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155 results for “interaction scale”
Data from: The role of climate, water and biotic interactions in shaping biodiversity patterns in arid environments across spatial scales
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Do large-scale associations in birds imply biotic interactions or environmental filtering?
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Benchmark dataset for pore-scale CO2-water interaction
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Scale dependency of joint species distribution models challenges interpretation of biotic interactions
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Data from: Magnitude and direction of stream-forest community interactions change with time scale
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Small-scale fires interact with herbivore feedbacks to create persistent grazing lawn environments
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Multiple spatial scales affect direct and indirect interactions between a non-native and a native species
Plant–plant interactions influence community assembly and species responses to environmental change. However, species interactions are complex phenomena influenced by context and scale. We conducted a one-year replacement experiment between two grasses in subtropical grasslands (native Axonopus fissifolius and non-native Paspalum notatum) in central Florida, USA. We evaluated interactions between these species at three ecological scales, ‘pairwise interactions’, ‘patch’ (33 cm x 33 cm) and ‘plot’ (1m x 3m), and along a gradient (15 levels) of increasing non-native and decreasing native plot groundcover within enclosures in semi-native pastures. We transplanted 18 individuals of each species per plot (18 × 30 plots = 1080 plants in total) in a 2×2 design intersecting direct pairwise interactions (additional transplanted neighbor: absent/present) with recipient patch type (Axonopus fissifolius/Paspalum notatum). Leaf length, leaf number and plant biomass were measured at the beginning and the end of the experiment along with soil nutrients and pH at patch level. Over 92% of the transplants survived. We observed an interactive effect between patch type (non-native vs. native dominated) and plant abundance at plot level on plant performance, suggesting that indirect effects at larger spatial scales can influence effects at smaller scales. Surprisingly, both species exhibited enhanced performance with increasing abundance of the non-native species at plot level. We discuss several mechanisms explaining these indirect effects including Paspalum notatum induced changes in soil pH, soil feedbacks from the soil microbial community, preconditioning effects of the native species on the recipient soil, and positive density dependence effects after transplantation.
Surface water chemistry:Scale Dependent Nutrient Interactions among Lacustrine Communities
E280 is a long-term study, initiated in 2013, to determine how nutrient retention vs. export in the uplands affects downslope aquatic communities. Experimental work will focus on stoichiometry and patterns of nutrient limitation at different observational scales. Our proposed work will test the hypothesis that with increasing spatial and temporal scale, interactions among limiting nutrients diminish and single factor limitation is increasingly prevalent.
Large-scale metabolic interaction network of the mouse and human gut microbiota
<p>The role of our gut microbiota in health and disease is largely attributed to the collective metabolic activities of the inhabitant microbes. A system-level framework of the microbial community structure, mediated through metabolite transport, would provide important insights into the complex microbe-microbe and host-microbe chemical interactions. This framework, if adaptable to both mouse and human systems, would be useful for mechanistic interpretations of the vast amounts of experimental data from gut microbiomes in murine animal models, whether humanized or not. Here, we constructed a literature-curated, interspecies network of the mammalian gut microbiota for mouse and human hosts, called NJC19. This network is an extensive data resource, encompassing 838 microbial species (766 bacteria, 53 archaea, and 19 eukaryotes) and 6 host cell types, interacting through 8,224 small-molecule transport and macromolecule degradation events. Moreover, we compiled 912 negative associations between organisms and metabolic compounds that are not transportable or degradable by those organisms. Our network may facilitate experimental and computational endeavors for the mechanistic investigations of host-associated microbial communities.</p>
Temperature and predator cues interactively affect ontogenetic metabolic scaling of aquatic amphipods
<p>A common belief is that body-mass scaling of metabolic rate results chiefly from intrinsic body-design constraints. However, several studies have shown that multiple ecological factors affect metabolic scaling. The mechanistic basis of these effects is largely unknown. Here, we explore whether abiotic and biotic environmental factors have interactive effects on metabolic scaling. To address this question, we studied the simultaneous effects of temperature and predator cues on the ontogenetic metabolic scaling of amphipod crustaceans inhabiting two different aquatic ecosystems, a freshwater spring and a saltwater lagoon. We assessed effects of phenotypic plasticity on metabolic scaling by exposing amphipods in the laboratory to water with and without fish-cues at multiple temperatures. Temperature interacts significantly with predator cues to affect metabolic scaling. Our results suggest that metabolic scaling is highly malleable in response to short-term acclimation. The interactive effects of temperature and predators show the importance of studying effects of global warming in realistic ecological contexts.</p>
Data from: Density-dependent offspring interactions do not explain macroevolutionary scaling of adult size and offspring size
Most lifeforms exhibit a correlated evolution of adult size (AS) and size at independence (SI), giving rise to AS-SI scaling relationships. Theory suggests that scaling arises because relatively large adults have relatively high reproductive output, resulting in strong density-dependent competition in early life, where large size at independence provides a competitive advantage to juveniles. The primary goal of our study is to test this Density Hypothesis, using large datasets that span the vertebrate tree of life (fishes, amphibians, reptiles, birds, and mammals). Our secondary goal is to motivate new hypotheses for AS-SI scaling, by exploring how subtle variation in life-histories among closely-related species is associated with variation in scaling. Our phylogenetically-informed comparisons do not support the Density Hypothesis. Instead, exploration of AS-SI scaling among life-history variants suggests that steeper AS-SI scaling slopes are associated with evolutionary increases in size at independence. We suggest that a positive association between size at independence and juvenile growth rate may represent an important mechanism underlying AS-SI scaling, a mechanism that has been underappreciated by theorists. If faster juvenile growth is a consequence of evolutionary increases in size at independence, this may help offset the cost of delayed maturation, leading to steeper AS-SI scaling slopes.
Data from: Helianthus maximiliani and species fine-scale spatial pattern affect diversity interactions in reconstructed tallgrass prairies
1. Biodiversity and Ecosystem Function analyses aim to explain how individual species and their interactions affect ecosystem function. With this study we asked in what ways do species interact, are these interactions affected by species planting pattern, and are initial (planted) proportions or previous year (realized) proportions a better reference point for characterizing grassland diversity effects? 2. We addressed these questions with experimental communities compiled from a pool of 16 tallgrass prairie species. We planted all species in monocultures and mixtures that varied in their species richness, evenness, and spatial pattern. We recorded species-specific biomass production over three growing seasons and fitted Diversity-Interactions (DI) models to annual plot biomass yields. 3. In the establishment season, all species interacted equally to form the diversity effect. In years 2 and 3, each species contributed a unique additive coefficient to its interaction with every other species to form the diversity effect. These interactions were affected by H. maximiliani and the species planting pattern. Models based on species planted proportions better-fit annual plot yields than models based on species previous contributions to plot biomass. 4. Outcomes suggest that efforts to plant tallgrass prairies to maximize diversity effects should focus on the specific species present and in what arrangement they are planted. Furthermore, for particularly diverse grasslands, the effort of collecting annual species biomass data may not be necessary when quantifying diversity effects with Diversity-Interactions models.
Data from: Frugivore biodiversity and complementarity in interaction networks enhance landscape-scale seed dispersal function
1. Animal biodiversity matters for the provision of ecosystem functions derived from trophic activity. However, the mechanisms underlying this pattern remain elusive since animal abundance and diversity, which are the components commonly used for representing biodiversity, provide poor information about ecological complementarity in species assemblages. An approach based on species interaction networks may overcome this constraint. 2. Here, we relate frugivore biodiversity and frugivore-plant network structure with landscape-scale seed dispersal function. We sampled, for two years, and at fourteen plots with variable assemblages of frugivores and plants in the Cantabrian Range (N Spain), data on the abundance and diversity of frugivorous birds, the consumption of fleshy fruits of woody plants, and the landscape-scale patterns of avian seed deposition. As a measure of interaction complementarity in seed dispersal networks, we estimated the degree to which frugivore and plant species specialize in their interacting partners. 3. Specialization varied strongly across the seed dispersal networks of the different plots, being higher in networks harboring smaller bird species that dispersed mostly small-fruited plants, and also in networks with late-ripening, dominant fruiting species dispersed mostly by wintering birds. 4. Bird abundance markedly affected seed deposition. Plots harboring more birds received a higher density of dispersed seeds, and showed higher probabilities of seed arrival and seed deposition in open microhabitats. Bird diversity also had a positive effect on the density of dispersed seed and, to a lesser extent, seed arrival probability. Independently of frugivore abundance and diversity, the density of dispersed seeds increased in plots where seed dispersal networks showed a higher degree of specialization. 5. This study considers the structure of interaction networks to re-address the relationship between biodiversity and ecosystem functionality, evidencing that specialization in frugivore-plant networks drives the large-scale process of seed dispersal. These results encourage the consideration of interaction complementarity as an underlying mechanism linking animal biodiversity and trophic-related functions.
Data from: Local and landscape-scale heterogeneity shape spotted wing drosophila (Drosophila suzukii) activity and natural enemy abundance: implications for trophic interactions
Like natural enemies, invasive polyphagous pests may respond positively to local and landscape-scale diversity, making them more serious challenges to sustainable management than specialists. Yet the current view of landscape effects on pests rarely considers perennial systems or polyphagous pests. We investigated Drosophila suzukii (SWD) and natural enemy distributions and trophic interactions in blueberry systems of the southeast US in relation to local management and landscape structure. Fields were nested in 1-km landscapes along gradients of crop and forest heterogeneity (landscape compositional diversity) and field border and crop border lengths (landscape configurational diversity). Yeast-sugar bait traps were used to collect SWD and canopy suction sampling for natural enemies. Management practices at the local scale did not influence SWD abundance, but natural enemy abundance was higher in organic systems and fields with vegetation present between rows. Landscape configurational diversity and greater proportion of non-cropping habitat promoted higher SWD populations. Natural enemy communities were composed of highly generalized species, and contrary to our predictions, we observed lower abundances in landscapes with higher proportion of non-cropping area. Few predators were detected to have fed on SWD, and communities were dominated by predators with low specialization on prey in blueberry. Our results indicate that local and landscape features in blueberry landscapes have differential effects on a polyphagous pest and generalist natural enemies. Our initial analysis of predator diets, using a metabarcoding approach, suggests spatial structure in specialization on prey with high diversity of prey in predators collected in forested margins.
Data from: Functional outcomes of mutualistic network interactions: a community-scale study of frugivore gut passage on germination
1. Current understanding of mutualistic networks is grounded largely in data on interaction frequency, yet mutualistic network dynamics are also shaped by interaction quality—the functional outcomes of individual interactions on reproduction and survival. The difficulty of obtaining data on functional outcomes has resulted in limited understanding of functional variation among a network's pairwise species interactions, of the study designs that are necessary to capture major sources of functional variation, and of predictors of functional variation that may allow generalization across networks. 2. In this community-scale study, we targeted a key functional outcome in plant-frugivore networks: the impact of frugivore gut passage on seed germination. We used captive frugivore feeding trials and germination experiments in an island ecosystem, attaining species-level coverage across all extant native frugivores and the plants they consume to 1) assess sources of functional variation, 2) separate effects of pulp removal from those of scarification via gut passage, and 3) test trait-based correlates of gut passage effect sizes. 3. We found antagonistic seed predation effects of a frugivore previously assumed to be a seed disperser, highlighting the need to consider functional outcomes rather than interaction frequency alone. The other frugivores each exhibited similar impacts for individual plant species, with benefits primarily caused by pulp removal rather than scarification, supporting the use of animal functional groups in this context. In contrast, plant species varied widely in impacts of gut passage on germination. Species with smaller seeds and more frugivore partners had larger benefits of gut passage, showing promise for network metrics and functional traits to predict functional variation among plants. 4. Synthesis. Combining network and demographic approaches, we assessed the degree and sources of variation in a key functional outcome of plant-frugivore interactions across an entire network. Using a detailed study design, our work shows how simpler study designs can capture primary sources of functional variation and that functional traits and network metrics may allow generalization across networks. Efficiently measuring and generalizing sources of functional variation within mutualistic networks will strengthen our ability to model network dynamics and predict mutualist responses to global change.
Data from: Detecting small-scale genotype-environment interactions in apomictic dandelion (Taraxacum officinale) populations
Studies of genotype × environment interactions (G×E) and local adaptation provide critical tests of natural selection's ability to counter opposing forces such as gene flow. Such studies may be greatly facilitated in asexual species, given the possibility for experimental replication at the level of true genotypes (rather than populations) and the possibility of using molecular markers to assess genotype-environment associations in the field (neither of which is possible for most sexual species). Here we tested for G×E in asexual dandelions (Taraxacum officinale) by subjecting six genotypes to experimental drought, mown, and benign (control) conditions, and subsequently using microsatellites to assess genotype-environment associations in the field. We found strong G×E, with genotypes that performed poorly under benign conditions showing the highest performance under stressful conditions (drought or mown). Our six focal genotypes comprise >80% of plants in local populations. The most common genotype in the field showed its highest relative performance under mown conditions (the most common habitat in our study area), and almost all plants of this genotype in the field were found growing in mowed lawns. Genotypes performing best under benign experimental conditions were found most frequently in unmown conditions in the field. These results are strongly indicative of local adaptation at a very small scale, with unmown microsites of only a few square meters typically embedded within larger mown lawns. By studying an asexual species we were able to map genotypes with known ecological characteristics to environments with high spatial precision.
Data from: Spatial and temporal aridity gradients provide poor proxies for plant-plant interactions under climate change: a large-scale experiment
1. Plant-plant interactions may critically modify the impact of climate change on plant communities. However, the magnitude and even direction of potential future interactions remains highly debated, especially for water limited ecosystems. Predictions range from increasing facilitation to increasing competition with future aridification. 2. The different methodologies used for assessing plant-plant interactions under changing environmental conditions may affect the outcome but they are not equally represented in the literature. Mechanistic experimental manipulations are rare compared to correlative approaches that infer future patterns from current observations along spatial climatic gradients. 3. Here, we utilize a unique climatic gradient in combination with a large-scale, long-term experiment to test whether predictions about plant-plant interactions yield similar results when using experimental manipulations, spatial gradients or temporal variation. We assessed shrub-annual interactions in three different sites along a natural rainfall gradient (spatial) during 9 years of varying rainfall (temporal) and 8 years of dry and wet manipulations of ambient rainfall (experimental) that closely mimicked regional climate scenarios. 4. The results were fundamentally different among all three approaches. Experimental water manipulations hardly altered shrub effects on annual plant communities for the assessed fitness parameters biomass and survival. Along the spatial gradient, shrub effects shifted from clearly negative to mildly facilitative towards drier sites, whereas temporal variation showed the opposite trend: more negative shrub effects in drier years. 5. Based on our experimental approach, we conclude that shrub-annual interaction will remain similar under climate change. In contrast, the commonly applied space-for time approach based on spatial gradients would have suggested increasing facilitative effects with climate change. We discuss potential mechanisms governing the differences among the three approaches. 6. Our study highlights the critical importance of long-term experimental manipulations for evaluating climate change impacts. Correlative approaches, e.g. along spatial or temporal gradients, may be misleading and overestimate the response of plant-plant interactions to climate change.
Data from: Prey limitation drives variation in allometric scaling of predator-prey interactions
Ecologists have long searched for a universal size-scaling constant that governs trophic interactions. Although this is an appealing theoretical concept, Predator-Prey Size Ratios (PPSR) vary strikingly across and within natural food webs, meaning that predators deviate from their optimal prey size by consuming relatively larger or smaller prey. Here, we suggest that this unexpected variation in allometric scaling of trophic interactions can be predicted by gradients of prey limitation consistent with predictions from the Optimal Foraging Theory. We analyzed >6,000 trophic interactions of 52 populations from four tropical frog species along a gradient of prey limitation. Mean of PPSR and its variance differed up to two orders of magnitude across and within food webs. Importantly, as prey availability decreased across food webs, PPSR and its variance became more size-dependent. Thus, trophic interactions did not follow a fixed allometric scaling but changed predictably with the strength of prey limitation. Our results emphasize the importance of ecological contexts in arranging food webs and the need to incorporate ecological drivers of PPSR and its variance in food web and community models.
FIGURES 39–44. T. lomalarga-ants interactions. Scale 2 in Natural history of the mistletoe-feeding Thereus lomalarga (Lepidoptera, Lycaenidae, Eumaeini) in Colombia
FIGURES 39–44. T. lomalarga-ants interactions. Scale 2mm; arrow points to DNO. 39. 4 th instar with Camponotus. 40. Idem, with Pheidole. 41. Idem, with Wasmannia. 42. Secretion droplet. 43. Crematogaster ants tending both early 3 rd instar of Th. lomalarga brown morph and scale insects. Larva of T. lomalarga is close to a stem at the base of the inflorescence; arrows point to larva and Coccidae. 44. 4 th instar with Crematogaster.
A cavity-microscope for micrometer-scale control of atom-photon interactions
<p>Data corresponding to the article "A cavity-microscope for micrometer-scale control of atom-photon interactions".</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.