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”
Figure 2 from: Vázquez-López M, Morrone JJ, Ramírez-Barrera SM, López-López A, Robles-Bello SM, Hernández-Baños BE (2020) Multilocus, phenotypic, behavioral, and ecological niche analyses provide evidence for two species within Euphonia affinis (Aves, Fringillidae). ZooKeys 952: 129-157. https://doi.org/10.3897/zookeys.952.51785
Figure 2 Ultrametric phylogenetic tree obtained by BEAST using ND2, ODC, and GAPDH concatenated matrix. The rhombus node represents the calibration point 17.1104 My with a 95% HPD of (14.7743, 19.6278) (see methods), dark gray circle node represents the E. affinis origin and light gray circle node represents the break between E. a. godmani and E. a. affinis. Above the branch the diversification dates (My) and in brackets the 95% HPD. Below branch the number indicated the posterior probability. The green area corresponds to the period when lowland dry forests had a greater expansion in Western Mexico.
Using naturalistic incubation temperatures to demonstrate how variation in the timing and continuity of heat wave exposure influences phenotype
<p>Most organisms are exposed to bouts of warm temperatures during development, yet we know little about how variation in the timing and continuity of heat exposure influences biological processes. If heat waves increase in frequency and duration as predicted, it is necessary to understand how these bouts could affect thermally sensitive species, including reptiles with temperature-dependent sex determination (TSD). In a multi-year study using fluctuating temperatures, we exposed <i>Trachemys scripta</i> embryos to cooler, male-producing temperatures interspersed with warmer, female-producing temperatures (heat waves) that varied in either timing during development or continuity and then analyzed resulting sex ratios. We also quantified the expression of genes involved in testis differentiation (<i>Dmrt1</i>) and ovary differentiation (<i>Cyp19A1</i>) to determine how heat wave continuity affects the expression of genes involved in sexual differentiation. Heat waves applied during the middle of development produced significantly more females compared to heat waves that occurred just 7 days before or after this window, and even short gaps in the continuity of a heat wave decreased the production of females. Continuous heat exposure resulted in increased <i>Cyp19A1 </i>expression while discontinuous heat exposure failed to increase expression in either gene over a similar time course. We report that even small differences in the timing and continuity of heat waves can result in drastically different phenotypic outcomes. This strong effect of temperature occurred despite the fact that embryos were exposed to the same number of warm days during a short period of time, which highlights the need to study temperature effects under more ecologically relevant conditions where temperatures may be elevated for only a few days at a time. In the face of a changing climate, the finding that subtle shifts in temperature exposure result in substantial effects on embryonic development becomes even more critical.</p>
The Ubiquitin Ligase WWP1 Contributes to Shifts in Matrix Proteolytic Profiles and a Myocardial Aging Phenotype with Diastolic Heart Failure
<p><strong><em>Aims</em></strong>. Ubiquitylation is a key event that regulates protein turnover, and induction of the ubiquitin ligase E3 WWP1 has been associated with age. Left ventricular hypertrophy (LVH) commonly occurs as a function of age and can cause heart failure with a preserved ejection fraction (EF; HFpEF). We hypothesized that overexpression (O/E) of WWP1 in the heart would cause LVH as well as functional and structural changes consistent with the aging HFpEF phenotype.</p> <p><strong><em>Methods and Results.</em></strong> Global WWP1 O/E was achieved in mice (n=11) and echocardiography (40 MHz) performed to measure LV mass, EF, Doppler velocities (early-E, late/atrial-A), myocardial relaxation (E’), and isovolumetric relaxation time (IVRT) at 4, 6, and 8 weeks. Age matched wild type animals (n=15) were included as referent controls. LV EF was identical (60+1% vs 60+1%, p>0.90) with no difference in LV mass (67+3 vs 75+5, p>0.25) at 4 weeks. However, at 8 weeks of age, LV mass increased by over two-fold, E/A fell (impaired passive filling), and E/E’ was lower and IVRT prolonged (impaired LV relaxation) - all p<0.05. Collagen percent area increased by over two-fold and fibrillar collagen expression (rtPCR) by over 1.5 fold (p<0.05) with WWP1 O/E. WWP1 with an anti-WWP1 antibody could be identified in isolated cardiac fibroblasts with WWP1 increased by over two-fold in O/E fibroblasts (p<0.05).</p> <p><strong><em>Conclusion.</em></strong> Inducing WWP1 expression caused LVH, preserved systolic function, but impaired diastolic dysfunction, consistent with the HFpEF phenotype. Targeting the WWP1 pathway may be a novel therapeutic target for this intractable form of HF associated with aging.</p>
Data from: Oxidative stress experienced during early development influences the offspring phenotype
<p>Oxidative stress (OS) experienced early in life can affect an individual's phenotype. However, its consequences for the next generation remain largely unexplored. We manipulated the OS level endured by zebra finches (<i>Taeniopygia guttata</i>) during their development by transitorily inhibiting the synthesis of the key antioxidant glutathione ('early-high-OS'). The offspring of these birds and control parents were cross-fostered at hatching to enlarge or reduce its brood size. Independently of parents' early-life OS levels, the chicks raised in enlarged broods showed lower erythrocyte glutathione levels, revealing glutathione sensitivity to environmental conditions. Control ("early-low-OS") biological mothers produced females, not males, that attained a higher body mass when raised in a benign environment (i.e. the reduced brood). In contrast, biological mothers exposed to early-life OS produced heavier males, not females, when allocated in reduced broods. Early-life OS also affected the parental rearing capacity because 12d-old nestlings raised by a foster pair with both early-high-OS members grew shorter legs (tarsus) than chicks from other groups. The results indicate that environmental conditions during development can affect early glutathione levels, which may, in turn, influence the next generation through both pre- and postnatal parental effects. The results also demonstrate that early-life OS can constrain the offspring phenotype.</p>
Phylogeographic analysis of character displacement in feeding phenotypes of snail-feeding Acoptolabrus ground beetles: Morphological measurements
<p>Ecological character displacement predicts that interspecific resource competition results in greater trait divergence between species in sympatry than in allopatry. In this study, we characterize character displacement in 8 species of snail-feeding <i>Acoptolabrus</i> ground beetles (Coleoptera, Carabidae, genus <em>Carabus</em>) in the Far East. <i>Acoptolabrus</i> exhibit divergent feeding phenotypes, including species with a slender forebody for intruding large shells and species with stout heads and mandibles for crushing small shells. Distance measurements (in mm) deposited here are for evaluating body shape variation among 8 <em>Acoptolabrus</em> species.</p>
Data from: Ecology shapes epistasis in a genotype-phenotype-fitness map for stick insect colour
<p>Genetic interactions such as epistasis are widespread in nature and can shape evolutionary dynamics. Epistasis occurs due to non-linearity in biological systems, which can arise via cellular processes that convert genotype to phenotype and via selective processes that connect phenotype to fitness. Few studies in nature have connected genotype to phenotype to fitness for multiple potentially interacting genetic variants. Thus, the causes of epistasis in the wild remain poorly understood. Here, we show that epistasis for fitness is an emergent and predictable property of non-linear selective processes. We do so by measuring the genetic basis of cryptic colouration and survival in a field experiment with stick insects. We find that colouration exhibits a largely additive genetic basis, but with some effects of epistasis that enhance differentiation between colour morphs. In terms of fitness, different combinations of loci affecting colouration confer high survival in one host-plant treatment. Specifically, non-linear correlational selection for specific combinations of colour traits in this treatment drives the emergence of pairwise and higher-order epistasis for fitness at loci underlying colour. In turn, this results in a rugged fitness landscape for genotypes. In contrast, fitness epistasis was dampened in another treatment, where selection was weaker. Patterns of epistasis that are shaped by ecologically based selection could be common, and central to understanding fitness landscapes, the dynamics of evolution, and potentially other complex systems.</p>
Data from: High content imaging of unbiased chemical perturbations reveals that the phenotypic plasticity of the actin cytoskeleton is constrained
Although F-actin has a large number of binding partners and regulators, the number of phenotypic states available to the actin cytoskeleton is unknown. Here, we quantified 74 features defining F-actin and cellular morphology in >25 million cells after treatment with a library of 114,400 structurally diverse compounds. After reducing the dimensionality of these data, we found that only ~25 recurrent F-actin phenotypes emerged, each defined by distinct quantitative features that could be machine learned. We identified 2003 unknown compounds as inducers of actin-related phenotypes, including two that directly bind talin, a core regulator of integrin activity. Moreover, we observed that compounds with distinct molecular mechanisms could induce equivalent phenotypes and that initially divergent cellular responses could converge over time. These findings suggest a conceptual parallel between the actin cytoskeleton and gene regulatory networks; where the theoretical plasticity of interactions is nearly infinite, yet phenotypes observed in vivo are constrained into a limited subset of practicable configurations.
Data from: Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass
<p><span>Germplasm from perennial ryegrass (<i>Lolium perenne</i> L.) natural populations is useful for breeding because of its adaptation to a wide range of climates. Climate-adaptive genes can be detected from associations between genotype, phenotype and climate but an integrated framework for the analysis of these three sources of information is lacking.</span></p> <p><span>We used two approaches to identify adaptive loci in perennial ryegrass and their effect on phenotypic traits. First, we combined Genome-Environment Association (GEA) and GWAS analyses. Then, we implemented a new test based on a Canonical Correlation Analysis (CANCOR) to detect adaptive loci. Furthermore, we improved the previous perennial ryegrass gene set by <i>de novo</i> gene prediction and functional annotation of 39,967 genes.</span></p> <p><span>GEA-GWAS revealed eight outlier loci associated with both an environmental variable and a phenotypic trait. CANCOR retrieved 633 outlier loci associated with two climatic gradients, characterized by cold-dry vs mild-wet winter and long rainy season vs long summer, and pointed out traits putatively conferring adaptation at the extremes of these gradients. Our CANCOR test also revealed the presence of both polygenic and oligogenic climatic adaptations. Our gene annotation revealed that 374 of the CANCOR outlier loci were positioned within or close to a gene. Co-association networks of outlier loci revealed a potential utility of CANCOR for investigating the interaction of genes involved in polygenic adaptations.</span></p> <p><span>The CANCOR test provides an integrated framework to analyze adaptive genomic diversity and phenotypic responses to environmental selection pressures that could be used to facilitate the adaptation of plant species to climate change.</span></p>
Linkage maps and phenotypic data for Bainbridge et al. 2020
Limited genetic parallels underlie convergent evolution of quantitative pattern variation in mimetic butterflies <p>Mimetic systems allow us to address the question of whether the same genes control similar phenotypes in different species. Although widespread parallels have been found for major effect loci, much less is known about genes that control quantitative trait variation. In this study, we identify and compare the loci that control subtle changes in the size and shape of forewing pattern elements in two <i>Heliconius</i> butterfly co-mimics. We use quantitative trait locus (QTL) analysis with a multivariate phenotyping approach to map the variation in red pattern elements across the whole forewing surface of <i>Heliconius erato</i> and <i>Heliconius melpomene</i>. These results are compared to a QTL analysis of univariate trait changes, and show that our resolution for identifying small effect loci is somewhat improved with the multivariate approach, but also that different loci are detected with these different approaches. QTL likely corresponding to the known patterning gene <i>optix</i> were found in both species but otherwise, a remarkably low level of genetic parallelism was found. This lack of similarity indicates that the genetic basis of convergent traits may not be as predictable as assumed from studies that focus solely on Mendelian traits.</p>
Do heterogeneous seascapes of carbonate conditions across biogeographic breaks influence divergent phenotypic plasticity in natural populations?
<p><b>Aim:</b> Understanding how environmental variability influences stress tolerance, local adaptation, and phenotypic variation among populations is a key challenge for evolutionary ecology and climate change biology. Coastal biogeographic breaks are natural laboratories to explore this fundamental research question due to the contrasting environmental conditions experienced by natural populations across these regions.</p> <p><b>Location:</b> In the South East Pacific (SEP) coast a major break (30º-32ºS) is characterized by extreme natural variability in seawater carbonate chemistry parameters related to temporal and spatial dynamics in upwelling events. Mollusk species that reach their range limit at this zone are exposed to naturally acidified waters that can be corrosive and impact their calcification, physiology, and fitness, making them particularly prone to the effects of ocean acidification (OA). We investigated to what extent the interplay between biogeographic breaks and local variability of seawater carbonate conditions influences the tolerances and sensitivity of populations of the limpet <i>Scurria araucana</i> to OA.</p> <p><b>Methods: </b>During two years, we conducted field surveys of limpet populations at sites across the SEP break (27ºS, 30ºS and 32ºS). We collected individuals from each population to test for geographic differences in morphometric (e.g., total buoyancy weight, shell length) and physiological (e.g., oxygen consumption rate, cardiac activity, and thermal performance curves; TPC) responses to local conditions and to simulated OA scenarios.</p> <p><b>Results:</b> Analysis of the cardiac activity indicates that limpets from the central part of the break (30ºS) exhibit higher thermal performance compared to limpets from populations at both sides of the break. Thus, heterogeneous seascape of carbonate conditions and sea surface temperature across a biogeographic break in the SEP coast influence phenotypic differences among populations of this ecosystem engineer.</p> <p><b>Main Conclusions:</b> Natural environmental variation might be the underpinning driver of the high tolerance to OA evidenced by populations of the limpet <i>Scurria araucana </i>along the SEP.</p>
Data from: Ecotypes or phenotypic plasticity - the aquatic and terrestrial forms of Helosciadium repens (Apiaceae)
<p> </p> <p>• Morphological and ecological differences of two forms of Helosciadium repens are known and described in the literature: aquatic and terrestrial. However, their taxonomic status is currently unknown. The question whether they are genotypically adapted to specific environmental conditions or are those differences a result of phenotypic plasticity is addressed in this study.<br> • SSR and ISSR data were used to uncover genotypic differences. Data from drought stress experiments (system water content and relative water content of leaves) were used to evaluate the response to water as an environmental factor. The stomatal index of both forms grown under different water treatments was analysed.<br> • The principal component analysis of the SSR and ISSR data revealed no clustering that would correspond with ecotypes. The diversity parameters of the SSR data showed no significant differences. Contrary to the expected pattern, the aquatic populations showed a tendency towards heterozygosity while the terrestrial ones showed a bias towards homozygosity. Both forms responded similarly to the changes in water availability, with newly produced leaves after drought stress that were better adapted to repeated drought stress. Stomatal indices were higher in plants from aquatic habitats, but these difference disappeared when the plants were grown in soil.<br> • The observed responses indicate that the differences between forms are due to phenotypic plasticity.</p> <p> </p>
Figure 6. Thelogresponsecurvesfor R. darlingi. A in Phenotypic Convergence in Genetically Distinct Lineages of a Rhinolophus Species Complex (Mammalia, Chiroptera)
Figure 6. Thelogresponsecurvesfor R. darlingi. A) R. darlingi; (i) annual precipitation, (ii) precipitationof thewettestquarter, (iii) temperature seasonality when all locality records were used to build the model (temperature seasonality (Coefficient of Variation) is the standard deviation of the monthly temperature estimates expressed as a percentage of the mean of those estimates (i.e., the annual mean); and B) R. damarensis; (i) annual precipitation, (ii), precipitation of thewettest quarter, and (iii) mean temperature of the wettest quarter when all locality records were used to build the model. doi: 10.1371/journal. pone.0082614.g006
Figure 3 in Phenotypic Convergence in Genetically Distinct Lineages of a Rhinolophus Species Complex (Mammalia, Chiroptera)
Figure 3. Plot of canonical scores extracted by Discriminant Function Analysis from 24 skull and external parameters. Species abbreviations are the same as those in Table S1 (Supporting Information). Museum accession numbers relate to holotypes (See legend of Figure 1). doi: 10.1371/journal.pone.0082614.g003
Figure 2 in Phenotypic Convergence in Genetically Distinct Lineages of a Rhinolophus Species Complex (Mammalia, Chiroptera)
Figure 2. Bayesian consensus topology of Rhinolophus spp. based on cytochrome b. Values above nodes indicate Bayesian posterior probabilities (> 0.80) and below nodes report parsimony bootstrap support. Branch lengths are proportional to average number of substitutions per site. Divergence times (millions years ago, Mya) were estimated for three nodes of interest: node A = 4.8 Mya (95% HPD; 2.69–7.52), B = 9.68 Mya (95% HPD; 5.87–10.04), C = 10.51 Mya (95% HPD; 6.65–15.43). The split between the Hipposideridae (outgroup) and the Rhinolophidae together with fossil dates for R. ferrumequinum were used as calibration points; calibration points are indicated on the tree with an asterisk *. Sequences from the type localities for R. darlingi darlingi (TM2476) and R. darlingi damarensis (TM9474) are indicated on the tree in bold. The eastern R. darlingi darlingi subspecies forms a single clade together with R. fumigatus, R. eloquens and R. hildebrandti (blue) while R. damarensis damarensis, distributed in the western region of southern Africa, is composed of two very well supported clades that subdivide into northern and southern lineages (red) that diverged in the late Miocene. doi: 10.1371/journal. pone.0082614.g002
Figure 5 in Phenotypic Convergence in Genetically Distinct Lineages of a Rhinolophus Species Complex (Mammalia, Chiroptera)
Figure 5. Probability of occurrence for A) R. darlingi and B) R. damarensis in southern Africa. The predictions (Low-High) show a suitability gradient from 0–1 based on environmental suitability where 0 (low) indicates a zero probability of occurrence and 1 (high) indicates maximum probability of occurrence. White circles indicate locality records used for modelling the species. Dotted white triangles indicate locality records from where DNA sequences were obtained. Variables used in the final model include annual mean temperature, isothermality, temperature seasonality, temperature annual range, mean temperature of thewettest quarter, mean temperature of the driest quarter, mean temperature of the warmest quarter, mean temperature of the coldest quarter, annual precipitation, precipitation seasonality, precipitation of the wettest quarter, precipitation of the driest quarter, and precipitation of the coldest quarter.
Figure 1 in Phenotypic Convergence in Genetically Distinct Lineages of a Rhinolophus Species Complex (Mammalia, Chiroptera)
Figure 1. The distribution of R. darlingi (shaded areas) and sample localities (symbols). Squares = eastern R. darlingi; Circles (southern lineage) and triangles (northern lineage) = western R. darlingi (R. damarensis; Fig. 2). TM 9474 = holotype R. d. damarensis Namibia), TM 2476 = holotype of R. d. barbetonensis South Africa. doi: 10.1371/journal.pone.0082614.g001
Field-based individual plant phenotyping of herbaceous species by unmanned aerial vehicle
<p>1. Recent advances in Unmanned Aerial Vehicle (UAVs) and image processing have made high-throughput field phenotyping possible at plot/canopy level in the mass grown experiment. Such techniques are now expected to be used for individual level phenotyping in the single grown experiment.</p> <p>2. We found two main challenges of phenotyping individual plants in the single grown experiment: plant segmentation from weedy backgrounds and the estimation of complex traits that are difficult to measure manurally.</p> <p>3. In this study, we proposed a methodological framework for field-based individual plant phenotyping by UAV. Two contributions, which are weed elimination for individual plant segmentation, and complex traits (volume and outline) extraction, have been developed. The framework demonstrated its utility in the phenotyping of<i> Helianthus tuberosus</i>(Jerusalem artichoke), an herbaceous perennial plant species.</p> <p>4. The proposed framework can be applied to either small and large scale phenotyping experiments.</p>
Data from: Phenotypic plasticity in sexual communication signal of a noctuid moth
Variability within sex pheromone signalling systems is generally believed to be low because of strong stabilizing selection; yet the noctuid moth Heliothis subflexa (Hs) shows significant intraspecific variation. One possible explanation is that females may alter their sex pheromone blend depending on prevailing olfactory cues in the habitat, which we termed the "experience hypothesis". This could be adaptive if Hs females experiencing the pheromone of another species, Heliothis virescens (Hv), responded to reduce the frequency of heterospecific matings. We exposed Hs females to no pheromone, Hs pheromone, or Hv pheromone in the first 3 days of their adult lives. Hs females in the latter treatment produced signficantly more of the acetate Z11-16:OAc, which inhibits the attraction of Hv males. To our knowledge, this is the first study showing adaptive phenotypic plasticity in a moth sex pheromone, and suggests that behavioral differentiation may precede genetic divergence in the sexual signals of moths.
Links between prey assemblages and poison frog toxins: a landscape ecology approach to assess how biotic interactions affect species phenotypes
<p>Ecological studies of species pairs showed that biotic interactions promote phenotypic change and eco-evolutionary feedbacks. However, it is unclear how phenotypes respond to synergistic interactions with multiple taxa. We investigate whether interactions with multiple prey species explain spatially structured variation in the skin toxins of the Neotropical poison frog <i>Oophaga pumilio</i>. Specifically, we assess how dissimilarity (i.e., beta diversity) of alkaloid-bearing arthropod prey assemblages (68 ant species) and evolutionary divergence between frog populations (from a neutral genetic marker) contribute to frog poison dissimilarity (toxin profiles composed of 230 different lipophilic alkaloids sampled from 934 frogs at 46 sites). We find that models that incorporate spatial turnover in the composition of ant assemblages explain part of the frog alkaloid variation, and we infer unique alkaloid combinations across the range of <i>O. pumilio</i>. Moreover, we find that alkaloid variation increases weakly with the evolutionary divergence between frog populations. The analytical framework proposed here can be extended to other multi-trophic systems, coevolutionary mosaics, microbial assemblages, and ecosystem services.</p>
Data from: Phenotypic plasticity, but not adaptive tracking, underlies seasonal variation in post-cold hardening freeze tolerance of Drosophila melanogaster
<p> In temperate regions, an organism's ability to rapidly adapt to seasonally varying environments is essential for its survival. In response to seasonal changes in selection pressure caused by variation in temperature, humidity, and food availability, some organisms exhibit plastic changes in phenotype. In other cases, seasonal variation in selection pressure can rapidly increase the frequency of genotypes that offer survival or reproductive advantages under the current conditions. Little is known about the relative influences of plastic and genetic changes in short lived organisms experiencing seasonal environmental fluctuations. Cold hardening is a seasonally relevant plastic response in which exposure to cool, but nonlethal, temperatures significantly increases the organism's ability to later survive at freezing temperatures. In the present study, we demonstrate seasonal variation in cold hardening in <em>Drosophila melanogaster</em> and test the extent to which plasticity and adaptive tracking underlie that seasonal variation. We measured the post-cold hardening freeze tolerance of flies from outdoor mesocosms over the summer, fall, and winter. We bred outdoor mesocosm-caught flies for two generations in the lab and matched each outdoor cohort to an indoor control cohort of similar genetic background. We cold hardened all flies under controlled laboratory conditions and then measured their post-cold hardening freeze tolerance. Comparing indoor and field-caught flies and their laboratory-reared G1 and G2 progeny allowed us to determine the roles of seasonal environmental plasticity, parental effects, and genetic changes on cold hardening. We also tested the relationship between cold hardening and other factors, including age, developmental density, food substrate, presence of antimicrobials, and supplementation with live yeast. We found strong plastic responses to a variety of field- and lab-based environmental effects, but no evidence of seasonally varying parental or genetic effects on cold hardening. We therefore conclude that seasonal variation in post-cold hardening freeze tolerance results from environmental influences and not genetic changes. </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.