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644 results for “Shrubs”
Data and scripts for the article entitled "Arctic heatwaves could significantly influence the isoprene emissions from shrubs"
<p>The package includes the data and scripts for generating the figures for the paper entitled "Arctic heatwaves could significantly influence the isoprene emissions from shrubs".</p>
263 MAG annotations for three nested metagenomic studies describe crop-shrub-microbe interactions in an agroecology system in the Sahel
<p>The Sahel region of West Africa is a vulnerable eco-region, where climate change induced drought and a rapidly growing population pose serious threats to food security and contribute to soil degradation. Local and biologically based systems are necessary to maintain crop yields and soil health, and intercropping with native woody shrubs Guiera senegalensis has been discovered as a solution. We have previously shown that soil microbial communities are significantly altered by the presence of shrubs, and that these organisms may have plant growth promoting properties. Here, we augment those data with metagenomic and metatranscriptomic data across three nested experiments: a landscape scale experiment across a rainfall and soil type gradient, a long-term experimental site, and a growth chamber simulated drought experiment. We recovered 263 95% ANI dereplicated metagenome-assembled genomes (MAGs) of medium and high quality to evaluate their relative enrichment and what their encoded metabolisms reveal about mechanisms of microbiome millet support. These data contribute to our understanding of the role of the microbial community crop drought resilience in the Sahel and in semi-arid cropping systems globally. Here we present the DRAM annotations of each MAG, all associated metadata, viral genes and vOTUs from the Optimized Shrub Intercropping Study (OSS), and eukaryotic contigs from the OSS</p>
Original data for the paper "Ericaceous dwarf shrubs in drained forested peatlands: distribution, dynamics and key factors in a restoration experiment"
Open the record for dataset details and reuse information.
Advancing shrub dendroecology: a cutting-edge machine learning method for measuring shrub rings
<p>This dataset contains the original data used for the manuscript "<span>Advancing shrub dendroecology: a cutting-edge machine learning method for measuring shrub rings". Image labels is structured as follows: </span></p> <p><span>Site code - Species - sample number </span></p> <p><span>Sites: </span></p> <ul> <li><span>F stands for Finse</span></li> <li><span>A stands for Abisko</span></li> </ul> <p><span>Species :</span></p> <ul> <li><span>DO stands fro Dryas octopetala </span></li> <li><span>EH for Empetrum hermaphroditum</span></li> </ul>
Data for Holdrege et al: Precipitation intensification increases shrub dominance in arid, not mesic, ecosystems
<p>Data and code for the Holdrege et al. (2022) manuscript entitled 'Precipitation intensification increases shrub dominance in arid, not mesic, ecosystems' published in <em>Ecosystems </em>(doi: 10.1007/s10021-022-00778-1). This repository contains the results from simulations of sagebrush dominated plant communities conducted across 200 sites in the western United States. Simulations were run for ambient conditions as well as increased precipitation intensity and warming. Refer to the manuscript for details on the methods. This repository contains the summarized model output (data) and the R code that uses this data to compute the statistics and create the figures presented in the manuscript. See the README.md and data_dictionary.md files for more information on the code and data, respectively. Note, the .git subfolder provided here contains the git (version control history) files, and the users can ignore these. </p>
Dataset of very-high-resolution satellite RGB images to train deep learning models to detect and segment high-mountain juniper shrubs in Sierra Nevada (Spain)
<p>This dataset provides annotated very-high-resolution satellite RGB images extracted from Google Earth to train deep learning models to perform instance segmentation of Juniperus communis L. and Juniperus sabina L. shrubs. All images are from the high mountain of Sierra Nevada in Spain. The dataset contains 810 images (.jpg) of size 224x224 pixels. We also provide partitioning of the data into Train (567 images), Test (162 images), and Validation (81 images) subsets. Their annotations are provided in three different .json files following the COCO annotation format.</p>
Dataset of very-high-resolution satellite RGB images to train deep learning models to recognize high-mountain juniper shrubs from Sierra Nevada (Spain)
<p>This dataset provides annotated very-high-resolution satellite RGB images extracted from Google Earth to train deep learning models to recognize Juniperus communis L. and Juniperus sabina L. shrubs. All images are from the high mountain of Sierra Nevada in Spain. The dataset contains 2000 images (.jpg) of size 512x512 pixels partitioned into two classes: Shrubs and NoShrubs. We also provide partitioning of the data into Train (1800 images), Test (100 images), and Validation (100 images) subsets.</p>
Data from: Diversity among rare and common congeneric plant species from the Garry oak and Okanagan shrub-steppe ecosystems in British Columbia: implications for conservation
<p>Using universal non-coding chloroplast DNA markers (cpDNA), we investigated genetic diversity and genetic structure in four rare and common plant species pairs inhabiting threatened ecosystems (Garry Oak and Okanagan shrub-steppe) in British Columbia. <span>The species found in the Garry oak ecosystem are:</span><span> </span><em>Sanicula bipinnatifida </em><span>(purple sanicle; Apiaceae; rare),</span><span> </span><em>Sanicula crassicaulis </em><span>(Pacific sanicle; Apiaceae; common), and</span><span> </span><em>Balsamorhiza deltoidea </em><span>(deltoid balsamroot; Asteraceae; rare). The species found in the Okanagan shrub-steppe ecosystem are:</span><span> </span><em>Balsamorhiza sagittata </em><span>(arrowleaf balsamroot; Asteraceae; common),</span><span> </span><em>Orthocarpus barbatus </em><span>(Grand Coulee owl-clover; Orobanchaceae; rare),</span><span> </span><em><u>Orthocarpus </u>luteus </em><span>(yellow owl-clover; Orobanchaceae; common),</span><span> </span><em>Phacelia ramosissima </em><span>(branching phacelia; Hydrophyllaceae; rare), and</span><span> </span><em>Phacelia linearis </em><span>(thread-leaved phacelia; Hydrophyllaceae; common). </span>Eight cpDNA regions were sequenced for each study species. Sequences were aligned and concatenated within each species, and single nucleotide polymorphisms (SNPs) were used to analyze patterns of regional genetic diversity and phylogeographic structure within genera and species. Results include: total gene diversity (Ht), nucleotide diversity (π), number of private alleles, haplotype networks, isolation by distance, and analysis of molecular variance. </p> <p> </p>
Scale insects support natural enemies in both landscape trees and shrubs below them
<p>Scale insects are frequently abundant on urban trees. Although scales can worsen tree condition, some tree species tolerate moderate scale densities. Scales are prey for many natural enemies. Therefore, scale-infested trees may conserve natural enemies in their canopies and in nearby plants. We examined if scale-infested oaks—<em>Quercus</em> <em>phellos</em> L.—hosted more natural enemies than scale-uninfested oaks—<em>Q</em>. <em>acutissima</em> Carruth. and <em>Q</em>. <em>lyrata Walter</em> in Raleigh, NC. USA. We also tested if natural enemies were more abundant in holly shrubs (<em>Ilex</em> spp.) planted below scale-infested compared to scale-uninfested oaks. We collected natural enemies from the canopies of both tree types and from holly shrubs planted below these trees. To determine if tree type affected the abundance of natural enemies that passively dispersed to shrubs, we created hanging cup traps to collect arthropods as they fell from trees. To determine if enemies became more abundant on shrubs below scale-infested compared to scale-uninfested trees over short time scales, we collected natural enemies from holly shrubs below each tree type at three to six-day intervals. Scale-infested trees hosted more natural enemies than scale-uninfested trees and shrubs below scale-infested trees hosted more natural enemies than shrubs under scale-uninfested trees. Natural enemy abundance in hanging cup traps did not differ by tree type; however, shrubs underneath scale-infested trees accumulated more natural enemies than shrubs under scale-uninfested trees in six to nine days. Tolerating moderate pest densities in urban trees may support natural enemy communities, and thus biological control services, in shrubs below them.</p>
Ungulates mitigate the effects of drought and shrub encroachment on the fire hazard of Mediterranean oak woodlands
<p>Dataset included: Shrub density; Shrub biomass; Fuel load of <em>Cistus ladanifer</em>; Fuel load herbs; Fuel load litter</p>
Data and model scripts for "Temporal shifts in iso/anisohydry revealed from daily observations of plant water potential in a dominant desert shrub"
<p>Model code and data as used for the first revision submitted to New Phytologist, Sept. 2019. </p> <p>Models are coded in JAGS and run in R via the package "rjags." Two model versions are presented:</p> <p>1) "mod_SAM.R" and "script_SAM.R" run the full, time-varying SAM model, utilizing both the plant water potential ("res.Rdata") and the environmental covariate data ("cov2.Rdata") and associated initial values ("initsSAM.Rdata")</p> <p>2) "mod_SIMPLE.R" and "script_SIMPLE.R" run the simple, time-invariant model, utilizing only the plant water potential data ("res.Rdata") and associated initial values ("initsSIMPLE.Rdata")</p>
Fig. 3 in Insect herbivory following fire on Lyonia fruticosa, an ericaceous shrub of Florida scrub
Fig. 3. Lyonia fruticosa traits with time-since-fire: (A) height, (B) number of stems, (C) proportion of plants flowering, and (D) leaf area. For all panels, points show the mean ± 1 SE of plants within a management unit. Generalized additive models were fitted using the mean values for each management unit to avoid pseudoreplication. Solid regression lines and the shaded areas show the predicted values with 1 SE.
Fig. 2 in Insect herbivory following fire on Lyonia fruticosa, an ericaceous shrub of Florida scrub
Fig. 2. Time-since-fire and herbivore damage by type across whole plants. Points show the mean ± 1 SE of plants within a management unit. Generalized additive models were fitted using the mean values for each management unit to avoid pseudoreplication. When significant, solid regression lines and the shaded areas show the predicted values with 1 SE.
Fig. 1 in Insect herbivory following fire on Lyonia fruticosa, an ericaceous shrub of Florida scrub
Fig. 1. Time-since-fire and herbivory across whole plants. (A) Percent herbivory with time-since-fire; (B) proportion of leaves damaged with time-since-fire. For both panels, points show the mean ± 1 SE of plants within a management unit. Generalized additive models were fitted using the mean values (see text for details). Solid regression lines and the shaded areas show the predicted values with 1 SE.
Datasets and R Code for native-invasive shrub analysis
<p>Datasets and R code to reproduce statistical analysis comparing functional traits of native and invasive shrub and liana species of North America.</p>
Modified Ecosystem Demography (ED2) model with sagebrush (shrub) parameters
<p># Original Ecosystem Demography (ED2) model was developed by Moorcroft et al., 2001 and Medvigy et al., 2009, and team, which is available at github (https://github.com/EDmodel/ED2).</p> <p># This repository contains modified Ecosystem Demography (ED2) model for sagebrush (shrub) PFT. In order to do so we primarily updated ed_params.F90 with additional PFT, which is represented by number '18'. For the initial works, we selected allometrics equations for temperate PFTs in ED2 to develop coefficients (parameters) related to allometric relationships (such as dbh to height , dbh to leaf biomass etc). We used cube root of volume to represent diameter to calculate allometric equations for shrubs, since they do not have clear main trunk like trees. Another source code ed_max_dims.F90 was also changed to update PFT dimensions. </p> <p># This repository also includes namelist (ED2IN) file used to run sensitivity and optimization of sagebrush parameters. </p> <p>References</p> <p>Medvigy, D., Wofsy, S. C., Munger, J. W., Hollinger, D. Y., and Moorcroft, P. R.: Mechanistic scaling of ecosystemfunction and dynamics in space and time: Ecosystem Demography model version 2, J. Geophys. Res., 114, G01002, doi:10.1029/2008JG000812, 2009.</p> <p>Moorcroft, P. R., Hurtt, G. C., Pacala, S. W.: A method for scaling vegetation dynamics: the Ecosystem Demography model (ED), Ecol. Monogr., 71, 557–586, <a href="https://doi.org/10.1890/0012-9615(2001)071%5b0557:AMFSVD%5d2.0.CO;2">https://doi.org/10.1890/0012-9615(2001)071[0557:AMFSVD]2.0.CO;2</a>, 2001.</p>
Data from: Assessing the mechanisms and impacts of shrub invasion in forests: A meta-analysis
<ol> <li>The encroachment of invasive shrubs in forest understories can have detrimental effects on native plant recruitment. As a result, removal of invasive species is a common practice although long-lasting success is rare. In order to effectively conserve and manage invaded forests, it is crucial to understand the mechanisms that drive shrub invasion, i.e., high propagule pressure, low native resistance, and exploitation of empty niches.</li> <li>To gain a deeper understanding of the invasion process in forest ecosystems we conducted a meta-analysis of the work done in this topic. We collected data on invasive species and native community performance and on the abiotic conditions of forest understories under low and high levels of shrub invasion. We analyzed data from 124 articles that yielded 377 unique observations.</li> <li>Our results revealed that while invader performance did not vary by the mechanism of invasion, the impact on the native community was significantly detrimental when invasion occurred via low biotic resistance, and only marginally significant via propagule pressure. Invasive species performance was associated with increases in light availability, but not with other resources (soil water, or nutrients). When assessing impact on native performance as a function of invasive performance, results were again only significant under the low biotic resistance mechanism. Lastly, impacts were stronger when invasion took place by a single invader.</li> <li> <em>Synthesis and applications</em>: Taken together, these results suggest that restoration efforts should focus on (i) increasing the presence of strong native competitors or functionally diverse native communities, (ii) decreasing sources of invasive shrub propagules while keeping the canopies closed when invasion occurs via high propagule pressure, (iii) avoiding management techniques that degrade or diminish canopy cover, and (iv) prioritizing management of forest understories dominated by particularly impactful invasive shrubs.</li> </ol>
Urban tree pests can support biological control services in landscape shrubs
<p>Scale insects are common tree pests in urban ecosystems. Although severe scale infestations can worsen tree condition, trees can tolerate moderate scale densities. Scale insects are prey for many arthropod natural enemies that also feed on plant pests throughout urban landscapes. Because scale-infested trees support natural enemy communities, they may support biological control services on nearby plants and function analogously to banker plants in greenhouse production systems. In this study, we tested if sentinel insect prey were more likely to be removed on shrubs below scale-infested trees compared to scale-uninfested trees. We conducted several biological control experiments from 2019–2021 using fruit flies, aphids, and caterpillars in potted and planted holly shrubs below scale-infested and scale-uninfested oak trees. We found that caterpillars in potted shrubs and fruit flies in planted landscape shrubs were more likely to be removed underneath scale-infested trees compared to scale-uninfested trees. Caterpillars were also more likely to be removed from landscape <em>Ilex</em> <em>vomitoria</em> shrubs compared to <em>I</em>. <em>cornuta</em> shrubs. In all other experiments, we found no effect of scale infestation status or shrub species on prey removal. Our results suggest that scale-infested trees can support biological control services in shrubs below them but that this effect can vary depending on prey and shrub species. The natural enemy communities in urban trees and shrubs appear to be linked and tolerating tree pests can favor conservation biological control services in urban landscapes.</p>
Scale insects contribute to spider conservation in urban trees and shrubs
<p>Urbanization filters arthropod communities and selects for species tolerant of urban conditions. Spiders are key generalist predators in urban ecosystems, but certain spider families are rare in cities compared to rural areas. The unique arthropod communities found in different tree species likely affect their ability to conserve spiders by providing different prey resources. If arthropods disperse from trees to plants growing below trees, the conservation benefits of the arthropod communities found in trees may also extend to plants growing beneath them. Certain urban tree species can host high densities of scale-insects and other arthropods that may provide important prey resources for spiders. To assess the conservation value of different arthropod communities in urban trees, we collected spiders from scale-infested and scale-uninfested trees and from shrubs under these trees. We used hanging cup traps to collect spiders that fell from both tree types. Spider abundance was greater within, and in shrubs below, scale-infested compared to scale-uninfested trees. Scale-infested trees hosted more orb web weaving spiders than scale-uninfested trees. Shrubs under scale-infested trees hosted more hunting, orb web weaving, and space web weaving spiders than shrubs under uninfested trees. Our findings suggest that scale-infested urban trees, and the robust arthropod communities they support, conserve certain spider guilds, and these benefits extend to other plants in the landscape.</p> <p><strong>Implications for insect conservation:</strong> The ability of urban trees to conserve spider communities is in part attributable to the abundance of potential prey available within trees. Therefore, tolerating pests such as scale insects in urban trees can conserve spider communities both within trees and in shrubs planted below these trees.</p>
Effects of nurse shrubs and biochar on planted conifer seedling survival and growth in a high-severity burn patch in New Mexico, USA
<p>The synergistic effects of widespread high-severity wildfire and anthropogenic climate change are driving large-scale vegetation conversion. In the southwestern United States, areas that were once dominated by conifer forests are now shrub- or grasslands after high-severity wildfire, an ecosystem conversion that could be permanent without human intervention. Yet, the reforestation of these landscapes is rarely successful, with a mean planted seedling survival of just 25 %. Given these low rates, we carried out a planting experiment to quantify the impacts of biochar as a soil amendment and shrubs as nurse plants on planted conifer seedling survival and growth following high-severity wildfire. We planted 1200 seedlings of three species (<em>Pinus</em> <em>ponderosa</em>, <em>P. strobiformis</em>, and <em>Pseudotsuga</em> <em>menziesii</em>) in a 2-ha area within the footprint of the Las Conchas fire in New Mexico, USA. We used four treatments: under shrubs, or in the open and with or without biochar in a full-factorial design. We found that planting tree seedlings underneath shrubs increased tree seedling survival by 46 % after 3 years, with some marginal evidence that shrubs inhibited seedling diameter growth (mean <em>R<sup>2</sup></em> = 0.08). The addition of biochar increased seedling survival by 11 % but had no effect on seedling growth. Our study suggests that planted seedling survival in post-wildfire areas can be increased by planting under shrubs in soil amended with biochar. The widespread adoption of these methods may improve the success rates of post-wildfire reforestation efforts in semi-arid areas, regaining some of the ecosystem services lost to high-severity wildfire.</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.
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.