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.
6,234
datasets available to search
ShareScore release 0.9.0
Dataset results
6,234 results for “phenotypes”
A modified fluctuation assay reveals a natural mutator phenotype that drives mutation spectrum variation within Saccharomyces cerevisiae
<p>Although studies of <em>Saccharomyces cerevisiae</em> have provided many insights into mutagenesis and DNA repair, most of this work has focused on a few laboratory strains. Much less is known about the phenotypic effects of natural variation within <em>S. cerevisiae</em>'s DNA repair pathways. Here, we use natural polymorphisms to detect historical mutation spectrum differences among several wild and domesticated <em>S. cerevisiae</em> strains. To determine whether these differences are likely caused by genetic mutation rate modifiers, we use a modified fluctuation assay with a <em>CAN1</em> reporter to measure de novo mutation rates and spectra in 16 of the analyzed strains. We measure a 10-fold range of mutation rates and identify two strains with distinctive mutation spectra. These strains, known as AEQ and AAR, come from the panel's 'Mosaic beer' clade and share an enrichment for C > A mutations that is also observed in rare variation segregating throughout the genomes of several Mosaic beer and Mixed origin strains. Both AEQ and AAR are haploid derivatives of the diploid natural isolate CBS 1782, whose rare polymorphisms are enriched for C > A as well, suggesting that the underlying mutator allele is likely active in nature. We use a plasmid complementation test to show that AAR and AEQ share a mutator allele in the DNA repair gene <em>OGG1</em>, which excises 8-oxoguanine lesions that can cause C > A mutations if left unrepaired.</p>
Census and phenotype data supporting Drosophila adaptive tracking
<p>Direct observation of evolution in response to natural environmental change can resolve <span>fundamental questions about adaptation including its pace, temporal dynamics, and underlying</span> p<span>henotypic and genomic architecture. </span>W<span>e tracked evolution of fitness-associated phenotypes and</span> <span>allele frequencies genome-wide in ten replicate field populations of <i>Drosophila melanogaster</i></span><i> </i><span>over ten generations from summer to late fall. Adaptation </span><span>was evident over each sampling</span> <span>interval (1-4 generations) with exceptionally rapid phenotypic adaptation and large allele frequency shifts at many independent loci. The direction and basis of the adaptive response</span> <span>shifted repeatedly over time, consistent with the action of strong and rapidly fluctuating</span> <span>selection. Overall, we find clear phenotypic and genomic evidence of a</span><span>daptive tracking</span> <span>occurring contemporaneously with environmental change, demonstrating the temporally dynamic</span> <span>nature of adaptation.</span></p>
Single Cell Phenotypic Profiling to Identify a Set of Immune Cell Protein Biomarkers for Relapsed and Refractory Diffuse Large B Cell Lymphoma: A Single-Center Study
<p>Diffuse large B-cell lymphoma (DLBCL) is the most common invasive type of non-Hodgkin lymphoma. Cell-of-origin (COO) classification is related to patients’ prognoses. Primary drug resistance in treatment for DLBCL has been observed. The specific serum biomarkers in these patients who suffer from relapsed and refractory (R/R)-DLBCL remains unclear. In the current study, using single-cell RNA sequencing (scRNA-seq) and mass cytometry (CyTOF), we determined and verified immune cell biomarkers at the mRNA and protein levels in single-cell resolution from 18 diagnostic peripheral blood mononuclear cell (PBMC) specimens collected from patients with R/R DLBCL. As controls, five PBMC specimens from healthy volunteers were obtained. We identified a panel of 35 surface marker genes for the features of R/R DLBCL unique cell cluster by scRNA-seq of eight R/R DLBCL patient samples and validated its efficiency in an external cohort consisting of 10 R/R DLBCL patients by CyTOF. The cell clustering and dimension reduction were compared among R/R DLBCL samples in CyTOF Space with COO as well as the C-MYC expression designation. Immune cells from each patient occupied unique regions in the 32-dimensional phenotypic space with no apparent clustering of samples into discrete subtypes. Significant heterogeneity observed in subgroups was mainly attributed to individual differences among samples and not to expression differences in a single, homogeneous immune cell subpopulation. The marker panel showed reliability in labeling R/R DLBCL without any influence from COO stratification and C-MYC expression designation. Furthermore, we compared all the markers between R/R DLBCL and normal samples. A total of 12 biomarkers were significantly overexpressed in R/R DLBCL relative to the normal samples. Therefore, we further optimized the diagnostic biomarker panel of R/R DLBCL comprising CD82, CD55, CD36, CD63, CD59, IKZF1, CD69, CD163, CD14, CD226, CD84, and CD31. In summary, we developed a novel set of biomarkers for the diagnoses of patients with R/R DLBCL. Detections procedures at single-cell resolution provide precise biomarkers which may substantially overcome intertumoral and intratumoral heterogeneity among primary samples. The findings confirmed that each case was unique and may comprise multiple, genetically distinct subclones.</p> <p>Here we uploaded the dataset of CyTOF for external validation. For more detailed information, please contact Dr zheng (zenki_zheng@163.com)</p> <p> </p>
Data from: Thyroid hormone tinkering elicits integrated phenotypic changes potentially explaining rapid adaptation of color vision in cichlid fish
Vision is critical for most vertebrates, including fish. One challenge that aquatic habitats pose is the high variability in spectral properties depending on depth, turbidity and composition of the water body. By altering opsin gene expression and chromophore usage, cichlid fish modulate visual sensitivities to maximize sensory input from the available light in their respective habitat. Thyroid hormone (TH) has been proposed to play a role in governing adaptive diversification in visual sensitivity in Nicaraguan Midas cichlids, which evolved in less than ~3,100 generations. As suggested by indirect measurements of TH levels (i.e., expression of deiodinases), populations adapted to short wavelength light in clear lakes have lower TH levels than ones inhabiting turbid lakes enriched in long-wavelength light. We experimentally manipulated TH levels by exposing two-week-old Midas cichlids to exogenous TH or a TH-inhibitor and measured opsin gene expression and chromophore usage (via cyp27c1 expression). Whereas exogenous TH induces long-wavelength sensitivity by changing opsin gene expression and chromophore usage in a concerted manner, TH-inhibited fish exhibit a visual phenotype with sensitivities shifted to shorter-wavelengths. Tinkering with TH levels in eyes results in concerted phenotypic changes that can provide a rapid mechanism of adaptation to novel light environments. --
Population genomic consequences of life history and mating system adaptation to a geothermal soil mosaic in yellow monkeyflowers (common garden phenotype data)
<p>Local selection can promote phenotypic divergence despite gene flow across habitat mosaics, but adaptation itself may generate substantial barriers to genetic exchange. In plants, life-history, phenology, and mating system divergence have been proposed to promote genetic differentiation in sympatry. In this study, we investigate phenotypic and genetic variation in <em>Mimulus guttatus</em> (yellow monkeyflowers) across a geothermal soil mosaic in Yellowstone National Park (YNP). Plants from thermal annual and nonthermal perennial habitats were heritably differentiated for life history and mating system traits, consistent with local adaptation to the ephemeral thermal-soil growing season. However, genome-wide genetic variation primarily clustered plants by geographic region, with little variation sorting by habitat. The one exception was an extreme thermal population also isolated by a 200m geographical gap of no intermediate habitat. Individual inbreeding coefficients (F<sub>IS</sub>) were higher (and predicted by trait variation) in annual plants and annual pairs showed greater isolation by distance at local (<1km) scales. Finally, YNP adaptation does not re-use a widespread inversion that underlies <em>M. guttatus</em> life-history ecotypes range-wide, suggesting a novel genetic mechanism. Overall, this work suggests that life history and mating system adaptation strong enough to shape individual mating patterns does not necessarily generate incipient speciation without geographical barriers.</p>
SARS-CoV-2 antigen exposure history shapes phenotypes and specificity of memory CD8 T cells
<p>This dataset contains aggregated CellRanger output for six 10x Genomics (5'GEX+abTCR+Feature barcoding) experiments from the study by Minervina, Pogorelyy et al (<a href="https://www.medrxiv.org/content/10.1101/2021.07.12.21260227v3">medrxiv</a>). <br> The scripts to process it further are available at github (<a href="https://github.com/pogorely/COVID_vax_CD8">repository</a>). <br> Raw sequencing data is available at SRA (acc. PRJNA744851)</p>
Datasets and scripts from: Sensory-based quantification of male colour patterns in Trinidadian guppies reveals no support for parallel phenotypic evolution in multivariate trait space
<p>Parallel evolution, in which independent populations evolve along similar phenotypic trajectories, offers insights into the repeatability of adaptive evolution. Here, we revisit a classic example of parallelism, that of repeated evolution of brighter males in the Trinidadian guppy (<em>Poecilia reticulata</em>). In guppies, colonisation of low predation habitats is associated with emergence of 'more colourful' phenotypes since predator-induced viability selection for crypsis weakens while sexual selection by female preference for conspicuousness remains strong. Our study differs from previous investigations in three respects. First, we adopt a multivariate phenotyping approach to characterise parallelism in multi-trait space. Second, we use ecologically-relevant colour traits defined by the visual systems of the two selective agents (i.e. guppy, predatory cichlid). Third, we estimate population genetic structure to test for adaptive (parallel) evolution against a model of neutral phenotypic divergence. We find strong phenotypic differentiation that is inconsistent with a neutral model but very limited support for the predicted pattern of greater conspicuousness at low predation. Effects of predation regime on each trait were in the expected direction, but weak, largely non-significant, and explained little among-population variation. In multi-trait space, phenotypic trajectories of lineages colonising low from high predation regimes were not parallel. Our results are consistent with reduced predation risk facilitating adaptive differentiation, potentially by female choice, but suggest that this proceeds in independent directions of multi-trait space across lineages. Pool-sequencing data also revealed SNPs showing greater differentiation than expected under neutrality, among which some are found in genes contributing to colour pattern variation, presenting opportunities for future genetic study.</p>
Hair phenotype diversity across Indriidae lemurs
<p><strong><span>Objectives: </span></strong><span>Hair (i.e., pelage/fur) is a salient feature of primate (including human) diversity and evolution—serving functions tied to thermoregulation, protection, camouflage, and signaling—but wild primate pelage evolution remains relatively understudied. Specifically, assessing multiple hypotheses across distinct phylogenetic scales is essential but is rarely conducted. We examine whole body hair color and density variation across Indriidae (<em>Avahi</em>, <em>Indri</em>, <em>Propithecus</em>)—a lineage that, like humans, exhibits vertical posture (i.e., their whole bodies are vertical to the sun).</span></p> <p><strong><span>Materials and Methods: </span></strong><span>Our analyses considers multiple phylogenetic scales (family-level, genus-level) and hypotheses (e.g., Gloger's rule, the body cooling hypotheses). We obtain hair color and density from museum and/or wild animals, opsin genotypes from wild animals, and climate data from WorldClim. To analyze our data, we use </span>phylogenetic generalized linear mixed models (PGLMM) using Markov chain Monte Carlo algorithms.</p> <p><strong><span>Results: </span></strong><span>Our results show that across the Indriidae family, darker hair is typical in wetter regions. However, within <em>Propithecus</em>, dark black hair is common in colder forest regions. Results also show pelage redness increases in populations exhibiting enhanced color vision. Lastly, we find follicle density on the crown and limbs increases in dry and open environments. </span></p> <p><strong><span>Discussion: </span></strong><span>This study highlights how different selective pressures across distinct phylogenetic scales have likely acted on primate hair evolution. Specifically, our data across <em>Propithecus</em> may implicate thermoregulation and is the first empirical evidence of Bogert's rule in mammals. Our study also provides rare empirical evidence supporting an early hypothesis on hominin hair evolution. </span></p>
Unravelling processes between phenotypic plasticity and population dynamics in migratory birds
<p>Populations can rapidly respond to environmental change via adaptive phenotypic plasticity, which can also modify interactions between individuals and their environment, affecting population dynamics. Bird migration is a highly plastic resource-tracking tactic in seasonal environments. However, the link between the population dynamics of migratory birds and migration tactic plasticity is not well understood.</p> <p>The quality of staging habitats affects individuals' migration timing and energy budgets in the course of migration, and can consequently affect individuals' breeding and overwintering performance, and impact population dynamics. Given staging habitats being lost in many parts of the world, our goal is to investigate responses of individual migration tactics and population dynamics in the face of loss of staging habitat, and to identify the key processes connecting them.</p> <p>We started by constructing and analysing a general full-annual-cycle individual-based model with a stylized migratory population to generate hypotheses on how changes in the size of staging habitat might drive changes in individual stopover duration and population dynamics. Next, through the interrogation of survey data, we tested these hypotheses by analysing population trends and stopover duration of migratory waterbirds experiencing loss of staging habitat.</p> <p>Our modelling exercise led to us posing the following hypotheses: the loss of staging habitat generates plasticity in migration tactics, with individuals remaining on the staging habitat for longer to obtain food due to a reduction in per capita food availability. The subsequent increasing population density on the staging habitat has knock on effects on population dynamics in the breeding and overwintering stage. Our empirical results were consistent with the modelling predictions.</p> <p>Our results demonstrate how environmental change that impacts one energetically costly life history stage in migratory birds can have population dynamics impacts across the entire annual cycle via phenotypic plasticity.</p>
Data for Rapid phenotypic differentiation and local adaptation in Japanese knotweed s.l. (Reynoutria japonica and R. × bohemica, Polygonaceae) invading novel habitats
<p><span><strong>PREMISE:</strong> Many plant invaders like the Japanese knotweeds are thought to colonize new habitats with low genetic diversity. Such species provide an opportunity to study rapid adaptation to complex environmental conditions.</span></p> <p><span><strong>METHODS:</strong> Using replicate reciprocal transplants of clones across three habitats, we described patterns of phenotypic response and assessed degree of local adaptation.</span></p> <p><span><strong>KEY RESULTS:</strong> We found plants from beach habitats had decreased height, number of leaves, leaf area, and biomass allocation to roots and shoots compared to plants from marsh and roadside habitats when grown in their home habitat. In the marsh habitat, marsh plants were generally larger than beach plants, but not different from roadside plants. There were no differences among plants from different habitats grown in the roadside habitat. Despite this evidence of differentiation in beach and marsh habitats, we found mixed evidence for local adaptation. In their "home site" plants from the marsh habitat had greater biomass than plants from the beaches but not compared to plants from roadsides. Biomass comparisons in other habitats were either maladaptive or not significant. However, plants from the roadside had greater survival in their "home site" compared to foreign plants. There were no differences in survival in the other habitats.</span></p> <p><span><strong>CONCLUSIONS:</strong> We found phenotypic differentiation associated with habitats despite the low reported genetic diversity for these populations. Our results partially support the hypothesis of local adaptation in marsh and roadside habitats. Identifying whether these patterns of differentiation result from genetic or heritable non-genetic mechanisms will require further work.</span></p>
Wildfire as a natural stressor and its effect on female phenotype and ornament development
<p>Controlled low-intensity fires are commonly used in ecosystem management for both habitat restoration and wildfire management. Animals in those ecosystems may respond to fire by shifting energy allocation away from reproduction and growth, and toward maintenance. Stress-induced shifts in energy allocation may affect expression of condition-dependent sexual signals, which are sensitive to energetic and physiological trade-offs mediated by glucocorticoids. Here, we examine the effect of fire on ornament expression, corticosterone, and other phenotypic traits in a population of striped plateau lizards, <i>Sceloporus virgatus</i>, affected by the Horseshoe 2 Fire in the Chiricahua Mountains, Arizona, USA. The condition-dependent female ornament was significantly smaller the month following the fire than two years prior, and was both smaller and less orange on the burned site relative to a nearby unburned site. These patterns are similar to those found in a previous experimental study examining the response of the ornament to corticosterone manipulations. Yet, in the current study, corticosterone levels were not different in lizards on the burned and unburned sites. Perhaps glucocorticoid levels already returned to baseline, or do not adequately track environmental change. Females tended to be smaller and lighter on the burned site than the unburned site, however the year after the fire, body condition was higher for females on the burned site, indicating a rapid recovery and potential long-term benefits in response to low-intensity fires in this fire-adapted ecosystem. We found that the lizards adjusted energy allocation away from sexual signaling and growth in response to low-intensity fires. As fires and fire management are likely to increase in response to changing fire regimes across the globe, it will be important to consider behavioral and physiological responses of impacted species, as well as population, community, and ecosystem level responses.</p>
Metabolomics-based phenotypic screens for evaluation of drug synergy via DIMS
<p>Drugs used in combination can synergize to increase efficacy, decrease toxicity, and prevent drug resistance. While conventional high-throughput screens relied on univariate data are incredibly valuable to identify promising drug candidates, phenotypic screening methodologies could be beneficial to provide deep insight into the molecular response of drug combination with a likelihood of improved clinical outcomes. We developed a high-content metabolomics drug screening platform using stable isotope tracer direct infusion mass spectrometry that informs a novel algorithm to determine synergy from multivariate phenomics data. Using a cancer drug library, we validated the drug screening integrating isotope enriched metabolomics data and computational data mining on a panel of prostate cell lines and verified the synergy between CB-839 and docetaxel both in vitro (three-dimensional model) and in vivo. The proposed unbiased metabolomics screening platform can be used to rapidly generate phenotype-informed datasets and quantify synergy for combinatorial drug discovery. Drugs used in combination can synergize to increase efficacy, decrease toxicity, and prevent drug resistance. While conventional high-throughput screens relied on univariate data are incredibly valuable to identify promising drug candidates, phenotypic screening methodologies could be beneficial to provide deep insight into the molecular response of drug combination with a likelihood of improved clinical outcomes. We developed a high-content metabolomics drug screening platform using stable isotope tracer direct infusion mass spectrometry that informs a novel algorithm to determine synergy from multivariate phenomics data. Using a cancer drug library, we validated the drug screening integrating isotope enriched metabolomics data and computational data mining on a panel of prostate cell lines and verified the synergy between CB-839 and docetaxel both in vitro (three-dimensional model) and in vivo. The proposed unbiased metabolomics screening platform can be used to rapidly generate phenotype-informed datasets and quantify synergy for combinatorial drug discovery.</p>
Rapid evolution of thermal tolerance and phenotypic plasticity in variable environments
<p>These are the data and code to go with "<strong>Rapid evolution of thermal tolerance and phenotypic plasticity in variable environments</strong>"</p> <p><strong>Figure 01 takes the following data/scripts:</strong></p> <p><a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/20210610_Thally02_Figure01_plot_and_stats.R">20210610_Thally02_Figure01_plot_and_stats.R </a> with <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/track_keeper.csv">track_keeper.csv </a> and <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/corr_Response%20growth%20.csv">corr_Response growth .csv </a>. These files contain growth rates per transfers for all selection environments throughout the experiment and growth rates in correlated environments during reciprocal transplants, respectively. </p> <p><strong>Figure 02 takes the following data/scripts:</strong></p> <p> </p> <p><a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/20210610_Thally02_Figure02_plot_and_stats.R">20210610_Thally02_Figure02_plot_and_stats.R </a> with <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/20161120_res_logis_t000.csv">20161120_res_logis_t000.csv </a>and <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/20161123_resloglint300.csv">20161123_resloglint300.csv .</a> These files contain the output of the shapes of the growth curves (i.e. information on lag time , growth at µmax, K etc) for all samples in all selection environments at t0 and t300, respectively</p> <p><strong>The remaining figures - position not clear at time of submission - take the following data/script. </strong></p> <p>For plasticity in FRRF data, the script 20181204_FRRF_plasticity.R takes the FRRF raw data contained in <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/allfvfmdata_thally_t300_t000.csv">allfvfmdata_thally_t300_t000.csv </a>. Extracted parameters are in files <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/CvaluesThally02.csv">CvaluesThally02.csv</a>, <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/psiPSI_slope_intercept.csv">psiPSI_slope_intercept.csv</a>, and <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/rP_extracted_values.csv">rP_extracted_values.csv </a> and can be analysed using the R script <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/extracted%20parameter%20plots.R">extracted parameter plots.R .</a> R script <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/FRRF%20visualisation%20only%20.R">FRRF visualisation only .R </a> is for visualisation only, as the title suggests. </p> <p>For comparing plasticity/growth , the data are in <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/20170327_giantbigtable.csv">20170327_giantbigtable.csv </a>, and can be visualised/analysed in <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/plast%20vs%20growth.R">plast vs growth.R </a></p> <p>In order to recreate the AMOVAS based on SNVs, use <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/all_variants_fixed-only_using_5x_depth_threshold.csv?versionId=01cbf6bf-fe16-4e7d-aae8-58c527596ebb">all_variants_fixed-only_using_5x_depth_threshold.cvs </a> with <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/amova%20thally02.R?versionId=e9c21378-ee37-4418-9ce1-76db821e645a">amova thally02.R </a></p> <p>For additional information, please contact elisa.schaum@uni-hamburg.de </p>
Phenotypic but no genetic adaptation in zooplankton 24 years after an abrupt +10°C climate change
<p>Data and scripts for Pais-Costa et al 2022</p>
Data and code from: Opposite, but insufficient, phenological responses to climate in two circumpolar seabirds: relative roles of phenotypic plasticity and selection
<p><span>The magnitude of climate change has been greatest in the Arctic, accelerating climate-induced shifts in phenology, but wildlife responses vary. Variation may be due to the relative importance of phenotypic plasticity or phenotypic selection.</span></p> <p><span>Here, we examine and contrast the environmental drivers of plasticity in breeding phenology of two circumpolar seabirds at their receding summer range limit using unique datasets of marked individuals </span><span>covering </span><span>25 and 30</span><span> years</span><span>. Based on prior knowledge of the local ecosystems, we predicted that climate would generate opposing patterns of plasticity in the two populations.</span></p> <p><span>Laying phenology of kittiwakes in the Gulf of Alaska was associated with a large-scale climate oscillation (Pacific Decadal Oscillation) while the Arctic-breeding murres adjusted </span><span>laying to sea-ice conditions. Kittiwakes laid earlier after experiencing colder climate about two years prior and laying dates did not advance over the study, but murres laid earlier when warmer climate led to earlier spring sea-ice break-up, and murre laying dates advanced by one week since 1990. Selection favoured earlier laying in both species.</span></p> <p><span>Both populations adjusted breeding phenology to environmental variation, but we anticipate opposing effects on phenology with continued climate change. Ice-constrained species can likely adapt to some extent because plasticity can provide the necessary shift to this physical barrier, although individuals were only able to adjust by ~one week while ice conditions advanced by over a month</span><span>. </span><span>In more temperate regions</span><span>,</span><span> where phenology is driven by bottom-up effects, plasticity and selection counteract one another leading to limited adaptability. We provide insights into the likely adjustments by Arctic marine animals to an increasingly warmer and ice-less summer.</span></p>
Fig. 4 in Phenotypic Diversities Of Four Populations Of Clarias Gariepinus (Siluriformes, Clariidae) Obtained From Ogun And Ondo State Waterbodies In South-Western Nigeria
Fig. 4. PCA loadings for meristics of Clarias gariepinus obtained from the four rivers.
Fig. 2 in Phenotypic Diversities Of Four Populations Of Clarias Gariepinus (Siluriformes, Clariidae) Obtained From Ogun And Ondo State Waterbodies In South-Western Nigeria
Fig. 2. PCA loadings for the morphometrics of Clarias gariepinus obtained from the four rivers.
Phenotypic and genotypic divergence of plant-herbivore interactions along an urbanization gradient
<p class="MsoNormal"><span>Urban environments provide challenging conditions for species survival, including increased temperatures, drought, and pollution. Species can deal with these conditions through evolution across generations or the immediate expression of phenotypic plasticity. The resulting phenotypic changes are key to the performance of species and their interactions with other species in the community. We here document patterns of herbivory in <em>Arabidopsis thaliana</em> along a rural-urban gradient, and tested the genetic background and ecological consequences of traits related to herbivore resistance. Aphid densities increased with urbanization levels along the gradient while plant size did not change. Offspring of urban mothers, raised under common garden conditions, were larger and had a decreased trichome density and seed set but a higher caterpillar (<em>Pieris brassicae</em>) tolerance. In contrast, no urban evolution was detected for defenses against aphids (<em>Myzus persicae</em>). Aphids reduced seed set more strongly in urban offspring, but this effect disappeared in second-generation plants. In general, urban adaptations as expressed in size and caterpillar tolerance were found, but these adaptations were associated with smaller inflorescences. The maternal effect on the response of seed set to aphid feeding demonstrates the relevance of intergenerational plasticity as a direct ecological consequence of herbivory. Our study demonstrates that the urban environment interacts with the plant's genotype and the extended phenotype as determined by ecological interactions.</span></p>
The phenotypic plasticity of an evolving digital organism
<p>Data set and R code used in the analysis reported in the manuscript entitled "<em>The phenotypic plasticity of an evolving digital organism</em>", which has been accepted in Proc. R. Open. Sci. for publication.</p>
Unraveling the roles of genotype and environment in the expression of plant defense phenotypes
<p>1. Phenotypic variability results from interactions between genotype and environment and is a major driver of ecological and evolutionary interactions. Measuring the relative contributions of genetic variation, the environment, and their interaction to phenotypic variation remains a fundamental goal of evolutionary ecology.</p> <p>2. In this study, we assess the question: How do genetic variation and local environmental conditions interact to influence phenotype within a single population? We explored this question using seed from a single population of common milkweed, <i>Asclepias syriaca</i>, in northern Michigan. We first measured resistance and resistance traits of 14 maternal lines in two common garden experiments (field and greenhouse) to detect genetic variation within the population. We carried out a reciprocal transplant experiment with three of these maternal lines to assess effects of local environment on phenotype. Finally, we compared the phenotypic traits measured in our experiments with the phenotypic traits of the naturally-growing maternal genets to be able to compare relative effect of genetic and environmental variation on naturally-occurring phenotypic variation. We measured defoliation levels, arthropod abundances, foliar cardenolide concentrations, foliar latex exudation, foliar carbon and nitrogen concentrations, and plant growth.</p> <p>3. We found a striking lack of correlation in trait expression of the maternal lines between the common gardens, or between the common gardens and the naturally-growing maternal genets, suggesting that environment plays a larger role in phenotypic trait variation of this population. We found evidence of significant genotype-by-environment interactions for all traits except foliar concentrations of nitrogen and cardenolide. Milkweed resistance to chewing herbivores was associated more strongly with the growing environment. We observed no variation in foliar cardenolide concentrations among maternal lines but did observe variation among maternal lines in foliar latex exudation.</p> <p>4. Overall, our data reveal powerful genotype-by-environment interactions on the expression of most resistance traits in milkweed.</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.