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364 results for “Network interaction”
Data and Code for Inequality is rising where social network segregation interacts with urban topology
<p>This folder contains data and code to reproduce results of the paper "Inequality is rising where social network segregation interacts with urban topology". arXiv version: https://arxiv.org/abs/1909.11414.</p>
Data from: Plant interactions shape pollination networks via nonadditive effects
Plants grow in communities where they interact with other plants and with other living organisms such as pollinators. On the one hand, studies of plant–plant interactions rarely consider how plants interact with other trophic levels such as pollinators. On the other, studies of plant–animal interactions rarely deal with interactions within trophic levels such as plant–plant competition and facilitation. Thus, to what degree plant interactions affect biodiversity and ecological networks across trophic levels is poorly understood. We manipulated plant communities driven by foundation species facilitation and sampled plant–pollinator networks at fine spatial scale in a field experiment in Sierra Nevada, Spain. We found that plant–plant facilitation shaped pollinator diversity and structured pollination networks. Nonadditive effects of plant interactions on pollinator diversity and interaction diversity were synergistic in one foundation species networks while they were additive in another foundation species. Nonadditive effects of plant interactions were due to rewiring of pollination interactions. In addition, plant facilitation had negative effects on the structure of pollination networks likely due to increase in plant competition for pollination. Our results empirically demonstrate how different network types are coupled, revealing pervasive consequences of interaction chains in diverse communities.
Data from: Empirical evaluation of neutral interactions in host-parasite networks
While niche-based processes have been invoked extensively to explain the structure of interaction networks, recent studies propose that neutrality could also be of great importance. Under the neutral hypothesis, network structure would simply emerge from random encounters between individuals and thus would be directly linked to species abundance. We investigated the impact of species abundance distributions on qualitative and quantitative metrics of 113 host-parasite networks. We analysed the concordance between neutral expectations and empirical observations at interaction, species and network levels. We found that species abundance accurately predicts network metrics at all levels. Despite host-parasite systems being constrained by physiology and immunology, our results suggest that neutrality could also explain, at least partially, their structure. We hypothesize that trait-matching would determine potential interactions between species, while abundance would determine their realization.
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: 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".
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: Experimental evidence for fundamental, and not realised, niche partitioning in a plant-herbivore community interaction network
Patterns of niche partitioning can result from local ecological interactions (e.g. interspecific competition) occurring within a contemporary time frame (realised niche partitioning). Alternatively they may represent the end-product of historical processes acting over long time frames (fundamental niche partitioning). Niche partitioning is often detected by analysing patterns of resource use within communities, but experiments are rarely conducted to test whether patterns of non-overlapping resource use reflect realised or fundamental niche partitioning. We studied a community of restio leafhoppers from the genus Cephalelus, and their host plants, the Restionaceae (restios). We used network and experimental approaches to determine whether network modularity (a measure of niche partitioning within local communities) reflects fundamental or realised niche partitioning. Using a weighted modularity index for two party networks (e.g. insect - plant) we determined whether the network of this community is modular (i.e. consists of groups of species interacting strongly, with weak interactions between groups). We also aimed to identify specific Cephalelus - restio modules (groups). Using knowledge of module membership to design experiments, we tested whether Cephalelus species from two different modules, C. uncinatus and C. pickeri, prefer and perform better on restios from their own modules versus restios from other modules. These experiments were performed under controlled conditions, eliminating the influences of competition and predation on host choices. The Cephalelus – restio community was modular, implying niche partitioning. Cephalelus also preferred and performed better on restios from their own modules in the absence of local contemporary factors. Most niche partitioning in the investigated Cephalelus community, is not caused by local interactions, and thus host use patterns represent fundamental niches. Our findings highlight the importance of understanding local community structure in the light of processes extrinsic to the local community context.
Data from: Interaction networks of macrofungi and mycophagous beetles reflect diurnal variation and the size and spatial arrangement of resources
Ecological networks are useful for characterizing interspecific associations and predicting the resilience of ecological communities. We evaluated how such networks vary with the size, spatial distribution, and timing of availability of resources, with a focus on beetle-macrofungal associations. We used 2 y of field experiments to construct ecological networks based on manipulated sporocarp baits (resources; Pleurotus ostreatus) and natural communities of beetles (consumers) in a temperate forest. Centrality and interaction strength increased with resource size, but were associated weakly with resource density and isolation, and not at all with position within patches. Whole-network connectance was greater in mornings (when beetle richness and abundance were high) than evenings. Interannual differences in networks were consistent with differences in beetle communities between years. The capacity of networks to vary temporally, spatially, and as a function of resource traits is examined in light of understanding beetle-macrofungal associations, which are important components of fungal ecology.
Data from: Invariant antagonistic network structure despite high spatial and temporal turnover of interactions
Recent work has suggested that emergent ecological network structure exhibits very little spatial or temporal variance despite changes in community composition. However, the changes in network interactions associated with turnover in community composition have seldom been assessed. Here we examine whether changes in ecological networks are best detected by standard emergent network metrics or by assessing internal network changes (i.e. interaction and composition turnover). To eliminate possible spatial or phylogenetic effects, that in large-scale studies may obscure mechanisms structuring networks and interactions, we sampled multiple antagonistic (plant-herbivore) networks for a single diverse plant family (the Restionaceae) in the hyperdiverse Cape Floristic Region. These are the first plant-herbivore networks constructed for this global biodiversity hotspot. We found invariant emergent network structure despite considerable changes in insect and plant composition across communities over time and space. In contrast, there was high interaction turnover between networks. Seasonally, this was driven by turnover in insect species and insect host switching. Spatially, this was driven by simultaneous turnover in plant and insect species, suggesting that many insects are host specific or that both groups exhibit parallel responses to environmental gradients. Spatial interaction turnover was also driven by turnover in plants, showing that many insects can utilise multiple (possibly closely related) hosts and this may create divergent selection gradients that promote insect speciation. Thus we show highly variable interaction fidelity, despite invariant emergent network structure. We suggest that evaluating internal network changes may be more effective at elucidating the processes structuring networks, and many fine-scale changes may be obscured when only calculating emergent network metrics.
Data from: Rate of inter-sex interactions affects injury likelihood in Tasmanian devil contact networks
Identifying the types of contacts that result in disease transmission is important for accurately modelling and predicting transmission dynamics and disease spread in wild populations. We investigated contacts within a population of adult Tasmanian devils (Sarcophilus harrisii) over a six-month period and tested whether individual-level contact patterns were correlated with accumulation of bite wounds. Bite wounds are important in the spread of devil facial tumour disease (DFTD), a clonal cancer cell line transmitted through direct inoculation of tumour cells when susceptible and infected individuals bite each other. We used multi-model inference and network autocorrelation models to investigate the effects of individual-level contact patterns, identities of interacting partners, and position within the social network on the propensity to be involved in bite-inducing contacts. We found that males were more likely to receive potentially disease-transmitting bite wounds than females, particularly during the mating season when males spend extended periods mate-guarding females. The number of bite wounds individuals received during the mating season was unrelated to any of the network metrics examined. Our approach illustrates the necessity for understanding which contact types spread disease in different systems to assist the management of this and other infectious wildlife diseases.
Data from: A dedicated network for social interaction processing in the primate brain
Primate cognition requires interaction processing. Interactions can reveal otherwise hidden properties of intentional agents, such as thoughts and feelings, and of inanimate objects, such as mass and material. Where and how interaction analyses are implemented in the brain is unknown. Using whole-brain functional magnetic resonance imaging in macaque monkeys, we discovered a network centered in the medial and ventrolateral prefrontal cortex that is exclusively engaged in social interaction analysis. Exclusivity of specialization was found for no other function anywhere in the brain. Two additional networks, a parieto-premotor and a temporal one, exhibited both social and physical interaction preference, which, in the temporal lobe, mapped onto a fine-grain pattern of object, body, and face selectivity. Extent and location of a dedicated system for social interaction analysis suggest that this function is an evolutionary forerunner of human mind-reading capabilities.
Replication data and analysis code for the article "Insect-habitat-plant interaction networks provide guidelines to mitigate the risk of transmission of Xylella fastidiosa to grapevine in Southern France"
<p>This deposit contains the dataset used in the article "Insect-habitat-plant interaction networks provide guidelines to mitigate the risk of transmission of Xylella fastidiosa to grapevine in Southern France" in the form of a RData file, directly loadable in R, as well as the Rmd script used to analyse the data and produce the figures.</p>
Datasets for "Physicochemical graph neural network for learning protein-ligand interaction fingerprints from sequence data"
<div> <p>Datasets used for implementing the <a href="https://github.com/huankoh/PSICHIC">PSICHIC</a> experiments shown in the <a href="https://doi.org/10.1101/2023.09.17.558145">manuscript</a>.</p> <p> </p> </div>
HerpesFolds: All-versus-all protein interaction network - VZV
<p>For VZV, all possible protein-protein combinations within the species were structurally predicted with AlphaFold 2.3. A user interface and network visualization can be found at: https://herpesfolds.org/</p>
PoxFolds: All-versus-all protein interaction network - MPOX
<p>For MPOX, all possible protein-protein combinations within the species were structurally predicted with AlphaFold 2.3. A user interface and network visualization can be found at: https://www.poxfolds.org/</p>
Data in support of: Species-specific interactions in an avian-bryophyte dispersal network
<p>Animal dispersal of plant propagules fundamentally alters the success of dispersal events, and thus shapes plant community composition through time. While this is well-documented in seed plants, spore-bearing plants have received little attention with regard to this phenomenon. Birds are particularly attractive as a potential bryophyte dispersal vector given their highly motile nature as well as their association with bryophytes when foraging and building nests. Despite this, species-specific dispersal relationships between birds and bryophytes have never been examined. We captured birds in Gifford Pinchot National Forest in the Pacific Northwest of the United States to sample their legs and tails for bryophyte spores. We found 24 bryophyte species across 34 species of bird. We examined the level of specialization 1) within the overall interaction network to assess community-level patterns and 2) at the plant species level to determine the effect of bird behavioral type on the plant-animal interaction. Our results suggest that associations within the network are more constrained (specialized) than expected by chance. Additionally, we found that avian foraging guild impacted the variety of bryophytes found on an individual bird. Foliage gleaners and ground foragers had particularly specialized associations within the overall disperser-bryophyte network. Our findings suggest that diffuse bird-bryophyte dispersal networks are likely to be common in habitats where birds readily encounter bryophytes and that further work aimed at understanding individual bird-bryophyte species relationships may prove valuable in determining nuance within this newly described dispersal mechanism.</p>
Screencast of the Lokahi2 Prototype: Search Engine with Interactive Knowledge Network Browser Extracted from Text
<p>This video shows a recording of the prototype system Lokahi2. It supports concept surfing for interacting with the search engine, automated document tagging, exploring tags, generating tags for text, and changing depth and dimension of the graph.</p>
Relative species abundance successfully predicts nestedness and interaction frequency of monthly pollination networks in an alpine meadow
<p>Plant-pollinator networks have been repeatedly reported as cumulative ones that are described with >1 years observations. However, such cumulative networks are composed of pairwise interactions recorded at different periods, and thus may not be able to reflect the reality of species interactions in nature (e.g., early-flowering plants typically do not compete for shared pollinators with late-flowering plants, but they are assumed to do so in accumulated networks). Here, we examine the monthly sampling structure of an alpine plant-pollinator bipartite network over a two-year period to determine whether relative species abundance and species traits better explain the network structure of monthly networks than yearly ones. Although community composition and species abundance varied from one month to another, the monthly networks (as well as the yearly networks described with annual pooled data) had a highly nested structure, in which specialists directly interact with generalist partners. Moreover, relative species abundance predicted the nestedness in both the monthly and yearly networks and accounted for a statistically significant percentage of the variation (i.e., 20%-44%) in the pairwise interactions of monthly networks, but not yearly networks. The combination of relative species abundance and species traits (but not species traits only) showed a similar prediction power in terms of both network nestedness and pairwise interaction frequencies. Considering the previously recognized structural pattern and associated mechanisms of plant-pollinator networks, we propose that relative species abundance may be an important factor influencing both nestedness and interaction frequency of pollination networks.</p>
Western Diamondback Rattlesnake interaction matrices for network analysis
<p>Social network ecology is a powerful framework to assess patterns of interconnectedness and identify group-level interactions. We investigated social network structure in a pitviper (<em>Crotalus atrox</em>) to determine if group-level interactions result in network structures for denning, pairing, and parentage. We tested if network centrality was influenced by body length, sex, home range size/location, or generic relatedness. We revealed that networks were structurally modular but not nested. Sex was the only significant predictor of centrality in the parentage network, likely due to high levels of multiple paternity. Genotypic data revealed interacting focal individuals were unlikely to be related in networks; however, analysis of a larger group of subjects suggests kin-association at communal dens. Den selection may be driven by a combination of social preference, experience, and/or genetic relatedness. We demonstrated strong fission-fusion dynamics connected to annual migrations to summer home ranges and use of communal winter dens. Furthermore, both sexes show high fidelity to home ranges and dens, but females occasionally alter den sites, indicating active manipulation of their social environment. Our study illustrates that comprehensive, long-term datasets incorporating social network analysis with spatial and genetic information provide robust and unique insights to understanding social structure of understudied, cryptic taxa.</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.