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30 results for “Species interaction networks”
Geographic range size and species morphology determines the organization of sponge host-guest interaction networks across tropical coral reefs (Raw data)
<p>Datasets for the analysis developed in the Article "<em><strong>Geographic range size and species morphology determines the organization of sponge host-guest interaction networks across tropical coral reefs</strong></em>". For more information, please refer to the original publication.</p> <p>Network_Structural_Index_&_SpogeTraits.csv <- Structural Index for the sponge-dwelling fauna network, sponge accumulated area and sponges’ morphology.</p> <p>NWTA_CoralReefs_Sponges_ interactions.csv <- Relationship between host sponges and guest fauna in the Northwester Atlantic coral reefs</p> <p>NWTA_CoralReefs_Sponge_reacords.csv <- Sponge species incidence records in the Northwester Atlantic coral reefs</p> <p>sponges_morphological_description.csv <- Sponge morphological standardization</p> <p>Network.html <- Interactive sponge-dwelling fauna network</p> <p>Enjoy!<br> </p>
Data and code corresponding to the article "Interaction network structure explains species temporal persistence in empirical plant-pollinator communities"
<p>This upload contains the Datasets and code to generate the results of the article "Interaction network structure explains species temporal persistence in empirical plant-pollinator communities".</p><p>The database comprises two files containing the abundances of plants and pollinators, and one containing the interaction networks among plants and pollinators. </p><p>The code folder contains the code to generate the results, and to generate the figures of the manuscript. </p>
Stable species and interactions in plant-pollinator networks deviate from core position in fragmented habitats
<p><span>S</span><span>pecies</span><span> and their interactions are more dynamic over time and space</span> <span>in</span><span> fragmented habitats </span><span>than</span><span> in continuous habitats</span><span>.</span> <span>In fragmented habitats,</span><span> the</span> <span>low </span><span>nestedness</span> <span>of </span><span>mutualistic</span><span> networks may be related to the</span> <span>position</span><span> change</span> <span>of stable (high persistence over time/space) species and interactions in </span><span>the</span><span> network</span><span>s.</span><span> Previous studies</span> <span>have shown that </span><span>s</span><span>table species </span><span>and</span><span> interactions tend to </span><span>be in</span><span> the core position </span><span>of</span> <span>mutualistic</span><span> networks</span><span>. </span><span>H</span><span>owever</span><span>, </span><span>in fragmented habitats</span><span>, </span><span>it remains unknown whether </span><span>stable species or interactions still </span><span>tend to </span><span>be in</span><span> the core position.</span><span> </span><span>To address this gap,</span> <span>here</span><span> we evaluated </span><span>the correlation between the position of proximity to the network core and the temporal/spatial stability of </span><span>species and interactions</span><span>, </span><span>using</span> <span>the </span><span>observation of 42 plant-pollinator networks conducted in a fragmented island landscape over 3 years</span><span>.</span> <span>We showed that temporally/spatially </span><span>stable </span><span>species </span><span>and</span><span> interactions </span><span>deviated from the network core</span><span> to varying degrees</span><span>. Temporally stable plants</span><span> were</span> <span>most likely to deviate from the network core, followed by</span> <span>pollinators and</span> <span>interactions</span><span>, while only </span><span>spatially stable </span><span>pollinators</span><span> tend to </span><span>deviate from the network core</span><span>. </span><span>When unstable species (</span><span>present in few time/space points</span><span>, </span><span>typically specialists) and interactions occupy the network core,</span> <span>they cannot interact with most species in the network </span><span>as</span><span> generalists</span> <span>do</span><span>, </span><span>result</span><span>ing</span> <span>in</span> <span>the</span> <span>decrease of network nestedness. Therefore, from the perspective of</span><span> position and stability,</span><span> s</span><span>table species and interactions </span><span>deviate from the network core</span> <span>in</span> <span>fragmented habitats</span><span>, which </span><span>is an important reason for</span><span> the</span><span> decrease of</span><span> nestedness in </span><span>mutualistic</span><span> networks</span><span>.</span><span> </span><span>Our study</span><span> suggests that protecting</span> <span>plants that</span><span> occupy the core in large plant-pollinator networks is </span><span>essential for</span> <span>maintaining the network persistence in fragmented habitats.</span></p>
Data from: Abundant top predators increase species interaction network complexity in Northeastern Chinese forests
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Stable species and interactions in plant-pollinator networks deviate from core position in fragmented habitats
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Data from: Seed-dispersal networks in tropical forest fragments: area effects, remnant species, and interaction diversity
<p>Seed dispersal interactions involve key ecological processes in tropical forests that help to maintain ecosystem functioning. Yet this functionality may be threatened by increasing habitat loss, defaunation and fragmentation. However, generalist species, and their interactions, can benefit from the habitat change caused by human disturbance while more specialized interactions mostly disappear. Therefore changes in the structure of the local, within fragment, networks can be expected. Here we investigated how the structure of seed-dispersal networks changes along a gradient of increasing habitat fragmentation. We analysed 16 bird seed-dispersal assemblages from forest fragments of a biodiversity-rich ecosystem. We found significant species-, interaction- and network-area relationships, yet the later was determined by the number of species remaining in each community. The number of frugivorous bird and plant species, their interactions, and the number of links per species decreases as area is lost in the fragmented landscape. In contrast, network nestedness has a negative relationship with fragment area, suggesting an increasing generalization of the network structure in the gradient of fragmentation. Network specialization was not significantly affected by area, indicating that some network properties may be invariant to disturbance. Still, the local extinction of partner species, paralleled by a loss of interactions and specialist-specialist bird-plant seed dispersal associations suggests the functional homogenization of the system as area is lost. Our study provides empirical evidence for network-area relationships driven by the presence/absence of remnant species and the interactions they perform.</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.
Downscaling mutualistic networks from species to individuals reveals consistent interaction niches and roles within plant populations.
<p>Repository containing dataset and code for the manuscript entitled <em>Downscaling mutualistic networks from species to individuals reveals consistent interaction niches and roles within plant populations</em>.</p> <p>For this study, we compiled 46 empirical individual-based networks on plant-animal seed dispersal mutualism, encompassing 1037 plant individuals across 29 species from various regions. We compare the structure of individual-based networks to that of species-based networks and by extending the niche concept to interaction assemblages, we explore levels of individual plant specialization. We examine how individual variation influences network structure and how plant individuals "explore" the interaction niche of the population.</p> <p>Please refer to <strong>makefile.R</strong> for project outline, explanation and codes used, and to the <strong>README</strong> in networks folder for data structure and compilation.</p>
Legacy effects of seed dispersal mechanisms shape the spatial interaction network of plant species in Mediterranean forests
<p>1. Seed dispersal by frugivores plays a key role in structuring and maintaining tree diversity in forests. However, little is known about how the spatial legacy of seed dispersal and early recruitment shapes spatial patterns and the spatial interaction network of plant species in mature forest communities.</p> <p>2. We analysed two fully mapped mixed Pine-Oak forest communities using spatial point pattern analysis to determine (i) the detailed structure of the intraspecific spatial patterns of saplings and adults, (ii) the intra- and interspecific spatial interaction of saplings, adults, and saplings relative to adults, (iii) the spatial patterns of species richness at the community level, and (iv) whether seed dispersal mechanisms affect the plant-plant interaction networks and the ratio of adult to sapling neighbourhood densities used as surrogate for spatial self-thinning.</p> <p>3. The intraspecific spatial patterns of saplings and adults showed in general complex nested cluster structures that were similar for sapling and adult stages, despite of substantial self-thinning in some dry-fruited species. The spatial network of saplings was characterized by positive spatial interactions. Adults of several tree species facilitated saplings in their proximity; however, adults of dry-fruited species, but not those of fleshy-fruited ones, lost almost all positive interactions that occurred at the sapling stage. Besides, interaction strength between adults was positive and often significantly stronger if both species were fleshy-fruited. At the community level, the forests were structured into multispecies clumps across all life stages.</p> <p>4. Synthesis. Our analyses highlight the importance of the spatial legacy of seed dispersal and early recruitment in the assembly of plant communities. Particularly, animal seed dispersal can lead to multispecies clusters and positive spatial associations across life stages in Mediterranean forests, with surprisingly little signatures of negative interactions. Our analysis suggests that changes of the spatial structure across plant life stages are driven by seed dispersal mechanisms and subsequent spatial self-thinning, generating a spatial footprint at the sapling stage that conditions the long-term interactions between adult plants. Combining spatial point pattern analysis with network analysis and species traits is a promising way to disentangle the processes underlying observed patterns of local diversity. </p>
Bacterial Community Diversity and Bacterial Interaction Network in Eight Mosquito Species
<p>Sequences of the V4 region of 16S rRNA from 111 mosquito samples. </p> <p>This dataset was used for analysis of bacterial diversity and bacterial interaction network in eight mosquito species. Result of the analysis is in the article "Bacterial Community Diversity and Bacterial Interaction Network in Eight Mosquito Species" (Genes 2022, 13(11), 2052; https://doi.org/10.3390/genes13112052).</p>
Data for: Honey bees (Apis mellifera) modify plant-pollinator network structure, but do not alter wild species' interactions
<p>Honey bees (<em>Apis mellifera</em>) are widely used for honey production and crop pollination, raising concern for wild pollinators, as honey bees may compete with wild pollinators for floral resources. The first sign of competition, before changes appear in wild pollinator abundance or diversity, may be changes to wild pollinator interactions with plants. Such changes for a community can be measured by looking at changes to metrics of resource use overlap in plant-pollinator interaction networks. Studies of honey bee effects on plant-pollinator networks have usually not distinguished whether honey bees alter wild pollinator interactions, or if they merely alter total network structure by adding their own interactions. To test this question, we experimentally introduced honey bees to a Canadian grassland and measured plant-pollinator interactions at varying distances from the introduced hives. We found that honey bees increased the network metrics of pollinator and plant functional complementarity and decreased interaction evenness. However, in networks constructed from just wild pollinator interactions, honey bee abundance did not affect any of the metrics calculated. Thus, all network structural changes to the full network (including honey bee interactions) were due only to honey bee-plant interactions, and not to honey bees causing changes in wild pollinator-plant interactions. Given widespread and increasing use of honey bees, it is important to establish whether they affect wild pollinator communities. Our results suggest that honey bees did not alter wild pollinator foraging patterns in this system, even in a year that was drier than the 20-year average.</p>
Data from: Honey bees (Apis mellifera) modify plant-pollinator network structure, but do not alter wild species’ interactions
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Data from: Non-native species spread in a complex network: the interaction of global transport and local population dynamics determines invasion success
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Data from: Genetics-based interactions of foundation species affect community diversity, stability, and network structure
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Data from: Seed-dispersal networks in tropical forest fragments: area effects, remnant species, and interaction diversity
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Data and R code from: Downscaling species to individual-level networks reveals the importance of population-level processes in mediating generalized community-wide interaction patterns
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Data from: Estimated missing interactions change the structure and alter species roles in one of the world’s largest seed-dispersal networks
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Legacy effects of seed dispersal mechanisms shape the spatial interaction network of plant species in Mediterranean forests
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Data from: Species traits and abundances predict metrics of plant–pollinator network structure, but not pairwise interactions
Plant–pollinator mutualistic networks represent the ecological context of foraging (for pollinators) and reproduction (for plants and some pollinators). Plant–pollinator visitation networks exhibit highly conserved structural properties across diverse habitats and species assemblages. The most successful hypotheses to explain these network properties are the neutrality and biological constraints hypotheses, which posit that species interaction frequencies can be explained by species relative abundances, and trait mismatches between potential mutualists respectively. However, previous network analyses emphasize the prediction of metrics of qualitative network structure, which may not represent stringent tests of these hypotheses. Using a newly documented temporally explicit alpine plant–pollinator visitation network, we show that metrics of both qualitative and quantitative network structure are easy to predict, even by models that predict the identity or frequency of species interactions poorly. A variety of phenological and morphological constraints as well as neutral interactions successfully predicted all network metrics tested, without accurately predicting species observed interactions. Species phenology alone was the best predictor of observed interaction frequencies. However, all models were poor predictors of species pairwise interaction frequencies, suggesting that other aspects of species biology not generally considered in network studies, such as reproduction for dipterans, play an important role in shaping plant–pollinator visitation network structure at this site. Future progress in explaining the structure and dynamics of mutualistic networks will require new approaches that emphasize accurate prediction of species pairwise interactions rather than network metrics, and better reflect the biology underlying species interactions.
Data from: Selective logging in tropical forests decreases the robustness of liana-tree interaction networks to the loss of host tree species
Selective logging is one of the major drivers of tropical forest degradation, causing important shifts in species composition. Whether such changes modify interactions between species and the networks in which they are embedded remain fundamental questions to assess the 'health' and ecosystem functionality of logged forests. We focus on interactions between lianas and their tree hosts within primary and selectively logged forests in the biodiversity hotspot of Malaysian Borneo. We found that lianas were more abundant, had higher species richness and different species compositions in logged than in primary forests. Logged forests showed heavier liana loads disparately affecting slow-growth tree species, which could exacerbate the loss of timber value and carbon storage already associated to logging. Moreover, simulation scenarios of host tree local species loss indicated that logging might decrease the robustness of liana-tree interaction networks if heavily infested trees (i.e. the most connected ones) are more likely to disappear. This effect is partially mitigated in the short term by the colonization of host trees by a greater diversity of liana species within logged forests, yet this might not compensate for the loss of preferred tree hosts in the long term. As a consequence, species interaction networks may show a lagged response to disturbance, which may trigger sudden collapses in species richness and ecosystem function in response to additional disturbances, representing a new type of "extinction debt".
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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)
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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.