A flexible consistent framework for modelling multiple interacting environmental responses to management in space and time.

Management of resources is often a large-scale task addressed using many small-scale interventions. The range of scales at which organisms respond to those interventions, along with the many outcomes which management aims to achieve can make determining the success of management complex. Environmental flow is an example of management where there is a recognized need for managers to demonstrate the impact of their actions by integrating different types of environmental responses. Here, we aim to support decision making in environmental management via the development of a new modelling framework (eFlowEval). It has the capacity to capture best-available knowledge, to scale it in space and time, explore interactions among species, compare scenarios, and account for uncertainty. Thus, it provides a basis for including multiple target groups in a common system. The framework is readily updatable as new information becomes available and can identify where data are insufficient to be scientifically robust. We demonstrate the eFlowEval framework using three very different environmental responses: 1) metabolism, which is a measure of the energy produced and then used in an ecosystem, 2) favorability for a bird species of interest (royal spoonbill Platalea regia), and 3) competing wetland plants (Centipeda cunninghamii and lippia Phyla canescens). These demonstrations illustrate the capability of the eFlowEval framework but the specific outputs shown here should not be used to assess environmental responses to management. Using these demonstrations, we illustrate the capacity of the eFlowEval framework to provide assessments across a range of scales (local to landscape) and from short time frames (weeks to months) to multi-year assessments. Further, we illustrate the ability to: i) scale responses from local to basin scales, ii) vary driver-response model types, iii) represent uncertainty, iv) compare scenarios, v) accommodate variable parameter values at different locations, and vi) incorporate spatial and temporal dependencies and dependencies among species. We also illustrate the framework's ability to capture inter- and intraspecific interactions and their impact in space and time. The eFlowEval framework extends the capacity of the component response models to provide novel modeling capabilities for management at scale. It allows for interactions among species or processes to be incorporated, as well as in space and time. A large degree of flexibility is offered by the framework, in terms of driver-response model types, input data, and aggregation methods. Thus, the eFlowEval framework provides a mechanism to enhance the transparency of environmental watering decision making, capture institutional knowledge, enhance adaptive management and undertake evaluation of the impact of environmental watering at a range of spatial and temporal scales.

Treating gaps and biases in biodiversity data as a missing data problem.

Big biodiversity data sets have great potential for monitoring and research because of their large taxonomic, geographic and temporal scope. Such data sets have become especially important for assessing temporal changes in species' populations and distributions. Gaps in the available data, especially spatial and temporal gaps, often mean that the data are not representative of the target population. This hinders drawing large-scale inferences, such as about species' trends, and may lead to misplaced conservation action. Here, we conceptualise gaps in biodiversity monitoring data as a missing data problem, which provides a unifying framework for the challenges and potential solutions across different types of biodiversity data sets. We characterise the typical types of data gaps as different classes of missing data and then use missing data theory to explore the implications for questions about species' trends and factors affecting occurrences/abundances. By using this framework, we show that bias due to data gaps can arise when the factors affecting sampling and/or data availability overlap with those affecting species. But a data set per se is not biased. The outcome depends on the ecological question and statistical approach, which determine choices around which sources of variation are taken into account. We argue that typical approaches to long-term species trend modelling using monitoring data are especially susceptible to data gaps since such models do not tend to account for the factors driving missingness. To identify general solutions to this problem, we review empirical studies and use simulation studies to compare some of the most frequently employed approaches to deal with data gaps, including subsampling, weighting and imputation. All these methods have the potential to reduce bias but may come at the cost of increased uncertainty of parameter estimates. Weighting techniques are arguably the least used so far in ecology and have the potential to reduce both the bias and variance of parameter estimates. Regardless of the method, the ability to reduce bias critically depends on knowledge of, and the availability of data on, the factors creating data gaps. We use this review to outline the necessary considerations when dealing with data gaps at different stages of the data collection and analysis workflow.

Predicting emergent animal biodiversity patterns across multiple scales.

Restoring biodiversity-based resilience and ecosystem multi-functionality needs to be informed by more accurate predictions of animal biodiversity responses to environmental change. Ecological models make a substantial contribution to this understanding, especially when they encode the biological mechanisms and processes that give rise to emergent patterns (population, community, ecosystem properties and dynamics). Here, a distinction between 'mechanistic' and 'process-based' ecological models is established to review existing approaches. Mechanistic and process-based ecological models have made key advances to understanding the structure, function and dynamics of animal biodiversity, but are typically designed to account for specific levels of biological organisation and spatiotemporal scales. Cross-scale ecological models, which predict emergent co-occurring biodiversity patterns at interacting scales of space, time and biological organisation, is a critical next step in predictive ecology. A way forward is to first capitalise on existing models to systematically evaluate the ability of scale-explicit mechanisms and processes to predict emergent patterns at alternative scales. Such model intercomparisons will reveal mechanism to process transitions across fine to broad scales, overcome approach-specific barriers to model realism or tractability and identify gaps which necessitate the development of new fundamental principles. Key challenges surrounding model complexity and uncertainty would need to be addressed, and while opportunities from big data can streamline the integration of multiple scale-explicit biodiversity patterns, ambitious cross-scale field studies are also needed. Crucially, overcoming cross-scale ecological modelling challenges would unite disparate fields of ecology with the common goal of improving the evidence-base to safeguard biodiversity and ecosystems under novel environmental change.

The cumulative niche approach: A framework to assess the performance of ecological niche model projections.

Ecological Niche Models (ENMs) are often used to project species distributions within alien ranges and in future climatic scenarios. However, ENMs depend on species-environment equilibrium, which may be absent for actively expanding species. We present a novel framework to estimate whether species have reached environmental equilibrium in their native and alien ranges. The method is based on the estimation of niche breadth with the accumulation of species occurrences. An asymptote will indicate exhaustive knowledge of the realised niches. We demonstrate the CNA framework for 26 species of mammals, amphibians, and birds. Possible outcomes of the framework include: (1) There is enough data to quantify the native and alien realised niches, allowing us to calculate niche expansion between the native and alien ranges, also indicating that ENMs can be reliably projected to new environmental conditions. (2) The data in the native range is not adequate but an asymptote is reached in the alien realised niche, indicating low confidence in our ability to evaluate niche expansion in the alien range but high confidence in model projections to new environmental conditions within the alien range. (3) There is enough data to quantify the native realised niche, but not enough knowledge about the alien realised niche, hindering the reliability of projections beyond sampled conditions. (4) Both the native and alien ranges do not reach an asymptote, and thus few robust conclusions about the species' niche or future projections can be made. Our framework can be used to detect species' environmental equilibrium in both the native and alien ranges, to quantify changes in the realised niche during the invasion processes, and to estimate the likely accuracy of model projections to new environmental conditions.

Erratum: Publisher Correction: wMel replacement of dengue-competent mosquitoes is robust to near-term climate change.

[This corrects the article DOI: 10.1038/s41558-023-01746-w.].

Ecology needs to overcome siloed modelling.

Bahlburg et al. re-implemented eight growth models of Antarctic krill and showed that their predictions are all over the place. The authors discuss the reasons for this and how more coherence in modelling could be achieved through systematic model comparison and integration. For this, we need a common language.

Robust steady states in ecosystems with symmetries.

Steady states of dynamical systems, whether stable or unstable, are critical for understanding future evolution. Robust steady states, ones that persist under small changes in the model parameters, are desired when modelling ecological systems, where it is common for accurate and detailed information on functional form and parameters to be unavailable. Previous work by Jahedi et al. [Robustness of solutions of almost every system of equations, SIAM J. Appl. Math. 82(5) (2022), pp. 1791-1807; Structured systems of nonlinear equations, SIAM J. Appl. Math. 83(4) (2023), pp. 1696-1716.] has established criteria to imply the prevalence of robust steady states for systems with minimal predetermined structure, including conventional structured systems. We review that work and extend it by allowing symmetries in the system structure, which present added obstructions to robustness.

wMel replacement of dengue-competent mosquitoes is robust to near-term change.

Rising temperatures are impacting the range and prevalence of mosquito-borne diseases. A promising biocontrol technology replaces wild mosquitoes with those carrying the virus-blocking Wolbachia bacterium. Because the most widely used strain, wMel, is adversely affected by heat stress, we examined how global warming may influence wMel-based replacement. We simulated interventions in two locations with successful field trials using Coupled Model Intercomparison Project Phase 5 climate projections and historical temperature records, integrating empirical data on wMel's thermal sensitivity into a model of Aedes aegypti population dynamics to evaluate introgression and persistence over one year. We show that in Cairns, Australia, climatic futures necessitate operational adaptations for heatwaves exceeding two weeks. In Nha Trang, Vietnam, projected heatwaves of three weeks and longer eliminate wMel under the most stringent assumptions of that symbiont's thermal limits. We conclude that this technology is generally robust to near-term (2030s) climate change. Accelerated warming may challenge this in the 2050s and beyond.

A gradual migratory divide determines not only the direction of migration but also migration strategy of a social migrant bird.

Migratory divides separate populations of migratory animals, facilitating the evolution of intraspecific differences in migration strategies. Migration strategies are expected to be different for birds using different flyways and environments, but the knowledge regarding the impact of the flyway on individual migration strategies is scarce. By using satellite tracking and neckband resightings, we reveal the existence and structure of a gradual migratory divide between two European flyway populations of greylag geese Anser anser. Birds breeding at the far end of the Gulf of Bothnia in the Baltic Sea coast use the Western Flyway, those breeding in the Gulf of Finland the Central Flyway and those breeding between these extremes scatter to the two flyways. By using Gaussian process modelling, we show that migration strategies differed between the flyways. The birds using the Western Flyway migrated earlier in autumn, performed longer annual migration and made a clear stopover during migration, whereas the birds using the Central Flyway flew directly to their wintering sites. The gradual migratory divide that also divides migration strategies provides insights into migratory divides on birds with learned migration. Distinct migration strategies in different flyways provide exciting possibilities to further study the factors driving migration strategies.

Taxonomy and distribution of Taraxacum sect. Erythrosperma (Asteraceae) in Poland.

The dandelions from Taraxacumsect.Erythrosperma are taxonomically well distinguished and ecologically restricted to warm and sunlit habitats of steppes, dry and sandy grasslands, and distributed in temperate regions of Europe and Central Asia, with some being introduced to North America. Despite the long tradition of botanical research, the taxonomy and distribution of dandelions of T.sect.Erythrosperma is still underexplored in central Europe. In this paper, by combining traditional taxonomic studies supported by micromorphological, molecular and flow cytometry analyses as well as potential distribution modelling we shed light on taxonomical and phylogenetical relationships between members of T.sect.Erythrosperma in Poland. We also provide an identification key, species-checklist, detailed descriptions of morphology and occupated habitats as well as distribution maps for 14 Polish erythrosperms (T.bellicum, T.brachyglossum, T.cristatum, T.danubium, T.disseminatum, T.dissimile, T.lacistophyllum, T.parnassicum, T.plumbeum, T.proximum, T.sandomiriense, T.scanicum, T.tenuilobum, T.tortilobum). Finally, conservation assessments performed using the IUCN method and threat categories for all the examined species are proposed.

Modifying and parameterizing the individual-based model inSTREAM for Atlantic salmon and brown trout in the regulated Gullspång River, Sweden.

We modified, parameterized, and applied the individual-based model inSTREAM version 6.1 for lake-migrating populations of landlocked Atlantic salmon (Salmo salar) and brown trout (S. trutta) in a residual flow stretch of the hydropower-regulated Gullspång River, Sweden. This model description is structured according to the TRACE model description framework. Our aim was to model responses in salmonid recruitment to alternative scenarios of flow release and other environmental alterations. The main response variable was the number of large out-migrating juvenile fish per year, with the assumption that individuals are more inclined to out-migrate the larger they get, and that migration is an obligatory strategy. Population and species-specific parameters were set based on local electrofishing surveys, redd surveys, physical habitat surveys, broodstock data as well as scientific literature.•Simulations were set to run over 10 years, with sub-daily time steps, in this spatially and temporally explicit model.•Model calibration and validation of fish growth was done using data on juvenile fish from electrofishing.•The results were found to be sensitive to parameter values for aggregated fish, i.e., "superindividuals" and for the high temperature limit to spawning.

Ecological indicators reveal historical regime shifts in the Black Sea ecosystem.

Background: The Black Sea is one of the most anthropogenically disturbed marine ecosystems in the world because of introduced species, fisheries overexploitation, nutrient enrichment via pollution through river discharge, and the impacts of climate change. It has undergone significant ecosystem transformations since the 1960s. The infamous anchovy and alien warty comb jelly Mnemiopsis leidyi shift that occurred in 1989 is the most well-known example of the drastic extent of anthropogenic disturbance in the Black Sea. Although a vast body of literature exists on the Black Sea ecosystem, a holistic look at the multidecadal changes in the Black Sea ecosystem using an ecosystem- and ecology-based approach is still lacking. Hence, this work is dedicated to filling this gap. Methods: First, a dynamic food web model of the Black Sea extending from 1960 to 1999 was established and validated against time-series data. Next, an ecological network analysis was performed to calculate the time series of synthetic ecological indicators, and a regime shift analysis was performed on the time series of indicators. Results: The model successfully replicated the regime shifts observed in the Black Sea. The results showed that the Black Sea ecosystem experienced four regime shifts and was reorganized due to effects instigated by overfishing in the 1960s, eutrophication and establishment of trophic dead-end organisms in the 1970s, and overfishing and intensifying interspecies trophic competition by the overpopulation of some r-selected organisms (i.e., jellyfish species) in the 1980s. Overall, these changes acted concomitantly to erode the structure and function of the ecosystem by manipulating the food web to reorganize itself through the introduction and selective removal of organisms and eutrophication. Basin-wide, cross-national management efforts, especially with regard to pollution and fisheries, could have prevented the undesirable changes observed in the Black Sea ecosystem and should be immediately employed for management practices in the basin to prevent such drastic ecosystem fluctuations in the future.

Using a dynamic energy budget model to investigate the physiological mode of action of lead (Pb) to Lymnaea stagnalis.

Lymnaea stagnalis is a notably sensitive species for a variety of metals, including lead (Pb). However, the mechanism(s) of lead toxicity to L. stagnalis currently remain incompletely understood. Under dynamic energy budget (DEB) theory, different physiological modes of action (PMoAs) result in the emergence of distinct changes to the life histories of exposed organisms. This work aims to better understand the PMoA of lead toxicity to L. stagnalis by applying DEB modeling to previously published datasets. After calibration, the model was utilized to evaluate the relative likelihood of several PMoAs. Assuming decreased assimilation, the L. stagnalis DEB model was able to capture most, but not all, trends in experimentally observed endpoints, including growth, reproduction, and food ingestion. The weight-of-evidence suggests that decreased assimilation via a decrease in food ingestion is the most plausible PMoA for chronic lead toxicity in L. stagnalis. Collectively, our results illustrate how mechanistic modeling can create added value for conventional individual-level toxicity test data by enabling inferences about potential physiological mechanisms of toxicity.

Climate-ecosystem modelling made easy: The Land Sites Platform.

Dynamic Global Vegetation Models (DGVMs) provide a state-of-the-art process-based approach to study the complex interplay between vegetation and its physical environment. For example, they help to predict how terrestrial plants interact with climate, soils, disturbance and competition for resources. We argue that there is untapped potential for the use of DGVMs in ecological and ecophysiological research. One fundamental barrier to realize this potential is that many researchers with relevant expertize (ecology, plant physiology, soil science, etc.) lack access to the technical resources or awareness of the research potential of DGVMs. Here we present the Land Sites Platform (LSP): new software that facilitates single-site simulations with the Functionally Assembled Terrestrial Ecosystem Simulator, an advanced DGVM coupled with the Community Land Model. The LSP includes a Graphical User Interface and an Application Programming Interface, which improve the user experience and lower the technical thresholds for installing these model architectures and setting up model experiments. The software is distributed via version-controlled containers; researchers and students can run simulations directly on their personal computers or servers, with relatively low hardware requirements, and on different operating systems. Version 1.0 of the LSP supports site-level simulations. We provide input data for 20 established geo-ecological observation sites in Norway and workflows to add generic sites from public global datasets. The LSP makes standard model experiments with default data easily achievable (e.g., for educational or introductory purposes) while retaining flexibility for more advanced scientific uses. We further provide tools to visualize the model input and output, including simple examples to relate predictions to local observations. The LSP improves access to land surface and DGVM modelling as a building block of community cyberinfrastructure that may inspire new avenues for mechanistic ecosystem research across disciplines.

Unlocking environmental contamination of animal tuberculosis hotspots with viable mycobacteria at the intersection of flow cytometry, PCR, and ecological modelling.

Mycobacterium bovis, a member of the Mycobacterium tuberculosis complex (MTBC), circulates in multi-host mammal communities. While interactions between different host species are mainly indirect, current knowledge postulates interspecific transmission is favored by animal contact with natural substrates contaminated with droplets and fluids from infected animals. However, methodological constraints have severely hampered monitoring of MTBC outside its hosts and the subsequent validation of this hypothesis. In this work, we aimed to evaluate the extent to which environmental contamination with M. bovis occurs in an endemic animal TB setting, taking advantage of a new real-time monitoring tool we recently developed to quantify the proportion of viable and dormant MTBC cell fractions in environmental matrices. Sixty-five natural substrates were collected nearby the International Tagus Natural Park region, in the epidemiological TB risk area in Portugal. These included sediments, sludge, water, and food deployed at unfenced feeding stations. The tripartite workflow included detection, quantification, and sorting of different M. bovis cell populations: total, viable, and dormant. Real-time PCR targeting IS6110 to detect MTBC DNA was performed in parallel. The majority of samples (54 %) contained metabolically active or dormant MTBC cells. Sludge samples had a higher burden of total MTBC cells and a high concentration of viable cells (2.3 × 104 cells/g). Ecological modelling informed by climate, land use, livestock and human disturbance data suggested eucalyptus forest and pasture cover as potential major factors affecting the occurrence of viable MTBC cells in natural matrices. Our study demonstrates, for the first time, the widespread environmental contamination of animal TB hotspots with viable MTBC bacteria and with dormant MTBC cells that are able to recover metabolic activity. Further, we show that viable MTBC cell load in natural substrates is superior to the estimated minimum infective dose, providing real-time insights into the potential magnitude of environmental contamination for indirect TB transmission.

Setting sustainable limits on anchoring to improve the resilience of coral reefs.

Boat anchoring is common at coral reefs that have high economic or social value, but anchoring has received relatively little attention in reef resilience studies. We developed an individual-based model of coral populations and simulated the effects of anchor damage over time. The model allowed us to estimate the carrying capacity of anchoring for four different coral assemblages and different starting levels of coral cover. The carrying capacity of small to medium-sized recreational vessels across these four assemblages was between 0 and 3.1 anchor strikes ha-1 day-1. In a case study of two Great Barrier Reef archipelagos, we modelled the benefits of anchoring mitigation under bleaching regimes expected for four climate scenarios. The partial mitigation of even a very mild anchoring incidence (1.17 strikes ha-1 day-1) resulted in median coral gains of 2.6-7.7 % absolute cover under RCP2.6, though benefits varied temporally and depended on the Atmosphere-Ocean General Circulation Model used.

Japanese Encephalitis Enzootic and Epidemic Risks across Australia.

Japanese encephalitis virus (JEV) is an arboviral, encephalitogenic, zoonotic flavivirus characterized by its complex epidemiology whose transmission cycle involves reservoir and amplifying hosts, competent vector species and optimal environmental conditions. Although typically endemic in Asia and parts of the Pacific Islands, unprecedented outbreaks in both humans and domestic pigs in southeastern Australia emphasize the virus' expanding geographical range. To estimate areas at highest risk of JEV transmission in Australia, ecological niche models of vectors and waterbirds, a sample of piggery coordinates and feral pig population density models were combined using mathematical and geospatial mapping techniques. These results highlight that both coastal and inland regions across the continent are estimated to have varying risks of enzootic and/or epidemic JEV transmission. We recommend increased surveillance of waterbirds, feral pigs and mosquito populations in areas where domestic pigs and human populations are present.

Prediction of the Potential Distributions of Prunus salicina Lindl., Monilinia fructicola, and Their Overlap in China Using MaxEnt.

Prunus salicina Lindl. (P. salicina) is an essential cash crop in China, and brown rot (BR) is one of its most important diseases. In this study, we collected geographic location information on P. salicina and Monilinia fructicola (G. Winter) Honey (M. fructicola), one of the BR pathogenic species, and applied the MaxEnt model to simulate its potential suitable distribution in China. There have been discussions about the dominant environmental variables restricting its geographical distribution and their overlap. The results showed that the mean temperature of the coldest quarter, precipitation of the warmest quarter, precipitation in July, and minimum temperatures in January and November were the main climatic variables affecting the potential distribution of P. salicina, while the coldest quarter, precipitation of the driest month, precipitation of March, precipitation of October, maximum temperatures of February, October, and November, and minimum temperature of January were related to the location of M. fructicola. Southern China had suitable conditions for both P. salicina and M. fructicola. Notably, the overlap area of P. salicina and M. fructicola was primarily located southeast of 91°48' E 27°38' N to 126°47' E 41°45' N. The potential overlap area predicted by our research provided theoretical evidence for the prevention of BR during plum planting.

Future supply of boreal forest ecosystem services is driven by management rather than by climate change.

Forests provide a wide variety of ecosystem services (ES) to society. The boreal biome is experiencing the highest rates of warming on the planet and increasing demand for forest products. To foresee how to maximize the adaptation of boreal forests to future warmer conditions and growing demands of forest products, we need a better understanding of the relative importance of forest management and climate change on the supply of ecosystem services. Here, using Finland as a boreal forest case study, we assessed the potential supply of a wide range of ES (timber, bilberry, cowberry, mushrooms, carbon storage, scenic beauty, species habitat availability and deadwood) given seven management regimes and four climate change scenarios. We used the forest simulator SIMO to project forest dynamics for 100 years into the future (2016-2116) and estimate the potential supply of each service using published models. Then, we tested the relative importance of management and climate change as drivers of the future supply of these services using generalized linear mixed models. Our results show that the effects of management on the future supply of these ES were, on average, 11 times higher than the effects of climate change across all services, but greatly differed among them (from 0.53 to 24 times higher for timber and cowberry, respectively). Notably, the importance of these drivers substantially differed among biogeographical zones within the boreal biome. The effects of climate change were 1.6 times higher in northern Finland than in southern Finland, whereas the effects of management were the opposite-they were three times higher in the south compared to the north. We conclude that new guidelines for adapting forests to global change should account for regional differences and the variation in the effects of climate change and management on different forest ES.

The effects of intraspecific variation on forecasts of species range shifts under climate change.

As global climate change is altering the distribution range of macroalgae across the globe, it is critical to assess its impact on species range shifts to inform the biodiversity conservation of macroalgae. Latitude/environmental gradients could cause intraspecific variability, which may result in distinct responses to climate change. It remains unclear whether geographical variation occurs in the response of species' populations to climate change. We tested this assumption using the brown alga Sargassum thunbergii, a habitat-forming macroalgae encompassing multiple divergent lineages along the Northwest Pacific. Previous studies revealed a distinct lineage of S. thunbergii in rear-edge populations. Given the phylogeographic structure and temperature gradients, we divided these populations into the southern and northern groups. We assessed the physiological responses of the two groups to temperature changes and estimated their niche differences using n-dimensional hypervolumes. A higher photosynthetic rate and antioxidative abilities were detected in the southern group of S. thunbergii than in the northern group. In addition, significant niche differentiation was detected between the two groups, suggesting the possibility for local adaptation. Given these results, we inferred that the southern group (rear-edge populations) may be more resilient to climate change. To examine climate-driven range shifts of S. thunbergii, we constructed species- and lineage-level species distribution models (SDMs). Predictions of both levels showed considerable distribution contracts along the Chinese coasts in the future. For the southern group, the lineage-level model predicted less habitat loss than the species-level model. Our results highlight the importance of considering intraspecific variation in climate change vulnerability assessments for coastal species.