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85 results for “niche analysis”
Data for: Range and niche expansion through multiple interspecific hybridization - a genotyping by sequencing analysis of Cherleria (Caryophyllaceae)
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Data from: Spider webs, stable isotopes and molecular gut content analysis: multiple lines of evidence support trophic niche differentiation in a community of Hawaiian spiders
1. Adaptive radiations are typically characterized by niche partitioning among their constituent species. Trophic niche partitioning is particularly important in predatory animals, which rely on limited food resources for survival. 2. We test for trophic niche partitioning in an adaptive radiation of Hawaiian Tetragnatha spiders, which have diversified in situ on the Hawaiian Islands. We focus on a community of nine species belonging to two different clades, one web building and the other actively hunting, which co-occur in wet forest on East Maui. We hypothesize that trophic niches differ significantly both 1) among species within a clade, indicating food resource partitioning, and 2) between the two clades, corresponding with their differences in foraging strategy. 3. To assess niches of the spider species, we measure a) web architecture, the structure of the hunting tool, and b) site choice, the physical placement of the web in the habitat. We then test whether differences in these parameters translate into meaningful differences in trophic niche by measuring c) stable isotope signatures of carbon and nitrogen in the spiders' tissues, and d) gut content of spiders based on metabarcoding data. 4. We find significant interspecific differences in web architecture and site choice. Importantly, these differences are reflected in stable isotope signatures among the five web-building species, as well as significant isotopic differences between web-builders and active hunters. Gut content data also show interspecific and inter-clade differences. Pairwise overlaps of web architecture between species are positively correlated with overlaps of isotopic signature. 5. Our results reveal trophic niche partitioning among species within each clade, as well as between the web-building and actively hunting clades. Based on the correlation between web architecture and stable isotopes, it appears that the isotopic signatures of spiders' tissues are influenced by architectural differences among their webs. Our findings indicate an important link between web structure, microhabitat preference and diet in the Hawaiian Tetragnatha.
Targeted DNA-seq analysis was performed on sorted population of CD45+/CD34+ HSPCs from control or FLI-1 modified mRNA treated mPB after co-culture with vascular niche cells
<p>Human mPB HSPCs were harvested isolated and transduced with either control or FLI-1 modified mRNA. HSPCs were introduced into co-culture with vascular niche ECs. Cultures were harvested and CD45+/CD34+ HSPCs were resoerted and processed for trageted DNA-seq analysis. Contains raw FASTQ sequencing files, unfiltered VCFs, and curated results in an excel.</p>
Multiplexed imaging mass cytometry analysis characterizes the vascular niche in pancreatic cancer
<p>All data supporting the publication: "Multiplexed imaging mass cytometry analysis characterizes the vascular niche in pancreatic cancer."</p><p>1. Fully_Processed_OME.TIFF: This folder contains the OME.TIFF files with all markers after compensation and hot pixel removal for visualization of the data. These can be opened with QuPath and other software. </p><p>2. PDAC_IMC_Seurat_FINAL.rds: Seurat object of all cells included in the analysis with cell type and neighborhood annotations, and unintegrated and rPCA-integrated UMAP reductions. </p><p>3. Raw_Data_TIFF_Files: All raw individual TIFF files from the image acquisition</p><p>4. ROI_Selection: Brightfield and IHC images of individual samples showing where the ROIs for each sample are collected </p><p>5. Segmentation_Files: All relevant segmentation files from Mesmer for nuclear and whole cell segmentation. </p><p>6. H&E Images for each case scanned at 40x </p>
VCF datasets and analysis scripts for: The combination of genomic offset and niche modelling provides insights into climate change-driven vulnerability
<p>Global warming is increasingly exacerbating biodiversity loss. Populations locally adapted to spatially heterogeneous environments may respond differentially to climate change, but this intraspecific variation has only recently been considered when modelling vulnerability under climate change. Here, we incorporate intraspecific variation in genomic offset and ecological niche modelling to estimate climate change-driven vulnerability in two bird species in the Sino-Himalayan Mountains. We found that the cold-tolerant populations show higher genomic offset but risk less challenge for niche suitability decline under future climate than the warm-tolerant populations. Based on a genome-niche index estimated by combining genomic offset and niche suitability change, we identified the populations with the least genome-niche interruption as potential donors for evolutionary rescue, i.e., the populations tolerant to climate change. We evaluated potential rescue routes via a landscape genetic analysis. Overall, we demonstrate that the integration of genomic offset, niche suitability modelling, and landscape connectivity can improve climate change-driven vulnerability assessments and facilitate effective conservation management.</p>
Supporting data and analysis for, "An atlas of healthy and injured cell states and niches in the human kidney"
<p>Online repository for contents associated with kidney cell state atlas: </p> <p>This combines the image datasets used for the manuscript describing an approach for the integrated tissue cytometry analysis of mesoscale confocal imaging datasets.</p> <p>Linked deposits:</p> <table> <tbody> <tr> <td>Zenodo Extended Data figures</td> <td>10.5281/zenodo.7120908</td> </tr> <tr> <td>3D Cytometry and neighborhood analysis</td> <td>10.5281/zenodo.7120941</td> </tr> <tr> <td>Github repository, "Cell-State-Atlas_2022"</td> <td>https://github.com/KPMP/Cell-State-Atlas-2022</td> </tr> </tbody> </table> <p> </p> <p> </p>
Figure 7 in Analysis of the spatial organization of Vallonia pulchella (Muller, 1774) ecological niche in Technosols (Nikopol manganese ore basin, Ukraine)
Figure 7. Results of MADIFA-mapping of Vallonia pulchella ecological niche.
Comparative genome analysis of Lactococcus lactis indicates niche adaptation and resolves genotype/phenotype disparity
<p>This publication describes the comparative genome analysis of 43 L. lactis strains</p> <p>The data stored here are individual alignments (alignments.zip) and the output files from gene trait matching (GTM_output.zip) used in this study.</p>
Data from: Spider webs, stable isotopes and molecular gut content analysis: multiple lines of evidence support trophic niche differentiation in a community of Hawaiian spiders
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VCF datasets and analysis scripts for: The combination of genomic offset and niche modelling provides insights into climate change-driven vulnerability
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Biogeography and ecological niche evolution in Diapensiaceae inferred from phylogenetic analysis
<p>Diapensiaceae (Ericales) are a small family of about 15 species. Within this clade, two species are broadly distributed throughout the Northern Hemisphere, while the remaining species have a disjunct distribution between eastern North America and eastern Asia. To address patterns and processes of diversification in Diapensiaceae, we conducted biogeographic analyses and inferred shifts in ecological niche across the phylogeny of the clade. Although Diapensiaceae have been the focus of multiple phylogenetic and biogeographic studies, previous studies were taxonomically limited. We greatly improve the phylogenetic underpinning for Diapensiaceae with the most inclusive taxonomic sampling thus far, employing both nuclear and plastid gene sequence data for at least one sample per species in the family. Our estimates indicate that genera of Diapensiaceae variously diverged in the Eocene, Oligocene, and early to mid-Miocene. Biogeographic analysis suggests that the probable ancestor of the Diapensiaceae crown clade originated in the Nearctic, with vicariance events contributing to the current distribution of the disjunct taxa. Ecological niche, when considered in a phylogenetic context, clustered based on biogeographic realm. In general, greater ecological overlap was found at younger nodes and greater niche divergence was found among distantly related species. Diversification in Diapensiaceae appears to have been shaped by both large-scale biogeographic factors, such as vicariance, and divergence in ecological niche among closely related species.</p>
Distribution maps and climatic niches analysis of Heliconius butterflies
<p>Distribution maps of <em>Heliconius</em> butterflies and climatic niches analysis between co-occurring and hybridizing species.</p>
Data from: Is there a correlation between abundance and environmental suitability derived from ecological niche modelling? A meta-analysis
It is thought that species abundance is correlated with environmental suitability and that environmental variables, scale, and type of model fitting can confound this relationship. We performed a meta-analysis to (i) test whether species abundance is positively correlated with environmental suitability derived from correlative ecological niche models (ENM), (ii) test whether studies encompassing large areas within a species range (>50%) exhibited higher AS correlations than studies encompassing small areas within a species range (<50%), (iii) assess which modelling method provided higher AS correlation, and (iv) compare strength of the AS relationship between studies using only climatic variables and those that used both climatic and other environmental variables to derive suitability. We used correlation coefficients to measure the relationship between abundance and environmental suitability derived from ENM. Each correlation coefficient was considered an effect size in a random-effects multivariate meta-analysis. In all cases we found a significantly positive relationship between abundance and suitability. This relationship was consistent regardless of scale of study, ENM method, or set of variables used to derive suitability. There was no difference in strength of correlation between studies focusing on large or small areas within a species' range or among ENM methods. Studies using other variables in combination with climate exhibited higher AS correlations than studies using only climatic variables. We conclude that occurrence data can be a reasonable proxy for abundance, especially for vertebrates, and the use of local variables increases the strength of the AS relationship. Use of ENMs can significantly decrease survey costs and allow the study of large-scale abundance patterns using less information. Including only climatic variables in ENM may confound the relationship between abundance and suitability when compared to studies including variables taken locally. However, modelers and conservationists must be aware that high environmental suitability does not always indicate high abundance.
Data from: Do deposit-feeders compete? Isotopic niche analysis of an invasion in a species-poor system
Successful establishment of invasive species is often related to the existence of vacant niches. Competition occurs when invaders use the same limiting resources as members of the recipient community, which will be reflected in some overlap of their trophic niches. The concept of isotopic niche has been used to study trophic niche partitioning among species. Here, we present a two-year field study comparing isotopic niches of the deposit-feeding community in a naturally species-poor system. The isotopic niche analyses showed no overlap between a recent polychaete invader and any of the native species suggesting that it has occupied a vacant niche. Its narrow isotopic niche suggests specialized feeding, however, the high d15N values compared to natives are most likely due to isotope fractionation effects related to nitrogen recycling and a mismatch between biological stoichiometry of the polychaete and the sediment nitrogen content. Notably, highly overlapping isotopic niches were inferred for the native species, which is surprising in a food-limited system. Therefore, our results demonstrate that invaders may broaden the community trophic diversity and enhance resource utilization, but also raise questions about the congruence between trophic and isotopic niche concepts and call for careful examination of assumptions underlying isotopic niche interpretation.
Characterizing Spatially Continuous Variations in Tissue Microenvironment through Niche Trajectory Analysis - Dataset
<p><span>Recent technological developments have made it possible to map the spatial organization of a tissue at the single-cell resolution. However, computational methods for analyzing spatially continuous variations in tissue microenvironment are still lacking. Here we present ONTraC as a strategy that constructs niche trajectories using a graph neural network-based modeling framework. Our benchmark analysis shows that ONTraC performs more favorably than existing methods for reconstructing spatial trajectories. Applications of ONTraC to public spatial transcriptomics datasets successfully recapitulated the underlying anatomical structure, and further enabled detection of tissue microenvironment-dependent changes in gene regulatory networks and cell-cell interaction activities during embryonic development. Taken together, ONTraC provides a useful and generally applicable tool for the systematic characterization of the structural and functional organization of tissue microenvironments.</span></p>
3D tissue cytometry analysis files for, "An atlas of healthy and injured cell states and niches in the human kidney"
<p>This deposit contains the supporting records of analysis for 3D cytometry presented in, "An atlas of healthy and injured cell states and niches in the human kidney". </p> <p>Contents:</p> <p>1) a collection of .zip files contains the 3D tissue cytometry files for tissue analyzed in the preprint doi: 10.1101/2021.07.28.454201. This collection includes the individual tissue specimens, XX-XXXX.zip, further described in detail in "Supplementary Table 2. 3D imaging and spatial transcriptomic experiments." </p> <p>2) neighborhoods by specimen as indicated above and calculated by Volumetric Tissue Exploration and Analysis (VTEA) for a radius of 50 voxels(accounting for anisotropy of voxels) or ~25 um as described in the methods of the preprint, doi: 10.1101/2021.07.28.454201.</p> <p>3) R environment file (.RData as a .zip file) for regenerating analysis from code at: https://github.com/KPMP/Cell-State-Atlas-2022</p> <p>Contents of XX-XXXX.zip files:</p> <p>1) maximum projections as used in the manuscript (all archived at kpmp.org)<br> 2) .obx and a .tif file which includes the segmented objects and associated measurements for use by VTEA (https://vtea.wiki/)<br> 3) .csv file including all the segmented objects and associated measurements<br> 4) .csv file including the neighborhood analysis results also found in the combined .zip file<br> 5) folder of ImageJ/FIJI folder which includes the expert ROIs and the pixel-wise consensus of ROIs drawn by experts used in cell classification strategy outlined in the methods<br> 6) folder of VTEA gate files and images of gating .png files used to label objects and used in cell classification strategy outlined in the methods of doi: 10.1101/2021.07.28.454201</p> <p>Please address any concerns or questions to the authors listed in the deposit or manuscript, doi: 10.1101/2021.07.28.454201.</p> <p> </p> <p> </p>
Isotope analysis combined with DNA barcoding provide new insights into the dietary niche of khulan in the Mongolian Gobi
<p><span>With increasing livestock numbers, competition and avoidance are increasingly shaping resource availability for wild ungulates. Shifts in the dietary niche of wild ungulates are likely and can be expected to negatively affect their fitness. The Mongolian Gobi constitutes the largest remaining refuge for several threatened ungulates, but unprecedentedly high livestock numbers are sparking growing concerns over rangeland health and impacts on threatened ungulates like the Asiatic wild ass (khulan).</span></p> <p><span>Previous stable isotope analysis of khulan tail hair from the Dzungarian Gobi suggested that they graze in summer but switch to a poorer mixed C3 grass / C4 shrub diet in winter, most likely in reaction to local herders and their livestock. Here we attempt to validate these findings with a different methodology, DNA metabarcoding. Further, we extend the scope of the original study to the South Gobi Region, where we expect higher proportions of low-quality browse in the khulan winter diet due to a higher human and livestock presence.</span></p> <p><span>Barcoding confirmed the assumptions behind the seasonal diet change observed in the Dzungarian Gobi isotope data, and new isotope analysis revealed a strong seasonal pattern and higher C4 plant intake in the South Gobi Region, in line with our expectations. However, DNA barcoding revealed C4 domination of winter diet was due to C4 grasses (rather than shrubs) for the South Gobi Region. Slight climatic differences result in regional shifts in the occurrence of C3 and C4 grasses and shrubs, which do not allow for an isotopic separation along the grazer-browser continuum over the entire Gobi. </span></p> <p><span>Our findings do not allow us to confirm human impacts upon dietary preferences in khulan as we lack seasonal samples from the South Gobi Region. However, these data provide novel insight into khulan diet, raise new questions about plant availability versus preference, and provide a cautionary tale about indirect analysis methods if used in isolation or extrapolated to the landscape level. Good concordance between relative read abundance of C4 genera from barcoding and proportion of C4 plants from isotope analysis adds to a growing body of evidence that barcoding is a promising quantitative tool to understand resource partitioning in ungulates.</span></p>
Data from: Genomic analysis of demographic history and ecological niche modeling in the endangered Sumatran Rhinoceros Dicerorhinus sumatrensis
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Data from: A comparative analysis reveals little evidence for niche conservatism in aquatic macrophytes among four areas on two continents
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Isotope analysis combined with DNA barcoding provide new insights into the dietary niche of khulan in the Mongolian Gobi
Open the record for dataset details and reuse information.
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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.