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251 results for “spatial heterogeneity”
Data from: Multiple scales of spatial heterogeneity control soil respiration responses to precipitation across a dryland rainfall gradient
<p><i>Aims –</i> Soil respiration (R<sub>s</sub>) is a major pathway for releasing fixed carbon back to the atmosphere. However, controls over R<sub>s</sub> are poorly understood in arid and hyper-arid systems where microbial activity is frequently constrained by moisture. We addressed key uncertainties in R<sub>s</sub>: 1) How do short-term rainfall pulses affect R<sub>s</sub> at sites that differ in long-term precipitation inputs?, 2) how do R<sub>s</sub> responses to short and long-term rainfall differ across soil surfaces?, and 3) how are R<sub>s</sub> responses affected by local-scale attributes?</p> <p><i>Methods – </i>We measured R<sub>s</sub> responses to rainfall pulses over a 48 h period. Working across a climate gradient, we compared R<sub>s </sub>responses on two contrasting soil surfaces which both had two vegetation/soil morphology patch types that differed in organic matter inputs and accumulation.</p> <p><i>Results – </i>Rates of R<sub>s </sub>were low, but highly responsive to rainfall pulses. Stimulation of R<sub>s </sub>by rainfall was generally greater in areas with higher annual rainfall. However, patterns for R<sub>s </sub>responses to rainfall differed greatly on the two soil surfaces and among patch types.</p> <p><i>Conclusions – </i>The strong role of patch type and soil surface in controlling R<sub>s</sub> points to the need to carefully consider small-scale spatial and temporal variation when interpreting dryland biogeochemical fluxes.</p>
Data from: Spatial analyses of two color polymorphisms in an alpine grasshopper reveal a role of small‐scale heterogeneity
Discrete color polymorphisms represent a fascinating aspect of intraspecific diversity. Color morph ratios often vary clinally, but in some cases, there are no marked clines and mixes of different morphs occur at appreciable frequencies in most populations. This poses the questions of how polymorphisms are maintained. We here study the spatial and temporal distribution of a very conspicuous color polymorphism in the club‐legged grasshopper Gomphocerus sibiricus. The species occurs in a green and a nongreen (predominately brown) morph, a green–brown polymorphism that is common among Orthopteran insects. We sampled color morph ratios at 42 sites across the alpine range of the species and related color morph ratios to local habitat parameters and climatic conditions. Green morphs occurred in both sexes, and their morph ratios were highly correlated among sites, suggesting shared control of the polymorphism in females and males. We found that in at least 40 of 42 sites green and brown morphs co‐occurred with proportions of green ranging from 0% to 70% with significant spatial heterogeneity. The proportion of green individuals tended to increase with decreasing summer and winter precipitations. Nongreen individuals can be further distinguished into brown and pied individuals, and again, this polymorphism is shared with other grasshopper species. We found pied individuals at all sites with proportions ranging from 3% to 75%, with slight, but significant variation between years. Pied morphs show a clinal increase in frequency from east to west and decreased with altitude and lower temperatures and were more common on grazed sites. The results suggest that both small‐scale and large‐scale spatial heterogeneity affects color morph ratios. The almost universal co‐occurrence of all three color morphs argues against strong effects of genetic drift. Instead, the data suggest that small‐scale migration–selection balance and/or local balancing selection maintain populations polymorphic.
Data from: Landscape heterogeneity and local adaptation define the spatial genetic structure of Pacific salmon in a pristine environment
Identifying the spatial distribution of genetic variation across the landscape is an essential step in informing species conservation. Comparison of closely related and geographically overlapping species can be particularly useful in cases where landscape may similarly influence genetic structure. Congruent patterns among species highlight the importance that landscape heterogeneity plays in determining genetic structure whereas contrasting patterns emphasize differences in species-specific ecology and life-history or the importance of species-specific adaptation to local environments. We examined the interacting roles of demography and adaptation in determining spatial genetic structure in two closely related and geographically overlapping species in a pristine environment. Using single nucleotide polymorphism (SNP) loci exhibiting both neutral and putative adaptive variation, we evaluated the genetic structure of sockeye salmon in the Copper River, Alaska; these data were compared to existing data for Chinook salmon from the same region. Overall, both species exhibited patterns of isolation by distance; the spatial distribution of populations largely determined the distribution of genetic variation across the landscape. Further, both species exhibited largely congruent patterns of within- and among-population genetic diversity, highlighting the role that landscape heterogeneity and historical processes play in determining spatial genetic structure. Potential adaptive differences among geographically proximate sockeye salmon populations were observed when high FST outlier SNPs were evaluated in a landscape genetics context. Results were evaluated in the context of conservation efforts with an emphasis on reproductive isolation, historical processes, and local adaptation.
Data from: Examining the full effects of landscape heterogeneity on spatial genetic variation: a multiple matrix regression approach for quantifying geographic and ecological isolation
Understanding the effects of landscape heterogeneity on spatial genetic variation is a primary goal of landscape genetics. Ecological and geographic variables can contribute to genetic structure through geographic isolation, in which geographic barriers and distances restrict gene flow, and ecological isolation, in which gene flow among populations inhabiting different environments is limited by selection against dispersers moving between them. Although methods have been developed to study geographic isolation in detail, ecological isolation has received much less attention, partly because disentangling the effects of these mechanisms is inherently difficult. Here, I describe a novel approach for quantifying the effects of geographic and ecological isolation using multiple matrix regression with randomization. I explored the parameter space over which this method is effective using a series of individual-based simulations and found that it accurately describes the effects of geographic and ecological isolation over a wide range of conditions. I also applied this method to a set of real-world datasets to show that ecological isolation is an often overlooked but important contributor to patterns of spatial genetic variation and to demonstrate how this analysis can provide new insights into how landscapes contribute to the evolution of genetic variation in nature.
Data from: Geographical isolation and environmental heterogeneity contribute to the spatial genetic patterns of Quercus kerrii (Fagaceae)
Southwest China is one of the major global biodiversity hotspots. The Tanaka line, extending within southwestern China from its northwest to its southeast, is an important biogeographical boundary between the Sino-Japanese and Sino-Himalayan floristic regions. Understanding the evolutionary history of the regional keystone species would assist with both reconstructing historical vegetation dynamics and ongoing biodiversity management. In this research, we combined phylogeographic methodologies and species distribution models (SDMs) to investigate the spatial genetic patterns and distribution dynamics of Quercus kerrii, a dominant evergreen oak inhabiting southwest China lowland evergreen broadleaved forests (EBLFs). A total of 403 individuals were sampled from 44 populations throughout southwest China. SDMs and mismatch distribution analysis indicated that Q. kerrii has undergone northward expansion since the Last Glacial Maximum (LGM). Quantitative analysis revealed that the range expansion of Q. kerrii since the LGM exceeded that of the sympatric mid-elevation species Quercus schottkyana, likely owing to their contrasting distribution elevations and habitat availabilities. The historical climate change since the LGM and the latitude gradient of the region played an important role in shaping the genetic diversity of Q. kerrii. The genetic differentiation index and genetic distance surface of Q. kerrii populations east of the Tanaka line exceeded those to its west. The long-term geographic isolation and environmental heterogeneity between the two sides of the Tanaka line might increase species divergence patterns and local adaptation. This study provides new insights into the historical dynamics of subtropical EBLFs and the changing biota of southwest China.
Data from: Spatial soil heterogeneity has a greater effect on symbiotic arbuscular mycorrhizal fungal communities and plant growth than genetic modification with Bacillus thuringiensis toxin genes
Maize, genetically modified with the insect toxin genes of Bacillus thuringiensis (Bt), is widely cultivated, yet its impacts on soil organisms are poorly understood. Arbuscular mycorrhizal fungi (AMF) form symbiotic associations with plant roots and may be uniquely sensitive to genetic changes within a plant host. In this field study, the effects of nine different lines of Bt maize and their corresponding non-Bt parental isolines were evaluated on AMF colonization and community diversity in plant roots. Plants were harvested 60 days after sowing, and data were collected on plant growth and per cent AMF colonization of roots. AMF community composition in roots was assessed using 454 pyrosequencing of the 28S rRNA genes, and spatial variation in mycorrhizal communities within replicated experimental field plots was examined. Growth responses, per cent AMF colonization of roots and AMF community diversity in roots did not differ between Bt and non-Bt maize, but root and shoot biomass and per cent colonization by arbuscules varied by maize cultivar. Plot identity had the most significant effect on plant growth, AMF colonization and AMF community composition in roots, indicating spatial heterogeneity in the field. Mycorrhizal fungal communities in maize roots were autocorrelated within approximately 1 m, but at greater distances, AMF community composition of roots differed between plants. Our findings indicate that spatial variation and heterogeneity in the field has a greater effect on the structure of AMF communities than host plant cultivar or modification by Bt toxin genes.
Data from: Spatially heterogeneous selection in nature favors phenotypic plasticity in anuran larvae
Theory holds that adaptive phenotypic plasticity evolves under spatial or temporal variation in natural selection. I tested this prediction in a classic system of predator-induced plasticity: frog tadpoles (Rana temporaria) reacting to predaceous aquatic insects. An outdoor mesocosm experiment manipulating exposure to Aeshna dragonfly larvae revealed plasticity in most characters: growth, development, behavior, and external morphology. I measured selection by placing 1927 tadpoles into enclosures within natural ponds; photographs permitted identification of the survivors 6–9 days later. Fitness was defined as a linear combination of growth, development, and survival that correlates with survival to age 2 in another anuran species. In enclosures with many predators, selection favored character values similar to those induced by exposure to Aeshna in mesocosms. The shift in selection along the predation gradient was strongest for characters that exhibited high predator-induced plasticity. A field survey of 50 ponds revealed that predator density changes over a spatial scale relevant for movement of individual adults and larvae: 17% of variation in predation risk was among ponds separated by tens to thousands of meters and 81% was among sites ≤10m apart within ponds. These results on heterogeneity in the selection regime confirm a key tenant of the standard model for the evolution of plasticity.
Data from: Functional responses in animal movement explain spatial heterogeneity in animal-habitat relationships
1. Understanding why heterogeneity exists in animal-habitat spatial relationships is critical for identifying the drivers of animal distributions. Functional responses in habitat selection – whereby animals adjust their habitat selection depending on habitat availability – are useful for describing animal-habitat spatial heterogeneity. However, they could be yielded by different movement tactics, involving contrasting inter-specific interactions. 2. Identifying functional responses in animal movement, rather than in emergent spatial patterns like habitat selection, could disentangle the effects of different movement behaviours on spatial heterogeneity in animal-habitat relationships. This would clarify how functional responses in habitat selection emerge and provide a general tool for understanding the mechanistic drivers of animal distributions. 3. We tested this approach using data from GPS-collared woodland caribou (Rangifer tarandus), a prey species under top-down control. We tested how caribou selected and moved with respect to a key resource (lichen-conifer stands) as a function of the availability of surrounding refuge land-cover (closed-conifer stands), using step selection functions. 4. Caribou selected resource patches more strongly in areas richer in refuge land-cover – a functional response in habitat selection. However, adjustments in multiple movement behaviours could have generated this pattern: stronger directed movement towards resources patches and/or longer residency within resource patches, in areas richer in refuges. Different contributions of these behaviours would produce contrasting forager spatial dynamics. 5. We identified functional responses in both movement behaviours: caribou were more likely to move towards resource patches in areas richer in refuge land-cover, and to remain in these patches during movement steps. This tactic enables caribou to spend longer foraging in safer areas where they could rapidly seek refuge in dense cover when predators are detected. 6. Our study shows that functional responses in movement can expose the context-dependent movement decisions that generate heterogeneity in animal-habitat spatial relationships. We used these functional responses to characterise anti-predator movement tactics employed by a large herbivore, but they could be applied in many different scenarios. The movement rules from functional responses in movement are well-suited to integration in spatial explicit individual-based models for forecasting animal distributions in landscapes undergoing environmental change.
Data from: Spatial genetic and morphologic structure of wolves and coyotes in relation to environmental heterogeneity in a Canis hybrid zone
Eastern wolves have hybridized extensively with coyotes and gray wolves and are listed as a 'species of special concern' in Canada. However, a distinct population of eastern wolves has been identified in Algonquin Provincial Park (APP) in Ontario. Previous Canis studies have not linked genetic analysis with field data to investigate genotype-specific morphology or determine how resident animals of different ancestry are distributed across the landscape in relation to heterogeneous environmental conditions. Accordingly, we studied resident wolves and coyotes in and adjacent to APP to identify distinct Canis types, clarify the occurrence of eastern wolves adjacent to APP, and investigate spatial genetic structure and landscape-genotype associations in the hybrid zone. We documented 3 genetically distinct Canis types that also differed morphologically, corresponding to putative gray wolves, eastern wolves, and coyotes. We also documented a substantial number of hybrid individuals (36%). Breeding eastern wolves were less common outside of APP, but occurred in some unprotected areas. We identified a steep cline extending west from APP where the dominant genotype shifted abruptly from eastern wolves to coyotes and hybrids. The genotypic pattern to the south and northwest was a more complex mosaic of alternating genotypes. We modeled genetic ancestry in response to prey availability and human disturbance and found positive and negative associations between wolf ancestry and 1) moose density and 2) road densities, respectively. Our results clarify the structure of the Canis hybrid zone adjacent to APP and provide unique insight into environmental conditions influencing hybridization dynamics between wolves and coyotes.
Data from: Whether larval amphibians school does not affect the parasite aggregation rule: testing the effects of host spatial heterogeneity in field and experimental studies
Almost all macroparasites show over-dispersed infections within natural host populations such that most parasites are distributed among a few heavily-infected individuals. Despite the importance of parasite aggregation for understanding system stability, the potential for population regulation, and super-spreading events, many questions persist about its underlying drivers. Theoretically, aggregation results from heterogeneity in host exposure, resistance, and tolerance. However, few studies have examined how host spatial arrangement – which likely affects both parasite encounter and density-dependent interactions – influences infection and dispersion, representing a critical gap in our current knowledge regarding the possible drivers of parasite aggregation. Using field data from over 165 ponds and 8,000 hosts, we evaluated how the spatial clustering of amphibian larvae within ponds 1) varied among different amphibian species, and 2), affected the distribution of parasites within the host population using Taylor's Power Law. A complementary mesocosm experiment used field-guided manipulations of the spatial arrangement of larval amphibians to create a gradient in host clustering while controlling host density, thereby testing for spatial effects on both infection success and aggregation by three different trematode species. Our field data indicated that larval amphibians exhibited significant spatial clustering that was well captured by Taylor's Power Law (R2 0.92 to 0.97 for different host species), but the residual variation only weakly correlated with observed patterns of trematode parasite over-dispersion. Correspondingly, experimental manipulation of host clustering had no effects on parasite infection success or the degree of parasite aggregation among cages or mesocosms. Given the importance of parasite over-dispersion for host populations and disease dynamics, we advocate for further investigations of host and parasite spatial aggregation, particularly studies that incorporate and/or control for heterogeneity in exposure and susceptibility.
Data from: Spatial heterogeneity in soil nutrient supply modulates nutrient and biomass responses to multiple global change drivers in model grassland communities
Changes in the atmospheric concentration of carbon dioxide ([CO2]), nutrient availability and biotic diversity are three major drivers of the ongoing global change impacting terrestrial ecosystems worldwide. While it is well established that soil nutrient heterogeneity exerts a strong influence on the development of plant individuals and communities, it is virtually unknown how nutrient heterogeneity and global change drivers interact to affect plant performance and ecosystem functioning. We conducted a microcosm experiment to evaluate the effect of simultaneous changes in [CO2], nutrient heterogeneity (NH), nutrient availability (NA) and species evenness on the biomass and nutrient uptake patterns of assemblages formed by Lolium perenne, Plantago lanceolata and Holcus lanatus. When the nutrients were heterogeneously supplied,assemblages exhibited precise root foraging patterns, and had higher above- and belowground biomass (average increases of 32% and 29% for above- and belowground biomass, respectively). Nutrient heterogeneity also modulated the effects of NA on biomass production, complementarity in nitrogen uptake and below: aboveground ratio, as well as those of [CO2] on the nutrient use efficiency at the assemblage level. Our results show that nutrient heterogeneity has the potential to influence the response of plant assemblages to simultaneous changes in [CO2], nutrient availability and biotic diversity, and suggest that it is an important environmental factor to interpret and assess plant assemblage responses to global change.
Data from: Recent range expansion and agricultural landscape heterogeneity have only minimal effect on the spatial genetic structure of the plant pathogenic fungus Mycosphaerella fijiensis
Understanding how geographical and environmental features affect genetic variation at both the population and individual levels is crucial in biology, especially in the case of pathogens. However, distinguishing between these factors and the effects of historical range expansion on spatial genetic structure remains challenging. In the present study, we investigated the case of Mycosphaerella fijiensis-a plant pathogenic fungus that has recently colonized an agricultural landscape characterized by the presence of potential barriers to gene flow, including several commercial plantations in which disease control practises such as the use of fungicides are applied frequently, and low host density areas. We first genotyped 300 isolates sampled at a global scale on untreated plants in 2 dimensions over a 50x80 Km area. Using two different clustering algorithms, no genetic structure was detected in the studied area, suggesting expansion of large populations and/or no influ ence of potential barriers. Second, we investigated the potential effect of disease control practises on M. fijiensis diversity by comparing populations sampled in commercial vs. food-crop plantations. At this local scale, we detected significantly higher allelic richness inside commercial plantations compared to the surrounding food-crop plantation populations. Analysis of molecular variance (AMOVA) indicated that 99% of the total genetic variance occurred within populations. We discuss the suggestion that high population size and/or high migration rate between populations might be responsible for the absence of any effect of disease control practises on genetic diversity and differentiation.
Data from: Modelling unbiased dispersal kernels over continuous space by accounting for spatial heterogeneity in marking and observation efforts
1. Although a key demographic trait determining the spatial dynamics of wild populations, dispersal is notoriously difficult to estimate in the field. Indeed, dispersal distances obtained from the monitoring of marked individuals typically lead to biased estimations of dispersal kernels as a consequence of i) restricted spatial scale of the study areas compared to species potential dispersal and ii) heterogeneity in marking and observation efforts and therfore in detection probability across space. 2. Here we propose a novel method to circumvent these issues that does not require data on observation effort per se, to correct for the variability in detection of marked individuals across space. Observed dispersal events were weighted by the distribution of departure points and an eroded spatial window approach was applied so as to deal with border effect. We conducted a set of simulations which indicated that our method was successful in correcting the effect of spatially heterogeneous detectability and produce unbiased dispersal kernels. 3. We applied this method to a real dataset on Montagu's harrier (>5000 chicks tagged), providing ca. 6000 resightings collected in entire France by a network of 1200 volunteers within a citizen-science program. The median dispersal distance observed was 32 km (range: 0.1-627 km). Once corrected for spatial heterogeneity in marking and observation efforts and border effect, the modelled dispersal kernel indicated a median dispersal distance of 78-123 km depending on the spatial scale considered (constrained within French borders or not, respectively). 4. Synthesis and applications: The current rise of citizen-science programs is likely to stretch our estimate of the ecologically-relevant spatial scale at which dispersal takes place for many taxa. Our method is particularly suited for such large scale data that typically suffer from high spatial heterogeneity in marking and observation efforts and offers the possibility to derive unbiased dispersal kernels, a key component for modelling population dynamics and species distribution in a context of environmental change. Currently, our method assumes homogeneity in both habitat and dispersal behaviour across individuals. We discuss however how to relax these hypotheses to further investigate the effect of e.g. local conspecific density or habitat quality on dispersal propensity.
Data from: Spatially heterogeneous perturbations homogenize the regulation of insect herbivores
Anthropogenic influences on resources and consumers can affect food web regulation, with impacts on trophic structure and ecosystem processes. Identifying how these impacts unfold is challenging because alterations to one or both resources and consumers can similarly transform community structure, especially for intermediate consumers. To date, empirical testing of perturbations on trophic regulation has been limited by the difficulty in separating the direct effect of perturbations on species composition and diversity from those unfolding indirectly via altered feeding pathways. Moreover, disentangling the independent and interactive impacts of covarying stressors that characterize human-altered systems has been an ongoing analytical challenge. We used a large-scale metacommunity experiment in grasslands to test how resource inputs, stand perturbation, and spatial factors affect regulation of insect herbivores in tritrophic grassland food webs. Using path-model comparisons, we observed significant simplification of food web regulation on insect herbivores, shifting from mixed predator-resource regulation in unaltered mainland areas to strictly resource-based regulation with landscape perturbation and fragmentation. Most changes were attributed to homogenization of plant community caused by landscape fragmentation and the deterministic influence of eutrophication that reduced among-patch beta diversity. This led to a simplified food web dominated by fewer but more abundant herbivore taxa. Our work implies that anthropogenic perturbation relating to resources and spatial isolation can transform the regulation of food web diversity, structure, and function.
Data from: Highly diverse and spatially heterogeneous mycorrhizal symbiosis in a rare epiphyte is unrelated to broad biogeographic or environmental features
Symbiotic interactions are common in nature. In dynamic or degraded environments, the ability to associate with multiple partners (i.e. broad specificity) may enable species to persist through fluctuations in the availability of any particular partner. Understanding how species interactions vary across landscapes is necessary to anticipate direct and indirect consequences of environmental degradation on species conservation. We asked whether mycorrhizal symbiosis by populations of a rare epiphytic orchid (Epidendrum firmum) is related to geographic or environmental heterogeneity. The latter would suggest that interactions are governed by environmental conditions rather than historic isolation of populations and/or mycorrhizal fungi. We used DNA-based methods to identify mycorrhizal fungi from eleven E. firmum populations in Costa Rica. We used molecular and phylogenetic analyses to compare associations. Epidendrum firmum exhibited broad specificity, associating with diverse mycorrhizal fungi, including six Tulasnellaceae molecular operational taxonomic units (MOTUs), five Sebacinales MOTUs and others. Notably, diverse mycorrhizal symbioses formed in disturbed pasture and roadside habitats. Mycorrhizal fungi exhibited significant similarity within populations (spatial and phylogenetic autocorrelation) and significant differences among populations (phylogenetic community dissimilarity). However, mycorrhizal symbioses were not significantly associated with biogeographic or environmental features. Such unexpected heterogeneity among populations may result from complex combinations of fine-scale environmental factors and macro-evolutionary patterns of change in mycorrhizal specificity. Thus, E. firmum exhibits broad specificity and the potential for opportunistic associations with diverse fungi. We suggest that these characteristics could confer symbiotic assurance when mycorrhizal fungi are stochastically available, which may be crucial in dynamic or disturbed habitats such as tropical forest canopies.
Data from: Spatial heterogeneity in landscape structure influences dispersal and genetic structure: empirical evidence from a grasshopper in an agricultural landscape
Dispersal may be strongly influenced by landscape and habitat characteristics that could either enhance or restrict movements of organisms. Therefore, spatial heterogeneity in landscape structure could influence gene flow and the spatial structure of populations. In the past decades, agricultural intensification has led to the reduction in grassland surfaces, their fragmentation and intensification. As these changes are not homogeneously distributed in landscapes, they have resulted in spatial heterogeneity with generally less intensified hedged farmland areas remaining alongside streams and rivers. In this study, we assessed spatial pattern of abundance and population genetic structure of a flightless grasshopper species, Pezotettix giornae, based on the surveys of 363 grasslands in a 430-km² agricultural landscape of western France. Data were analysed using geostatistics and landscape genetics based on microsatellites markers and computer simulations. Results suggested that small-scale intense dispersal allows this species to survive in intensive agricultural landscapes. A complex spatial genetic structure related to landscape and habitat characteristics was also detected. Two P. giornae genetic clusters bisected by a linear hedged farmland were inferred from clustering analyses. This linear hedged farmland was characterized by high hedgerow and grassland density as well as higher grassland temporal stability that were suspected to slow down dispersal. Computer simulations demonstrated that a linear-shaped landscape feature limiting dispersal could be detected as a barrier to gene flow and generate the observed genetic pattern. This study illustrates the relevance of using computer simulations to test hypotheses in landscape genetics studies.
Temporal and spatial heterogeneity of atmospheric environmental and meteorological field in the urban street canyon——dataset
<p>Here are the datasets related to the article, "Temporal and spatial heterogeneity of atmospheric environmental and meteorological field in the urban street canyon". The datasets contain two part:</p> <ol> <li>The observation data and the analysis processing scripts (Folder observation).</li> <li>The data used for figures (Folder Fig_data).</li> </ol> <p>The CFD simulation configuration files can be found at https://doi.org/10.5281/zenodo.10841653.</p>
Temporal and spatial heterogeneity of atmospheric environmental and meteorological field in the urban street canyon——CFD configuration
<p>This dataset is about the configuration files for simulations conducted in OpenFOAM-v8 in multiple scenarios, categorized into the "wd" folder for simulating the wind field and the "conc" folder for the concentration field.</p>
Profiling the heterogeneity of colorectal cancer consensus molecular subtypes using spatial transcriptomics: fastq & bam files - Sample S5_Rec
<p>You can find here the fastq and bam files related to the datasets used in the publication: </p> <p>In this particular upload, you can find the fastq (version1) and bam (version2) files of the two replicates of sample S5_Rec (A121573)</p> <p><strong>Valdeolivas, A., Amberg, B., Giroud, N. <em>et al.</em> Profiling the heterogeneity of colorectal cancer consensus molecular subtypes using spatial transcriptomics. <em>npj Precis. Onc.</em> 8, 10 (2024). https://doi.org/10.1038/s41698-023-00488-4</strong></p> <p> </p> <p> </p>
Spatial Transcriptomics in Breast Cancer Reveals Tumour Microenvironment-Driven Drug Responses and Clonal Therapeutic Heterogeneity
<p>We acquired 10x Visium spatial transcriptomics (ST) data from 9 patients with invasive adenocarcinomas [1–5] to explore the role of the tumour microenvironment (TME) on intratumor heterogeneity (ITH) and drug response in breast cancer. By leveraging a new version of Beyondcell [6] (<a href="https://github.com/cnio-bu/beyondcell" target="_blank" rel="noopener">cnio-bu/beyondcell</a>), a tool for identifying tumour cell subpopulations with distinct drug response patterns, we predicted sensitivity to over 1,200 drugs while accounting for the spatial context and interaction between the tumour and TME compartments. Moreover, we also used Beyondcell to compute spot-wise functional enrichment scores and identify niche-specific biological functions.</p> <p>Here, you can find:</p> <p>In signatures folder:</p> <ul> <li><strong>SSc breast:</strong> Collection of gene signatures used to predict sensitivity to > 1,200 drugs derived from breast cancer cell lines.</li> <li><strong>Functional signatures:</strong> Collection of gene signatures used to compute enrichment in different biological pathways.</li> </ul> <p>In visium folder:</p> <ul> <li><strong>Visium objects:</strong> Processed ST Seurat objects with deconvoluted spots, SCTransform-normalised counts, and clonal composition predicted with SCEVAN [7]. These objects, together with the signatures, were used to compute the Beyondcell objects.</li> </ul> <p>In single-cell folder:</p> <ul> <li><strong>Single-cell objects:</strong> Raw and filtered merged single-cell RNA-seq (scRNA-seq) Seurat objects with unnormalised counts used as a reference for spot deconvolution.</li> </ul> <p>In beyondcell folder:</p> <ul> <li><strong>Beyondcell </strong><strong>sensitivity </strong><strong>objects</strong> with prediction scores for all drug response signatures in SSc breast.</li> <li><strong>Beyondcell functional objects </strong>with enrichment scores for all functional signatures.</li> </ul>
ScienceDex guides
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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.