Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
43
datasets available to search
ShareScore release 0.9.0
Dataset results
43 results for “herbivore performance”
Linking diet switching to reproductive performance across populations of two Critically Endangered mammalian herbivores
<p>Data associated with Harvey Sky, N., Britnell, J., Antwis, R. <em>et al.</em> Linking diet switching to reproductive performance across populations of two critically endangered mammalian herbivores. <em>Commun Biol</em> <strong>7</strong>, 333 (2024). https://doi.org/10.1038/s42003-024-05983-3</p> <p>The data deposited here includes raw metabarcoding output fasta files and some processed metabarcoding and sample data in xslx files. We include a more detailed description of each file below.</p> <p>Data regarding Kenyan black rhino and Grevy’s zebra are treated as sensitive and confidential. There are therefore restrictions on the data that we can make available. Due to these confidentiality considerations, the sample data stored here does not include locations of sample collection within each reserve for either species, or the identity or breeding data for black rhino. It also only includes the final processed values for NDVI and rainfall. The remote sensing data is available from the repositories cited in the methods, but we cannot provide the shapefiles or other data used to calculate the final values for each sample. </p> <p><em><strong>Raw fasta files_plants.zip</strong></em></p> <p>A zipped folder containing the raw fasta files which were the output from the MiSeq sequencing of dietary plants in the faecal samples for both black rhino and Grevy's zebra. Within the zipped folder, the first part of the title of each fasta.gz file is the sample code (S1, S2, S3 etc), which allows you to cross reference these files with the sample data and processed sequencing data in the xslx files. Files with R1 in the title are foward reads, and R2 are reverse reads. </p> <p><em><strong>Raw fasta files_bacteria.zip</strong></em></p> <p>A zipped folder containing the raw fasta files which were the output from the MiSeq sequencing of microbiome bateria in the faecal samples for both black rhino and Grevy's zebra. Within the zipped folder, the first part of the title of each fasta.gz file is the sample code (S1, S2, S3 etc), which allows you to cross reference these files with the sample data and processed sequencing data in the xslx files. Files with R1 in the title are foward reads, and R2 are reverse reads. </p> <p><em><strong>Sample data and processed metabarcoding data_Black rhino.xlsx</strong></em></p> <p><em>Sample data tab</em></p> <p>The data that we are able to share that is associated with each black rhino sample.</p> <p>SampleID - The code used to identiy each sample which allows it be cross-referenced with other tabs and the fasta files. </p> <p>IndividualID - We are not able to share rhino names or other identifiers, but we have given each individual a unique number so that it can be seen which samples came from the same individuals. </p> <p>NDVI - Mean NDVI of each individual's area of utilisation in the 10-day period within which the sample was collected. The method used to calculate this is described in the methods of the article. </p> <p>Rainfall - Cumulative rainfall over the 30 days previous to sample collection for the 0.05 degree pixel under the sample. The method used to calculate this is described in the methods of the article. </p> <p>Season - Post is the post-rain sampling season June-July 2018. Pre is the pre-rain sampling season January-March 2019. </p> <p>Reserve - The reserve that the sample was collected on. </p> <p>Date - The date of sample collection. </p> <p>Dietary breadth - Shannon-Wiener index of dietary alpha diversity. The method used to calculate this is described in the methods of the article. NA signifies that the number of reads returned for that sample was under the threshold that signified sequencing failure for the dietary plant metabarcoding.</p> <p>Poaceae, Fabaceae, Ebenaceae - The relative abundance of each of these three dietary plant families that were the focus of our analyses. The method used to calculate these is described in the methods of the article. NA signifies that the number of reads returned for that sample was under the threshold that signified sequencing failure for the dietary plant metabarcoding.</p> <p><em>Bacteria numbers of reads</em></p> <p>The number of reads assigned to each bacterial ASV found in each sample. </p> <p><em>Bacteria sequences and reads</em></p> <p>The sequence of each ASV, and the taxa assigned to each sequence in the microbiome metabarcoding. The method for taxonomic assignment is described in the methods of the article. </p> <p><em>Plant numbers of reads</em></p> <p>The number of reads assigned to each dietary plant ASV found in each sample. </p> <p><em>Plant sequences and reads</em></p> <p>The sequence of each ASV, and the taxa assigned to each sequence in the dietary plant metabarcoding. The method for taxonomic assignment is described in the methods of the article. </p> <p> </p> <p><em><strong>Sample data and processed metabarcoding data_Grevy's zebra.xlsx</strong></em></p> <p><em>Sample data tab</em></p> <p>The data that we are able to share that is associated with each Grevy's zebra sample.</p> <p>Sample ID - The code used to identiy each sample which allows it be cross-referenced with other tabs and the fasta files. </p> <p>NDVI - Mean NDVI of each individual's area of utilisation in the 10-day period within which the sample was collected. The method used to calculate this is described in the methods of the article. </p> <p>Rainfall - Cumulative rainfall over the 30 days previous to sample collection for the 0.05 degree pixel under the sample. The method used to calculate this is described in the methods of the article. </p> <p>Reserve - The reserve that the sample was collected on. </p> <p>Season - Post is the post-rain sampling season July-August 2018. Pre is the pre-rain sampling season January-February 2019. </p> <p>Date - The date of sample collection. </p> <p>Dietary breadth - Shannon-Wiener index of dietary alpha diversity. The method used to calculate this is described in the methods of the article. </p> <p>Poaceae, Fabaceae - The relative abundance of each of these two dietary plant families that were the focus of our analyses. The method used to calculate these is described in the methods of the article. NA signifies that the number of reads returned for that sample was under the threshold that signified sequencing failure for the dietary plant metabarcoding.</p> <p>Indigofera - The relative abundance of each of this Fabaceae genus was included in our analyses. The method used to calculate these is described in the methods of the article. NA signifies that the number of reads returned for that sample was under the threshold that signified sequencing failure for the dietary plant metabarcoding.</p> <p><em>Bacteria numbers of reads</em></p> <p>The number of reads assigned to each bacterial ASV found in each sample. </p> <p><em>Bacteria sequences and reads</em></p> <p>The sequence of each ASV, and the taxa assigned to each sequence in the microbiome metabarcoding. The method for taxonomic assignment is described in the methods of the article. </p> <p><em>Plant numbers of reads</em></p> <p>The number of reads assigned to each dietary plant ASV found in each sample. </p> <p><em>Plant sequences and reads</em></p> <p>The sequence of each ASV, and the taxa assigned to each sequence in the dietary plant metabarcoding. The method for taxonomic assignment is described in the methods of the article. </p> <p> </p>
Large differences in herbivore performance emerge from simple herbivore behaviors and fine-scale spatial heterogeneity in phytochemistry
Open the record for dataset details and reuse information.
Data from: Will like replace like? linking thermal performance to ecological function across predator and herbivore populations
The inability of species to adapt to changing climate may cause ecological communities to disassemble and lose ecological functioning. However, theory suggests that communities may be resilient whenever populations within species exhibit variation in thermal plasticity or adaptation whereby thermally tolerant populations replace thermally sensitive ones. But will they maintain the functional roles of the populations being replaced? This study evaluated whether "like replaces like" functionally by measuring how four populations of a grasshopper herbivore and its co-occurring spider predator cope with environmental warming. The study occurred across a latitudinal gradient bounded by southerly, warmer Connecticut and northerly, cooler New Hampshire, USA. The study compared the survival rates, thermal performance, habitat usage, and food chain interactions of each grasshopper and spider population between its home field site (field of origin) and a Connecticut transplant site, and the native Connecticut population. Three grasshopper populations exhibited physiological plasticity by adjusting metabolic rates. The fourth population selected cooler habitat locations. Spider populations did not alter their metabolism, and instead selected cooler habitat locations thereby altering spatial overlap with their prey and food chain interactions. Grasshopper populations that coped physiologically consumed plants in different ratios than the fourth population and the Connecticut population. Hence "like may not replace like" whenever populations adapt physiologically to warming.
Root-knot nematode infection of Brassica rapa enhances the performance of a specialist root herbivore via systemically induced responses
<p>Herbivores sharing host plants are often temporally and spatially separated, limiting direct interactions between them. Nevertheless, they can reciprocally influence each other via systemically induced plant responses, as observed in numerous study systems. In contrast, examples of such plant-mediated interactions between belowground herbivores are scarce, but we postulated that they similarly occur given the large diversity of root-interacting soil organisms. To test this hypothesis, we analyzed the performance of <em>Delia radicum</em> larvae feeding on main roots of <em>Brassica rapa </em>plants whose fine roots were infected by the root-knot nematode <em>Meloidogyne incognita</em>. Simultaneously, we studied the effects of <em>M. incognita</em> on <em>D. radicum</em>-induced defense responses and the accumulation of primary metabolites in the main root. We observed that almost 1.5 times as many <em>D. radicum</em> adults emerged from nematode-infected plants, indicating a facilitation effect of <em>M. incognita</em> infection.<em> </em>Although we observed increases in the accumulation of proteins and two essential amino-acids, the strongest effect of nematode-infection was visible in the defense response to <em>D. radicum</em>. We observed a 1.5 times higher accumulation of the defense-related phytohormone JA-Ile in response to <em>D. radicum</em> on nematode-infected plants, coinciding with a 75% increase in indole glucosinolate concentrations. Contrastingly, concentrations of aliphatic glucosinolates, secondary metabolites negatively affecting <em>D. radicum</em>, were 10-25% lower in nematode<em>-</em>infected plants. We hypothesize that the attenuated aliphatic glucosinolate concentrations result from antagonistic interactions between biosynthetic pathways of both glucosinolate classes, which was reflected in the expression of key biosynthesis genes. Our results provide explicit evidence of plant-mediated interactions between belowground organisms via systemically induced responses in roots.</p>
Nitrogen fertilization and high plant growing temperature increase herbivore performance
<p>Global environmental change exerts growing pressure on biodiversity. Anthropogenic climate and land use change are particularly important drivers of biodiversity loss. While their effects on biodiversity have been widely studied individually, interactions among them are poorly understood. Here, we investigate the effects of two common drivers of global change, increased temperature and nitrogen fertilization, on host-plant quality and herbivore performance in the butterfly <i>Lycaena tityrus</i>. We show that butterfly performance was positively affected by plants grown at increased temperatures and nitrogen fertilization, the latter being in line with the nitrogen limitation hypothesis. Effects were largely consistent across treatments, i.e. nitrogen deposition and temperature did not interact strongly to affect herbivore performance. Overall, females suffered more strongly than males from poor host-plant quality. Our study demonstrates changes in host-plant quality caused by variation in temperature and nitrogen availability, which induced indirect effects in an herbivore. Such indirect effects of global environmental change are an important source of variation and should be considered in order to reduce uncertainties with regard to the effects of global change on biodiversity.</p>
Data from: Predator performance and fitness Is dictated by herbivore prey type plus indirect effects of their host plant
<p>Animals, including herbivores and predators, use diet-mixing to balance their macro- and micronutrient intake. Recent work demonstrated that lady beetles fed only pea aphids from fava beans had reduced fitness caused by a deficiency of dietary sterols. However, beetles redressed this deficit by eating fava bean leaves. In the current study we used Coccinella septempunctata as a model to test the hypotheses that pea aphids are a poor sterol resource independent of their host plant, and that fava beans produce low quality prey regardless of aphid species. Additionally, we tested the reproductive rescue capacity of alfalfa and barley foliage compared to fava, and profiled the sterols of phloem exudates, foliage, and aphids reared on these different hosts. Beetle fecundity and egg viability was significantly better when provided pea aphids reared on alfalfa (compared to fava beans) and green peach aphids reared on fava plants. Alfalfa and barley leaves were not consumed by beetles and did not support beetle reproduction. The sterol profile of aphids largely reflected their host plant phloem. However, green peach aphids from fava acquired 125-times more sterol than pea aphids from fava. Our findings show how the sterol content of different host-plants can affect the third trophic level. Our results suggest that 1) prey quality varies depending on prey species, even when they occur on the same plant, 2) plant species can mediate prey quality, 3) host plant-mediated effects on prey quality partially drive omnivory, and 4) diet-mixing benefits growth and reproduction by redressing micronutrient deficits.</p>
Data for: Simulating effects of agricultural intensification and climate change: Nitrogen fertilization and drought stress decrease insect herbivore performance
<p>Biodiversity is globally under pressure, and the current decline in insect biomass and diversity is likely caused by human activities. Key drivers of biodiversity loss include agricultural intensification and anthropogenic climate change. Nevertheless, a thorough understanding of potential interactions between both factors and the mechanisms underlying insect declines in general is still lacking.</p> <p>Here, we investigate the combined effects of nitrogen fertilization and drought, as applied to host plants, on the preference and performance of the butterfly <em>Lycaena tityrus</em>.</p> <p>Individuals performed best on plants having received medium nitrogen levels, while performance was reduced by either a lack of or strong fertilization, the former potentially caused by nitrogen limitation and the latter by increased concentrations of toxic allelochemicals. Female oviposition preference though was positively related to nitrogen fertilization, resulting in a mismatch between preference and offspring performance at high nitrogen levels. Plant drought stress additionally reduced herbivore performance, and females appeared to suffer more from low-quality food than males.</p> <p>Our results indicate that increasing nitrogen fertilization, as applied in intensive agriculture, may substantially reduce host-plant quality for insect herbivores, which may be exaggerated in the course of climate change due to the more frequent occurrence of droughts. Our study thus contributes to a better understanding of the mechanisms underlying human-driven insect declines in agricultural landscapes and beyond.</p>
The plant toxin 4-methylsulfinylbutyl isothiocyanate decreases herbivore performance and modulate cellular and humoral immunity
<p class="MsoNormal"><span>Insect herbivores frequently encounter plant defense molecules, but the physiological and ecological consequences for their immune systems are not fully understood. The majority of studies attempting to relate levels of plant defensive chemistry to herbivore immune responses have used natural population or species-level variation in plant defensive chemistry. Yet, this potentially confounds the effects of plant defense chemistry with other potential traits that may affect the expression of herbivore immunity such as development time and nutritional quality. We have used an artificial diet containing known quantities of a plant toxin (4-methylsulfinylbutyl isothiocyanate; 4MSOB-ITC or ITC), an isothiocyanate present in many plants in the genus <em>Brassica</em>, to explicitly explore the effects of a plant toxin on the cellular and humoral immune responses of the generalist herbivore <em>Trichoplusia ni</em> (Lepidoptera: Noctuidae) that frequently feeds on glucosinolate-containing plants. Caterpillars feeding on diets with high concentrations of ITC experienced reduced survivorship and growth rates. High concentrations of ITC suppressed the appearance of several types of hemocytes and melanization activity, which are critical defenses against parasitic Hymenoptera and microbial pathogens. In terms of </span><em><span>T. ni</span></em><span> humoral immunity, only </span><span>the antimicrobial peptide (AMP) genes <em>lebocin</em> and <em>gallerimycin </em>were significantly upregulated in caterpillars fed on diets </span><span>containing high levels of 4MSOB-ITC relative to caterpillars that were provided with ITC-free diet</span><span>. Surprisingly, challenging </span><span>caterpillars</span><span> </span><span>with a non-pathogenic strain of </span><em><span>Escherichia coli</span></em><span> resulted in the upregulation of the AMP gene <em>cecropin</em>. Feeding on high concentrations of plant toxins hindered caterpillar development and decreased cellular immunity but conferred mixed effects on humoral immunity. Our findings provide novel insights into the effects of herbivore diet composition on insect performance demonstrating the role of specific plant defense toxins that shape herbivore immunity and trophic interactions. </span></p>
Performance and preference of four above- and below-ground invertebrate and generalist herbivores on regionally and locally rare plant species
<ol> <li>Rare plant species are suggested to be less resistant to herbivores than common species. Their lower apparency and the fact that they often live in isolated populations, resulting in fewer herbivore encounters, might have led to the evolution of reduced defences. Moreover, their frequently lower levels of genetic diversity compared with common species could negatively affect their resistance against enemies. However, the hypothesis that plant resistance depends on plant regional and local rarity, independently of habitat and competitive and growth strategy, lacks evidence.</li> <li>To test this hypothesis, we assessed the performance and preference of one belowground and three aboveground generalist invertebrate herbivores from different taxonomic groups as indicators of plant resistance. Herbivores were fed a total of 62 regionally and locally rare and common plant species from Switzerland. We accounted for differences in a plant's growth and competitive strategy and habitat resource availability.</li> <li>We found that regionally and locally rare and common plant species did not generally differ in their resistance to most generalist herbivores. However, one herbivore species even performed better and preferred locally and regionally common plant species over rarer ones, indicating that common species are not more resistant, but tend to be less resistant. We also found that all herbivore species consistently performed better on competitive and large plant species, although different herbivore species generally preferred and performed better on different plant species. The latter indicates that the use of generalist herbivores as indicators of plant-resistance levels can be misleading.</li> <li> <em>Synthesis</em>: Our results show that rare plant species are not inherently less resistant than common ones to herbivores. Instead, our results suggest that the ability of plants to allocate resources away from defence towards enhancing their competitive ability might have allowed plants to tolerate herbivory, and to become locally and regionally common.</li> </ol>
Specialist herbivore performance on introduced plants during native host decline
Open the record for dataset details and reuse information.
Data from: Will like replace like? linking thermal performance to ecological function across predator and herbivore populations
Open the record for dataset details and reuse information.
Nitrogen fertilization and high plant growing temperature increase herbivore performance
Open the record for dataset details and reuse information.
Data for: Simulating effects of agricultural intensification and climate change: Nitrogen fertilization and drought stress decrease insect herbivore performance
Open the record for dataset details and reuse information.
Using dynamic foodscape models to assess bottom-up constraints on population performance of herbivores
Open the record for dataset details and reuse information.
Data from: Predator performance and fitness Is dictated by herbivore prey type plus indirect effects of their host plant
Open the record for dataset details and reuse information.
Performance and preference of four above- and below-ground invertebrate and generalist herbivores on regionally and locally rare plant species
Open the record for dataset details and reuse information.
The plant toxin 4-methylsulfinylbutyl isothiocyanate decreases herbivore performance and modulate cellular and humoral immunity
Open the record for dataset details and reuse information.
Work that body: fin and body movements determine herbivore feeding performance within the natural reef environment
<p>Herbivorous fishes form a keystone component of reef ecosystems, yet the functional mechanisms underlying their feeding performance are poorly understood. In water, gravity is counter-balanced by buoyancy, hence fish are recoiled backwards after every bite they take from the substrate. To overcome this recoil and maintain contact with the algae covered substrate, fish need to generate thrust while feeding. However, the locomotory performance of reef herbivores in the context of feeding has hitherto been ignored. We used a 3D high-speed video system to track mouth and body kinematics during <i>in-situ</i> feeding strikes of fishes in the genus <i>Zebrasoma</i>, while synchronously recording the forces exerted on the substrate. These herbivores committed stereotypic and coordinated body and fin movements when feeding off the substrate and these movements determined algal biomass removed. Specifically, the speed of rapidly backing away from the substrate was associated with the magnitude of the pull force and the biomass of algae removed from the substrate per feeding bout. Our new framework for measuring biting performance <i>in-situ</i> demonstrates that coordinated movements of the body and fins play a crucial role in herbivore foraging performance and may explain major axes of body and fin shape diversification across reef herbivore guilds.</p>
Data from: Loss of heterosis and family-dependent inbreeding depression in plant performance and resistance against multiple herbivores under drought stress
1. Inbreeding depression (ID), outbreeding depression (OD) and heterosis can occur concurrently in plant populations. ID often increases under environmental stress, but the combined effects of inbreeding, outbreeding between populations and environmental stress, such as drought, on plant performance and herbivore resistance remain unclear. 2. In order to determine environment-dependent and family-dependent ID, OD and heterosis we conducted a common garden experiment with plants from five populations of Brassica nigra. Inbred, within-population outbred and between-population outbred plant families were exposed to drought or ambient water levels. We recorded the abundance and damage caused by specialist herbivores from contrasting feeding guilds, i.e. the phloem-feeding Brevicoryne brassicae, the leaf-chewing Psylliodes chrysocephalus and the stem-boring Ceutorhynchus quadridens larvae. 3. Drought stress had negative effects on growth, herbivore resistance and resistance against B. brassicae and positive effects on investments in reproductive output and plant secondary metabolites (sinigrin). We found drought stress-induced loss of heterosis for plant height and investment in reproductive output. Between-population outbred plants were more sensitive to drought stress in terms of above-ground biomass compared to within-population outbred plants. 4. Drought and inbreeding synergistically negatively influenced traits related to growth and reproductive output (environment-dependent inbreeding depression, EDID). There was high variation among families within populations in the degree of ID and EDID. Genetic variation in EDID could buffer the negative effects of genetic stress associated with habitat fragmentation and concurrent environmental stress. In order to capture fully the effects of both inbreeding and between-population outbreeding under stress the different spatial scales of the effects of inbreeding and between-population outbreeding should be taken into account. 5. Synthesis. Our results indicate that drought stress influences not only inbreeding depression (ID), but also heterosis. These findings shed new light on the combined effects of anthropogenic environmental change and the genetic consequences of habitat fragmentation on plants and their interactions with other organisms. Conservation programmes aiming to restore genetically degraded populations with the translocation of individuals between populations should consider environmental stress as a risk factor.
Beneficial worm allies warn plants of parasite attack belowground and reduce aboveground herbivore preference and performance
<p>We investigated responses of tomato (<i>Solanum lycopersicum</i>) to two functional guilds of nematodes - plant parasite (<i>Meloidogyne javanica</i>) and entomopathogens (<i>Heterorhabditis bacteriophora</i>, <i>Steinernema feltiae</i> belowground, and <i>S. carpocapsae</i>) - as well as a leaf mining insect (<i>Tuta absoluta</i>) aboveground. Our results indicate that entomopathogenic nematodes (EPNs): 1) induced plant defense responses, 2) reduced root knot nematode (RKN) infestation belowground and 3) reduced herbivore (<i>T. absoluta</i>) host preference and performance aboveground. Concurrently, we investigated the plant signaling mechanisms underlying these interactions using biochemical and transcriptome analyses. We found that both entomopathogen and parasite triggered immune responses in plant roots with shared gene expression. Tomato plants responded similarly to presence of RKN or EPN in the rootzone, by rapidly activating polyphenol oxidase (PPO) and guaiacol peroxidase (GP) activity in roots, but simultaneously suppressed this activity in aboveground tissues. We quantified changes in gene expression in tomato that may play essential roles in defense response to RKN, which were also coincidentally triggered by EPN. <span>For example, <i>PR-14</i> expression was greater in plants inoculated with EPN than in plants co-inoculated with </span>both nematode functional guilds<span>. Overall, EPN inoculation directly mediated enhanced plant defense and </span>reduced subsequent RKN infection. Likewise, we show that EPNs modulate plant defense against RKN invasion, in part, by suppressing active expression of antioxidant enzymes. Inoculation of tomato roots with EPNs belowground reduced both host preference and performance of the aboveground herbivore, <i>T. absoluta</i>. Inoculations of roots with EPN also triggered an immune response in tomato via up-regulated phenylpropanoid metabolism and synthesis of protease inhibitors (PIs) in plant tissues, which could explain an observed decrease in egg laying and developmental performance exhibited by herbivores on EPN-inoculated plants. Our results support the hypothesis that subterranean EPNs activate a battery of plant defenses associated with systemic acquired resistance (SAR) and/or induced systemic resistance (ISR) with concomitant antagonistic effects on temporally co-occurring subterranean plant pathogenic nematodes and terrestrial herbivores.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.