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106 results for “community stability”
MCR LTER: Coral Reef: Asynchrony in coral community structure contributes to reef‑scale community stability, data for Srednick et al., Nature 2023
These data were generated in support of the manuscript: Srednick G, Davis K, and Edmunds P, Nature To evaluate whether spatial insurance effects are important on coral reefs, we explored variation over 2006–2019 in coral community structure and environmental conditions in Moorea, French Polynesia. We studied coral community structure at a single site with fringing, back reef, and fore reef habitats, and used this system to explore associations among community asynchrony, asynchrony of environmental conditions, and community stability. The daily range in seawater temperature among habitats suggests it could be a factor contributing to the variation in coral community structure. Wave-forced seawater flow facilitated larval exchange among connected habitats, differing in strength among years, and accentuated periodic connectivity among habitats at 1-7 year intervals. At this site, connected habitats harboring taxonomically similar coral assemblages and exhibiting asynchronous population dynamics can provide insurance against extirpation and may promote community stability. If these effects apply at larger spatial scale, then among-habitat community asynchrony is likely to play an important role in determining reef-wide coral community resilience. This manuscript uses data collected by the U.S. National Science Foundation's (NSF) Moorea Coral Reef Long Term Ecological Research (MCR LTER) site under Grant No. OCE 2224354 (and earlier awards). Additional financial support to the MCR LTER site was provided through a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2023).
Plant community compositional stability over 40 years in a Fraser River Estuary tidal freshwater marsh
<p class="MsoNormal"><span>Long-term data sets documenting temporal changes in vegetation communities are uncommon, yet imperative for understanding trends and triggering potential conservation management interventions. For example, decreasing species diversity and increasing non-native species abundance may be indicative of decreasing community stability. We explored long-term plant community change over a 40-year period through the contribution of data collected in 2019 to two historical datasets collected in 1979 and 1999 to evaluate decadal changes in plant community biodiversity in a tidal freshwater marsh in the Fraser River Estuary in British Columbia, Canada. We found that plant assemblages were characterized by similar indicator species, but most other indicator species changed, and that overall </span><span>α-diversity</span><span> decreased while </span><span>β</span><span>-diversity increased. Further, we found evidence for plant assemblage homogenization through the increased abundance of invasive species such as yellow flag iris (<em>Iris pseudacorus</em>), and reed canary grass (<em>Phalaris arundinacea</em>). These observations may inform concepts of habitat stability in the absence of direct anthropogenic disturbance and corroborate globally observed trends of native species loss and non-native species encroachment. Our results indicate that within the Fraser River Estuary, active threat management may be necessary in areas of conservation concern in order to prevent further native species biodiversity loss. </span></p>
Data from: Wildlife fecal microbiota exhibit community stability across a semi-controlled longitudinal non-invasive sampling experiment
<p>Wildlife microbiome studies are being used to assess microbial links with animal health and habitat. The gold standard of sampling microbiomes directly from captured animals is ideal for limiting potential abiotic influences on microbiome composition, yet fails to leverage the many benefits of non-invasive sampling. Application of microbiome-based monitoring for rare, endangered, or elusive species creates a need to non-invasively collect scat samples shed into the environment. Since controlling sample age is not always possible, the potential influence of time-associated abiotic factors was assessed. To accomplish this, we analyzed partial 16S rRNA genes of fecal metagenomic DNA sampled non-invasively from Rocky Mountain elk (<em>Cervus canadensis</em>) near Yellowstone National Park. We sampled pellet piles from four different elk, then aged them in a natural forest plot for 1, 3, 7, and 14 days, with triplicate samples at each time point (i.e., a blocked, repeat measures (longitudinal) study design). We compared microbiomes of each elk through time with point estimates of diversity, bootstrapped hierarchical clustering of samples, and a version of ANOVA–simultaneous components analysis (ASCA) with PCA (LiMM-PCA) to assess the variance contributions of time, individual and sample replication. Our results showed community stability through days 0, 1, 3 and 7, with a modest but detectable change in abundance in only 2 genera (<em>Bacteroides</em> and <em>Sporobacter</em>) at day 14. The total variance explained by time in our LiMM-PCA model across the entire 2-week period was not statistically significant (p>0.195) and the overall effect size was small (<10% variance) compared to the variance explained by the individual animal (p<0.0005; 21% var.). We conclude that non-invasive sampling of elk scat collected within one week during winter/early spring provides a reliable approach to characterize microbiome composition in a 16S rDNA survey and that sampled individuals can be directly compared across unknown time points with minimal bias. Further, point estimates of microbiome diversity were not mechanistically affected by sample age. Our assessment of samples using bootstrap hierarchical clustering produced clustering by animal (branches) but not by sample age (nodes). These results support greater use of non-invasive microbiome sampling to assess ecological patterns in animal systems.</p>
Stability of rocky intertidal communities in response to species removal varies across spatial scales
<p>Improving our understanding of stability across spatial scales is crucial in the current scenario of biodiversity loss. Still, most empirical studies of stability target small scales. Here we experimentally removed the local space-dominant species (macroalgae, barnacles, or mussels) at eight sites spanning more than 1000 km of coastline in north- and south-central Chile, and quantified the relationship between area (the number of aggregated sites) and stability in aggregate community variables (total cover) and taxonomic composition. Resistance, recovery, and invariability increased nonlinearly with area in both functional and compositional domains. Yet, the functioning of larger areas achieved a better, albeit still incomplete, recovery than composition. Compared with controls, smaller disturbed areas tended to overcompensate in terms of total cover. These effects were related to enhanced available space for recruitment (resulting from the removal of the dominant species), and to increasing beta diversity and decaying community-level spatial synchrony (resulting from increasing area). This study provides experimental evidence for the pivotal role of spatial scale in the ability of ecosystems to resist and recover from chronic disturbances. This knowledge can inform further ecosystem restoration and conservation policies.</p>
Data from: Plant community stability is associated with a decoupling of prokaryote and fungal soil networks
<p>Data from the manuscript Plant community stability is associated with a decoupling of prokaryote and fungal soil networks: https://doi.org/10.1101/2022.06.21.496867</p>
Examining the diversity, stability and functioning of marine fish communities across a latitudinal gradient
<p><strong>Aim</strong>: As anthropogenic stressors on the biosphere intensify, understanding how communities respond to disturbances is critical. Biodiversity is often thought to promote the stability of communities over time and enhance ecosystem functioning. However, results have been inconsistent, and the multifaceted linkages among diversity, stability, and functioning under acute disturbances remain poorly understood. We experimentally tested the responses of marine fish communities to disturbance (i.e., acute habitat loss) across a diversity gradient spanning 35º degrees of latitude in the western Atlantic Ocean to assess the diversity-stability relationship and the interplay between diversity, stability, and fish biomass recovery (as a proxy for function) in marine fish communities.</p> <p><strong>Location</strong>: Western Atlantic Ocean (Maine, Massachusetts, North Carolina, Florida [USA], Belize, and Panama).</p> <p><strong>Time</strong> <strong>period</strong>: 2016 – 2017</p> <p><strong>Major taxa studied</strong>: Small, bottom-dwelling ('cryptobenthic') fishes</p> <p><strong>Results</strong>: Diversity showed a negative effect on community stability at both the regional (across docks) and local (within docks) scales. Similarly, local diversity was negatively correlated with ecosystem function. These effects are exacerbated by the habitat loss imposed via our experimental treatment.</p> <p><strong>Main</strong> <strong>conclusions</strong>: Our results suggest that habitat loss may more intensively re-shuffle diverse, tropical communities, which impacts biomass recovery, our proxy of functioning. Contrary to ecological theory, in small-bodied, benthos-associated vertebrate communities, biodiversity may neither promote stability nor functioning, suggesting that human disturbances may be particularly impactful in tropical, high-diversity ecosystems.</p>
Data for "Species richness and food-web structure jointly drive community biomass and its temporal stability in fish communities"
<p>Data for the paper "Species richness and food-web structure jointly drive community biomass and its temporal stability in fish communities" which is in minor revision in Ecology Letters (manuscript id:ELE-00589-2021.R1). A doi will be provided upon publication.</p> <p>Current citation: Danet, A., Mouchet, M., Bonnaffé, W., Thébault, E., & Fontaine, C. (In revision) Species<br> richness and food-web structure jointly drive total biomass and its temporal stability in<br> fish communities Minor revision in Ecology Letters.</p> <p>The repository constains data describing fish community monitoring across stream sections in metropolitan France over the period 1995-2018 by the French Office of Water and Aquatic Ecosystems (ONEMA) using electrofishing.</p> <p>The repository contains:</p> <ul> <li> description of fishing: fishing_protocol.csv <ul> <li>surface: sampled surface</li> <li>opcod: fishing operation code, a unique identifier for each sampling event</li> <li>station: unique identifier for each site</li> <li>nb_sp, nb_ind: number of species, number of individuals</li> </ul> </li> <li>geographical information: station_basin.csv <ul> <li>X, Y: spatial coordinates of the station, expressed in metres in Lambert93 (epsg:2154)</li> <li>basin: name of the hydrographic basin</li> </ul> </li> <li>environment: environment.csv ( _mean: mean, _med: median, _cv: coefficient of variation) <ul> <li>alt: altitude</li> <li>d_source: distance to source</li> <li>strahler: strahler order</li> <li>BOD: Biological Oxygen Demand</li> <li>temperature: water temperature</li> <li>flow: water flow</li> </ul> </li> <li>community data: community_data.csv <ul> <li>species: three digits code corresponding to a given species (see Table S1, Danet et al. in revision)</li> <li>nind: number of individuals</li> <li>biomass: biomass in gram</li> </ul> </li> <li>Length of each fish individual: fish_length.csv <ul> <li>length: length of the fish in millimeter</li> </ul> </li> <li>Inferred food-web: class_network.rda <ul> <li>data: <ul> <li>class_id: size class of a fish individual</li> </ul> </li> <li>network: these data.frame can be handled by igraph::graph_from_data_frame() <ul> <li>from, to: "to" eats "from"</li> </ul> </li> <li>composition: <ul> <li>sp_class: concatenation of species and class_id columns</li> <li>bm_std: biomass reported to the sampled surface</li> </ul> </li> </ul> </li> </ul> <p> </p> <p> </p>
Long-term coastal macrobenthic Community Trajectory Analysis reveals habitat-dependent stability patterns
<p>Long-term monitoring programs are fundamental to detecting changes in ecosystem health and understanding ecological processes. In the current context of increasing anthropogenic threats on marine ecosystems, understanding the dynamics and response of communities becomes essential. We used data collected over 14 years in the REBENT benthic coastal invertebrates monitoring program, at a regional scale in the North-East Atlantic, covering a total of 26 sites and 979 taxa. Four distinct habitats were studied: two biogenic habitats associated with foundation species in the intertidal and subtidal zones and two bare sedimentary habitats in the same respective tidal zones. We used Community Trajectory Analysis, a statistical approach that allows for quantitative measures and comparisons of temporal trajectories of ecosystems. We compared observed community trajectories to trajectories simulated under a non-directional null model in order to better understand the dynamics of the communities, their potential drivers, and the role of the studied habitats in these dynamics. Despite strong differences in the community compositions between sites and habitats, the communities followed non-directional dynamics during the 14 years monitored, which suggested stability at the regional scale. However, the shape, size, and direction of the trajectories of benthic communities were more similar within than among habitats, also suggesting the influence of the nature of the habitat on community dynamics. Results showed a higher variability in community composition in the first years of the monitoring in the intertidal bare habitat and confirmed the role of biogenic habitats in maintaining temporal stability. They also highlighted the need to apprehend the role of transient and rare species and the scale of observation in temporal beta diversity analyses. Finally, our study confirmed the usefulness of Community Trajectory Analysis to link observed trajectory patterns to fundamental ecological processes.</p>
Examining the diversity, stability and functioning of marine fish communities across a latitudinal gradient
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Long-term coastal macrobenthic Community Trajectory Analysis reveals habitat-dependent stability patterns
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Plant community compositional stability over 40 years in a Fraser River Estuary tidal freshwater marsh
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Network specificity decreases community stability and competition among avian haemosporidian parasites and their hosts
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Stability of rocky intertidal communities in response to species removal varies across spatial scales
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Data from: Wildlife fecal microbiota exhibit community stability across a semi-controlled longitudinal non-invasive sampling experiment
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Code and data for: Exposure to climate change drives stability or collapse of desert mammal and bird communities
<p>The following code and data are used to generate the results for the publication "Exposure to climate change drives stability or collapse of desert mammal and bird communities". Climate_Data.zip contains the monthly minimum and maximum temperatures, vegetation data, and soil thickness data to generate microclimates. NicheMapR_code_and_files.zip contains the script and data necessary to generate the microhabitats. Endoscape.zip contains the data and script necessary to run the heat flux models. Resurvey_data.zip contains the jags data to run the occupancy models for small mammals and birds. The read_me file contains the descriptions of all data and script necessary to reproduce the data from the publication.</p>
Contrasting latitudinal patterns in diversity and stability in a high-latitude species-rich moth community
<p>Aim: Biodiversity is currently undergoing rapid restructuring across the globe. However, the nature of biodiversity change is not well understood, as community-level changes may hide differential responses in individual population trajectories. Here, we quantify spatio-temporal community and stability dynamics using a long-term high-quality moth monitoring dataset. Location: Finland, Northern Europe. Time period: 1993-2012. Major taxa studied: Nocturnal moths (Lepidoptera). Methods: We quantify patterns of change in species richness, total abundance, dominance and temporal variability at different organisational levels over a 20-year period and along a 1100-km latitudinal gradient. We used mixed-effects and linear models to quantify temporal trends for the different community and stability metrics and to test for latitudinal (or longitudinal) effects. Results: We find contrasting patterns for different community metrics, and strong latitudinal patterns. While total moth abundance has declined, species richness has simultaneously increased over the study period, but with rates accelerating with latitude. Additionally, we reveal a latitudinal pattern in temporal variability – the northernmost locations exhibited higher variability over time, as quantified by both metrics of richness and aggregated species populations trends. Main Conclusions: When combined, our findings likely reflect an influx of species expanding their ranges poleward in response to warming. The overall decline in abundance and the latitudinal effect on temporal variability highlight potentially severe consequences of global change for community structure and integrity across high-latitude regions. Importantly, our results underscore that increases in species richness may be paralleled by a loss of individuals, which in turn might affect higher trophic levels. Our findings suggest that the ongoing global species redistribution is affecting both community structure and stability over time, leading to compounded and partly opposing effects of global change depending on what biodiversity dimension we focus on.</p>
Data from: Genetics-based interactions of foundation species affect community diversity, stability, and network structure
We examined the hypothesis that genetics-based interactions between strongly interacting foundation species, the tree Populus angustifolia and the aphid Pemphigus betae, affect arthropod community diversity, stability and species interaction networks of which little is known. In a 2-year experimental manipulation of the tree and its aphid herbivore four major findings emerged: (i) the interactions of these two species determined the composition of an arthropod community of 139 species; (ii) both tree genotype and aphid presence significantly predicted community diversity; (iii) the presence of aphids on genetically susceptible trees increased the stability of arthropod communities across years; and (iv) the experimental removal of aphids affected community network structure (network degree, modularity and tree genotype contribution to modularity). These findings demonstrate that the interactions of foundation species are genetically based, which in turn significantly contributes to community diversity, stability and species interaction networks. These experiments provide an important step in understanding the evolution of Darwin's 'entangled bank', a metaphor that characterizes the complexity and interconnectedness of communities in the wild.
River dams and the stability of bird communities: A hierarchical Bayesian analysis in a tropical hydroelectric power plant
<ol> <li>The effects of anthropogenic disturbance upon the stability of wildlife communities depend on the heterogeneity and connectivity of habitat remnants on multiple scales. The number of hydroelectric dams in biodiversity hotspots (Africa, South America and Asia) is growing rapidly. To establish their environmental impact, it is essential to understand the dynamics of wildlife communities before and following the establishment of dams.</li> <li>We evaluated the impacts of the filling of the Serra do Facão hydroelectric reservoir in the São Marcos river, central Brazil, upon the bird community. Using data from 1,145 surveys across 20 sampling sites over eight years, two years before and six years after the filling of the reservoir, we assessed the resistance, i.e., maintenance close to an equilibrium state during the disturbance, and resilience, i.e., ability to return to the original state following the disturbance, of the bird community. We used spatiotemporal hierarchical Bayesian models to assess the effects of reservoir filling on five community parameters: abundance, richness, phylogenetic diversity, functional diversity and species composition.</li> <li>In the period subsequent to reservoir filling, there was (i) a marked reduction in bird abundance, richness, phylogenetic diversity and functional diversity, and (ii) a reduction in the proportion of forest species, coupled with an increase in the proportion of savanna species. Except for bird abundance, none of the other community attributes returned to their original levels, even after six years. Our findings indicate that Cerrado bird communities have both low resistance and low resilience to habitat loss associated with the establishment of hydroelectric reservoirs.</li> <li> <i>Synthesis and applications.</i> The environmental costs of hydroelectric dams are still underestimated or neglected in Brazil. A new paradigm in the assessment of their environmental impacts is warranted, incorporating (i) models of spatiotemporal variations based on long-term monitoring with surveys initiated before disturbances and (ii) measures of functional and phylogenetic diversity, such that society can understand the costs and benefits of the establishment of new hydroelectric dams and make informed decisions. Biodiversity loss could be minimized by ensuring the preservation and connectivity of alluvial habitats, capable of maintaining the supply of resources and the functional and phylogenetic attributes of bird communities associated with such habitats.</li> </ol>
Complex landscapes stabilize farm bird communities and their expected ecosystem services
<p>1. Birds play many roles within agroecosystems including as consumers of crops and pests, carriers of pathogens, and beloved icons. Birds are also rapidly declining across North America, in part due to agricultural intensification. Thus, it is imperative to identify how to manage agroecosystems to best support birds for multi-functional outcomes (e.g., crop production and conservation). Both the average amounts of services/disservices provided and their temporal stability are important for effective farm planning.</p> <p>2. Here, we conducted point-count surveys for four years across 106 locations on 27 diversified farms in Washington and Oregon, USA. We classified birds as ecosystem service or disservice providers using indices spanning supporting, regulating, provisioning, and cultural services/disservices. We then examined service/disservice index pairwise correlations and assessed the relative importance of local, farm, and landscape complexity on the average and temporal stability of avian service/disservice provider indices.</p> <p>3. Generally, service provider indices (production benefitting birds, grower appreciation, and conservation scores) were positively correlated with each other. Foodborne pathogen risk, grower disapproval, and identity/iconic value indices were also positively correlated with each other. However, the crop damaging bird index generally had low correlations with other indices.</p> <p>4. Farms that implemented more conservation-friendly management practices generally had higher average service provider indices, but farm management did not impact disservice provider indices, except for grower disapproval. Average disservice provider indices were lower on farms in complex landscapes.</p> <p>5. Local vertical vegetation complexity tended to increase the temporal stability of service provider indices but did not affect the disservice provider indices. Greater landscape complexity was generally associated with increased temporal stability of service and disservice provider indices. Increased landscape complexity may stabilize bird communities by increasing bird community evenness, which in turn, positively predicted temporal stability of all service/disservice provider indices.</p> <p>6. <i>Policy implications</i>: Our results suggest that farmers can effectively manage their farms to harness ecosystem services from birds through farm diversification. Disservices provided by birds, however, appear to be most negatively impacted by landscape-level complexity. Thus, greater incentives for farmers to increase seminatural cover at the landscape-scale are likely necessary to achieve multifunctional outcomes for conservation and agriculture.</p>
Intra- and interspecific variability of specific leaf area mitigate the reduction of community stability in response to warming and nitrogen addition
<p><span>Global environmental changes are reducing the diversity and affecting the functioning of natural ecosystems as well as their ability to reliably provide ecosystem functions and services to mankind. Many studies have shown that a greater plant diversity can stabilize community productivity against environmental fluctuations. However, most of these studies focused on plant species richness, thus overlooking the potential role of functional traits in stabilizing community productivity against environmental fluctuations.</span> <span>Whether and how functional trait mean and variability influence community stability in response to environmental changes and their relative contributions to community stability are largely unknown. Here, we used a 10-year experiment to investigate the role of species richness, as well as functional mean and intra- and interspecific variability of specific leaf area (SLA) of plants within- and among communities in driving community stability in response to nitrogen (N) addition and warming.</span> <span>We found that both N addition and warming reduced the temporal stability of community productivity by reducing species richness and its contribution to species asynchrony and species stability. In contrast, changes in the mean and variability of SLA in response to N addition and warming mitigated the reduction of community stability. Specifically, N addition reduced variation in SLA both by reducing interspecific differences in SLA within communities and differences in mean values of SLA among communities. Warming increased intraspecific differences in SLA among communities, leading to higher species stability that partly buffered the reduction of community stability.</span><span> Our study demonstrates the role of trait mean and variability in mitigating the reduction of community stability in response to two pervasive global environmental changes. Gaining a deeper understanding of the processes linking global changes and the stability of our ecosystems requires integrating both trait mean values and trait variability.</span></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.