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403 results for “Occurrence Data”
Data from: Bedrock geological map predictions for Phanerozoic fossil occurrences
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Data from: Integrating variation in bacterial-fungal co-occurrence network with soil carbon dynamics
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The occurrence data of Ageratina adenophora in China and Mexico
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Data from: Occurrence, morphology, and taxonomy of the late Cambrian Laurentian dikelocephalid trilobite Osceolia Walcott, 1914
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Data from: Combining past and contemporary species occurrences with ordinal species distribution modeling to investigate responses to climate change
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Occurrence data on chlorinated paraffins in feed and food
<p>This Annex is an excel file which presents tables on chlorinated paraffins on occurrence data in food and dietary exposure assessment for humans.</p>
SCINDA GPS and UHF data supporting analysis in "On the assessment of daily Equatorial Plasma Bubble occurrence modeling and forecasting"
<p>This dataset consists of ionospheric scintillation data collected from August 1, 2013 until July 25, 2014 by a collection of GPS and UHF receiver stations in the Scintillation Network Decision Aid (SCINDA) network (Groves et al., 1997). This particular dataset supports the analysis conducted in Carter et al. (2020).</p> <p><br> Carter, B.A., J.L. Currie, T. Dao, E. Yizengaw, J.M. Retterer, M. Terkildsen, K. Groves and R. Caton (2020), On the assessment of daily Equatorial Plasma Bubble occurrence modeling and forecasting, Submitted to Space Weather, Jun 2020.</p> <p>Groves, K.M., S. Basu, E. J. Weber, M. Smitham, H. Kuenzler, C.E. Valladares, R. Sheehan, E. MacKenzie, J.A. Secan, P. Ning, W.J. McNeill, D.W. Moonan, and M.J. Kendra (1997), Equatorial scintillation and systems support, Radio Science, 32, 2047-2064, doi:10.1029/97RS00836.</p>
Data from: Metabolically similar cohorts of bacteria exhibit strong co-occurrence patterns with diet items and eukaryotic microbes in lizard guts
Gut microbiomes perform essential services for their hosts, including helping them to digest food and manage pathogens and parasites. Performing these services requires a diverse and constantly changing set of metabolic functions from the bacteria in the microbiome. The metabolic repertoire of the microbiome is ultimately dependent on the outcomes of the ecological interactions of its member microbes, as these interactions in part determine the taxonomic composition of the microbiome. The ecological processes that underpin the microbiome's ability to handle a variety of metabolic challenges might involve rapid turnover of the gut microbiome in response to new metabolic challenges, or it might entail maintaining sufficient diversity in the microbiome that any new metabolic demands can be met from an existing set of bacteria. To differentiate between these scenarios, we examine the gut bacteria and resident eukaryotes of two generalist-insectivore lizards, while simultaneously identifying the arthropod prey each lizard was digesting at the time of sampling. We find that the cohorts of bacteria that occur significantly more or less often than expected with arthropod diet items or eukaryotes include bacteria species that are highly similar to each other metabolically. This pattern in the bacteria microbiome could represent an early step in the taxonomic shifts in bacteria microbiome that occur when host lineages change their in diet niche over evolutionary timescales.
Occurrence data of nitrate and nitrite in feed
<p><strong>Annex_III_occurrence data.xlsx</strong></p> <p>This Annex is an excel file presenting tables on occurrence data on nitrate and nitrite in feed.</p> <p> </p> <p><strong>Nitrate Nitrite_OCC_ZENODO.CSV</strong></p> <p>Contains the raw (no data cleaning applied to it) occurrence dataset on nitrate and nitrite as extracted from EFSA DWH on 03 December 2019 in feed samples presented in the opinion as described in its section 3.2.2. The data is provided <em>in csv format</em>. This dataset is compliant with EFSA SSD model and contains two additional columns documenting issues identified in the cleaning process (column: issue) and the action taken (column: action) to address the issue (e.g. delete record or update values in specific fields).</p> <p>The link to the catalogues of controlled terminologies can be found under "Related identifiers”.</p>
Occurrence data on nickel in food
<p>Nickel_OCC_ZENODO.CSV</p> <p>Contains the raw (no data cleaning applied to it) occurrence dataset on nickel as extracted from EFSA DWH on 7 February 2020 in food samples presented in the opinion as described in its section 3.2.1. The data is provided in csv format. This dataset is compliant with EFSA SSD model and contains two additional columns documenting issues identified in the cleaning process (column: issue) and the action taken (column: action) to address the issue (e.g. delete record or update values in specific fields).</p> <p>The link to the catalogues of controlled terminologies can be found under "Related identifiers”.</p>
The fate of páramo plant assemblages in the sky islands of the northern Andes - Appendix S1. Vegetation and occurrence data used in this study
<p><strong>Aims:</strong> Assessing climate change impacts on biodiversity is a main scientific challenge, especially in the tropics, therefore, we predicted the future of plant species and communities on the unique páramo sky islands. We implemented the <i>Spatially Explicit Species Assemblage Modelling</i> framework, by i) calculating species' maximum dispersal distance, ii) modelling species distributions at present up to 2100, iii) assembling models into communities. Finally, we assessed the vulnerability of sky islands based on richness and composition changes.</p> <p><strong>Location: </strong>Ecuadorian super-páramo (>4200 m)</p> <p><strong>Methods:</strong> Using species trait data, the maximum dispersal distance of 435 species was calculated. Species distribution models (SDM) were fitted to obtain current and future distribution predictions based on dispersal and bioclimatic factors. The final assemblages for present and 2100 were achieved by stacking all probabilistic SDMs and applying the probability ranking rule. The vulnerability of each sky island was evaluated by quantifying richness and composition changes.</p> <p><strong>Results: </strong>Maximum dispersal distances ranged between 0.008-6027 m/year, and across all scenarios, 70% of models showed a net loss in species distribution while 9% of all species were predicted to undergo extinction by 2100. Local richness was estimated to decrease by 56.63% on average, and composition changes in each sky island suggested a mean loss of 64.74% of their original species pool against a 12.97% gain. Finally, 5% of the sky island floras reconverted from high-elevation to low-elevation species. These numbers were usually more important for high-elevation species and the mountains Pichincha, Ilinizas and Antisana.</p> <p><strong>Conclusions:</strong> Our study is methodologically pioneer and provides novel insight on the future of páramo biodiversity. Significant losses in species distribution and changes in community richness and composition suggest drastic impacts and call for further study considering additional factors, such as land-use. Finally, we recommend focusing monitoring and conservation strategies on the northern sky islands in priority.</p>
Data from: Revisiting the relative growth rate hypothesis for gymnosperm and angiosperm species co‐occurrence
Premise of the study: It is unclear to what extent the co-occurrence of angiosperm and gymnosperm species in some marginal ecosystems is explained by reduced growth in angiosperms due to carbon (C) limitation, and by high stress tolerance in gymnosperms associated with lack of vessels and resource conservation. Methods: We examined growth patterns and traits associated with C balance in four evergreen angiosperm species (including one vesselless species, Drimys winteri) and three gymnosperm tree species of a cold-temperate rainforest in southern Chile. We measured the mean basal area increment for the first 50 (BAI50) and the last 10 years (BAI10), wood density, leaf lifespan, and non-structural carbohydrate (NSC) concentrations in different organs. Key results: BAI50 was 6-fold higher in angiosperms than in gymnosperms, and c. 4-fold higher in Drimys than in the fastest growing gymnosperm. BAI10 and aboveground NSC concentrations were significantly higher and leaf lifespan lower in angiosperms than in gymnosperms; these differences though were largely driven by the slow growth and low NSC concentrations of the Cupressaceae species (Pilgerodendron uviferum), while the two Podocarpaceae showed similar BAI10 and NSC concentrations to angiosperms. In angiosperms, NSC and starch concentrations were generally higher in species with lower BAI10, indicating no severe C limitation. Conclusions: The co-occurrence of angiosperms and gymnosperms in cold-temperate rainforests of southern Chile is not explained by growth disadvantages and C limitation in angiosperms. High leaf longevity, but not lack of vessels, appeared to favor resource conservation and C balance in some gymnosperms (Podocarpaceae). In compliance with data protection regulations, please contact the publication office if you would like to have your personal information removed from the database.
Data from: Co-occurrence of related asexual, but not sexual, lineages suggests that reproductive interference limits coexistence
We used randomizations to analyse patterns of co-occurrence of sexual and apomictic (asexual) members of the North American Crepis agamic complex (Asteraceae). We expect strong asymmetry in reproductive interactions in Crepis: apomicts produce clonal seeds with no need for pollination and are not subject to reproductive interference from co-occurring relatives. However, because they still produce some viable pollen, apomicts can reduce reproductive success of nearby sexual relatives, potentially leading to eventual local exclusion of sexuals. Consistent with this, randomizations reveal that sexuals are over-represented in isolated sites, while apomicts freely co-occur. Incorporation of taxonomic and phylogenetic evidence indicates that this pattern is not driven by local origins of asexuals. Our evidence that patterns of local co-occurrence are structured by reproductive interference suggests an underappreciated role for these interactions in community assembly, and highlights the need for explicit tests of the relative contributions of ecological and reproductive interactions in generating patterns of limiting similarity.
Data from: Genetic diversity is largely unpredictable but scales with museum occurrences in a species-rich clade of Australian lizards
Genetic diversity is a fundamental characteristic of species and is affected by many factors, including mutation rate, population size, life history and demography. To better understand the processes that influence levels of genetic diversity across taxa, we collected genome-wide restriction-associated DNA data from more than 500 individuals spanning 76 nominal species of Australian scincid lizards in the genus Ctenotus. To avoid potential biases associated with variation in taxonomic practice across the group, we used coalescent-based species delimitation to delineate 83 species-level lineages within the genus for downstream analyses. We then used these genetic data to infer levels of within-population genetic diversity. Using a phylogenetically informed approach, we tested whether variation in genetic diversity could be explained by population size, environmental heterogeneity or historical demography. We find that the strongest predictor of genetic diversity is a novel proxy for census population size: the number of vouchered occurrences in museum databases. However, museum occurrences only explain a limited proportion of the variance in genetic diversity, suggesting that genetic diversity might be difficult to predict at shallower phylogenetic scales.
Data from: Can collective memories shape fish distributions? A test, linking space-time occurrence models and population demographics
Social learning can be fundamental to cohesive group living, and schooling fishes have proven ideal test subjects for recent work in this field. For many species, both demographic factors, and inter- (and intra-) generational information exchange are considered vital ingredients in how movement decisions are reached. Yet key information is often missing on the spatial outcomes of such decisions, and questions concerning how migratory traditions are influenced by collective memory, density-dependent and density-independent processes remain open. To explore these issues, we focused on Atlantic herring (Clupea harengus), a long-lived, dense-schooling species of high commercial importance, noted for its unpredictable shifts in winter distribution, and developed a series of Bayesian space-time occurrence models to investigate wintering dynamics over 23 years, using point-referenced fishery and survey records from Icelandic waters. We included covariates reflecting local-scale environmental factors, temporally-lagged prey biomass and recent fishing activity, and through an index capturing distributional persistence over time, derived two proxies for spatial memory of past wintering sites. The previous winter's occurrence pattern was a strong predictor of the present pattern, its influence increasing with adult population size. Although the mechanistic underpinnings of this result remain uncertain, we suggest that a 'wisdom of the crowd' dynamic may be at play, by which navigational accuracy towards traditional wintering sites improves in larger and/or denser, better synchronized schools. Wintering herring also preferred warmer, fresher, moderately stratified waters of lower velocity, close to hotspots of summer zooplankton biomass, our results indicative of heightened environmental sensitivity in younger cohorts. Incorporating spatiotemporal correlation structure and time-varying regression coefficients improved model performance, and validation tests on independent observations one-year ahead illustrate the potential of uniting demographic information and non-stationary models to quantify both the strength of collective memory in animal groups and its relevance for the spatial management of populations.
Data from: Understanding co-occurrence by modelling species simultaneously with a Joint Species Distribution Model (JSDM)
A primary goal of ecology is to understand the fundamental processes underlying the geographic distributions of species. Two major strands of ecology – habitat modelling and community ecology – approach this problem differently. Habitat modellers often use species distribution models (SDMs) to quantify the relationship between species' and their environments without considering potential biotic interactions. Community ecologists, on the other hand, tend to focus on biotic interactions and, in observational studies, use co‐occurrence patterns to identify ecological processes. Here, we describe a joint species distribution model (JSDM) that integrates these distinct observational approaches by incorporating species co‐occurrence data into a SDM. JSDMs estimate distributions of multiple species simultaneously and allow decomposition of species co‐occurrence patterns into components describing shared environmental responses and residual patterns of co‐occurrence. We provide a general description of the model, a tutorial and code for fitting the model in R. We demonstrate this modelling approach using two case studies: frogs and eucalypt trees in Victoria, Australia. Overall, shared environmental correlations were stronger than residual correlations for both frogs and eucalypts, but there were cases of strong residual correlation. Frog species generally had positive residual correlations, possibly due to the fact these species occurred in similar habitats that were not fully described by the environmental variables included in the JSDM. Eucalypt species that interbreed had similar environmental responses but had negative residual co‐occurrence. One explanation is that interbreeding species may not form stable assemblages despite having similar environmental affinities. Environmental and residual correlations estimated from JSDMs can help indicate whether co‐occurrence is driven by shared environmental responses or other ecological or evolutionary process (e.g. biotic interactions), or if important predictor variables are missing. JSDMs take into account the fact that distributions of species might be related to each other and thus overcome a major limitation of modelling species distributions independently.
Data from: Species interactions in occurrence data for a community of tick-transmitted pathogens
Interactions between species of ticks, their realised range of hosts, the pathogens they carry and transmit, as well as the geographical distribution of species in the Western Palearctic, have been obtained based on evidence published between 1970–2014. These relationships were linked to remotely-sensed features of temperature and vegetation and used to extract the network of interactions among the organisms. The resulting datasets were focussed on niche overlap among ticks and hosts, species interactions and the fraction of the environmental niche where tick-borne pathogens may circulate, as a result of interactions and environmental trait overlap. The presented datasets provide a valuable resource for researchers of tick-borne pathogens, as they conciliate the abiotic and biotic sides of their niche, allowing exploration of the importance of each species of vertebrate reservoir in the circulation of tick-transmitted pathogens at intervals of the environmental niche.
Data from: Social group signatures in hummingbird displays provide evidence of co-occurrence of vocal and visual learning
Vocal learning, in which animals modify their vocalizations based on social experience, has evolved in several lineages of mammals and birds, including humans. Despite much attention, the question of how this key cognitive trait has evolved remains unanswered. The motor theory for the origin of vocal learning posits that neural centers specialized for vocal learning arose from adjacent areas in the brain devoted to general motor learning. One prediction of this hypothesis is that visual displays that rely on complex motor patterns may also be learned in taxa with vocal learning. While learning of both spoken and gestural languages is well-documented in humans, the occurrence of learned visual displays has rarely been examined in non-human animals. We tested for geographic variation consistent with learning of visual displays in long-billed hermits (Phaethornis longirostris), a lek-mating hummingbird that, like humans, has both learned vocalizations and elaborate visual displays. We found lek-level signatures in both vocal parameters and visual display features, including element proportions, sequence syntax, and fine-scale parameters of elements. This variation was not associated with genetic differentiation between leks. In the absence of genetic differences, geographic variation in vocal signals at small scales is most parsimoniously attributed to learning, suggesting a significant role of social learning in visual display ontogeny. The co-occurrence of learning in vocal and visual displays would be consistent with a parallel evolution of these two signal modalities in this species.
Data from: Predicting species occurrences with habitat network models
1. Biodiversity conservation requires modelling tools capable of predicting the presence or absence (i.e. occurrence-state) of species in habitat patches. Local habitat characteristics of a patch (lh), the cost of traversing the landscape matrix between patches (weighted connectivity; (wc), and the position of the patch in the habitat network topology (nt) all influence occurrence-state. Existing models are data demanding or consider only local habitat characteristics. We address these shortcomings and present a network-based modelling approach, which aims to predict species occurrence-state in habitat patches using readily available presence-only records. 2. For the tree frog Hyla arborea on the Swiss Plateau, we delineated habitat network nodes from an ensemble habitat suitability model, and used different cost surfaces to generate the edges of three networks: one limited only by dispersal distance (Uniform), another incorporating traffic, and a third based on inverse habitat suitability. For each network, we calculated explanatory variables representing the three categories (lh, wc and nt). The response variable, occurrence-state, was parametrized by a sampling-intensity procedure assessing observations of comparable species over a threshold of patch visits. The explanatory variables from the three networks and an additional non-topological model were related to the response variable with boosted regression trees. 3. The habitat network models had a similar fit; they all outperformed the non-topological model. Habitat suitability index ((lh) was the most important predictor in all networks, followed by third-order neighborhood (nt). Patch size (lh) was unimportant in all three networks. 4. We found that topological variables of habitat networks are relevant for the prediction of species occurrence-state, a step-forward from models considering only local habitat characteristics. For any habitat patch, occurrence-state is most prominently influenced by its habitat suitability, and then by the number of patches in a wide neighborhood. Our approach is generic and can be applied to multiple species in different habitats.
Data from: Metapopulation dynamics of the mistletoe and its host in savanna areas with different fire occurrence
Mistletoes are aerial hemiparasitic plants which occupy patches of favorable habitat (host trees) surrounded by unfavorable habitat and may be possibly modeled as a metapopulation. A metapopulation is defined as a subdivided population that persists due to the balance between colonization and extinction in discrete habitat patches. Our aim was to evaluate the dynamics of the mistletoe Psittacanthus robustus and its host Vochysia thyrsoidea in three Brazilian savanna areas using a metapopulation approach. We also evaluated how the differences in terms of fire occurrence affected the dynamic of those populations (two areas burned during the study and one was fire protected). We monitored the populations at six-month intervals. P. robustus population structure and dynamics met the expected criteria for a metapopulation: i) the suitable habitats for the mistletoe occur in discrete patches; (ii) local populations went extinct during the study and (iii) colonization of previously non-occupied patches occurred. The ratio of occupied patches decreased in all areas with time. Local mistletoe populations went extinct due to two different causes: patch extinction in area with no fire and fire killing in the burned areas. In a burned area, the largest decrease of occupied patch ratios occurred due to a fire event that killed the parasites without, however, killing the host trees. The greatest mortality of V. thyrsoidea occurred in the area without fire. In this area, all the dead trees supported mistletoe individuals and no mortality was observed for parasite-free trees. Because P. robustus is a fire sensitive species and V. thyrsoidea is fire tolerant, P. robustus seems to increase host mortality, but its effect is lessened by periodic burning that reduces the parasite loads.
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Allen Brain Atlas
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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.
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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.
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