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1,069 results for “Data managment”
Data from: Knowledge co-production with traditional herders on cattle grazing behaviour for better management of species-rich grasslands
The research gap between rangeland/livestock science and conservation biology/vegetation ecology has led to a lack of evidence needed for grazing-related conservation management. Connecting scientific understanding with traditional ecological knowledge of local livestock keepers could help bridge this research and knowledge gap. 1. We studied the grazing behaviour (plant selection and avoidance) of beef cattle (ca. 33 000 bites) on species-rich lowland pastures in Central Europe and traditional herding practices. We also did >450 outdoor interviews with traditional herders about livestock behaviour, herders' decisions to modify grazing behaviour, and effects of modified grazing on pasture vegetation. 2. We found that cattle grazing on species-rich pastures displayed at least 10 different behavioural elements as they encountered 117 forage species from highly desired to rejected. The small discrimination error suggests that cattle recognize all listed plants 'by species'. 3. We also found that herders had broad knowledge of grazing desire and they consciously aimed to modify desire by slowing, stopping or redirecting the herd. Modifications were aimed at increasing grazing intensity in less desired patches and decreasing grazing selectivity in heterogenous swards. 4. Synthesis and applications: These traditional herd management practices have significant conservation benefits, such as avoiding under- and overgrazing, and targeted removal of pasture weeds, litter and enchroaching bushes, tall competitive plants and invasive species. We argue that knowledge co-production with traditional herders who belong to another knowledge system could help connect isolated scientific disciplines especially if ecologists and rangeland scientists work closely with traditional herders, co-designing research projects and working together in data collection, analysis and interpretation. Stronger links between these disciplines could help develop evidence-based, specific conservation management practices while herders could contribute with their practical experiences and with real world testing of new management techniques.04-May-2020
Data from: Recognition of endophytic Trichoderma species by leaf-cutting ants and their potential in a Trojan-horse management strategy
Interactions between leaf-cutting ants, their fungal symbiont (Leucoagaricus) and the endophytic fungi within the vegetation they carry into their colonies are still poorly understood. If endophytes antagonistic to Leucoagaricus were found in plant material being carried by these ants, then this might indicate a potential mechanism for plants to defend themselves from leaf-cutter attack. In addition, it could offer possibilities for the management of these important Neotropical pests. Here, we show that, for Atta sexdens rubropilosa, there was a significantly greater incidence of Trichoderma species in the vegetation removed from the nests—and deposited around the entrances—than in that being transported into the nests. In a no-choice test, Trichoderma-infested rice was taken into the nest, with deleterious effects on both the fungal gardens and ant survival. The endophytic ability of selected strains of Trichoderma was also confirmed, following their inoculation and subsequent reisolation from seedlings of eucalyptus. These results indicate that endophytic fungi which pose a threat to ant fungal gardens through their antagonistic traits, such as Trichoderma, have the potential to act as bodyguards of their plant hosts and thus might be employed in a Trojan-horse strategy to mitigate the negative impact of leaf-cutting ants in both agriculture and silviculture in the Neotropics. We posit that the ants would detect and evict such 'malign' endophytes—artificially inoculated into vulnerable crops—during the quality-control process within the nest, and, moreover, that the foraging ants may then be deterred from further harvesting of 'Trichoderma-enriched' plants.
Data from: Plant demographic and functional responses to management intensification: a long-term study in a Mediterranean rangeland
1. Understanding how functional traits, which are key for plant functioning, relate to demographic parameters of populations is central to tackle pending issues in plant ecology such as the forecast of the fate of populations and communities in a changing world, the quantification of community assembly processes or the improvement of species distribution models. We addressed this question in the case of species from a Mediterranean rangeland of southern France. 2. Changes in species abundance in response to management intensification (fertilization and increased grazing pressure) were followed over a 28-year period. Probabilities of presence, and elasticities of the changes in the probability of space occupancy to colonization and survival, which are analogues of demographic parameters, were calculated for 53 species from the time series of abundance data using a space occupancy model. Nine quantitative traits pertaining to resource use, plant morphology, regeneration and phenology were measured on these species and related to demographic parameters. 3. The long-term dynamics of species in response to management intensification was associated with major changes in functional traits and strategies. Changes in the probability of occurrence – analogous to population growth rate - were correlated with traits describing the fast-slow continuum of leaf functioning. The elasticity of population growth rate to colonization was significantly related to reproductive plant height and seed mass, and to a lower extent, to leaf carbon isotopic ratio. 4. Synthesis. The functional response of species to management intensification corresponds to a shift along the second axis of a recently identified global spectrum of plant form and function, which maps, to some extent, onto the fast-slow continuum of life-history strategies. By contrast, the elasticity of colonization relates to the global spectrum axis capturing the size of organs. Seed mass contributes to this axis and is assumed to relate to one of the important traits structuring the reproductive strategy axis of life histories as well, namely net reproductive rate. While this mapping between functional and life-history traits is appealing, further tests in contrasting types of communities are required to assess its degree of generality.
Training for RD Management: Comparative European Approaches, Raw data & Tidied Data
<p>Raw and tidied data of responses to the Knowledge Exchange survey around Training for Research Data management. The data accompanies the Knowledge Exchange report 'Training for RD Management: Comparative European Approaches' DOI: 10.5281/zenodo.50068</p> <p> </p>
Research Data Management: The Numbers
<p>Infographic illustrating the numbers associated with research data management. In particular the associated costs, the value and the volume of data</p>
Experimental results of "Managing variant calling datasets the big data way"
<p>Tomatula was demonstrated for retrieving the allele frequencies for a given region in the data from Aflitos et al (2014). We developed scripts to retrieve allele frequencies, either from the VCF file storage or Apache Parquet. We executed a series of experiments, querying for a region of 2000 bases in the file of chromosome 6, that corresponds to the approximate length of a gene. We compared both storage formats (VCF files and Parquet), two input sizes (104 and 1144 individuals), different cluster sizes varying between 2 and 150 executor nodes, and HDFS replication factor was set to 3, 5, 7, and 9, in order to examine four main factors that<br> can affect the performance of a Big Data cluster: (a) the storage format, (b) the size of the input files, (c) the number of computing nodes of the cluster, and (d) the replication factor of HDFS. The block size of the HDFS was kept at the default value of 128MB. All experiments were executed five times and the detailed results are provided here, along with a script that produces the corresponding figures.</p>
Data from: Effective population size of Culex quinquefasciatus under insecticide-based vector management and following Hurricane Harvey in Harris County, Texas
<div> <em>Culex quinquefasciatus</em> is mosquito species of significant public health importance due to its ability to transmit multiple pathogens that can cause mosquito-borne diseases, such as West Nile fever and St. Louis encephalitis. In Harris County, Texas, <em>Cx. quinquefasciatus</em> is a common vector species and is subjected to insecticide-based management by the Harris County Public Health Department. However, insecticide resistance in mosquitoes has increased rapidly worldwide and raises concerns about maintaining the effectiveness of vector control approaches. This concern is highly relevant in Texas, with its humid subtropical climate along the Gulf Coast that provides suitable habitat for <em>Cx. quinquefasciatus</em> and other mosquito species that are known disease vectors. Therefore, there is an urgent and ongoing need to monitor the effectiveness of current vector control programs. In this study, we evaluated the impact of vector control approaches by estimating the effective population size of <em>Cx. quinquefasciatus</em> in Harris County. We applied Approximate Bayesian Computation to microsatellite data to estimate effective population size. We collected <em>Cx. quinquefasciatus</em> samples from two mosquito control operation areas, 415 and 802, during routine vector monitoring in 2016 and 2017. No county mosquito control operations were applied at area 415 in 2016 and 2017, whereas extensive adulticide spraying operations were in effect at area 802 during the summer of 2016. We collected data for eighteen microsatellite markers for 713 and 723 mosquitoes at eight timepoints from 2016 to 2017 in areas 415 and 802, respectively. We also investigated the impact of Hurricane Harvey's landfall in the Houston area in August of 2017 on <em>Cx. quinquefasciatus</em> population fluctuation. Although we did not detect significant effects of vector control interventions, we found considerable influences of the winter season and a major hurricane on the effective population size of <em>Cx. quinquefasciatus</em>. The fluctuations in effective population size in both areas showed a significant seasonal pattern. Additionally, the significant population expansion following Hurricane Harvey in 2017 supports the necessity for post-hurricane vector-control interventions.</div>
Data Management Plan preliminary version (D1.3)
<p>First version of the Data Management Plan, to be updated twice in the project</p>
[VERSION 2] Data set and analytic codes supporting "How do management decisions impact butterfly assemblages in smallholding oil palm plantations in Peninsular Malaysia?"
<p>This is <strong>VERSION 2</strong> of data set and analytic codes (with a meta data [see the meta data from VERSION 1]) supporting "How do management decisions impact butterfly assemblages in smallholding oil palm plantations in Peninsular Malaysia?". We investigated the impacts of replanting and alternative replanting decisions (replanting with monoculture versus polyculture oil palm plantations) on within-plantation environmental conditions and butterfly assemblages (diversity, density, and composition). We also assessed the effects of habitat structure and complexity within plantations on butterfly assemblages. Apart from "BantingButterflies_ButterflyData", other data are the same as in VERSION 1.</p><p><strong>## List of changes:</strong></p><p># 1. <i>Tirumala septentrionis </i>was not included in the analyses because it should have been <i>Ideopsis vulgaris</i> (had been corrected),</p><p># 2. PC5 and PC6 (from PCA) were considered as predictors for the GLMs,</p><p># 3. The Mantel test was added.</p><p><strong>## Other notes:</strong></p><p># 1. Older version of ggiNEXT could work with facet.var = "site", now it needs to be "Assemblage"</p><p># 2. Older version of ggiNEXT could work with facet.var = "order", now it needs to be "Order.q"</p><p># 3. "set.seed(42)" function was used before running "iNEXT", ANOSIM, and the Mantel test to get reproducible outputs (exactly the same outputs every time each function is run).</p><p><strong>Funding and research permission:</strong> Jardine Foundation, the Cambridge Trust, and Tim Whitmore Fund provided funding for MFH, the Biotechnology and Biological Sciences Research Council (BBSRC) funded JS (USN: 304338625), and BBSRC (BB/T012366/1) provided funding for the establishment of the plots and surveys of environmental parameters. Research permission was provided by the Economic Planning Unit (EPU) of Malaysia's Prime Minister's Department for MFH (Ref: EPU 40/200/19/3727) and JS (Ref: MEA 40/200/19/3705).</p>
Research Data Management Workflow
<p>This diagram illustrates essential ideas and useful tools during the RDM cycle.</p>
Data from: Quantifying the impacts of management and herbicide resistance on regional plant population dynamics in the face of missing data
<p>A key challenge in the management of populations is to quantify the impact of interven-tions in the face of environmental and phenotypic variability. However, accurate estima-tion of the effects of management and environment, in large-scale ecological research is often limited by the expense of data collection, the inherent trade-off between quality and quantity, and missing data.</p> <p>In this paper we develop a novel modelling framework, and demographically informed imputation scheme, to comprehensively account for the uncertainty generated by miss-ing population, management, and herbicide resistance data. Using this framework and a large dataset (178 sites over 3 years) on the densities of a destructive arable weed (Alo-pecurus myosuroides) we investigate the effects of environment, management, and evolved herbicide resistance, on weed population dynamics.</p> <p>In this study we quantify the marginal effects of a suite of common management prac-tices, including cropping, cultivation, and herbicide pressure, and evolved herbicide re-sistance, on weed population dynamics.</p> <p>Using this framework, we provide the first empirically backed demonstration that herbi-cide resistance is a key driver of population dynamics in arable weeds at regional scales. Whilst cultivation type had minimal impact on weed density, crop rotation, and earlier cultivation and drill dates consistently reduced infestation severity.</p> <p>Synthesis and applications: As we demonstrate that high herbicide resistance levels can produce extremely severe weed infestations, monitoring of herbicide resistance is a pri-ority for famers across western Europe. Furthermore, developing non chemical control methods is essential to control current weed populations, and prevent further resistance evolution. We recommend that planning interventions that center on crop rotation and incorporate spring sewing and cultivation to provide the best reductions in weed densi-ties. More generally, by directly accounting for missing data our framework permits the analysis of management practices with data that would otherwise be severely compro-mised.</p>
Data from: navigating uncertainty: managing herbivore communities enhances savanna ecosystem resilience under climate change
<p>Savannas are characterized by water scarcity and degradation, making them highly vulnerable to increased uncertainties in water availability resulting from climate change. This poses a significant threat to ecosystem services and rural livelihoods that depend on them. In addition, the lack of consensus among climate models on precipitation change makes it difficult for land managers to plan for the future. Therefore, savanna rangeland management needs to develop strategies that can sustain savanna resilience and avoid tipping points under an uncertain future climate. Our study aims to analyze the impacts of climate change and rangeland management on degradation in savanna ecosystems of southern Africa, providing insights for the management of semi-arid savannas under uncertain conditions worldwide. To achieve this, we simulated the effects of projected changes in temperature and precipitation, as predicted by ten global climate models, on water resources and vegetation (cover, functional diversity, tipping points (transition from grass-dominated to shrub-dominated vegetation)). We simulated three different rangeland management options (herbivore community dominated by grazers, by browser and by mixed-feeders), each with low and high animal densities using the ecohydrological model EcoHyD. Our results identified intensive grazing as the primary contributor to the increased risk of degradation in response to changing climatic conditions across all climate change scenarios. This degradation encompassed a reduction in available water for plant growth within the context of predicted climate change. It also entails a decline in the overall vegetation cover, the loss of functionally important plant species, and the inefficient utilization of available water resources, leading to earlier tipping points. Our findings underscore that in the face of climate uncertainty, farmers' most effective strategy for securing their livelihoods and ecosystem stability is to integrate browsers and apply management of mixed herbivore communities. This management approach not only significantly delays or averts tipping points but also maintained greater plant functional diversity, fostering a more robust and resilient ecosystem that acts as a vital buffer against adverse climatic conditions.</p>
Data from: Social stability via management of natal males in captive rhesus macaques (Macaca mulatta)
<p>Keystone individuals are expected to disproportionately contribute to group stability. For instance, rhesus macaques (<em>Macaca mulatta</em>) who police conflict contribute towards stability. Not all individuals' motivations align with mechanisms of group stability. In wild systems, males typically disperse at maturity and attempt to ascend via contest competition. In a captive system, dispersal is not naturally enabled – individuals attempt to ascend in their natal groups, which can be enabled by matrilineal kin potentially destabilizing group dynamics. We relocated select high-ranking natal males from five groups and assessed group stability before and after. We quantified hierarchical metrics at the individual and group level. After removal, we found significantly higher aggression against the established hierarchy (reversals), indicative of opportunistic attempts to change the hierarchy. Mixed-sex social signaling became more hierarchical, but the strength of this effect varied. Stable structure was not uniformly reached across the groups and alpha males did not all benefit. Indiscriminate natal male removal is an unreliable solution to group instability. Careful assessment of how natal males are embedded within their group is necessary to balance individual and group welfare.</p>
Data from: Upland Sandpipers select for later time since fire and experience high nest survival in grasslands managed with patch-burn grazing
<p>Upland Sandpipers (<em>Bartramia longicauda</em>) are a grassland obligate shorebird that nests in dense vegetation structure near recently disturbed areas and could benefit from management practices that promote heterogenous vegetation structure. Although, Upland Sandpipers primary breeding range is generally managed for livestock production using traditional practices that lack patchy disturbances to facilitate higher levels of structural heterogeneity. Patch-burn grazing (PBG) could be an alternative management practice for Upland Sandpiper conservation for its ability to create areas of dense vegetation structure near recently disturbed areas. However, limited information is available regarding nest production of Upland Sandpipers within a PBG framework. To assess the compatibility of PBG with Upland Sandpiper conservation, we estimated nest site selection and survival of Upland Sandpiper nests on private lands managed with PBG in the unglaciated plains region of North Dakota. We located 59 nests from 2017–2020. Upland Sandpipers avoided 1 year since fire (YSF) patches and selected for 2 and 3 YSF patches for nest sites. Additionally, nest site selection decreased with increased bare ground and at intermediate distances to the nearest Upland Sandpiper nest. Upland Sandpipers experienced high overall nest survival during the study with 51 of 59 nests successfully hatching, which limited our ability to make inferences between daily survival rates and variables of interest. Our findings suggest that PBG can provide suitable nesting cover for Upland Sandpipers in later YSF patches despite annual prescribed fire and livestock grazing during the nesting season. PBG seems a suitable grassland management strategy that should be included in conservation planning within Upland Sandpiper's breeding distribution.</p>
Data for: Fire season and time since fire determine AM fungal trait responses to fire management
<p><strong>Rationale:</strong> AM fungi are common mutualists in grassland and savanna systems that are adapted to recurrent fire disturbance. This long-term adaptation to fire means that AM fungi display disturbance associated traits which are useful for understanding environmental and temporal effects on AM fungal community assembly. </p> <p><strong>Methods:</strong> In this work, we evaluated how fire driven ecological selection on AM fungal spore traits varies with fire season (Fall vs. Spring) and time since fire. We tested this by analyzing AM fungal spore traits (e.g., colorimetric, sporulation, and size) from a fire regime experiment. </p> <p><span><span> </span></span><strong>Key results:</strong> Immediately following Fall and Spring fires, spore pigmentation darkened; however, this did not mediate the observed differences between Fall burned and no burn communities. Six months after Fall fires, spores in burned plots were lower in volume, produced less color rich pigment, and had higher sporulation rates, and these differences in spore traits were associated with shifts in AM fungal spore communities.</p> <p><strong>Main conclusion:</strong> This shows that AM fungal responses to fire vary based on season (stronger effects in the Fall) and with time since fire. Variation in AM fungal responses to fire time may reflect greater exposure to fire in Fall, when sporulation is highest.</p>
IPBES Invasive Alien Species Assessment: Chapter 2. Figures, tables, captions and data management reports
<p>This folder contains the figures and tables included in Chapter 2 of the IPBES Invasive Alien Species and their Control Assessment Report. Each figure is provided in pdf and svg format. In addition, the R scripts and the data sets required to generate the figures are provided as well.</p><p>The figures and tables showing information about alien species numbers or distributions are all based on two data sets, which are stored on Zenodo folders. One data set contains the records of alien species per region worldwide (https://doi.org/10.5281/zenodo.7554428) and the workflow including R scripts have been published (https://doi.org/10.3897/neobiota.59.53578). This data set is called the 'chapter database'. Version 2.4.1 of this data set was used to extract the numbers shown in figures and tables of this chapter. The second data set (https://doi.org/10.5281/zenodo.6458083) contains coordinates of alien species occurrences worldwide and the workflow including R scripts have also been published elsewhere (https://doi.org/10.3897/neobiota.74.81082). Version 1.0.1 of this data set was used here.</p><p>The folder also contains the data management reports for the generation of the chapter database and figures.</p>
Appendix 1 to "The Status of Biological Invasions and their Management in South Africa in 2022"—Species level pathway data
<p>SANBI and CIB 2023. Appendix 1 to "The Status of Biological Invasions and their Management in South Africa in 2022"—Species level pathway data. South African National Biodiversity Institute, Kirstenbosch and DSI-NRF Centre of Excellence for Invasion Biology, Stellenbosch. http://dx.doi.org/10.5281/zenodo.8217192</p> <p>For more details see: http://iasreport.sanbi.org.za</p> <p>For the report itself see: http://dx.doi.org/10.5281/zenodo.8217182</p>
Aligning Data Management Plans with Community Standards using FAIR Implementation Profiles
<p>Here you can find the files corresponding to our submission titled 'Aligning DMPs with Community Standards using FIPs'.</p> <p>- VU DMP template and the mapping is included in the folder /VU-DMP-template-and-mapping</p> <p>- All the FAIR Implementation Profiles are included in the folder /FIPs.</p> <p>- The knowledge model we created for the project, and a small demo of the interface are in the folder /KM-and-demo.</p> <p>- The folder /user-study consists of the following:</p> <p> a) The mock DMPs we provided to the participants of this research are in /mock_DMPs.</p> <p> b) We downloaded the resulting DMPs after participants completed their DMPs, they are in the folder /resulting_DMPs.</p> <p> c) Survey results can be found in the folder /survey_results.</p> <p> d) Some Python scripts were used for the analysis of the survey results. They are in the folder /Python_script_for_analysis.</p> <p><br>The project is open source under the license CC-BY 4.0.</p> <p>Contact: Shuai Wang (shuai.wang@vu.nl)</p> <p> </p>
Data from: forest stand dynamics of a short-stature tree species: ecological knowledge for sustainable forest management
<p>This data set is a forest inventory of <em>Nothofagus antarctica</em> in southern Chile. More than 20 sites were selected. In each site, parallel transects were set and every 30 m a sampling point was set where the distance to the nearest four trees (in accordance with the cardinal points) were measured.</p>
Data from: Genetic analysis of red deer (Cervus elaphus) administrative management units in a human-dominated landscape - patterns of genetic diversity, population structure and gene flow
<p><span><span>Red deer (</span><span><em>Cervus elaphus</em></span><span>) throughout central Europe are</span> impacted by different anthropogenic activities including habitat fragmentation, selective hunting, and translocations<span>. This has substantial influences on genetic diversity and the long-term conservation of local populations of this species. Here we use genetic samples from 480 red deer individuals to assess the genetic diversity and differentiation of the 12 administrative management units located in Schleswig Holstein, the northernmost federal state in Germany. </span></span><span><span>We applied multiple analytical approaches and show that the history of local populations (i.e., translocations, culling of individuals outside of designated red deer zones, and anthropogenic infrastructures) has led to comparably low levels of genetic diversity. The mean expected heterozygosity was below 0.6 and we observed on average 4.2 alleles across 12 microsatellite loci. Effective population sizes below the recommended level of 50 were estimated for multiple local populations. </span></span><span><span>Our estimates of genetic structure and gene flow show that red deer in northern Germany are best described as a complex network of asymmetrically connected subpopulations, with high genetic exchange among some local populations and reduced connectivity of others. Genetic diversity was also correlated with population densities of neighboring management units. </span></span></p> <p><span><span>Based on these findings, we suggest that connectivity among existing management units needs to be considered in the practical management of the species, which means that some administrative management units should be managed together, while the effective isolation of other units needs to be mitigated.</span></span></p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.