Joint species distribution modelling with the r-package Hmsc

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.Peer reviewe

Joint species distribution modelling with the r-package Hmsc

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.Peer reviewe

Projecting terrestrial biodiversity intactness with GLOBIO 4

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.Peer reviewe

Conditional love? Co-occurrence patterns of drought-sensitive species in European grasslands are consistent with the stress-gradient hypothesis

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 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 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 associationsPeer reviewe

Projecting terrestrial biodiversity intactness with GLOBIO 4

.-- Schipper, Aafke M. et al.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 pressuresPeer reviewe

The potential of emerging bio-based products to reduce environmental impacts

Abstract 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

Projecting terrestrial biodiversity intactness with GLOBIO 4

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