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328 results for “ecological community”
Spatial distribution of benthic algae in the South China Sea: responses to gradually changing environmental factors and ecological impacts on coral communities
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Data from: The spatial patterns of community composition, their environmental drivers and their spatial scale dependence vary markedly between fungal ecological guilds
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Ecological network structure in response to community assembly processes over evolutionary time
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EAP21-0576.R1 - Implementing Community-Engaged Ecological Research in Proctor Creek, an Urban Watershed in Atlanta, GA
The Southeast Region of the U.S. Fish and Wildlife Service (USFWS) implemented community-engaged research in Proctor Creek, an urban watershed in Northwest Atlanta, Georgia, to sample for aquatic species of concern in Atlanta, Georgia’s Proctor Creek Watershed as a part of the Urban Waters Federal Partnership program. This research shifted the focus of the agency from the endangered and pristine natural spaces to a major city watershed negatively impacted by urbanization and other human influences for more than a century. Team members from USFWS, Proctor Creek Watershed residents, local students, and other stakeholders in the UWFP spent three months conducting stream surveys and participating in community-led events to build relationships and learn community priorities. The team collected data at 11 sites throughout the Proctor Creek Watershed, visually assessed each site, and collected aquatic species using dip nets, seines, and traps. We observed approximately 28 aquatic species, including 13 unique fish species, and eight macroinvertebrate species, including two unique crayfish species. We also observed varying degrees of ecological health throughout the watershed. Native aquatic animal species were found at all stream sites, no matter the condition of the stream. Through creating training resources and disseminating data among team members for future sampling, the team established pathways to keep natural resource stewardship sustainable outside of direct federal involvement. Through engaging in community-engaged research to achieve the mission of the agency, the USFWS Proctor Creek watershed survey helped shift the paradigm of how government agencies can connect their mission statements to the ever-changing complex needs of the American public.
Long Term Research in Environmental Biology (LTREB): California vernal pool plant community ecology and restoration, 2000-2017
This data set includes annual vegetation data and selected water depth data collected during the period 2000-2017 from vernal pool basins that were constructed in 1999 as part of a large-scale vernal pool mitigation effort at Travis Air Force Base, California. The constructed pools covered an area of about 15 Ha and were located adjacent to a complex of naturally-occurring pools, which were used as reference sites for comparison. Five plant species were intentionally seeded into the pools according to five seeding treatment protocols to assess the influence of order of colonization, frequency of colonization, and dispersal limitation on vernal pool plant community assembly. Because water depth was known to influence plant species distributions, water depth was recorded weekly during the winter wet season in selected years for each constructed and reference pool at the site. Seed plots were 50 cm x 50 cm and were permanently marked and used for repeated sampling of vegetation from 2000-2017. For each plant species that occurred in the plots, the frequency of occurrence was recorded as the number of squares out of a 100-cell grid laid over the plot in which that plant species appeared. For the five species that were planted into the plots, the frequency was recorded, as above, but in addition the number of individuals of that species in the plot was also recorded.
Ecological data from: Combining botanical collections and ecological data to better describe plant community diversity
<p>In this age of rapid biodiversity loss, we must continue to refine our approaches to describing variation in life on Earth. Combining knowledge and research tools from multiple disciplines is one way to better describe complex natural systems. Understanding plant community diversity requires documenting both pattern and process. We must first know which species exist, and where (i.e., taxonomic and biogeographic patterns), before we can determine why they exist there (i.e., ecological and evolutionary processes). Floristic botanists often use collections-based approaches to elucidate biodiversity patterns, while plant ecologists use hypothesis-driven statistical approaches to describe underlying processes. Because of these different disciplinary histories and research goals, floristic botanists and plant ecologists often remain siloed in their work. Here, using a case study from an urban greenway in Colorado, USA, we illustrate that the collections-based, opportunistic sampling of floristic botanists is highly complementary to the transect- or plot-based sampling of plant ecologists. We found that floristic sampling captured a community species pool four times larger than that captured using ecological transects, with rarefaction and non-parametric species estimation indicating that it would be prohibitive to capture the "true" community species pool if constrained to sampling within transects. We further illustrate that the discrepancy in species pool size between approaches led to a different interpretation of the greenway's ecological condition in some cases (e.g., transects missed uncommon cultivated species escaping from nearby gardens) but not others (e.g., plant species distributions among functional groups were similar between species pools). Finally, we show that while using transects to estimate plant relative abundances necessarily trades off with a fuller assessment of the species pool, it is an indispensable indicator of ecosystem health, as evidenced by three non-native grasses contributing to 50% of plant cover along the highly modified urban greenway. We suggest that actively fostering collaborations between floristic botanists and ecologists can create new insights into the maintenance of species diversity at the community scale.</p>
Diversity of response and effect traits provides complementary information about avian community dynamics linked to ecological function
<p>Functional diversity metrics based on species traits are widely used to investigate ecosystem functioning. In theory, such metrics have different implications depending on whether they are calculated from traits mediating responses to environmental change (response traits) or those regulating function (effect traits), yet trait choice in diversity metrics is rarely scrutinized. Here, we compile effect and response traits for British bird species supplying two key ecological services – seed dispersal and insect predation – to assess the relationship between functional diversity and both mean and stability of community abundance over time. As predicted, functional diversity correlates with stability in community abundance of seed dispersers when calculated using response traits. However, we found a negative relationship between functional diversity and mean community abundance of seed dispersers when calculated using effect traits. Subsequently, when combining all traits together, we found inconsistent results with functional diversity correlating with reduced stability in insectivores, but greater stability in seed dispersers. Our findings suggest that trait choice should be considered more carefully when applying such metrics in ecosystem management.</p>
Data from: Ecological sorting and character displacement contribute to the structure of communities of Clarkia species
Despite long‐standing interest in the evolutionary ecology of plants that share pollinators, few studies have explored how these interactions may affect communities during both community assembly (ecological sorting) and through ongoing, in situ evolution (character displacement), and how the effects of these interactions may change with community context. To determine if communities display patterns consistent with ecological sorting, we assessed the frequency of co‐occurrence of four species of Clarkia in the southern Sierra foothills (Kern County, CA, USA). To investigate potential character displacement, we measured pollination‐related traits on plants grown in a greenhouse common garden from seed collected in communities with one, two, or four Clarkia species. Among the four species of Clarkia in this region, the two species that are often found in multi‐species communities also co‐occur with one another more frequently than expected under a null model. This pattern is consistent with ecological sorting, although further investigation is needed to determine the role of pollinators in shaping community assembly. Patterns of trait variation in a common garden suggest that these two species have diverged in floral traits and converged in flowering time where they co‐occur, which is consistent with character displacement. Trait variation across community types also suggests that the process and outcome of character displacement may vary with community context. Because community context appears to affect both the direction and magnitude of character displacement, change in more species‐rich communities may not be predictable from patterns of change in simpler communities.
Ecological patterns of root nodule diversity in cultivated and wild rooibos populations: a community prediction approach
<p>There is interest in understanding the factors behind the biogeography of root-associated bacteria due to the joint effects that plant host, climate, and soil conditions can have on bacterial diversity. For legume crops with remaining wild populations, this is of even more importance, because the effects of cropping on undisturbed root-associated bacterial communities can be addressed. Here, we used a community prediction approach to describe the diversity of the root nodule bacterial communities of rooibos (<i>Aspalathus linearis</i>), an endemic legume crop from South Africa. The goal was to reveal whether patterns of root nodule community composition in paired cultivated and wild rooibos populations could be related to geographical distance, plant traits, and plant population type (i.e. cultivated or uncultivated). We identified a core of dominant and widespread <i>Mesorhizobium</i> ZOTUs that each defined one of 4 different root nodule community classes. Rooibos cultivation impacted root nodule bacterial diversity at regional and local scales, while the geographical origin of the root nodule communities was the strongest predictor of root nodule community structure. Beyond impacts of cultivation on root nodule bacterial diversity, this study suggests a mixture of dispersal limitation and ecological drift regionally, and selection by different plant populations locally, define the biogeography of rooibos root nodule bacterial communities. </p>
Data from: Relatedness with plant species in native community influences ecological consequences of range expansions
Global warming is enabling many plant species to expand their range to higher latitudes and altitudes, where they may suffer less from natural aboveground and belowground enemies. Reduced control by natural enemies can enable climate warming-induced range expanders to get an advantage in competition with natives and become disproportionally abundant in their new range. However, so far studies have examined individual growth of range expanders, which have common congeneric plant species in their new range. Thus it is not known how general is this reduced effect of above- and belowground enemies and how it operates in communities, where multiple plant species also interact with each other. Here we show that range-expanding plant species with and without congenerics in the invaded habitats differ in their ecological interactions in the new range. In a community-level experiment, range-expanding plant species, both with and without congenerics, suppressed the growth of a herbivore. However, only range expanders without congenerics reduced biomass production of the native plant species. In the present study, range expanders without congenerics allocated more biomass aboveground compared to native plant species, which can explain their competitive advantage. Competitive interaction and also biomass allocation of native plants and their congeneric range expanders were similar. Our results highlight that information about species phylogenetic relatedness with native flora can be crucial for improving predictions about the consequences of climate warming-induced range expansions.
Data from: Applying community ecological theory to maximize productivity of cultivated biocrusts
Degraded rangelands around the world may benefit from the reestablishment of lost biological soil crusts (biocrusts, soil surface cryptogamic-microbial communities). Cultivation of biocrust organisms is the first step in this process, and may benefit from harnessing species interactions. Species interactions are a dominant force structuring ecological communities. One key element of community structure, species richness, is itself important because it can promote the productivity of the entire community. Here, we use biological soil crusts as a model to test the effects of species interactions on production of biocrust materials for use in ecosystem rehabilitation. We screened eight different moss and lichen species from semi-arid rangelands of Montana, USA, for growth potential under two watering regimes. Mosses generally grew well, but we were unable to cultivate the selected lichen species. We produced a >400% increase in the biomass of one species (Ceratodon purpureus). We tested whether a parasite-host relationship between two lichens could be used to enhance productivity of the parasite species, but this also resulted in no net gain of lichen productivity. Finally, we constructed all possible community combinations from a pool of five moss species to test for overyielding (community productivity exceeding that expected from the growth of community members in monoculture), and to determine both if, and the mode in which, species richness increases productivity. Polycultures yielded more than would be expected based upon the production of community constituents in monoculture. Using structural equation models we determined that there was a modest effect of species richness on community productivity (r = 0.24-0.25), which was independent of a stronger effect of the identity of species in the community (r = 0.41-0.50). These results will contribute to the optimization of biocrust cultivation, promoting the development of this emerging ecological rehabilitation technology.
Ecological impacts of pesticide seed treatments on arthropod communities in a grain crop rotation
<p>1. While many studies have investigated non-target impacts of neonicotinoid seed treatments (NSTs), they usually take place within a single crop and focus on specific pest or beneficial arthropod taxa.</p> <p>2. We compared the impacts of three seed treatments to an untreated control: imidacloprid + fungicide products, thiamethoxam + fungicide products, and fungicide products alone in a three-year crop rotation of full-season soybean, winter wheat, double-cropped soybean and maize. Specifically, we quantified neonicotinoid residues in the soil and in weedy winter annual flower buds and examined treatment impacts on soil and foliar arthropod communities as well as on plant growth and yield.</p> <p>3. Unquantifiably low amounts of insecticide were found in winter annual flowers of one species in one site year, which did not correspond with our treatments. Although low levels of insecticide residues were present in the soil, residues were not persistent. Residues were highest in the final year of the study, suggesting some accumulation.</p> <p>4. We observed variable impacts of NSTs on the arthropod community; principle response curve and redundancy analyses exhibited occasional treatment effects, with treatments impacting the abundance of various taxa, including predators and parasitoids. Overall, foliar taxa were impacted more than soil taxa, and the fungicides occasionally effected communities and individual taxa.</p> <p>5. Pest pressure was low throughout the study, and although pest numbers were reduced by the insecticides, corresponding increases in yield were not observed.</p> <p>6. <i>Synthesis and applications.</i> Pesticide seed treatments can impact arthropod taxa, including important natural enemies even when environmental persistence and active ingredient concentrations are low. The foliar community in winter wheat showed that in some cases, these impacts can last for several months after planting. Given the low pest pressure and lack of yield improvement in full-season and double-cropped soybean, winter wheat, and maize, we did not observe benefits that could justify the risks associated with neonicotinoid seed treatment (NST) use. Our results suggest that NSTs are not warranted in Maryland grain production, outside of specific instances of high pest pressure.</p>
Data from: Precipitation alters interactions in a grassland ecological community
Climate change is transforming precipitation regimes world-wide. Changes in precipitation regimes are known to have powerful effects on plant productivity, but the consequences of these shifts for the dynamics of ecological communities are poorly understood. This knowledge gap hinders our ability to anticipate and mitigate the impacts of climate change on biodiversity. Precipitation may affect fauna through direct effects on physiology, behaviour or demography, through plant-mediated indirect effects, or by modifying interactions among species. In this paper, we examined the response of a semi-arid ecological community to a fivefold change in precipitation over 7 years. We examined the effects of precipitation on the dynamics of a grassland ecosystem in central California from 2007 to 2013. We conducted vegetation surveys, pitfall trapping of invertebrates, visual surveys of lizards and capture–mark–recapture surveys of rodents on 30 plots each year. We used structural equation modelling to evaluate the direct, indirect and modifying effects of precipitation on plants, ants, beetles, orthopterans, kangaroo rats, ground squirrels and lizards. We found pervasive effects of precipitation on the ecological community. Although precipitation increased plant biomass, direct effects on fauna were often stronger than plant-mediated effects. In addition, precipitation altered the sign or strength of consumer-resource and facilitative interactions among the faunal community such that negative or neutral interactions became positive or vice versa with increasing precipitation. These findings indicate that precipitation influences ecological communities in multiple ways beyond its recognized effects on primary productivity. Stochastic variation in precipitation may weaken the average strength of biotic interactions over time, thereby increasing ecosystem stability and resilience to climate change.
Common barriers, but temporal dissonance: genomic tests suggest ecological and paleo-landscape sieves structure a coastal riverine fish community
<p>Assessments of spatial and temporal congruency across taxa from genetic data provide insights into the extent to which similar processes structure communities. However, for coastal regions that are affected continuously by cyclical sea-level changes over the Pleistocene, congruent interspecific response will not only depend upon co-distributions, but also on similar dispersal histories among taxa. Here, we use SNPs to test for concordant genetic structure among four co-distributed taxa of freshwater fishes (Teleostei: Characidae) along the Brazilian Atlantic coastal drainages. Based on population relationships and hierarchical genetic structure analyses, we identify all taxa share the same geographic structure suggesting the fish utilized common passages in the past to move between river basins. In contrast to this strong spatial concordance, model-based estimates of divergence times indicate that despite common routes for dispersal, these passages were traversed by each of the taxa at different times resulting in varying degrees of genetic differentiation across barriers with most divergences dating to the Upper Pleistocene, even when accounting for divergence with gene flow. Interestingly, when this temporal dissonance is viewed through the lens of the species-specific ecologies, it suggests that an ecological sieve influenced whether species dispersed readily, with an ecological generalist showing the highest propensity for historical dispersal among the isolated rivers of the Brazilian coast (i.e., the most recent divergence times and frequent gene flow estimated for barriers). We discuss how our findings, and in particular what the temporal dissonance, despite common geographic passages, suggest about past dispersal structuring coastal communities as a function of ecological and paleo-landscape sieves.</p>
Dataset supplementing Lichtenberg et al. (2017) Foraging traits modulate stingless bee community disassembly under forest loss. Journal of Animal Ecology
<p>This dataset contains data and scripts that supplement the publication</p> <p>Lichtenberg et al. (2017) Foraging traits modulate stingless bee community disassembly under forest loss. Journal of Animal Ecology. DOI 10.1111/1365-2656.12747.</p> <p> </p> <p>Please cite the above article if you use any of the included data or code.</p> <p> </p> <p>Files are described in README.md.</p>
Data from: Geography and ecology shape the phylogenetic composition of Amazonian tree communities
<p><strong>Aim:</strong> Amazonia hosts more tree species, from numerous evolutionary lineages both young and ancient, than any other biogeographic region. Previous studies have shown that tree lineages colonised multiple edaphic environments and dispersed widely across Amazonia, leading to a hypothesis, which we test, that lineages should not be strongly associated with either geographic regions or edaphic forest types.</p> <p><strong>Location:</strong> Amazonia.</p> <p><strong>Taxon:</strong> Angiosperms (Magnoliids; Monocots; Eudicots).</p> <p><strong>Methods:</strong> Data for the abundance of 5,082 tree species in 1,989 plots were combined with a mega-phylogeny. We applied evolutionary ordination to assess how phylogenetic composition varies across Amazonia. We used variation partitioning and Moran's eigenvector maps (MEM) to test and quantify the separate and joint contributions of spatial and environmental variables to explain the phylogenetic composition of plots. We tested the indicator value of lineages for geographic regions and edaphic forest types and mapped associations onto the phylogeny.</p> <p><strong>Results:</strong> In the terra firme and várzea forest types, phylogenetic composition varies by geographic region, but the igapó and white-sand forest types retain a unique evolutionary signature regardless of region. Overall, we find that soil chemistry, climate, and topography explain 24% of the variation in phylogenetic composition, with 79% of that variation being spatially structured (R <sup>2</sup> = 19% overall for combined spatial/environmental effects). Phylogenetic composition also shows substantial spatial patterns not related to the environmental variables we quantified (R <sup>2</sup> = 28%). A greater number of lineages were significant indicators of geographic regions than forest types.</p> <p><strong>Main conclusions:</strong> Numerous tree lineages, including some ancient ones (>66 Ma), show strong associations with geographic regions and edaphic forest types of Amazonia. This shows that specialization on specific edaphic environments has played a long-standing role in the evolutionary assembly of Amazonian forests. Furthermore, many lineages, even those that have dispersed across Amazonia, dominate within a specific region, likely because of phylogenetically conserved niches for environmental conditions that are prevalent within regions. </p>
Data for Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach
<p>Environmental DNA (eDNA) is gaining a growing popularity among scientists but its applicability to biodiversity research and management remains limited in river systems by the lack of knowledge about the spatial extent of the downstream transport of eDNA.</p> <p>Here, we assessed the ability of eDNA inventories to retrieve spatial patterns of fish assemblages along two large and species rich Neotropical rivers. We first examined overall community variation with distance through the distance decay of similarity and compared this pattern to capture-based samples. We then considered previous knowledge on individual species distributions, and compared it to the eDNA inventories for a set of 53 species.</p> <p>eDNA collected from 28 sites in the Maroni and 25 sites in the Oyapock rivers permitted to retrieve a decline of species similarity with distance between sites. The distance decay of similarity derived from eDN<span>A </span>was similar, and even more pronounced, than that obtained with capture-based methods (gil-nets). In addition, the species upstream-downstream distribution range derived from eDNA matched to the known distribution of most species.</p> <p>Our results demonstrate that environmental DNA does not represent an integrative measure of biodiversity across the whole upstream river basin but provide a relevant picture of local fish assemblages. Importantly, the spatial signal gathered from eDNA was therefore comparable to that gathered with local capture based methods, which describes fish fauna over a few hundred metres.</p>
Ecological and evolutionary processes shape belowground springtail communities along an elevational gradient
<p> The data sets were analyzed during the current study. Data from: Ecological and evolutionary processes shape belowground springtail communities along an elevational gradient</p>
Distance decay 2.0 – a global synthesis of taxonomic and functional decay in ecological communities
<p>Datasets used in the analysis of the manuscript by Graco-Roza, C., Aarnio, S., Abrego, N., Acosta, A. T., Alahuhta, J., Altman, J., ... & Soininen, J. (2022). Distance decay 2.0–a global synthesis of taxonomic and functional turnover in ecological communities.<em> Global Ecology and Biogeography.</em></p> <p> </p> <p><strong>raw_data.zip - </strong>Includes the raw datasets used in the analysis. </p> <p><strong>processed_data.xlsx - </strong>Includes the results from the distance decay analysis, specifically: </p> <p>- Dataset : dataset code (same as in raw_data)</p> <p>- Beta_type: The component of beta diversity (i.e., total similarity, replacement, richness differences)</p> <p>- Level : Taxonomic (TAX) or functional (FUN)</p> <p>- Based: Occurrence (occ) or Abundance (abund)</p> <p>- Organism: Code used to describe organisms (see Appendix S1 of the paper)</p> <p>- Realm: Aquatic, Terrestrial, or Freshwaters</p> <p>- Body_size </p> <p>- Dispersal_mode: Seeds, Passive or Active</p> <p>- Latitude: Mean latitude of the dataset (average of all data points)</p> <p>- Latitude_range Distance in kilometres between the two vertically most distant points.</p> <p>- Longitude_range: Distance in kilometres between the two horizontally most distant points.</p> <p>- spa_min: minimum distance between sites (in kilometres) </p> <p>- spa_mean: average distance between sites (in kilometres) </p> <p>- spa_max: maximum distance between sites (in kilometres)</p> <p>- ext: area in kilometres covered by all sites in the dataset</p> <p>- n_sites: Number of sites in each dataset</p> <p>- n_var: Number of environmental variables in each dataset</p> <p>- gamma_spe: Number of species observed in each dataset</p> <p>- gamma_trait: Volume of the hypervolume constructed using the traits in each dataset</p> <p>- n_traits: Number of traits in each dataset</p> <p>- Intercept_spa: Intercept of GLM including community similarity and spatial distances</p> <p>- Slope_Spa: Slope of GLM including community similarity and spatial distances</p> <p>- R2_spa: R² of GLM including community similarity and spatial distances</p> <p>- Intercept_env: Intercept of GLM including community similarity and environmental distances</p> <p>- Slope_env: Slope of GLM including community similarity and environmental distances</p> <p>- R2_env: R² of GLM including community similarity and environmental distances</p> <p>- Mantel_spa: Mantel statistics of community similarity and spatial distances</p> <p>- spa_signif: Significance of Mantel statistics considering community similarity and spatial distances</p> <p>- Mantel_env: Mantel statistics considering community similarity and environmental distances</p> <p>- env_signif: Significance of Mantel statistics considering community similarity and environmental distances</p> <p><strong>Null_models.zip - </strong>Includes the results from the null models for each dataset.</p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p>
Determinism and stochasticity in the spatial-temporal continuum of ecological communities: the case of tropical mountains
<p>Ecological communities are assembled in a spatial-temporal continuum. However, we still have a poor understanding of the relative importance of different mechanisms structuring community composition (i.e., beta-diversity) in space and time. In this study, we start by introducing a conceptual model that capitalizes upon the core-occasional species concept to predict that the assembly process in tropical mountains is driven by the deterministic turnover of core species in space via habitat sorting, but the turnover of occasional species through time via stochastic events of colonization and local extinctions. We then propose a general analytical framework that allows assessing these predictions by partitioning the total variance of a species-by-site-by-time matrix (i.e., total beta-diversity) among its purely spatial (variation in space independent of time), purely temporal (variation in time independent of space), and spatiotemporal (i.e., variation across different sites across different moments in time) components. Through simulation models, we provided theoretical support that the proposed analytical framework is suitable to test the predictions derived from our conceptual model. We then used this framework to identify general patterns and quantify the relative importance of processes underlying the spatial and temporal organization of ten distinct insect metacommunities along a tropical elevational gradient. As predicted, we found that, across taxa, spatial beta-diversity was mainly explained by environmental variation alone: a pattern that indicates the spatial turnover of core species. In contrast, temporal beta-diversity could not be distinguished from the expectation of null models where communities are simply represented by random draws from species pools: a pattern that indicates a temporal turnover of occasional species within communities. Taken together, our findings illustrate how our conceptual model and quantitative framework can articulate a better understanding of community assembly in space and time.</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.