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1,868 results for “Spatial Data”
Data from: Integrating pheromonal and spatial information in the amygdalo-hippocampal network. Villafranca-Faus et al. 2021
<p>The local field potential (LFP) of the dorsal hippocampus (CA1) and cortical amygdala (PMCo) of mice, under head-fix recording and inmersed on a virtual environtmernt.</p> <p><strong>Paper Abstract</strong>: <br> Vomeronasal information is critical in mice for territorial behavior. Consequently, learning the territorial spatial structure should incorporate the vomeronasal signals indicating individual identity into the hippocampal cognitive map. In this work we show in mice that navigating a virtual environment induces synchronic activity, with causality in both directionalities, between the vomeronasal amygdala and the dorsal CA1 of the hippocampus in the theta frequency range. The detection of urine stimuli induces synaptic plasticity in the vomeronasal pathway and the dorsal hippocampus, even in animals with experimentally induced anosmia. In the dorsal hippocampus, this plasticity is associated with the overexpression of pAKT and pGSK3β. An amygdalo-entorhino-hippocampal circuit likely underlies this effect of pheromonal information on hippocampal learning. This circuit likely constitutes the neural substrate of territorial behavior in mice, and it allows the integration of social and spatial information.</p>
Data from: Restoring marine ecosystems: spatial reef configuration triggers taxon-specific responses among early colonizers
<p>1. The longstanding debate in conservation biology on the importance of single large or several small (SLOSS) habitats for preserving biodiversity remains highly relevant, given the ongoing degradation and loss of natural habitats worldwide. Restoration efforts are often constrained by limited resources, and insights from SLOSS studies therefore have important implications if restoration efforts can be optimized by manipulating the spatial configuration of restored habitats. Yet, the relevance of SLOSS for habitat restoration remains largely unexplored.</p> <p>2. Here, we report the effects of spatial reef configuration on early colonization of marine organisms after restoring boulder reef habitats. Reefs were restored in single large (SL) and several small (SS) designs in the western Baltic Sea, where century-long boulder extraction has severely degraded large reef areas and likely exacerbated regional declines in commercially important gadoids (<i>Gadidae spp.</i>). We sampled the field sites using remote underwater video systems in a before-after control-impact (BACI) design and obtained probabilistic inferences on restoration and SLOSS effects from Bayesian hierarchical models.</p> <p>3. Probabilities of a positive restoration effect were high (>95%) for gadoids, labrids and demersal gobies, moderate (60-75%) for species richness and sand gobies, and low (<5%) for flatfish abundance. Notably, gadoid abundance increased 60-fold and 129-fold on average at SL and SS, respectively. The species composition at restored reefs deviated from control sites, mainly driven by large-bodied piscivores.</p> <p>4. Spatial reef configuration had the strongest effect on small-bodied mesopredators, including gobies, which were more abundant and driving a distinct species assemblage at SS. In addition to providing suitable conditions for reef species, results suggest that SS can also benefit soft-bottom taxa, possibly through a dispersed predator-mediated effect relative to SL. </p> <p><i>5. Synthesis and applications.</i> This study demonstrates that boulder reef restoration can strongly promote the abundance of exploited gadoids and is therefore a promising management tool to support top-down controls by predatory fishes in degraded marine systems. The higher abundance of mesopredators at SS reefs suggests that SLOSS could have long-term implications for trophic structure and resilience of restored habitats, and should therefore become an important facet within restoration strategies. </p>
Data for: Using spatial patterns of seeds and saplings to assess the prevalence of heterospecific replacements among cloud forest canopy tree species
<p><b>Questions:</b> To gain insights into the role of species-by-species replacements in cloud forest community structuring, we asked: (1) What are the effects of the spatial distribution of standing individuals on the seed rain, soil seed bank, and sapling density and survival in this cloud forest? and (2) What is the prevalence of conspecific vs<i>.</i> heterospecific replacements in the regeneration of this forest?</p> <p><b>Location:</b> Santo Tomás Teipan, Oaxaca State, southern Mexico.</p> <p><b>Methods:</b> In a 1-ha cloud forest plot we assessed seed rain, seed bank, and sapling density and survival of four canopy tree species (<i>Chiranthodendron pentadactylon</i>, <i>Cornus disciflora</i>,<i> Quercus laurina</i>, <i>Oreopanax</i> <i>xalapensis</i>). All standing individuals of these and other tree species (dbh ≥ 2.5 cm) were mapped. We used neighbourhood models to examine the spatial patterns of the three life cycle stages relative to the spatial distribution of adults. The neighbourhood effect was assessed through the Neighbourhood Index, which integrates information on size (dbh) and distance to adults. Data analysis was based on maximum likelihood and model selection procedures.</p> <p><b>Results:</b> We found large between-species differences regarding the spatial patterns of seeds and saplings. Three species showed evidence for the Janzen-Connell effect operating at the seed (<i>C. pentadactylon</i> and <i>Q. laurina</i>) or sapling (<i>O.</i> <i>xalapensis</i>) stage. We also found support for a critical role of specific microsite factors (i.e., niche differentiation) in the regeneration of two species (<i>C. pentadactylon</i> and <i>C. disciflora</i>).</p> <p><b>Conclusions:</b> Seed and sapling distribution patterns suggest the prevalence of heterospecific replacements, and that both Janzen-Connell and niche differentiation effects contribute to this pattern. Our results largely support the notion that the prevalence of heterospecific replacements among canopy species promotes species coexistence in cloud forest.</p>
Data from: Fractal triads efficiently sample ecological diversity and processes across spatial scales
<p>The relative influence of ecological assembly processes, such as environmental filtering, competition, and dispersal, vary across spatial scales. Changes in phylogenetic and taxonomic diversity across environments provide insight into these processes, however, it is challenging to assess the effect of spatial scale on these metrics. Here, we outline a nested sampling design that fractally spaces sampling locations to concentrate statistical power across spatial scales in a study area. We test this design in northeast Utah, at a study site with distinct vegetation types (including sagebrush steppe and mixed conifer forest), that vary across environmental gradients. We demonstrate the power of this design to detect changes in community phylogenetic diversity across environmental gradients and assess the spatial scale at which the sampling design captures the most variation in empirical data. We find clear evidence of broad-scale changes in multiple features of phylogenetic and taxonomic diversity across aspect. At finer scales, we find additional variation in phylodiversity, highlighting the power of our fractal sampling design to efficiently detect patterns across multiple spatial scales. Thus, our fractal sampling design and analysis effectively identify important environmental gradients and spatial scales that drive community phylogenetic structure. We discuss the insights this gives us into the ecological assembly processes that differentiate plant communities found in northeast Utah.</p>
Data from: Spatial consistency in drivers of population dynamics of a declining migratory bird
<p>1. Many migratory species are in decline across their geographical ranges. Single-population studies can provide important insights into drivers at a local scale, but effective conservation requires multi-population perspectives. This is challenging because relevant data are often hard to consolidate, and state-of-the-art analytical tools are typically tailored to specific datasets.</p> <p>2. We capitalized on a recent data harmonization initiative (SPI-Birds) and linked it to a generalized modeling framework to identify the demographic and environmental drivers of large-scale population decline in migratory pied flycatchers (<em>Ficedula</em> <em>hypoleuca</em>) breeding across Britain.</p> <p>3. We implemented a generalized integrated population model (IPM) to estimate age-specific vital rates, including their dependency on environmental conditions, and total and breeding population size of pied flycatchers using long-term (34–64 years) monitoring data from seven locations representative of the British breeding range. We then quantified the relative contributions of different vital rates and population structures to changes in short- and long-term population growth rates using transient life table response experiments (LTREs).</p> <p>4. Substantial covariation in population sizes across breeding locations suggested that change was the result of large-scale drivers. This was supported by LTRE analyses, which attributed past changes in short-term population growth rates and long-term population trends primarily to variation in annual survival and dispersal dynamics, which largely act during migration and/or non-breeding season. Contributions of variation in local reproductive parameters were small in comparison, despite sensitivity to local temperature and rainfall within the breeding period.</p> <p>5. We show that both short- and longer-term population changes of British-breeding pied flycatchers are likely linked to factors acting during migration and in non-breeding areas, where future research should be prioritized. We illustrate the potential of multi-population analyses for informing management at (inter)national scales and highlight the importance of data standardization, generalized and accessible analytical tools, and reproducible workflows to achieve them.</p>
Data, code and supplementary material for "A data integration framework for spatial interpolation of temperature observations using climate model data"
<p>Each zipped file contains code and data to reproduce the results in the paper and supplementary material. The Cyprus folder contains also the files to run the model, as well as the associated results. The Morocco folder only contains the results and the code used to manipulate it. </p>
Code and data for: Emergence of spatially structured populations by area-concentrated search
<p>The idea that populations are spatially structured has become a very powerful concept in ecology, raising interest in many research areas. However, despite dispersal being a core component of the concept, it typically does not consider the movement behavior underlying any dispersal. Using individual-based simulations in continuous space, we investigate the emergence of a spatially structured population in landscapes with spatially heterogeneous resource distribution and with organisms following simple area-concentrated search (ACS); individuals do not, however, perceive or respond to any habitat attributes per se but only to their foraging success. We investigated effects of different resource clustering patterns in landscapes (single large cluster vs. many small clusters) and different resource densities on spatial structure of populations and movement between resource clusters of individuals. As the results, we found that foraging success increased with increasing resource density and decreasing number of resource clusters. In a wide parameter space, the system exhibited attributes of a spatially structured population with individuals concentrated in areas of high resource density, searching within areas of resources, and 'dispersing' in a straight line between resource patches. 'Emigration' was more likely from patches that were small or of low quality (low resource density), but we observed an interaction effect between these two parameters. With the ACS implemented, individuals tended to move deeper into a resource cluster in scenarios with moderate resource density than in scenarios with high resource density. 'Looping' from patches was more likely if patches were large and of high quality. Our simulations demonstrate that spatial structure in populations may emerge if critical resources are heterogeneously distributed and if individuals follow simple movement rules (such as ACS). Neither the perception of habitat nor an explicit decision to emigrate from a patch on the side of acting individuals is necessary for the emergence of spatial structure.</p>
Data for: Spatial and temporal genetic stock composition of river herring bycatch in southern New England Atlantic herring and mackerel fisheries
<p>Anadromous river herring (alewife and blueback herring) persist at historically low abundances and are caught as bycatch in commercial fisheries, potentially preventing recovery despite conservation efforts. We used newly established single-nucleotide polymorphism genetic baselines for alewife and blueback herring to define fine-scale reporting groups for each species. We then determined the occurrence of fish from these reporting groups in bycatch samples from a Northwest Atlantic fishery over four years.Within sampled bycatch events, the highest proportions of alewife were from the Block Island (34%) and Long Island Sound (22%) reporting groups, while for blueback herring the highest proportions were from the Mid-Atlantic (47%) and Northern New England (24%) reporting groups. We then quantified stock-specific mortality in a focal geographic area (~3500 km<sup>2</sup> including Block Island Sound) of high bycatch incidence and sampling effort, where the most accurate estimates of mortality could be made. During this period, we estimate that bycatch took about 4.6 million alewife and 1.2 million blueback herring, highlighting the need to reduce bycatch mortality for the most depleted river herring stocks.</p>
Data for accurate cell type deconvolution in spatial transcriptomics using a batch effect-free strategy
<p>Simulated and experimental data used in the ReSort manuscript. It is necessary and sufficient to reproduce the results in the paper.</p>
Data supplement to "Aromatics and agriculture: A spatial approach to long-distance trade and the local economy of the Nabataeans"
<p>Data used to analyze the role of long-distance trade in the local agricultural economy of the Nabataeans, as described in Weaverdyck, E. J. S. forthcoming. "Aromatics and agriculture: A spatial approach to long-distance trade and the local economy of the Nabataeans." In S. von Reden (ed.). <em>Handbook of Ancient Afro-Eurasian Economies</em>, vol. 3. Oldenbourg: De Gruyter.</p> <p>Data sources are provided in the chapter.</p> <p>With the exception of runoff, environmental variables are rasters created using the focal statistics tool to sum the number of cells within a radius around each cell. They are named according to the following convention: f{radius}_{factor abbreviation}_{variable}.tif</p> <p>Factor abbreviations:</p> <table> <tbody> <tr> <td>A</td> <td>Aspect</td> </tr> <tr> <td>D</td> <td>DEV geomorphological land form</td> </tr> <tr> <td>H</td> <td>Hydrology</td> </tr> <tr> <td>S</td> <td>Slope</td> </tr> <tr> <td>T</td> <td>TPI geomorphological land form</td> </tr> </tbody> </table> <p>Of these environmental variables, the following were used as background variables in the MaxEnt models:</p> <table> <thead> <tr> <th scope="col">ASKP-LA</th> <th scope="col">WHS</th> </tr> </thead> <tbody> <tr> <td>f500_H_prec_soak</td> <td>f500_H_Runoff</td> </tr> <tr> <td>f500_T_Valley</td> <td>f5k_D_Ridge</td> </tr> <tr> <td>f5k_T_Ridge</td> <td>f5k_H_Runoff</td> </tr> <tr> <td>f5k_H_Runoff</td> <td>f500_D_UpperSlope_or_low_rise</td> </tr> <tr> <td>f5k_A_Northeast</td> <td>f5k_A_Southwest</td> </tr> <tr> <td>f500_D_UpperSlope_or_low_rise</td> <td>f500_D_Valley</td> </tr> <tr> <td>f5k_H_springs</td> <td> </td> </tr> <tr> <td>f5k_D_Ridge</td> <td> </td> </tr> <tr> <td>f5k_A_South</td> <td> </td> </tr> <tr> <td>f5k_A_Southwest</td> <td> </td> </tr> <tr> <td>f5k_A_Northwest</td> <td> </td> </tr> <tr> <td>f500_T_UpperSlope_or_low_rise</td> <td> </td> </tr> <tr> <td>f500_D_Lower_slope_or_shallow_valley</td> <td> </td> </tr> <tr> <td>f5k_A_North</td> <td> </td> </tr> </tbody> </table> <p> </p>
Data set for paper "Spatial Mobility Capital: A Valuable Resource for the Social Mobility of Border-Crossing Migrant Entrepreneurs?"
<p>Data set for paper "Spatial Mobility Capital: A Valuable Resource for the Social Mobility of Border-Crossing Migrant Entrepreneurs?"</p>
Data for: The interactive effects of soil fertility and tree mycorrhizal association explain spatial variation of diversity-biomass relationships in a subtropical forest
<p><span>Observed biodiversity-ecosystem function (BEF) relationships are highly variable, particularly in natural forests. However, our understanding of the factors that generate these often contradictory patterns, especially the role of different mycorrhizal associations, is still limited. By relating tree species richness and aboveground biomass (AGB) in a fully-mapped 24-ha subtropical forest dynamics plot, we evaluated the impacts of soil fertility and tree mycorrhizal type in mediating BEF relationships at multiple spatial scales. Our results demonstrate a highly positive total richness effect on AGB for arbuscular mycorrhizal (AM) trees but a negative effect on AGB for ectomycorrhizal (EcM) trees, and their relationships were highly spatial scale dependent. However, the observed BEF relationships turned into positive at small spatial scales (i.e., 10 m and 20 m) after controlling for other confounding factors (i.e., topography, soil fertility, and AM proportion). In addition, we found significant interactions between soil fertility and species richness on AGB. Specifically, the positive effect of total species richness on AGB for major mycorrhizal types gradually weakened with increasing soil fertility, while the positive effect of EcM species richness on AM AGB gradually enhanced at small spatial scales, suggesting the observed diversity effects can be largely attributed to resource niche complementarity and the role of EcM fungi.</span></p> <p><span>Synthesis. We conclude that the variable BEF relationships among forest communities could be explained by spatial variation in abiotic environments and community mycorrhizal composition because different types of symbionts perform different nutrient uptake strategies and ability in protection from antagonists. Our findings provide novel insights into the understanding of the variation in the shape of BEF relationships in natural forests, which is critical for forest management, conservation, and restoration in a changing world.</span></p>
Data and scripts for: Quantifying annual spatial consistency in chick-rearing seabirds to inform important site identification
<p>Data derivates and analysis scripts (in R) used for the paper "Quantifying annual spatial consistency in chick-rearing seabirds to inform important site identification", published in Biological Conservation, on analyzing annual spatial overlap of 25 seabird populations across 23 species to assess variability and inform global efforts to improve spatial conservation measures.</p>
Scripts of data selection and analysis: role of community size in driving spatial variation in riverine fish metacommunities around the world
<p>Here we describe how we obtained and analyzed data for the manuscript: High compositional dissimilarity among small communities is decoupled from environmental variation, accepted for publication in Oikos. (10.1111/oik.09802). A preprint is also available: https://doi.org/10.32942/osf.io/vngse</p> <p>We investigated the role of community size in mediate the strength of ecological drift and environmental selection in driving community spatial variation in metacommunities. </p>
Mars Watershed boundary data for "Global Spatial Distribution of Hack's Law Exponent on Mars Consistent with Early Arid Climate "
<p>This is the watershed boundary data for Mars (along with Hack's Law exponent) as described in Luo et al. "Global Spatial Distribution of Hack’s Law Exponent on Mars Consistent with Early Arid Climate" accepted for publication in Geophysical Research Letters on 3/10/2023.</p> <p>The attributes are as follows:</p> <p>Id, gridcode = ID of basin</p> <p>Shape_Length = perimeter of the basin</p> <p>Shape_area = area of the basin</p> <p>geoArea = geodesic area of the basin</p> <p>geoLength = geodesic perimeter of the basin</p> <p>areaR = geoArea / Shape_area</p> <p>LengthR = geoLength / Shape_Length</p> <p>n_exponent = Hack’s Law Exponent (h in L = k A^h)</p> <p>n_coefficient = Hack’s Law exponent (k in L = k A^h)</p> <p>n_r2 = r^2 of the nonlinear fit (optimize.curve_fit function in SciPy)</p>
Data from: The spatial patterns of community composition, their environmental drivers and their spatial scale dependence vary markedly between fungal ecological guilds
<p><strong><span>Aim</span></strong></p> <p><span>How community composition varies in space and what governs the variation has been extensively investigated in macroorganisms. However, we have only limited knowledge for microorganisms, especially fungi, despite their ecological and economic significance. Based on previous research, we define and test a series of hypotheses regarding the composition of fungal communities, its most influential drivers and their spatial scale dependence. </span></p> <p><strong><span>Location</span></strong></p> <p><span>Czech Republic.</span></p> <p><strong><span>Time period</span></strong></p> <p><span>Present.</span></p> <p><strong><span>Taxa studied</span></strong></p> <p><span>Fungi.</span></p> <p><strong><span>Methods</span></strong></p> <p><span>We analyzed the distance decay relationships, community composition and its drivers (physical distance, litter and soil chemistry, tree composition, climate) in fungi, using multivariate analyses. We compared the results across three fungal ecological guilds (ectomycorrhizal fungi, saprotrophs and yeasts), two forest microhabitats (litter and bulk soil) and six spatial scales (from 5 m to 80 km) that comprehensively cover the Czech Republic.</span></p> <p><strong><span>Results</span></strong></p> <p><span>We found that, similar to macroorganisms, the ectomycorrhizal fungi and saprotrophs showed marked distance-decay relationships</span><span>,</span><span> and their community composition was driven mainly by vegetation and dispersal at local scales, but at regional scales, by environmental effects. In contrast, the third fungal guild, the unicellular yeasts, showed little distance decay, suggesting extraordinary spatial homogeneity, as often seen in microorganisms, such as bacteria.</span></p> <p><strong><span>Main conclusions</span></strong></p> <p><span>Our results underscore the remarkable variation in the community ecology of fungi, which seems to range well-known patterns both from the macro- and the microworld. Knowledge of these patterns advances our understanding of the ecology of fungi, rather understudied organisms of significant ecological and economic importance, which our findings identify as a potentially suitable model for bridging the gaps between the biogeography of micro- and macroorganisms. </span></p>
Data from: Using environmental DNA metabarcoding to monitor fish communities in small rivers and large brooks: Insights on the spatial scale of information
<p><span>Monitoring fish communities is central to the evaluation of ecological health of rivers. Not only presence/absence of species is important to assess, but also the species composition of local fish assemblages is a crucial parameter. Lotic fish communities are traditionally monitored via electrofishing, characterized by a known limited efficiency and high survey costs. The use of environmental DNA-based analyses could serve as a non-destructive alternative, but this approach requires further insights in practical sampling schemes incorporating transport and dilution of the eDNA fragments; as well as optimization of molecular detection in terms of predictive power and quality assurance. By introducing fifteen species known to occur in Belgian waters via a controlled cage experiment, we aim to extend the knowledge on streamreach of eDNA in small rivers and large brooks, as laid out in the European Water Framework Directive's water typology. Introducing fish communities in two transects of a species poor river characterized by contrasting river discharge rates, we found strong and significant correlations between the eDNA relative abundances and the relative biomass per species in the cage community. Despite a decreasing correlation over distance, the underlying community composition remained stable over a distance of 300 m up to 1 km downstream of the cages, depending on the river discharge rate. Such decrease in similarity between relative source biomass and the corresponding eDNA-based community profile with increasing distance downstream from the source, can partly be attributed to variation in species-specific eDNA persistence. Our findings offer novel insights on eDNA behaviour and characterization of riverine fish communities. We conclude that water sampled from a relatively small river offers an adequate snapshot of the total fish community composition occurring within an upstream perimeter ranging between 300 and 1000 meters. The potential application for other river systems is discussed in this study. </span></p>
Data for 'Deriving spatial features from in situ proteomics imaging to enhance cancer survival analysis'
<p>Additional data for 'Deriving spatial features from in situ proteomics imaging to enhance cancer survival analysis'</p>
Data from: Spatial localization of anterior precuneus for bodily self validated with brain stimulation
<div class="page"> <div class="section"> <div class="layoutArea"> <div class="column"> <p>The posteromedial cortex (PMC), comprising the precuneus, the posterior cingulate, and the retrosplenial regions, is known to be engaged in various self-referential functions. Recent observations have also suggested a link between PMC dysfunction and self-dissociation. To test the causal relevance of specific PMC locations for self- referential processing, we recruited nine neurosurgical participants with bilaterally implanted PMC electrodes. We applied focal electrical stimulation within discrete PMC sites while probing changes in the participants' subjective states. We found that, in all nine participants, the electrical perturbation of the anterior precuneus (aPCu), but not the other PMC sites, caused apparent dissociative changes in the physical and spatial bodily domain involving head, trunk, and legs. The responsive aPCu sites did not exhibit event-related activation during a cued autobiographical memory recall task. Furthermore, resting-state functional connectivity with functional Magnetic Resonance Imaging data and effective connectivity with single-pulse electrical stimulation procedures confirmed that the responsive aPCu sites were distinct from, while closely connected with, the adjacent PMC nodes of the default mode network (DMN). Based on these data, we conclude that the aPCu is a distinct functional unit within the PMC and causally important for processing self-referential information in the physical and spatial domains. Future larger-scale experimental studies are needed to explore how operations of distinct neuronal populations within the PMC are integral to various cognitive processes that require a reference to self in its various dimension.</p> </div> </div> </div> </div>
Input data, species level results and code accompanying paper: Drivers of the changing abundance of European birds at two spatial scales
<p>This repository contains the input data, species level results and code associated with the paper: <strong>Drivers of the changing abundance of European birds at two spatial scales. </strong></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.