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2,568 results for “niche”
Long time-series ecological niche modelling using archaeological settlement data.
<p><strong>CR_settlement_niche_[N]_[Yr]_[BC/AD].tif</strong></p> <p>Ecological niche models in GeoTIFF format generated with the MaxEnt software based using prehistoric settlement evidence as training data and environmental layers (elevation, mean annual precipitation, mean annual temperature, landscape water balance, soil types) as background data. Raster values represent the probability of presence of a settlement.<br> <strong>N</strong> - chronological ordering<br> <strong>Yr, BC/AD</strong> - calendar years BC or AD</p> <p> </p> <p><strong>CR_settlement_niche_combined.tif</strong></p> <p>All models combined by averaging.</p> <p> </p> <p><strong>CR_settlement_archeo.zip</strong></p> <p>Archaeological data used to train the MaxEnt models in ESRI SHP format with the following fields:</p> <p><strong>Site_Type:</strong> Cemetery or Settlement</p> <p><strong>Archeo_Dat:</strong> Archaeological dating (culture or period)</p> <p><strong>Source:</strong> Source dataset (AMCR or LONGWOOD)</p> <p>AMCR: Archeologická mapa České republiky – Archaeological Map of the Czech Republic. Retrieved from https://digiarchiv.aiscr.cz/.</p> <p>LONGWOOD: Kolář, J., Tkáč, P., Macek, M., & Szabó, P. (2016). Archaeology and Historical Ecology: the Archaeological Database of the LONGWOOD ERC Project. Archäologisches Korrespondenzblatt 46/4, 539-554.</p> <p><strong>Yrs_BP_Avg:</strong> Average dating in calendar years BP (based on the archaeological dating)</p> <p><strong>Yrs_BP_Unc:</strong> Temporal uncertainty of the dating (half of the culture or period's duration)</p> <p><strong>Loc_Accur:</strong> Spatial accuracy derived from the recorded degree of the accuracy of location (radius in meters around the center point)</p>
Rakhterā (रखतेरा or Rakhetrā, Ashoknagar). General view of the niche with foot prints near a large rock-cut image of Ādinātha.
<p><a href="https://siddham.network/object/vs1555/">OBIG1555</a> Rakhterā (रखतेरा or Rakhetrā, Ashoknagar). General view of the niche with foot prints near a large rock-cut image of Ādinātha.</p>
Spatial dataset for ecological niche and spatial distribution modeling of Herichthys bartoni (Cichliformes: Cichlidae) in the Media Luna spring, Mexico
<p>Dataset for the endangered endemic cichlid <em>Herichthys bartoni</em> in the Media Luna spring, Mexico. This data includes occurrences records by species life stage (adult, juvenile and fry), in three field sessions corresponding to the summer period, in the years 1999, 2009 and 2019.</p> <p>For more information about the codes where the previous datasets could be used, visit the following repository with URL: <a href="https://doi.org/10.5281/zenodo.7603557">https://doi.org/10.5281/zenodo.7603557</a>.</p> <p>Likewise, the UC and WDp variables used to run the ecological niche and spatial distribution model, by summer period, can be found in the following repository wirh URL: <a href="https://doi.org/10.5281/zenodo.7603890">https://doi.org/10.5281/zenodo.7603890</a>.</p>
Processed data to regenerate figures in Noecker et al, "Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta"
<p>This archive contains the processed source data for the publication by Noecker et al, "Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe <em>Eggerthella lenta</em>" (2023, in review). Data tables underlying each figure panel are included, except for the following panels:</p> <ul> <li>Figure S1A: Source data is in Table S1 of the publication</li> <li>Figure 6D: Source data can be found at NCBI GEO accession GSE212420 (supplementary counts data matrix)</li> </ul> <p>Raw metabolomics data can also be found at Metabolomics Workbench accession PR001620.</p> <p>Methods used to summarize these data and generate the figures are described in the manuscript Materials and Methods and figure captions. Code to generate all figures is also available at www.github.com/turnbaughlab/2022_Noecker_ElentaMetabolism and 10.5281/zenodo.7779454.</p>
Different facets of the same niche: integrating citizen science and scientific survey data to predict biological invasion risk under multiple global change drivers
<p>Raw data (occurrences and environmental predictors) used in the manuscript "Different facets of the same niche: integrating citizen science and scientific survey data to predict biological invasion risk under multiple global change drivers"</p>
Extra terrestrials: experimental drought creates niche space for rare invertebrates in terrestrialising stream channels
<p>The code and data for the paper entitled "Extra terrestrials: experimental drought creates niche space for rare invertebrates in terrestrialising stream channels" published in <em>Biology Letters</em>.</p>
Data supporting Comparison of feeding niches between Arctic and northward moving sub-Arctic marine mammals in Greenland
<p>Data supporting the paper:</p> <blockquote> <p>Land-Miller, H., A. Roos, M. Simon, R. Dietz, C. Sonne, S. Pedro, A. Rosing-Asvid, F. Rigét, and M. McKinney. 2023. Comparison of feeding niches between Arctic and northward moving sub-Arctic marine mammals in Greenland. Marine Ecology Progress Series.</p> </blockquote> <p>This data is in five files:</p> <p>1. <strong>greenland_marmam_metadata.csv</strong> contains metadata for all samples used in this project, including sample identifiers:</p> <ul> <li><em>Sample: </em>unique sample ID per individual animal</li> <li><em>Species</em></li> </ul> <p>and details of collection, including <em>Year, Location </em>(general area), <em>Lat, </em><em>Long, </em>and<em> </em><em>Date. </em>It also includes other data on the animal (<em>Sex, Age, Length</em>), when available, as well as the co-author who provided the sample to the project (<em>Sample sender</em>) and the tissues available/analyzed for each individual (<em>Tissues received</em>).</p> <p>2. <strong>all_sample_locations.csv</strong> includes latitude/longitude of each sample for mapping. Latitude and longitude are consistent with the full metadata file when coordinates were available, and estimated based on general sampling area (<em>Location </em>or <em>Area</em>) when not. The variable <em>estimate</em><strong> </strong>denotes samples for which coordinates were estimated.</p> <p>3. <strong>fatty_acids_greenland_marmams.csv </strong>contains fatty acid data for all samples. Variables <em>8:00</em> to <em>24:1n9</em> represent the proportion of each individual fatty acid, out of total fatty acids in that sample. Data are represented as whole number percents (i.e., 10 = 10% and all fatty acids sum to 100 for each sample). </p> <p>4. <strong>CNS_greenland_McGill.csv</strong> contains bulk stable isotope data for all samples analyzed at McGill. In addition to <em>Sample</em> and <em>Species</em>, this includes:</p> <ul> <li><em>treatment</em>: whether a sample was lipid-extracted (<em>LE</em>) or non-lipid-extracted (<em>nLE</em>) prior to analysis</li> <li><em>d15N</em>: stable isotope ratio δ<sup>15</sup>N</li> <li><em>d13C: </em>stable isotope ratio δ<sup>13</sup>C</li> <li><em>d34S: </em>stable isotope ratio δ<sup>34</sup>S</li> <li><em>perc.C: </em>mass percent of carbon in the sample</li> <li><em>perc.N: </em>mass percent of nitrogen in the sample</li> <li><em>perc.S: </em>mass percent of sulfur in the sample</li> <li><em>C.N.ratio: </em>mass ratio of carbon to nitrogen in the sample </li> </ul> <p>5. <strong>CN_greenland_nLE_copenhagen.csv</strong> contains stable isotope data for non-lipid-extracted samples analyzed at the University of Copenhagen for δ<sup>13</sup>C and δ<sup>15</sup>N. Variables <em>treatment</em>, <em>d13C</em>, and <em>d15N</em> are consistent with CNS_greenland_McGill.csv. </p>
Ecological niche models for American black bear, Rafinesque's big-eared bat, and timber rattlesnake
<p>This data set contains rasters that are predictive environmental suitability maps for three wildlife species: the American black bear (<i>Ursus americanus</i>), Rafinesque's big-eared bat (<i>Corynorhinus rafinesquii</i>), and Timber rattlesnake (<i>Crotalus horridus</i>). Rasters for each species include: individual prediction maps for each of 5 ENMs (GBM: generalized boosting model, GLM: generalized linear model, MARS: multivariate adaptive regression spline, MX: maximum entropy, and RF: random forest), as well as the ensemble prediction map from all five ecological niche models (ENMs).</p>
Data from: Foraging behaviour and habitat-use drives niche segregation in sibling seabird species
<p>To mediate competition, similar sympatric species are assumed to utilise different resources, or the same but geographically separated resources. The two giant petrels (<em>Macronectes</em> spp.) are intriguing in that they are morphologically similar seabirds with overlapping diets and distributions. To better understand the mechanisms allowing their co-existence, we investigated intra- and interspecific niche segregation at Marion Island (Southern Indian Ocean), one of the few localities where they breed in sympatry. We used GPS tracks from 94 individuals and remote-sensed environmental data to quantify habitat-use, combined with blood carbon and nitrogen stable isotope ratios from 90 individuals to characterise their foraging habitat and trophic ecology. Females of both species made distant at sea foraging trips and fed at a similar trophic level. However, they used distinct pelagic habitats. In contrast, males of both species mainly foraged on or near land, resulting in significant sexual segregation, but high interspecific habitat and diet overlap. However, some males showed flexible behavioural strategies, also making distant, pelagic foraging trips. Using contemporaneous tracking, environmental and stable isotope data we provide a clear example of how sympatric sibling species can be segregated along different foraging behaviour dimensions.</p>
Figure 2 in Food niche of Exomalopsis (Exomalopsis) fulvofasciata Smith (Hymenoptera: Apidae) in Brazilian savannah: the importance of oil-producing plant species as pollen sources
Figure 2. Estimated number of pollen types in each study area using extrapolation curves. ESP: Ecological Station of Panga, MG and SPSCN: State Park of Serra de Caldas Novas, GO.
Data from: Species distribution models of the Spotted Wing Drosophila (Drosophila suzukii, Diptera: Drosophilidae) in its native and invasive range reveal an ecological niche shift
<p>The Spotted Wing Drosophila (<em>Drosophila</em> <em>suzukii</em>) is native to Southeast Asia. Since its first detection in 2008 in Europe and North America, it has been a pest to the fruit production industry as it feeds and oviposits on ripening fruit. Here we aim to model the potential geographical distribution of <em>D. suzukii</em>. We performed an extensive literature review to map the current records. In total, 517 documented occurrences (96 native and 421 invasive) were identified spanning 52 countries. Next, we constructed three species distribution models (SDMs) based on occurrence records in: 1) the native range (SDMnative), 2) the invasive range in Europe (SDMEurope) and 3) a global model of all records (SDMglobal). The models aimed to investigate, whether this species will be able to occupy additional ecological niches beyond its native range and expand its current geographic distribution both globally and in Europe. The SDMs were generated using Maximum Entropy algorithms (Maxent) based on present occurrence records and bioclimatic variables (WorldClim). Predictions of habitat suitability vary greatly depending on the origins of occurrence records. According to all models, precipitation and low temperatures were key limiting factors for the distribution of <em>D. suzukii</em>, which suggests that this species requires a humid environment with mild winters in order to establish a permanent population in its invasive range. Several regions in the invasive range, not presently occupied by this species, were predicted highly suitable, especially in northern Europe, suggesting that <em>D. suzukii</em> is not occupying its full fundamental niche yet. Synthesis and applications. Based on these models of potential geographic distribution of the Spotted Wing Drosophila (<em>Drosophila</em> <em>suzukii</em>), we show a shift in the ecological niche in <em>D. suzukii</em> populations, emphasizing the importance of using presence and local environmental data. Further investigation regarding new occurrences is recommended to secure optimal pest management. Despite a continuing expansion, many countries still lack proper surveillance schemes, and we urge policymakers to initiate appropriate management programs.</p>
Model, data, and analysis for Negative Niche Construction Favors the Evolution of Cooperation
<p>This repository contains the model, data, and analysis corresponding to <em>Negative Niche Construction Favors the Evolution of Cooperation</em> as submitted for review by Brian D. Connelly, Katherine J. Dickinson, Sarah P. Hammarlund, and Benjamin Kerr. Contents are released to the public domain under the Creative Commons CC0 License.</p>
Udayagiri, Madhya Pradesh. Cave 7, subsidiary niches.
<p>Udayagiri, Madhya Pradesh. Cave 7, subsidiary niches, located to the immediate east of the cave, with damaged figures of Durgā and Gaṇeśa, probably 5th century. As documented in 11/2007.</p>
Paphos, Cyprus. Tomb niche, Latin church in the Chrysopolitissa complex.
<p>Paphos, Cyprus. Tomb niche, north side of the Latin church in the Chrysopolitissa complex, as documented in 1974.</p>
Integrative spatial omics reveals distinct tumor-promoting multicellular niches and immunosuppressive mechanisms in African American and European American patients with TNBC (Spatial Transcriptomic 10X Visium portion)
<p>Racial disparities in triple-negative breast cancer (TNBC) outcomes have been reported. However, the biological mechanisms underlying these disparities remain unclear. We integrated imaging mass cytometry and spatial transcriptomics, to characterize the tumor microenvironment (TME) of African American (AA) and European American (EA) patients with TNBC. The TME in AA patients was characterized by interactions between endothelial cells, macrophages, and mesenchymal-like cells, which were associated with poor patient survival. In contrast, the EA TNBC-associated niche is enriched in T-cells and neutrophils suggestive of an exhaustion and suppression of otherwise active T cell responses. Ligand-receptor and pathway analyses of race-associated niches found AA TNBC to be “immune cold” and hence immunotherapy resistant tumors, and EA TNBC as ‘inflamed’ tumors that evolved a distinctive immunosuppressive mechanism. Our study revealed the presence of racially distinct tumor-promoting and immunosuppressive microenvironments in AA and EA patients with TNBC, which may explain the poor clinical outcomes.</p> <p> </p> <p>This dataset contains the 10X Visium Spatial Transcriptomic data of TNBC patients. There are two cohorts.</p> <p> </p> <p><strong>Baylor Scott and White (BSW) cohort</strong>: <strong>10x.visium.tar.gz</strong>, containing 10 patients with TNBC from Baylor Scott and White affiliated Hospital. </p> <p>Each sample is made of Space Ranger processed spot-separated gene expression data (processed to HDF5 AnnData file). There are also H&E images, and spot coordinate files available. </p> <p> </p> <p>For <strong>Georgia validation cohort</strong>, 400 genes used for validation of ESG signatures (associated with BA-Community 1 and WA-Community-1) were obtained and provided by Ritu Aneja's lab. These 400 genes' spot-based expression data across Black and White TNBC patients are provided. See file <strong>georgia.validation.visium.tar.gz</strong>. Expression was normalized by total counts per spot, followed by log-normalization by Giotto.</p> <p> </p> <p>As well in our paper, we integrated a published racial TNBC cohort for deriving some of initial results in the paper. This refers to the Bassiouni et al (Cancer Research) paper in Carpten's group. <strong>GSM_giotto_processed.tar.gz</strong> refers to this dataset, which we deposit here. The data were normalized by Giotto using standard procedure.</p>
Figure 3 in Ecological niche differentiation among Aztec fruit-eating bat subspecies (Chiroptera: Phyllostomidae) in Mesoamerica
Figure 3. Niche overlap values for Schoener's D and Hellinger's I compared to a null distribution: (a) Artibeus a. aztecus (yellow) vs. A. a. minor (blue), (b) A. a. aztecus vs.A. A. major (red), (c) A. a. minor vs. A. a. major.
Figure 2 in Ecological niche differentiation among Aztec fruit-eating bat subspecies (Chiroptera: Phyllostomidae) in Mesoamerica
Figure 2. Maxent predicted potential distribution for (a) Artibeus a. aztecus, (b) A. a. minor, and (c) A. a. major.
Mural cells sustain a homeostatic vascular macrophage niche limiting chronic inflammation
<p>If you use any of these data, please cite the corresponding publication:</p><p><a href="https://doi.org/10.1016/j.immuni.2023.08.002">Mural cell-derived chemokines provide a protective niche to safeguard vascular macrophages and limit chronic inflammation</a><br><a href="https://doi.org/10.1016/j.immuni.2023.08.002">Pekayvaz et al., Immunity, 2023</a> . ( <a href="https://doi.org/10.1016/j.immuni.2023.08.002">https://doi.org/10.1016/j.immuni.2023.08.002</a> )</p><p><strong>scRNA-seq data</strong></p><p><i>processed:</i></p><p>processed_kidney_seurat.Rds<br>processed_lung_seurat.Rds</p><p><i>count matrices:</i></p><p>sample_M1_raw_feature_bc_matrix.h5<br>sample_M2_raw_feature_bc_matrix.h5</p><p><i>script:</i></p><p>process_sctransform.R</p><p>functions.R with helper functions (mainly for plotting) used in the process-script.</p><p><strong>RNA-seq</strong></p><p><i>macrophages:</i></p><p>macs_control_vs_knockout.hisat2.DirectDESeq2.tsv|xlsx (count data and DESeq2 results)</p><p><i>aorta:</i></p><p>aorta_control_vs_knockout.hisat2.DirectDESeq2.tsv|xlsx (count data and DESeq2 results)</p><p><i>Dead vs. Living:</i></p><p>peri_Dead_vs_Living.exon_all.DirectDESeq2.tsv|xlsx (count data and DESeq2 results)</p><p> </p>
Data from: Fluctuation of ecological niches and geographic range shifts along chile pepper's domestication gradient
<p>Domestication is an ongoing well-described process. However, while many have stud- ied the changes domestication causes in plant genetics, few have explored its impact on the portion of the geographic landscape in which the plants exist. Therefore, the goal of this study was to understand how the process of domestication changed the geographic space suitable for chile pepper (<em>Capsicum annuum</em>) in its center of origin (domestication). <em>C. annuum</em> is a major crop species globally whose center of domes- tication, Mexico, has been well-studied. It provides a unique opportunity to explore the degree to which ranges of different domestication classes diverged and how these ranges might be altered by climate change. To this end, we created ecological niche models for four domestication classes (wild, semiwild, landrace, modern cultivar) based on present climate and future climate scenarios for 2050, 2070, and 2090. Considering present environment, we found substantial overlap in the geographic niches of all the domestication classes. Yet, environmental and geographic aspects of the current ranges did vary among classes. Wild and commercial varieties could grow in desert conditions, while landraces could not. With projections into the future, habitat was lost asymmetrically, with wild, semiwild, and landraces at greater risk of territorial declines than modern cultivars. Further, we identified areas where future suitability overlap between landraces and wilds is expected to be lost. While range expansion is widely associated with domestication, we found little support of a con- stant niche expansion (either in environmental or geographical space) throughout the domestication gradient in chile peppers in Mexico. Instead, particular domestication transitions resulted in loss, followed by capturing or recapturing environmental or geographic space. The differences in environmental characterization among domes- tication gradient classes and their future potential range shifts increase the need for conservation efforts to preserve landraces and semiwild genotypes</p>
Identifying climatic drivers of hybridization with a new ancestral niche reconstruction method
<p>Applications of molecular phylogenetic approaches have uncovered evidence of hybridization across numerous clades of life, yet the environmental factors responsible for driving opportunities for hybridization remain obscure. Verbal models implicating geographic range shifts that brought species together during the Pleistocene have often been invoked, but quantitative tests using paleoclimatic data are needed to validate these models. Here, we produce a phylogeny for Heuchereae, a clade of 15 genera and 83 species in Saxifragaceae, with complete sampling of recognized species, using 277 nuclear loci and nearly complete chloroplast genomes. We then employ an improved framework with a coalescent simulation approach to test and confirm previous hybridization hypotheses and identify one new intergeneric hybridization event. Focusing on the North American distribution of Heuchereae, we introduce and implement a newly developed approach to reconstruct potential past distributions for ancestral lineages across all species in the clade and across a paleoclimatic record extending from the late Pliocene. Time calibration based on both nuclear and chloroplast trees recovers a mid- to late-Pleistocene date for most inferred hybridization events, a timeframe concomitant with repeated geographic range restriction into overlapping refugia. Our results indicate an important role for past episodes of climate change, and the contrasting responses of species with differing ecological strategies, in generating novel patterns of range contact among plant communities and therefore new opportunities for hybridization. The new ancestral niche method flexibly models the shape of niche while incorporating diverse sources of uncertainty and will be an important addition to the current comparative methods toolkit.</p>
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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.
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.