciones pareadas correspondientes a 126 publicaciones que estudiaron el efecto del enriquecimiento de nitrógeno en la riqueza (número de taxones) y/o abundancia (número de individuos por taxón) de artrópodos y/o nematodos. Encontramos que la respuesta de los invertebrados al enriquecimiento de nitrógeno depende en gran medida tanto de los rasgos de las especies como del clima local. La abundancia de artrópodos con metamorfosis incompleta, incluyendo especies que pueden crear plagas agrícolas, aumentó en respuesta al enriquecimiento de nitrógeno. Por el contrario, los artrópodos con metamorfosis completa o nula, incluidos polinizadores y detritívoros, mostraron una tendencia negativa de su abundancia con respecto al aumento de nitrógeno, especialmente en climas más cálidos. Además, no detectamos una respuesta general de la riqueza de artrópodos posiblemente por la variabilidad en respuestas observadas, tanto negativas como positivas. En el caso de los nematodos, la respuesta de sus abundancias al enriquecimiento de nitrógeno fue dependiente de la precipitación media anual y de su grupo trófico. En general, observamos una respuesta negativa de la abundancia de nematodos al enriquecimiento de nitrógeno en zonas secas y una tendencia positiva en zonas más húmedas, pero además los diferentes grupos tróficos estudiados presentaron diferentes respuestas. Por ejemplo, la abundancia de bacterívoros mostró una tendencia positiva en respuesta al enriquecimiento de nitrógeno bajo niveles medios de precipitación, mientras que la abundancia de fungívoros disminuyó. Además, observamos un descenso general de la riqueza de nematodos con más enriquecimiento de nitrógeno. Estos cambios inducidos por el nitrógeno en las comunidades de invertebrados podrían tener consecuencias negativas para diversas funciones y servicios de los ecosistemas, incluyendo aquellos que contribuyen a la producción de alimentos.
Anthropogenic increases in nitrogen (N) concentrations might affect terrestrial invertebrates, but the effect is unclear. We performed an exploratory meta‐analysis of 126 publications reporting on the diversity (richness) or abundance of terrestrial arthropods or nematodes in relation to N addition. We found diverging abundance responses to N addition between different groups of arthropods, as well as a modulating effect of temperature. We further observed an overall decline in nematode richness with N addition, while their abundance responses were depending on precipitation and varied between feeding guilds. These N‐induced changes in invertebrate communities could have consequences for ecosystem functions and services.
External nutrient loading can cause large changes in freshwater ecosystems. Many local field and laboratory experiments have investigated ecological responses to nutrient addition. However, these ...findings are difficult to generalize, as the responses observed may depend on the local context and the resulting nutrient concentrations in the receiving water bodies. In this research, we combined and analysed data from 131 experimental studies containing 3054 treatment‐control abundance ratios to assess the responses of freshwater taxa along a gradient of elevated nutrient concentrations. We carried out a systematic literature search in order to identify studies that report the abundance of invertebrate, macrophyte, and fish taxa in relation to the addition of nitrogen, phosphorus, or both. Next, we established mixed‐effect meta‐regression models to relate the biotic responses to the concentration gradients of both nutrients. We quantified the responses based on various abundance‐based metrics. We found no responses to the mere addition of nutrients, apart from an overall increase of total invertebrate abundance. However, when we considered the gradients of N and P enrichment, we found responses to both nutrients for all abundance metrics. Abundance tended to increase at low levels of N enrichment, yet decreased at the high end of the concentration gradient (1–10 mg/L, depending on the P concentration). Responses to increasing P concentrations were mostly positive. For fish, we found too few data to perform a meaningful analysis. The results of our research highlight the need to consider the level of nutrient enrichment rather than the mere addition of nutrients in order to better understand broad‐scale responses of freshwater biota to eutrophication, as a key step to identify effective conservation strategies for freshwater ecosystems.
In this study, we synthesized data from 131 experimental studies to explore how freshwater invertebrate and macrophyte abundance responds to a gradient of nitrogen and/or phosphorus enrichment. For N, we observed abundance mostly increased for low concentrations, with decreases at higher concentrations (1–10 mg/L), whereas for P, abundance mostly showed positive linear response relationships. Our findings highlight the need of studying eutrophication impacts along a gradient of nutrient concentrations, considering the combined effects of N and P.
Aim
The stress‐gradient hypothesis (SGH) postulates that species interactions shift from negative to positive with increasing abiotic stress. Interactions between species are increasingly being ...recognized as important drivers of species distributions, but it is still unclear whether stress‐induced changes in interactions affect continental‐to‐global scale species distributions. Here, we tested whether associations of vascular plant species in dry grasslands in Europe follow the SGH along a climatic water deficit (CWD) gradient across the continent.
Location
Dry grasslands in Europe.
Time period
Present.
Major taxa studied
Vascular plants.
Methods
We built a context‐dependent joint species distribution model (JSDM) to estimate the residual associations (i.e., associations that are not explained by the abiotic environment) of 161 plant species as a function of the CWD based on community data from 8,660 vegetation plots. We evaluated changes in residual associations between species for pairs and on the community level, and we compared responses for groups of species with different drought tolerances.
Results
We found contrasting shifts in associations for drought‐sensitive and drought‐tolerant species. For drought‐sensitive species, 21% of the pairwise associations became more positive with increasing CWD, whereas 17% became more negative. In contrast, only 17% of the pairwise associations involving drought‐tolerant species became more positive, whereas 27% became more negative in areas with a high CWD. Additionally, the incidence of positive associations increased with drought for drought‐sensitive species and decreased for drought‐tolerant species.
Main conclusions
We found that associations of drought‐sensitive plant species became more positive with drought, in line with the SGH. In contrast, associations of drought‐tolerant species became more negative. Additionally, changes in associations of single species pairs were highly variable. Our results indicate that stress‐modulated species associations might influence the distribution of species over large geographical extents, thus leading to unexpected responses under climate change through shifts in species associations.
Abstract
Land use is a major cause of biodiversity decline worldwide. Agricultural and forestry diversification measures, such as the inclusion of natural elements or diversified crop types, may ...reduce impacts on biodiversity. However, the extent to which such measures may compensate for the negative impacts of land use remains unknown. To fill that gap, we synthesised data from 99 studies that recorded mammal populations or assemblages in natural reference sites and in cropland and forest plantations, with or without diversification measures. We quantified the responses to diversification measures based on individual species abundance, species richness and assemblage intactness as quantified by the mean species abundance indicator. In cropland with natural elements, mammal species abundance and richness were, on average, similar to natural conditions, while in cropland without natural elements they were reduced by 28% and 34%, respectively. We found that mammal species richness was comparable between diversified forest plantations and natural reference sites, and 32% lower in plantations without natural elements. In both cropland and plantations, assemblage intactness was reduced compared with natural reference conditions, but the reduction was smaller if diversification measures were in place. In addition, we found that responses to land use were modified by species traits and environmental context. While habitat specialist populations were reduced in cropland without diversification and in forest plantations, habitat generalists benefited. Furthermore, assemblages were impacted more by land use in tropical regions and landscapes containing a larger share of (semi)natural habitat compared with temperate regions and more converted landscapes. Given that mammal assemblage intactness is reduced also when diversification measures are in place, special attention should be directed to species that suffer from land use impacts. That said, our results suggest potential for reconciling land use and mammal conservation, provided that the diversification measures do not compromise yield.
•We calculated the life cycle carbon efficiency of a Direct Air Capture (DAC) system.•The main GHG emissions of the system are from fossil energy requirements.•DAC, using hydroxide solutions, can ...help mitigate climate change.
Direct Air Capture (DAC) of carbon dioxide (CO2) from ambient air has the potential to combat climate change. DAC systems capture CO2 using a sorbent material and compress it for storage. In this study, we calculated the life cycle carbon efficiency (Ec) of a DAC system which equals the net amount of carbon stored per amount of carbon captured from capture to geological storage. We included greenhouse gas (GHG) emissions during construction of the necessary facilities as well as GHG emissions from energy, water and chemicals needed during operations. The system we analysed includes a hydroxide solution as sorbent material and utilizes the pelletized variant of the Kraft process to regenerate the sorbent and separate the CO2. To our knowledge, the potential climate benefit over the full life cycle of this DAC system has not been fully investigated up to now. Using the baseline scenario, we obtained a positive Ec of 62%. For the optimistic and pessimistic scenarios, we found a Ec of 93% and 10%, respectively. We conclude that this type of DAC system may be a feasible option to help keep limit global temperature increases to well below 2 °C.
To prioritize conservation efforts, it is important to know which plant species are most vulnerable to extinction. Intrinsic extinction vulnerabilities depend on demographic parameters, but for many ...species these demographic parameters are lacking. Body size has been successfully used as proxy of such parameters to estimate extinction vulnerability of birds and mammals. For plants, not all necessary demographic parameters have been related to size yet.
Here, we derived allometric relationships with maximum plant height for the intrinsic population growth rate and the carrying capacity. Furthermore, for the first time, we derived a relationship between the variance in population growth rate due to environmental stochasticity and plant height. These relationships were used to relate extinction vulnerability to maximum plant height.
Extinction vulnerability was found to be most sensitive to fluctuations in the population growth rate due to environmental stochasticity. Large plant species were less susceptible to environmental stochasticity, resulting in a lower vulnerability to extinction than small plant species. This negative relationship between plant size and extinction vulnerabilities is in contrast to previous results for mammals and birds.
These results increase our theoretical understanding of the relationship between plant functional traits and extinction vulnerabilities and may aid in assessments of data deficient species. The uncertainty in the allometric relationships is, however, too large to quantify true extinction vulnerabilities. Further investigation in the relationship between demographic parameters and plant traits other than height is needed to further enhance our understanding of plant species extinction vulnerabilities.
•We derived relationships between demographic rates and maximum plant height.•Large vascular plants are less susceptible to environmental stochasticity.•Plant growth form does not explain intrinsic population growth rates.•Plant height has a weak negative relationship with extinction vulnerability.
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