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.
21
datasets available to search
ShareScore release 0.9.0
Dataset results
21 results for “Cost of phenotype”
Image dataset for the evaluation of a low-cost high-throughput plant phenotyping system
<p>This dataset contains the raw and processed images from a low-cost high-throughput plant phenotyping (HTP) system, as well as the raw and processed images that were manually acquired for comparison. The HTP images were automatically and wirelessly acquired for entire benches of plants with a system composed of a Raspberry Pi and eight GoPro cameras. The entire file system of each GoPro camera was copied directly into a subfolder of finalGoProImages (numbered by camera). The raw HTP images were processed by correcting for lens distortion, computing the "greenness index" for each individual pixel, and filtering out extreme high and low values. These processed HTP images were then saved in the "greenness" subfolder of finalGoProImages. The manually acquired images in the finalDSLR folder each represent an individual plant from one of five time points during the same greenhouse experiment. The raw manually acquired images were processed in the same manner as the raw HTP images by computing the greenness index for each individual pixel and filtering out extreme high and low values. The two tab-delimited text files include the number of green pixels and mean greenness index for each HTP (greennessGoProTable2.txt) and manually acquired (greennessDSLRTable2.txt) image.</p>
Analysis scripts for the evaluation of a low-cost high-throughput plant phenotyping system
<p>Data analyses to complement "Image dataset for the evaluation of a low-cost high-throughput plant phenotyping system" (DOI: 10.5281/zenodo.5725224). "README_SetupAndAnalyses.pdf" contains instructions for setting up the high-throughput phenotyping (HTP) system and analyzing the resulting image datasets. The analyses are split into two parts. First, the automatically acquired HTP and manually acquired (DSLR) images are processed using the Python script labeled "finalGreennessAnalyses.py". The csv file labeled "labelTable.csv" is used to rename the DSLR images in terms of the date acquired and experimental conditions and must be included for the Python script to process the DSLR images. The output of the Python script includes "greennessGoProTable.txt" containing tab-delimited data regarding foliar size and greenness for each HTP image and "greennessDSLRTable.txt" containing tab-delimited data regarding foliar size and greenness for each DSLR image. The second step of the analyses includes inferential statistics (e.g., correlations and linear mixed effects modeling) and is based on the R script labeled "ghGoProAndDSLR_toPublish2.R". The csv file labeled "parAllBenches.csv" includes average solar daily light integral (solar DLI) data that were used as part of the linear mixed effects models in R.</p>
Learning‐induced switching costs in a parasitoid can maintain diversity of host aphid phenotypes although biocontrol is destabilized under abiotic stress
<p>Aphid populations frequently include phenotypes that are resistant to parasitism by hymenopterous parasitoid wasps, which is often attributed to the presence of 'protective' facultative endosymbionts residing in aphid tissues, particularly <em>Hamiltonella defensa</em>. In field conditions, under parasitoid pressure, the observed coexistence of aphids with and without protective symbionts cannot be explained by their difference in fitness alone.</p> <p>Using the cereal aphid <em>Rhopalosiphum padi</em> as a model, we propose an alternative mechanism whereby parasitoids are more efficient at finding common phenotypes of aphid and experience a fitness cost when switching to the less common phenotype.</p> <p>We construct a model based on delay differential equations and parameterise and validate the model with values within the ranges obtained from experimental studies. We then use it to explore possible effects on system dynamics under conditions of environmental stress, using our existing data on the effects of drought stress in crops as an example.</p> <p>We show the 'switching penalty' incurred by parasitoids leads to stable coexistence of aphids with and without <em>H. defensa</em> and provides a potential mechanism for maintaining phenotypic diversity amongst host organisms. We show that drought-induced reduction in aphid development time has little impact. However, greater reduction in fecundity on droughted plants of symbiont-protected aphids can cause insect population cycles when the system would be stable in the absence of drought stress.</p> <p>The stabilising effect of the increased efficiency in dealing with more commonly encountered host phenotypes is applicable to a broad range of consumer-resource systems and could explain stable coexistence in competitive environments. The loss of stable coexistence when drought has different effects on the competing aphid phenotypes highlights the importance of scenario testing when considering biocontrol for pest management.</p>
Data and Results for: Cost-effective, high-throughput fruit phenotyping system for three-dimensional reconstruction of fruit form
<p>The dataset contains the raw data used for generating the results in the paper, and the reconstructed results at 1mm and 2mm voxel resolution.</p> <p><strong>Raw data</strong>: Samples are gathered into groups of five, DataObjects1-5.zip, ... , DataObjects56-59.zip.</p> <p>Once uncompressed, each directory holds the images and configuration information used for each sample. For instance, '1_obj' is for the first sample, and the 'data' folder has the image files by camera. In this case one camera was used, 'cam2', and there are 62 images. 'pattern_square_mm_external.txt', 'pattern_square_mm_internal.txt', and 'rotate_specification_file.txt' are all configuration files needed for the calibration step.</p> <p> </p> <p><strong>Results</strong>: Reconstructions results are in compressed folders 'reconstruction-results-1mm.zip' and 'reconstruction-results-2mm.zip' for 1 mm and 2 mm voxel resolutions, respectively. These results are three-dimensional model files than can be viewed with a variety of software, we have used the free MeshLab: https://www.meshlab.net/ .</p> <p> </p> <p> </p> <p> </p>
Transgenerational phenotypic plasticity of diapause induction and related fitness cost in a commercial strain of the parasitoid Aphidius ervi Haliday
<p>Dataset.</p> <p>Diapause is an adaptation that insects have evolved to synchronize their life cycle with that of seasonal climatic changes and resources availability. However, cues for its induction are not always clear and, in some cases, a maternal effect may be involved. At the population level, just a part of the individuals may exhibit diapause with important consequences in terms of winter survival. Moreover, clear indicators of diapause state are difficult to identify. Diapause induction was thus investigated in the aphid parasitoid species Aphidius ervi Haliday (Hymenoptera: Braconidae) developing in the aphid Sitobion avenae (Hemiptera: Aphididae) at four crossed photothermal regimes (16 °C and 8 °C, 16:8 h L:D and 8:16 h L:D), and during 2 successive generations. We analyzed the reliability of changes in mummy color to assess for the diapausing state compared to dissections, and we measured parasitoid morphological and physiological traits. We observed that the proportion of dark brown mummies increased after one generation under low photothermal regime compared to other regimes. No diapause was recorded at 16 °C, 16:8 h L:D, while we observed 16.2% and 67.5% diapause incidence at 8 °C, 8:16 h L:D, at 1st and 2nd generation, respectively. Diapause induction is thus increased by short day-length conditions and low temperatures as well as by maternal effects. All parasitoid life-history traits (weight, size, fat content, water content, egg-load, and longevity) were affected by the photothermal regime and/or the generation. These results raise new questions on the environmental thresholds needed to induce diapause and on survival and adaptation potential of commercially available parasitoid strains in different environments.</p>
Experimental and theoretical support for costs of plasticity and phenotype in a nematode cannibalistic trait
<p>Developmental plasticity is the ability of a genotype to express multiple phenotypes under different environmental conditions and has been shown to facilitate the evolution of novel traits. However, while the associated cost of plasticity, i.e., the loss in fitness due to the ability to express plasticity in response to environmental change, and the cost of phenotype, i.e., the loss of fitness due to expressing a fixed phenotype across environments, have been theoretically predicted, empirically such costs remain poorly documented and little understood. Here, we use a plasticity model system, hermaphroditic nematode Pristionchus pacificus, to experimentally measure these costs in wild isolates under controlled laboratory conditions. P. pacificus can develop either a bacterial feeding or predatory mouth morph in response to different external stimuli, with natural variation of mouth-morph ratios between strains. We first demonstrated the cost of phenotype by analyzing fecundity and developmental speed in relation to mouth morphs across the P. pacificus phylogenetic tree. Then, we exposed P. pacificus strains to two distinct microbial diets that induce strain-specific mouth-form ratios. Our results indicate that the plastic strain does shoulder a cost of plasticity, i.e., the diet-induced predatory mouth morph is associated with reduced fecundity and slower developmental speed. In contrast, the non-plastic strain suffers from the cost of phenotype since its phenotype does not change to match the unfavorable bacterial diet but shows increased fitness and higher developmental speed on the favorable diet. Furthermore, using a stage-structured population model based on empirically derived life history parameters, we show how population structure can alleviate the cost of plasticity in P. pacificus. The results of the model illustrate the extent to which the costs associated with plasticity and its effect on competition depend on ecological factors. This study provides support for costs of plasticity and phenotype based on empirical and modeling approaches.</p>
Learning‐induced switching costs in a parasitoid can maintain diversity of host aphid phenotypes although biocontrol is destabilized under abiotic stress
Open the record for dataset details and reuse information.
Experimental and theoretical support for costs of plasticity and phenotype in a nematode cannibalistic trait
Open the record for dataset details and reuse information.
Data from: Phenotypic variation in overwinter environmental transmission of a baculovirus and the cost of virulence
A pathogen's ability to persist in the environment is an ecologically important trait, and variation in this trait may promote coexistence of different pathogen strains. We asked whether naturally occurring isolates of the baculovirus that infects gypsy moth larvae varied in their overwinter environmental transmission, and whether this variation was consistent with a tradeoff or an upper limit to virulence that might promote pathogen diversity. We used experimental manipulations to replicate the natural overwinter infection process using 16 field-collected isolates. Virus isolates varied substantially in the fraction of larvae infected, leading to differences in overwinter transmission rates. Furthermore, isolates that killed more larvae also had higher rates of early larval death in which no infectious particles were produced, consistent with a cost of high virulence. Our results thus support the existence of a cost that could impose an upper limit to virulence even in a highly virulent pathogen.
Genomic shifts, phenotypic clines and fitness costs associated with cold-tolerance in the Asian tiger mosquito
<p>Climatic variation is a key driver of genetic differentiation and phenotypic traits evolution, and local adaptation to temperature is expected in widespread species. We investigated phenotypic and genomic changes in the native range of the Asian tiger mosquito, <em>Aedes</em> <em>albopictus</em>. We first refine the phylogeographic structure based on genome-wide regions (1,901 double-digest restriction-site associated DNA single nucleotide polymophisms [ddRAD SNPs]) from 41 populations. We then explore the patterns of cold adaptation using phenotypic traits measured in common garden (wing size and cold tolerance) and genotype–temperature associations at targeted candidate regions (51,706 exon-capture SNPs) from nine populations. We confirm the existence of three evolutionary lineages including clades A (Malaysia, Thailand, Cambodia, and Laos), B (China and Okinawa), and C (South Korea and Japan). We identified temperature-associated differentiation in 15 out of 221 candidate regions but none in ddRAD regions, supporting the role of directional selection in detected genes. These include genes involved in lipid metabolism and a circadian clock gene. Most outlier SNPs are differently fixed between clades A and C, whereas clade B has an intermediate pattern. Females are larger at higher latitudes yet produce no more eggs, which might favor the storage of energetic reserves in colder climates. Nondiapausing eggs from temperate populations survive better to cold exposure than those from tropical populations, suggesting they are protected from freezing damages but this cold tolerance has a fitness cost in terms of egg viability. Altogether, our results provide strong evidence for the thermal adaptation of <em>A</em>. <em>albopictus</em> across its wide temperature range.</p>
Data from: Right phenotype, wrong place: predator-induced plasticity is costly in a mismatched environment
Open the record for dataset details and reuse information.
Data from: Relative costs and benefits of alternative reproductive phenotypes at different temperatures - genotype-by-environment interactions in a sexually selected trait
Open the record for dataset details and reuse information.
Data from: Phenotypic variation in overwinter environmental transmission of a baculovirus and the cost of virulence
Open the record for dataset details and reuse information.
Genomic shifts, phenotypic clines and fitness costs associated with cold-tolerance in the Asian tiger mosquito
Open the record for dataset details and reuse information.
Data from: Telomere length reflects phenotypic quality and costs of reproduction in a long-lived seabird
Telomere length is associated with cellular senescence, lifestyle and ageing. Short telomeres indicate poor health in humans and reduced life expectancy in several bird species, but little is known about telomeres in relation to phenotypic quality in wild animals. We investigated telomere lengths in erythrocytes of known-age common terns (Sterna hirundo), a migratory seabird, in relation to arrival date and reproductive performance. Cross-sectional data revealed that, independent of age, individuals with short telomeres performed better: they arrived and reproduced earlier in the season and had more chicks in the nest. The latter effect was stronger the older the brood and stronger in males, which do most of the chick provisioning. Longitudinal data confirmed this pattern: compared with birds that lost their brood, birds that raised chicks beyond the 10th nestling day experienced higher telomere attrition from one year to the next. However, more detailed analysis revealed that the least and most successful individuals lost the fewest base pairs compared with birds with intermediate success. Our results suggest that reproductive success is achieved at the expense of telomeres, but that individual heterogeneity in susceptibility to such detrimental effects is important, as indicated by low telomere loss in the most successful birds.
Data from: A costly chemical trait: phenotypic condition dependence of cuticular hydrocarbons in a dung beetle
Chemical traits are increasingly recognised as important cues used in mate choice. For example, the cuticular hydrocarbons (CHCs) of insects have been shown to influence mating success in a range of taxa. Less is known, however, about how CHCs are expressed in proportion to an individual's condition, and consequently whether CHCs can function as condition dependent signals of quality. We investigated this question using the dung beetle, Onthophagus taurus. CHCs are subject to sexual selection in this species through mate choice. A dietary manipulation revealed condition dependence of CHC expression for both sexes: dietary restriction decreased overall CHC production and altered the composition of CHCs. Furthermore, CHC production was associated with a measure of condition in beetles fed a limited diet but not those fed ad libitum. These results implicate a resource cost to CHC production that is likely to result in trade-offs with other fitness components in this species, as these respond similarly to a dietary restriction. The CHC profiles showed sexual dimorphism: males produced more CHCs and the sexes differed in the blend of compounds they produced. There was evidence for a male dimorphism in the CHC profile, in line with the presence of the alternative reproductive tactics (minor sneaks and major fighters) in this species. However, rather than mimicking a female CHC profile, minor males differed more from females than major males. Our results suggest that CHCs are a costly trait in O. taurus that has the potential to act as a condition dependent signal of quality.
Data from: Telomere length reflects phenotypic quality and costs of reproduction in a long-lived seabird
Open the record for dataset details and reuse information.
Data from: The social and ecological costs of an ‘over-extended’ phenotype
Open the record for dataset details and reuse information.
Data from: A costly chemical trait: phenotypic condition dependence of cuticular hydrocarbons in a dung beetle
Open the record for dataset details and reuse information.
Phenotypic and transcriptional profiling in Entamoeba histolytica reveal costs to fitness and adaptive responses associated with metronidazole resistance
GEO Series GSE35990. Entamoeba histolytica. 8 samples. Type: Expression profiling by array.
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.