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281 results for “community model”
The Community Coevolution Model with application to the study of evolutionary relationships between genes based on phylogenetic profiles
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A unified model explaining the unimodal relationship between productivity and species richness in fish communities
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Community Earth System Model (CESM) simulations disentangling CO2 effects - PHYS (2 of 4)
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Data from: Impacts of rainfall extremes predicted by climate-change models on major trophic groups in the leaf-litter arthropod community
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Community Earth System Model (CESM) simulations disentangling CO2 effects - PI (4 of 4)
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Data from: Disentangling elevational richness: a multi-scale hierarchical Bayesian occupancy model of Colorado ant communities
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Input data and model implementation from: How do terrestrial wildlife communities respond to small-scale Acacia plantations embedded in harvested tropical forest?
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Revealing the drivers of parasite community assembly: using avian haemosporidians to model global dynamics of parasite species turnover
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Data to replicate: Forecasting community reassembly using climate-linked spatio-temporal ecosystem models
Ecosystems are increasingly impacted by human activities, altering linkages among physical and biological components. Spatial community reassembly occurs when these human impacts modify the spatial overlap between system components, and there is need for practical tools to forecast spatial community reassembly at landscape scales using monitoring data. To illustrate a new approach, we extend a generalization of empirical orthogonal function (EOF) analysis, which involves a spatio-temporal ecosystem model that approximates coupled physical, biological, and human dynamics. We then demonstrate its application to five trophic levels for the eastern Bering Sea by fitting to multiple, spatially unbalanced datasets measuring physical characteristics (temperature measurements and climate-linked forecasts), primary producers (spring and fall size-fractionated chlorophyll-a), secondary producers (copepods), juveniles (age-0 walleye pollock), adult consumers (five commercially important fishes), human activities (seasonal fishing effort), and mobile predators (seabirds). We identify the spatial niche for each ecosystem component, as well as dominant modes of variability that are highly correlated with a known bottom-up driver of dynamics. We then measure spatial overlap between interacting variables (using Schoener's-D) and identify that age-0 pollock have decreased spatial overlap with copepods and increased overlap with adult pollock during warm years, and also that adult pollock have increased overlap with arrowtooth flounder and decreased overlap with catcher-processor fishing effort during these warm years. Given the warming conditions that are projected for the coming decade, the model forecasts increased prey and competitor overlap involving adult pollock (between age-0 pollock, adult pollock and arrowtooth flounder) and decreased overlap with the copepod forage base and with the catcher-processor fishery during future warming. We recommend that joint species distribution models be extended to incorporate "ecological teleconnections" (correlations between distant locations arising from known mechanisms) arising from behavioral adaptation by mobile animals as well as passive advection of nutrients and planktonic juvenile stages.
Data from: Abundance data applied to a novel model invertebrate host sheds new light on parasite community assembly in nature
<ol> <li>Understanding how environmental drivers influence the assembly of parasite communities, in addition to how parasites may interact at an infracommunity level, are fundamental requirements for the study of parasite ecology. Knowledge of how parasite communities are assembled will help to predict the risk of parasitism for hosts, and model how parasite communities may change under variable conditions. However, studies frequently rely on presence-absence data and examine multiple host species or sites, metrics which may be too coarse to characterise nuanced within-host patterns.</li> <li>We utilised a novel host system, the freshwater mussel <i>Anodonta anatina</i>, to investigate the drivers of community structure and explore parasite interactions. In addition, we aimed to highlight consistencies and inconsistencies between presence-absence and abundance data.</li> <li>Our analysis incorporated 14 parasite taxa and 720 replicate infracommunities. Using redundancy analysis, a joint species distribution model and a Markov random fields approach, we modelled the impact of both host-level and environment-level characteristics on parasite structure, as well as parasite-parasite correlations after accounting for all other factors. This approach was repeated for both the presence and abundance of all parasites.</li> <li>We demonstrated that the regional species pool, individual host characteristics (mussel length and gravidity) and predicted parasite-parasite interactions are all important but to varying degrees across parasite species, suggesting that applying generalities to parasite community construction is too simplistic. Further, we showed that presence-absence data fails to capture important density-dependent effects of parasite load for parasites with high abundance, and in general performs poorly for high-intensity parasites.</li> <li>Host and parasite traits, as well as broader environmental factors, all contribute to parasite community structure, emphasising that an integrated approach is required to study community assembly. However, care must be taken with the data used to infer patterns, as presence-absence data may lead to incorrect ecological inference.</li> </ol>
Community science validates climate suitability projections from ecological niche modeling
<p><span>Climate change poses an intensifying threat to many bird species, and projections of future climate suitability provide insight into how species may shift their distributions in response. Climate suitability is characterized using ecological niche models (ENMs), which correlate species occurrence data with current environmental covariates and project future distributions using the modeled relationships together with climate predictions. Despite their widespread adoption, ENMs rely on several assumptions that are rarely validated <i>in situ </i>and can be highly sensitive to modeling decisions, precluding their reliability in conservation decision-making. Using data from a novel, large-scale community science program, we developed dynamic occupancy models to validate near-term climate suitability projections for bluebirds and nuthatches in summer and winter. We estimated occupancy, colonization, and extinction dynamics across species' ranges in the United States in relation to projected climate suitability in the 2020s, and used a Gibbs variable selection approach to quantify evidence of species-climate relationships. We also included a Bird Conservation Region strata-level random effect to examine among-strata variation in occupancy that may be attributable to land-use and ecoregional differences. Across species and seasons, we found strong evidence that initial occupancy and colonization were positively related to 2020 climate suitability, illustrating an independent validation of projections from ENMs across a large geographic area. </span><span>Random strata effects revealed that occupancy probabilities were generally higher than average in core areas and lower than average in peripheral areas of species' ranges, and served as a first step in identifying spatial patterns of occupancy from these community science data. </span><span>Our findings lend much-needed support to the use of ENM projections for addressing questions about potential climate-induced changes in species' occupancy dynamics. More broadly, </span>our work highlights the value of community scientist observations for ground-truthing projections from statistical models and for refining our understanding of the processes shaping species' distributions under a changing climate.</p>
Data from: Spatial heterogeneity in soil nutrient supply modulates nutrient and biomass responses to multiple global change drivers in model grassland communities
Changes in the atmospheric concentration of carbon dioxide ([CO2]), nutrient availability and biotic diversity are three major drivers of the ongoing global change impacting terrestrial ecosystems worldwide. While it is well established that soil nutrient heterogeneity exerts a strong influence on the development of plant individuals and communities, it is virtually unknown how nutrient heterogeneity and global change drivers interact to affect plant performance and ecosystem functioning. We conducted a microcosm experiment to evaluate the effect of simultaneous changes in [CO2], nutrient heterogeneity (NH), nutrient availability (NA) and species evenness on the biomass and nutrient uptake patterns of assemblages formed by Lolium perenne, Plantago lanceolata and Holcus lanatus. When the nutrients were heterogeneously supplied,assemblages exhibited precise root foraging patterns, and had higher above- and belowground biomass (average increases of 32% and 29% for above- and belowground biomass, respectively). Nutrient heterogeneity also modulated the effects of NA on biomass production, complementarity in nitrogen uptake and below: aboveground ratio, as well as those of [CO2] on the nutrient use efficiency at the assemblage level. Our results show that nutrient heterogeneity has the potential to influence the response of plant assemblages to simultaneous changes in [CO2], nutrient availability and biotic diversity, and suggest that it is an important environmental factor to interpret and assess plant assemblage responses to global change.
Data from: Controlled comparison of species- and community-level models across novel climates and communities
Species distribution models (SDMs) assume species exist in isolation and do not influence one another's distributions, thus potentially limiting their ability to predict biodiversity patterns. Community-level models (CLMs) capitalize on species co-occurrences to fit shared environmental responses of species and communities, and therefore may result in more robust and transferable models. Here, we conduct a controlled comparison of five paired SDMs and CLMs across changing climates, using palaeoclimatic simulations and fossil-pollen records of eastern North America for the past 21 000 years. Both SDMs and CLMs performed poorly when projected to time periods that are temporally distant and climatically dissimilar from those in which they were fit; however, CLMs generally outperformed SDMs in these instances, especially when models were fit with sparse calibration datasets. Additionally, CLMs did not over-fit training data, unlike SDMs. The expected emergence of novel climates presents a major forecasting challenge for all models, but CLMs may better rise to this challenge by borrowing information from co-occurring taxa.
Data from: Using camera trapping and hierarchical occupancy modelling to evaluate the spatial ecology of an African mammal community
Emerging conservation paradigms have shifted from single to multi-species approaches focused on sustaining biodiversity. Multi-species hierarchical occupancy modelling provides a method for assessing biodiversity while accounting for multiple sources of uncertainty. We analysed camera trapping data with multi-species models using a Bayesian approach to estimate the distributions of a terrestrial mammal community in northern Botswana and evaluate community, group, and species-specific responses to human disturbance and environmental variables. Groupings were based on two life-history traits: body size (small, medium, large and extra-large) and diet (carnivore, omnivore and herbivore). We photographed 44 species of mammals over 6607 trap nights. Camera station-specific estimates of species richness ranged from 8 to 27 unique species, and species had a mean occurrence probability of 0·32 (95% credible interval = 0·21–0·45). At the community level, our model revealed species richness was generally greatest in floodplains and grasslands and with increasing distances into protected wildlife areas. Variation among species' responses was explained in part by our species groupings. The positive influence of protected areas was strongest for extra-large species and herbivores, while medium-sized species actually increased in the non-protected areas. The positive effect of grassland/floodplain cover, alternatively, was strongest for large species and carnivores and weakest for small species and herbivores, suggesting herbivore diversity is promoted by habitat heterogeneity. Synthesis and applications. Our results highlight the importance of protected areas and grasslands in maintaining biodiversity in southern Africa. We demonstrate the utility of hierarchical Bayesian models for assessing community, group and individual species' responses to anthropogenic and environmental variables. This framework can be used to map areas of high conservation value and predict impacts of land-use change. Our approach is particularly applicable to the growing number of camera trap studies world-wide, and we suggest broader application globally will likely result in reduced costs, improved efficiency and increased knowledge of wildlife communities.
Data from: Effects of seal predation on a modelled marine fish community and consequences for a commercial fishery
We constructed a size- and trait-based dynamic marine community model of the Celtic Sea/Biologically Sensitive Area, including grey seals Halichoerus grypus (Fabricius 1791) and harbour seals Phoca vitulina vitulina (Linnaeus 1758) to examine potential resource conflict between seals and commercial trawl fisheries. The model incorporates seal diet preference, population size and commercial fishery catch, with survey data to quantify ecological interactions between seals and fisheries. Total annual consumption by seals was an order of magnitude less than the catch of the modelled trawl fishery. Increasing fishing pressure reduced fish spawning stock biomass (SSB) much more than a proportionally equivalent increase in seal predation. For most fish species, quadrupling seal predation showed little effect on the predicted fishery catch. These results arise from relatively low seal abundance and partial niche partitioning. The fishery harvested a wider range of fish lengths and species than seals consumed. The fish community was dominated by small fish lengths and seals predated on these more than suggested by their calculated diet preference. Seal predation disproportionately affected several fish species not targeted by the fishery, but seal predation did not significantly affect the SSB of any of the species that constitute 90% of the total landings of the fishery. Synthesis and applications. Predation of fish by grey and harbour seals is unlikely to harm commercial trawl fisheries in south-west Irish waters. This conclusion differs from those of some model-based studies of other North Atlantic systems, demonstrating the need for ecosystem-specific evidence in considering such conflicts. In systems with low niche overlap between seals and fisheries, the two are largely decoupled in effect, leaving fishing pressure as the overwhelming determinant of targeted fish stock status.
Data from: How does spatial resolution affect model performance? A case for ensemble approaches for marine benthic mesophotic communities
Aim: To investigate how changing grid size can alter model predictions of the distribution of mesophotic taxa and how it affects different modelling methods. Location: Ningaloo Marine Park, Western Australia. Taxon: Benthic mesophotic taxa: corals, macroalgae, and sponges. Methods: We determined the distributions of the major benthic taxonomic groups: corals, macroalgae, and sponges, using a number of modelling techniques and an ensemble using the 'sdm' R package. A range of grid sizes were used (10 m, 50 m, 100 m, and 250 m) to identify how model predictions were altered. Models were evaluated using the area under the curve of a receiver operator characteristic plot (AUC) and the true skill statistic (TSS) using a spatially independent dataset. Results: Grid size had a large effect on model performance across the taxonomic groups. Model outputs were compared to null surfaces and 88.8% of models performed significantly better than null. Distribution of corals was best predicted using the finest grid size (10 m) regardless of modelling method, although a model ensemble produced the best results (AUC = 0.80, TSS = 0.52). Macroalgae and sponges were better predicted at coaster grids sizes (250 m). Again, ensembles performed well for both macroalgae (AUC = 0.83, TSS = 0.63) and sponges (AUC = 0.88, TSS = 0.66). Model ensembles maintained high accuracy across grid sizes and were consistently the best, or second-best, performing method. Main Conclusions: This study has shown how grid size should be considered when producing distribution models. Identifying the most relevant grid size and being aware of the influence it may have will provide more accurate predictions of the distributions of taxa. Ensemble methods maintained good performance across scenarios and thus provide a useful tool for conservation and management especially where single modelling methods showed high levels of variability.
Data from: Use of classical bird census transects as spatial replicates for hierarchical modeling of an avian community
New monitoring programs are often designed with some form of temporal replication to deal with imperfect detection by means of occupancy models. However, classical bird census data from earlier times often lack temporal replication, precluding detection-corrected inferences about occupancy. Historical data have a key role in many ecological studies intended to document range shifts, and so need to be made comparable with present‐day data by accounting for detection probability. We analyze a classical bird census conducted in the region of Murcia (SE Spain) in 1991 and 1992 and propose a solution to estimating detection probability for such historical data when used in a community occupancy model: the spatial replication of subplots nested within larger plots allows estimation of detection probability. In our study, the basic sample units were 1‐km transects, which were considered spatial replicates in two aggregation schemes. We fit two Bayesian multispecies occupancy models, one for each aggregation scheme, and evaluated the linear and quadratic effect of forest cover and temperature, and a linear effect of precipitation on species occupancy probabilities. Using spatial rather than temporal replicates allowed us to obtain individual species occupancy probabilities and species richness accounting for imperfect detection. Species‐specific occupancy and community size decreased with increasing annual mean temperature. Both aggregation schemes yielded estimates of occupancy and detectability that were highly correlated for each species, so in the design of future surveys ecological reasons and cost‐effective sampling designs should be considered to select the most suitable aggregation scheme. In conclusion, the use of spatial replication may often allow historical survey data to be applied formally hierarchical occupancy models and be compared with modern‐day data of the species community to analyze global change process.
Data from: Using filter-based community assembly models to improve restoration outcomes
1. Ecological filter models derived from community assembly theory can inform restoration planning by highlighting management actions most likely to affect community composition. Despite growing interest in these models, many restoration studies solely manipulate a single filter—the biotic filter by altering interspecific competition in studies—while ignoring abiotic and dispersal filters that may also influence restoration success. 2. To examine how manipulating all three filters (biotic, abiotic, dispersal) affected restoration in an annual-type grassland, we seeded native forbs from the same functional group as a target invader to increase biotic resistance to invasion (biotic filter), cut standing biomass and either removed it or returned it to plots as litter to alter light conditions (abiotic filter), and added native forbs at different seeding rates to alter density of establishing native populations (dispersal filter). We measured restoration success by recording native species and invader cover in plots. 3. The addition of native species with phenological and morphological traits similar to the target invader reduced invasion and increased native populations, but only in litter-free plots when high-densities of native seed were added. 4. Seeding two species with functional traits similar to the invader was more effective at reaching restoration goals than seeding just one functionally similar species. As such, trait differences among restoration species, even species belonging to the same functional group, may increase biotic resistance to invasion in restored communities. 5. Litter removal altered native-invader interactions. When litter was kept, added natives did not reduce invader cover. However, when litter was removed, added natives led to declines in invader cover. 6. Increasing native seeding rates led to larger native populations and increased invasion resistance. 7. Synthesis and applications. In this study, simultaneously manipulating biotic, abiotic and dispersal filters was necessary to optimize restoration outcomes. In particular, the biotic filter only contributed to successful restoration outcomes under abiotic and dispersal conditions that were created through management actions specifically targeting these two additional filters. Restoration planning based on filter models should incorporate actions that target all three filters, rather than solely focusing on the biotic filter.
Simulations Supporting 'Representing Intra-Hillslope Lateral Subsurface Flow in the Community Land Model', JAMES, 2019
<p>CLM5 Simulations used for the paper "Representing Intra-Hillslope Lateral Subsurface Flow in the Community Land Model". Files are in NetCDF format.</p> <p>Filenames beginning with 'RME_' contain single point simulations for the Reynolds Mountain East catchment. Filenames beginning with 'Global_' contains global simulations used in the sensitivity study. Filenames beginning with 'surfdata_' contain input surface data files used in CLM5 Hillslope simulations.</p>
Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches
<p>Generated draft and consensus reconstructions for the manuscript "Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches" (Hsieh, Tandon, Verbruggen, & Nikoloski).</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.