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470 results for “Spatial Patterns”
Data from: Linking habitat composition, local population densities and traffic characteristics to spatial patterns of ungulate-train collisions
1. Total length of railways worldwide exceeds 1 million kilometres and recent railway development directly impacts wildlife because of animal-train collisions. Few studies, however, have analysed factors driving ungulate-train collisions. 2. We analysed over 3500 ungulate-train collisions including roe deer, red deer, wild boar, and moose collected in 2012-2015 in Poland. We compared train traffic characteristics (e.g. traffic intensity, speed, rail curvature), land-use and habitat characteristics (e.g. share of forests and build-up areas) and local ungulate population densities at collision sites and random sites distributed along the rail network. 3. Forest coverage generally increased, while urban areas decreased ungulate collision risk. Local density of ungulate species was strongly positively related to the relative collision risk in all four ungulate species, but above certain densities, the risk levelled off for all four species. 4. Train speed and train traffic intensity were positively associated with elevated collision risk in all four species, but the latter in a non-linear manner reached an asymptote at the level of ca. 10 trains per day. Rail curvature also increased probability of collisions with roe deer and red deer and possibly also wild boar. 5. Mortality rate of ungulates on railways in Poland is estimated to be 0.13-0.42% of annual hunting bags of studied species assuming that only one individual is killed at each occasion and ignoring undetected collisions. These values are expected to increase in near future due to increasing train speed in Central European countries. 6. Synthesis and applications. Ungulate-train collisions spots are characterised by surrounding forest, rail curvature, high train speed, and a moderate to high train traffic intensity. To reduce collision risk in a cost-effective way, we suggest to prioritise mitigation actions at sections of the railway characterized by those factors, e.g. by fencing and various warning devices. Due to nonlinear correlation between collision risk and population density, reducing density of ungulates will most likely reduce collision risk only marginally, and only in regions of low population densities where collision risk is relatively low anyway.
Data from: Genetic relatedness does not retain spatial pattern across multiple spatial scales: dispersal and colonization in the coral, Pocillopora damicornis
Patterns of isolation-by-distance are uncommon in coral populations. Here, we depart from historical trends of large-scale, geographic genetic analyses by scaling down to a single patch reef in Kāne'ohe Bay, Hawai'i, and map and genotype all colonies of the coral, Pocillopora damicornis. Six polymorphic microsatellite loci were used to assess population genetic and clonal structure and to calculate individual colony pairwise relatedness values. Our results point to an inbred, highly clonal reef (between 53 and 116 clonal lineages out of 2352 genotyped colonies) with a very skewed genet frequency distribution (over 70% of the reef was composed of just seven genotypes). Spatial autocorrelation analyses revealed that corals found close together on the reef were more genetically related than corals further apart. Spatial genetic structure disappears, however, as spatial scale increases and then becomes negative at the largest distances. Stratified, random sampling of three neighbouring reefs confirms that reefs are demographically open and inter-reef genetic structuring was not detected. Attributing process to pattern in corals is complicated by their mixed reproductive strategies. Separate autocorrelation analyses, however, show that the spatial distribution of both clones and non-clones contribute to spatial genetic structure. Overall, we demonstrate genetic structure on an intra-reef scale and genetic panmixia on an inter-reef scale indicating that, for P. damicornis, small- and large-scale dispersal processes are likely not the same. By starting from an inter-individual, intra-reef level before scaling up to an inter-reef level, this study demonstrates that isolation-by-distance patterns for the coral P. damicornis are limited to small scales and highlights the importance of investigating genetic patterns and ecological processes at multiple scales.
Spatial point pattern analysis of traces (SPPAT): an approach for visualizing and quantifying site-selectivity patterns of drilling predators
<p>Site-selectivity analysis in drilling predation may provide useful behavioral information of a predator interacting with its prey. However, traditional approaches exclude some spatial information (i.e., oversimplified trace position) and are dependent on the scale of analysis (e.g., arbitrary grid system used to divide the prey skeleton into sectors). Here we introduce the spatial point pattern analysis of traces (<i>SPPAT</i>), an approach for visualizing and quantifying the distribution of traces on shelled invertebrate prey, which includes improved collection of spatial information inherent to drillhole location (morphometric-based estimation), improved visualization of spatial trends (Kernel density and hotspot mapping), and distance-based statistics for hypothesis testing (<i>K</i>-, <i>L</i>-, and pair correlation functions). We illustrate the <i>SPPAT</i> approach through case studies of fossil samples, modern beach-collected samples, and laboratory feeding trials of naticid gastropod predation on bivalve prey. Overall results show that Kernel density and hotspot maps enable visualization of subtle variations in regions of the shell with higher density of predation traces, which can be combined with the maximum clustering distance metric to generate hypotheses on predatory behavior and anti-predatory responses of prey across time and geographic space. Distance-based statistics also capture the major features in the distribution of traces across the prey skeleton, including aggregated and segregated clusters, likely associated with different combinations of two modes of drilling predation, edge- and wall-drilling. The <i>SPPAT </i>approach is transferrable to other paleoecologic and taphonomic data such as encrustation and bioerosion, allowing for standardized investigation of a wide range of biotic interactions.</p>
Data from: Spatial and temporal patterns of larval dispersal in a coral-reef fish metapopulation: evidence of variable reproductive success
Many marine organisms can be transported hundreds of kilometers during their pelagic larval stage, yet little is known about spatial and temporal patterns of larval dispersal. Although traditional population-genetic tools can be applied to infer movement of larvae on an evolutionary time scale, large effective population sizes and high rates of gene-flow present serious challenges to documenting dispersal patterns over shorter, ecologically-relevant, time scales. Here, we address these challenges by combining direct parentage analysis and indirect genetic analyses over a four-year period to document spatial and temporal patterns of larval dispersal in a common coral-reef fish: the bicolor damselfish (Stegastes partitus). At four island locations surrounding Exuma Sound, Bahamas, including a long-established marine reserve, we collected 3,278 individuals and genotyped them at 10 microsatellite loci. Using Bayesian parentage analysis, we identified eight parent-offspring pairs, thereby directly documenting dispersal distances ranging from 0 km (i.e., self-recruitment) to 129 km (i.e., larval connectivity). Despite documenting substantial dispersal and gene-flow between islands, we observed more self-recruitment events than expected if the larvae were drawn from a common, well-mixed pool (i.e., a completely open population). Additionally, we detected both spatial and temporal variation in signatures of sweepstakes and Wahlund effects. The high variance in reproductive success (i.e., "sweepstakes") we observed may be influenced by seasonal mesoscale gyres present in the Exuma Sound, which play a prominent role in shaping local oceanographic patterns. This study documents the complex nature of larval dispersal in a coral-reef fish, and highlights the importance of sampling multiple cohorts and coupling both direct and indirect genetic methods in order disentangle patterns of dispersal, gene-flow, and variable reproductive success.
Data from: Spatial pattern and scale influence invader demographic response to simulated precipitation change in an annual grassland community
It is important to predict which invasive species will benefit from future changes in climate, and thereby identify those invaders that need particular attention and prioritization of management efforts. Because establishment, persistence, and spread determine invasion success, this prediction requires detailed demographic information. Explicit study of the impact of pattern on demographic response is particularly important for species that are naturally patchy, such as the invasive grass, Aegilops triuncialis. In the northern California Coast Range, where climate change may increase or decrease mean annual rainfall, we conducted a field experiment to understand the interaction of climate change and local-scale patterning on the demography of A. triuncialis. We manipulated precipitation (reduced, ambient, or augmented), seed density, and seeding pattern. Demographic and environmental data were collected for three years following initial seeding. Pattern and scale figure prominently in the demographic response of A. triuncialis to precipitation manipulation. Pattern interacts with precipitation and seeding density in its influence on per-plant seed output. Although per-plot seed production was highest when seeds were not aggregated, per-plant seed output was higher in aggregated patches. Results suggest aggregation of invasive A. triuncialis reduces the detrimental impact of interspecific competition in its invaded community, and that interspecific competition per se has a stronger impact than intraspecific competition
Data from: Revisiting the provenance delineation of a widespread shrub, Frangula alnus—the role of spatial, temporal and environmental patterns
Including population genetic aspects into the selection of planting material within the framework of conservation and restoration measures is of vital importance for the long-term persistence of populations. This is especially true facing climate change since genetic diversity and the spread of potentially beneficial alleles are important for the adaptability of populations. Therefore, knowledge about genetic variability within and between populations is a critical aspect when determining provenance regions. In our study, we investigated the population genetic structure of a widespread, insect-pollinated and mainly bird-dispersed shrub species, Frangula alnus, on the basis of seven microsatellites and two chloroplast DNA markers throughout Germany. The aim was to determine the spatial, temporal and ecological processes genetically structuring populations to critically revise existing provenance regions. Therefore, we conducted analyses on different spatial scales (country-wide, regional and local) using the two different marker sets in addition to environmental variables. We detected distinct patterns on all spatial scales which indicated influences of historic recolonization processes, regional differences of seed dispersal across the landscape, as well as small-scale spatial genetic structures attributable to local dispersal processes. No relation of underlying environmental gradients such as temperature or precipitation and genetic patterns was found. We conclude that different aspects of historic and more recent gene flow shape population genetic structures and that a thorough analysis on a variety of spatial, temporal and environmental scales is necessary to appropriately select planting material for conservation and restoration measures. Correspondingly, management advice regarding provenance delineations will be provided.
Data from: Intraspecific interactions affect the spatial pattern of a dominant shrub in a semi-arid scrubland: a prospective approach
Dispersal, physical conditions and biotic interactions contribute to determine the spatial distribution of individuals in plant populations. Much of what we know has been learned from studies that retrospectively posit mechanisms presumed to have generated the observed spatial patterns. Here we present a prospective approach. We start by measuring spatial demographic effects and evaluate if they can generate observed spatial patterns. We evaluated the influence of interactions among conspecifics on vital rates, demography and spatial distribution of Croton aff. wagneri, a dominant shrub in dry Andean ecosystems. Recruitment, survival and growth varied in relation with distance to conspecifics neighbors and with their summed cover. We built a spatial individual-based model and simulated its population dynamics in 30 × 30 m plots for a 30 year periods. We compared the predicted spatial pattern from these demographic models with that observed among plants in sixteen independent plots with the same area. Simulated populations mimicked observed spatial patterns, although in plots at high elevations the simulated populations did not reproduce the observed inhibition at small scales. Observed and simulated patterns indicated differences between elevations in maximum aggregation and location of the distances with higher aggregation. We discuss how consideration of critical seed and juvenile stages and interspecific interactions could further improve our understanding of spatial pattern and recommend that these factors be considered in future models.
Data from: Patterns of diversity and spatial variability of β-defensin innate immune genes in a declining wild population of tree swallows
Assessing the genetic variation and distribution of immune genes across heterogeneous environmental conditions in wild species is essential to further our understanding of the role of pathogen pressure and potential resistance or prevalence in hosts. Researchers have recently investigated β-defensin genes in the wild, because their variability suggests that they may play an important role in innate host defense. This study investigated the variation occurring at 6 innate immune genes of the β-defensin family in a declining population of tree swallows (Tachycineta bicolor) in southern Québec, Canada (N = 160). We found that all 6 genes showed synonymous and nonsynonymous single nucleotide polymorphisms (SNPs) within the exon coding for the mature peptide. These results indicated that this group of genes was diverse in tree swallows. Our results suggested a potential interaction of this group of genes with fluctuating pathogen diversity, however, we found no sign of positive or negative selection. We assessed whether or not the distribution of genetic diversity of β-defensin genes in our study population differed between 2 regions that strongly differ in their level of agricultural intensification. Adults are highly philopatric to their breeding sites and their immunological responses differ between these 2 regions. However, we found little evidence that the level and distribution of genetic variability differed between these heterogeneous environmental conditions. Further studies should aim to assess the link between genetic diversity of β-defensin genes and fitness-related traits in wild populations.
Data from: The impact of spatial scale and habitat configuration on patterns of trait variation and local adaptation in a wild plant parasite
Theory indicates that spatial scale and habitat configuration are fundamental for coevolutionary dynamics and how diversity is maintained in host–pathogen interactions. Yet, we lack empirical data to translate the theory to natural host–parasite systems. In this study, we conduct a multiscale cross-inoculation study using the specialist wild plant pathogen Podosphaera plantaginis on its host plant Plantago lanceolata. We apply the same sampling scheme to a region with highly fragmented (Åland) and continuous (Saaremaa) host populations. Although theory predicts higher parasite virulence in continuous regions, we did not detect differences in traits conferring virulence among the regions. Patterns of adaptation were highly scale dependent. We detected parasite maladaptation among regions, and among populations separated by intermediate distances (6.0–40.0 km) within the fragmented region. In contrast, parasite performance did not vary significantly according to host origin in the continuous landscape. For both regions, differentiation among populations was much larger for genetic variation than for phenotypic variation, indicating balancing selection maintaining phenotypic variation within populations. Our findings illustrate the critical role of spatial scale and habitat configuration in driving host–parasite coevolution. The absence of more aggressive strains in the continuous landscape, in contrast to theoretical predictions, has major implications for long-term decision making in conservation, agriculture, and public health.
Spatial transcriptome mapping of the desmoplastic growth pattern of colorectal liver metastases by in situ sequencing - Image and In SItu Sequencing data
<p>Image and ISS data for Spatial transcriptome mapping of the desmoplastic growth pattern of colorectal liver metastases by in situ sequencing reveals a biologically relevant zonation of the desmoplastic rim.</p><p>Image data consists of:</p><ul><li>Nucler stain (DAPI)</li><li>Masks for liver, rim and tumor regions</li><li>H&E images of parallel tissue sections</li></ul><p>Gene and cluster marker data is collected in the <i>markers.h5ad</i> file which can be read using AnnData (<a href="https://anndata.readthedocs.io/en/latest/">https://anndata.readthedocs.io/en/latest/)</a>. </p><p> </p>
Processed datasets used in Almet et al. (2024), "Inferring pattern-driving intercellular flows from single-cell and spatial transcriptomics"
<p>These are the processed anndata objects used in Almet et al. (2024), "Inferring pattern-driving intercellular flows from single-cell and spatial transcriptomics".</p> <p>These datasets are stored as .h5ad files and are intended to be used with the <a href="https://scanpy.readthedocs.io/en/stable/api.html">Scanpy</a> package in Python. They contain all relevant cell type annotation, unnormalized and transformed gene expression counts, as well as the inferred intercellular fow networks inferred by FlowSig.</p>
Spatial patterns and effects of invasive plants on soil microbial activity and diversity along river corridors - dataset
<p>environmental data, plant community data, CLPP profiles, microbial activity data</p>
Data Artifact for "Gaze into the Pattern: Characterizing Spatial Patterns with Internal Temporal Correlations for Hardware Prefetching"
<p>This dataset contains the Ligra, PARSEC, GAP, and QMM traces used in our paper "Gaze into the Pattern: Characterizing Spatial Patterns with Internal Temporal Correlations for Hardware Prefetching", which is accepted by HPCA'25. These traces are provided as part of the AE proces.</p>
R script used for: Telomeres in a spatial context: a tool for understanding ageing pattern variation in wild populations
<p><span><span><span><span><span><span><span><span><span><span><span>Ageing refers to the loss of organismal functionality with age, a process that is characterised by decreased reproduction and survival probability. In natural populations, it is expected that environmental conditions influence an individual's ageing trajectory. Understanding the role of environmental heterogeneity on ageing variation could provide criticleinsights into population resilience and species distribution but remains overlooked. Telomeres, the end cap of chromosomes, are a promising integrative physiological marker of an individual's health and a possible proxy to aid the understanding of variation in ageing trajectories. Here, we review the existing information on telomere length and its dynamics in wild populations distributed across spatial scales. Despite a relative scarcity of information, there is evidence for divergence in telomere length between populations facing contrasting environments. Nonetheless, a higher spatial resolution and temporal replication is needed to fully understand the role that environmental conditions play on telomere length variation. Since most of the existing studies are correlational, future field and laboratory experiments are required. For the first time, we demonstrate the use of population telomere data to predict species habitat suitability through Species Distribution Models (SDMs). This represents a promising new research area in the study of ageing pattern variation in wild populations. Furthermore, the inclusion of telomere data in future physiological-SDMs may improve our understanding of species distribution and population resilience. However, the use of telomeres within this context could be limited if no previous knowledge on the relevance of telomeres as markers of health and survival at the species level is available. Finally, we suggest some key practical and theoretical considerations that, ideally, future studies combining biogeographic and telomere data should pay attention. </span></span></span></span></span></span></span></span></span></span></span></p>
Resource availability and heterogeneity shape the self‐organisation of regular spatial patterning
<p>Explaining large-scale ordered patterns and their effects on ecosystem functioning is a fundamental and controversial challenge in ecology. Here, we coupled empirical and theoretical approaches to explore how competition and spatial heterogeneity govern the regularity of colony dispersion in fungus-farming termites. Individuals from different colonies fought fiercely, and inter-nest distances were greater when nests were large and resources scarce—as expected if competition is strong, large colonies require more resources, and foraging area scales with resource availability. Building these principles into a model of inter-colony competition showed that highly ordered patterns emerged under high resource availability and low resource heterogeneity. Analysis of this dynamical model provided novel insights into the mechanisms that modulate pattern regularity and the emergent effects of these patterns on system-wide productivity. Our results show how environmental context shapes pattern formation by social-insect ecosystem engineers, which offers one explanation for the marked variability observed across ecosystems.</p>
Wildland-urban interface fire dynamics simulator input files for pyric tree spatial patterning interactions in historical and contemporary mixed conifer forests, California, USA
<p><span>Tree spatial patterns in dry coniferous forests of the western US, and analogous ecosystems globally, were historically aggregated, comprising a mixture of single trees and groups of trees. Modern forests, in contrast, are generally more homogeneous and overstocked than their historical counterparts. As these modern forests lack regular fire, pattern formation and maintenance is generally attributed to fire. Accordingly, fires in modern forests may not yield historically analogous patterns. However, direct observations on how selective tree mortality among pre-existing forest structure shapes tree spatial patterns is limited. In this study, we (1) simulated fires in historical and contemporary counterpart plots in a Sierra Nevadan mixed-conifer forest, (2) estimated tree mortality, and (3) examined tree spatial patterns of live trees before and after fire, and of fire-killed trees. Tree mortality in the historical period was clustered and density-dependent, because trees were aggregated and segregated by tree size before fire. Thus, fires maintained an aggregated distribution of tree groups. Tree mortality in the contemporary period was widespread, except for dispersed large trees, because most trees were a part of large, interconnected tree groups. Thus, post-fire tree patterns were more uniform and devoid of moderately sized tree groups. Post-fire tree patterns in the historical period, unlike the contemporary period, were within the historical range of variability identified for the western US. This divergence suggests that decades of forest dynamics without significant disturbances has altered the historical means of pyric pattern formation. Our results suggest that ecological silvicultural treatments, such as forest restoration thinnings, which emulate qualities of historical forests may facilitate the reintroduction of fire as a means to reinforce forest structural heterogeneity.</span></p>
Dataset for Spatial Heterogeneity of Uplift Pattern in the Western European Alps Revealed by InSAR Time Series Analysis
<p>ZIP file with InSAR raw and smoothed final velocity solution values</p>
Derived products from "Beyond glacier wide mass balances: parsing seasonal elevation change into spatially-resolved patterns of accumulation and ablation at Wolverine Glacier, Alaska"
<p>Distributed mass balances, emergence velocities, firn compaction rates, and co-registered 10 m resolution DEMs from "Beyond glacier wide mass balances: parsing seasonal elevation change into spatially-resolved patterns of accumulation and ablation at Wolverine Glacier, Alaska" (in review) (Zeller et al., 2022).</p>
Spatial patterns and quantification of lacustrine groundwater discharge determined based on 222Rn
<p>Shape of water pixels calculated by Modified Normalized Difference Water Index algorithm based on Landsat8 images</p>
Spatial patterns and quantification of lacustrine groundwater discharge determined based on 222Rn
<p>The field parameter [temperature (T), electrical conductivity (EC), pH, dissolved oxygen (DO), redox potential (Eh) and 222Rn concentration] were listed here. </p>
ScienceDex guides
Understand access before you commit
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.