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.
3,339
datasets available to search
ShareScore release 0.9.0
Dataset results
3,339 results for “heterogeneities”
Data from: The relative importance of modeling site pattern heterogeneity versus partition-wise heterotachy in phylogenomic inference
Large taxa-rich genome-scale data sets are often necessary for resolving ancient phylogenetic relationships. But accurate phylogenetic inference requires that they are analyzed with realistic models that account for the heterogeneity in substitution patterns amongst the sites, genes and lineages. Two kinds of adjustments are frequently used: models that account for heterogeneity in amino acid frequencies at sites in proteins, and partitioned models that accommodate the heterogeneity in rates (branch lengths) among different proteins in different lineages (protein-wise heterotachy). Although partitioned and site-heterogeneous models are both widely used in isolation, their relative importance to the inference of correct phylogenies has not been carefully evaluated. We conducted several empirical analyses and a large set of simulations to compare the relative performances of partitioned models, site-heterogeneous models and combined partitioned site heterogeneous models. In general, site-homogeneous models (partitioned or not) performed worse than site heterogeneous, except in simulations with extreme protein-wise heterotachy. Furthermore, simulations using empirically-derived realistic parameter settings showed a marked long-branch attraction (LBA) problem for analyses employing protein-wise partitioning even when the generating model included partitioning. This LBA problem results from a small sample bias compounded over many single protein alignments. In some cases, this problem was ameliorated by clustering similarly-evolving proteins together into larger partitions using the PartitionFinder method. Similar results were obtained under simulations with larger numbers of taxa or heterogeneity in simulating topologies over genes. For an empirical Microsporidia test data set, all but one tested site-heterogeneous models (with or without partitioning) obtain the correct Microsporidia+Fungi grouping, whereas site-homogenous models (with or without partitioning) did not. The single exception was the fully partitioned site-heterogeneous analysis that succumbed to the compounded small sample LBA bias. In general unless protein-wise heterotachy effects are extreme, it is more important to model site-heterogeneity than protein-wise heterotachy in phylogenomic analyses. Complete protein-wise partitioning should be avoided as it can lead to a serious LBA bias. In cases of extreme protein-wise heterotachy, approaches that cluster similarly-evolving proteins together and coupled with site-heterogeneous models work well for phylogenetic estimation.
Data from: Lifetime fitness in wild baboons: tradeoffs and individual heterogeneity in quality
Understanding the evolution of life histories requires information on how life histories vary among individuals, and how such variation predicts individual fitness. Using complete life histories for females in a well-studied population of wild baboons, we tested two non-exclusive hypotheses about the relationships among survival, reproduction, and fitness: the quality hypothesis, which predicts positive correlations between life history traits, mediated by variation in resource acquisition, and the tradeoff hypothesis, which predicts negative correlations between life history traits, mediated by tradeoffs in resource allocation. In support of the quality hypothesis, we found that females with higher rates of offspring survival were themselves better at surviving. Further, after statistically controlling for variation in female quality, we found evidence for two types of tradeoffs: females who produced surviving offspring at a slower rate had longer lifespans than those who produced surviving offspring at a faster rate, and females who produced surviving offspring at a slower rate had a higher overall proportion of offspring survive infancy than females who produced surviving offspring at a faster rate. Importantly, these tradeoffs were evident even when accounting for: (i) the influence of offspring survival on maternal birth rate, (ii) the dependence of offspring survival on maternal survival, and (iii) potential age-related changes in birth rate and/or offspring survival. Our results shed light on why tradeoffs are evident in some populations, while variation in individual quality masks tradeoffs in others.
Data from: Lizards paid a greater opportunity cost to thermoregulate in a less heterogeneous environment
The theory of thermoregulation has developed slowly, hampering efforts to predict how individuals can buffer climate change through behaviour. Mixed results of field and laboratory experiments underscore the need to test hypotheses about thermoregulation explicitly, while measuring costs and benefits in different thermal landscapes. We simulated body temperature and energy expenditure of a virtual lizard that either thermoregulates optimally or thermoconforms in a landscape of either low or high quality (one or four basking sites, respectively). We then compare the predicted values in each landscape with the observed values for real lizards in experimental arenas. Lizards thermoregulated more accurately in the high-quality landscape than they did on the low-quality landscape, albeit only slightly so, but spent similar amounts of energy in these landscapes. Basking, rather than shuttling between heat sources, accounted for the majority of the energy consumed in both landscapes. These results did not support the predictions of our model. In the low-quality landscape, real lizards thermoregulated intensely despite the potential to save energy by thermoconforming. In the high-quality landscape, lizards moved more than expected, suggesting that lizards explored their surroundings despite being able to thermoregulate without doing so. Our results suggest that non-energetic benefits drive thermoregulatory behaviour in costly environments, despite the missed opportunities arising from thermoregulation. We propose that energetic costs associated with thermoregulatory movement will become substantial in homogeneous environments such as flat plains and dense forests. The theory of thermoregulation should incorporate these aspects if biologists wish to predict responses of ectotherms to changing climates and habitats.
Data from: Host use dynamics in a heterogeneous fitness landscape generates oscillations in host range and diversification
Colonization of novel hosts is thought to play an important role in parasite diversification, yet little consensus has been achieved about the macroevolutionary consequences of changes in host use. Here we offer a mechanistic basis for the origins of parasite diversity by simulating lineages evolved in silico. We describe an individual-based model in which (i) parasites undergo sexual reproduction limited by genetic proximity, (ii) hosts are uniformly distributed along a one-dimensional resource gradient, and (iii) host use is determined by the interaction between the phenotype of the parasite and a heterogeneous fitness landscape. We found two main effects of host use on the evolution of a parasite lineage. First, the colonization of a novel host allowed parasites to explore new areas of the resource space, increasing phenotypic and genotypic variation. Second, hosts produced heterogeneity in the parasite fitness landscape, which led to reproductive isolation and therefore, speciation. As a validation of the model, we analyzed empirical data from Nymphalidae butterflies and their host plants. We then assessed the number of hosts used by parasite lineages and the diversity of resources they encompass. In both simulated and empirical systems, host diversity emerged as the main predictor of parasite species richness.
Data from: Heterogeneous models place the root of the placental mammal phylogeny
Heterogeneity among life traits in mammals has resulted in considerable phylogenetic conflict, particularly concerning the position of the placental root. Layered upon this are gene- and lineage-specific variation in amino acid substitution rates and compositional biases. Life trait variations that may impact upon mutational rates are longevity, metabolic rate, body size and germ line generation time. Over the past 12 years, three main conflicting hypotheses have emerged for the placement of the placental root. These hypotheses place: the Atlantogenata (common ancestor of Xenarthra plus Afrotheria), the Afrotheria, or the Xenarthra as the sister group to all other placental mammals. Model adequacy is critical for accurate tree reconstruction and by failing to account for these compositional and character exchange heterogeneities across the tree and dataset, previous studies have not provided a strongly supported hypothesis for the placental root. For the first time, models that accommodate both tree and dataset heterogeneity have been applied to mammal data. Here we show the impact of accurate model assignment and the importance of datasets in accommodating model parameters while maintaining the power to reject competing hypotheses. Through these sophisticated methods, we demonstrate the importance of model adequacy, dataset power and provide strong support for the Atlantogenata over other competing hypotheses for the position of the placental root.
Data from: Gametic selection, developmental trajectories, and extrinsic heterogeneity in Haldane's rule
Deciphering the genetic and developmental causes of the disproportionate rarity, inviability and sterility of hybrid males, Haldane's rule, is important for understanding the evolution of reproductive isolation between species. Moreover, extrinsic and pre-zygotic factors can contribute to the magnitude of intrinsic isolation experienced between species with partial reproductive compatibility. Here we use the nematodes Caenorhabditis briggsae and C. nigoni to quantify the sensitivity of hybrid male viability to extrinsic temperature and developmental timing, and test for a role of mito-nuclear incompatibility as a genetic cause. We demonstrate that hybrid male inviability manifests almost entirely as embryonic, not larval, arrest and is maximal at the lowest rearing temperatures, indicating an intrinsic-by-extrinsic interaction to hybrid inviability. Crosses using mitochondrial substitution strains that have reciprocally introgressed mitochondrial and nuclear genomes show that mito-nuclear incompatibility is not a dominant contributor to post-zygotic isolation and does not drive Haldane's rule in this system. Crosses also reveal that competitive superiority of X-bearing sperm provides a novel means by which post-mating pre-zygotic factors exacerbate the rarity of hybrid males. These findings highlight the important roles of gametic, developmental, and extrinsic factors in modulating the manifestation of Haldane's rule.
Data from: Environmental heterogeneity generates opposite gene-by-environment interactions for two fitness-related traits within a population
Theory predicts that environmental heterogeneity offers a potential solution to the maintenance of genetic variation within populations, but empirical evidence remains sparse. The livebearing fish Xiphophorus variatus exhibits polymorphism at a single locus, with different alleles resulting in up to five distinct melanistic "tailspot" patterns within populations. We investigated the effects of heterogeneity in two ubiquitous environmental variables (temperature and food availability) on two fitness-related traits (upper thermal limits and body condition) in two different tailspot types (wildtype and upper cut crescent). We found gene-by-environment (GxE) interactions between tailspot type and food level affecting upper thermal limits (UTL), as well as between tailspot type and thermal environment affecting body condition. Exploring mechanistic bases underlying these GxE patterns, we found no differences between tailspot types in hsp70 gene expression despite significant overall increases in expression under both thermal and food stress. Similarly, there was no difference in routine metabolic rates between the tailspot types. The reversal of relative performance of the two tailspot types under different environmental conditions revealed a mechanism by which environmental heterogeneity can balance polymorphism within populations through selection on different fitness-related traits.
Data for: Density dependence and spatial heterogeneity limit the population growth rate of invasive pines at the landscape scale
<p class="MsoBodyText"><span><span><span><span><span><span><span><span><span><span><span>Determining population growth across large scales is difficult because it is often impractical to collect data at large scales and over long timespans. Instead, the growth of a population is often only measured at a small, plot-level scale and then extrapolated to derive a mean field estimate. However, this approach is prone to error since it simplifies spatial processes such as the neighbourhood effects of density and dispersal. We present a novel approach that estimates how spatial processes derived from the effects of density and dispersal affect population growth between plot scales and landscape scales. The method is based on a scale transition theory and calculates a transition term to measure the spatial scaling of population growth, which we extend to unstable, expanding populations in order to assess whether landscape-scale population dynamics are different from those estimated at smaller spatial scales. We illustrate this approach using aerial imagery of eight locations in New Zealand experiencing non-native pine invasions. Analyses examined the dynamics at a plot scale (1 hectare) and compared this to estimates across entire landscapes (between 24 and 1600 hectares), in several cases for more than one time period. We used a Bayesian spatial random effects model to examine population growth and to account for neighbourhood effects and dispersal between plots in a rapidly changing system. </span></span></span></span></span></span></span></span></span></span></span></p> <p class="MsoBodyText"><span><span><span><span><span><span><span><span><span><span><span>We found that the estimates of the scale transition term were typically 10-25% of the mean field estimates, which led to mean field estimates of population growth extrapolated from plots being considerably higher than landscape estimates. The approach we have developed will not only have applications for predicting the populations' growth of invasive species, but also for studies examining the scaling of landscape-scale phenomena.</span></span></span></span></span></span></span></span></span></span></span></p>
Is shallow convection sensitive to environmental heterogeneities?
This dataset contains the data files that underlie the four figures that are included in the paper entitled "Is shallow convection sensitive to environmental heterogeneities?" (please see the "Related Links" section to access the paper). The data represents analysis of 3D large eddy simulation. These are either profiles (e.g., the cloud fraction) or evolutions (e.g., the mean liquid water path) of various model-predicted quantities. These typically include several dozen levels each. One figure includes 2D cross sections of predicted cloud water mixing ratio. The abstract of the paper is included as follows: "The key assumption underlying convection parameterizations is that rising plumes develop in a horizontally-homogeneous environment. With this in mind, we investigate the impact of environmental cloud-layer heterogeneities on shallow convection using large-eddy simulation that applies a master-slave methodology. In the master-slave approach, two independent sets of thermodynamic variables (master and slave) are driven by one dynamics (coupled with the master) to remove the impact of internal variability of the dynamical system considered. The two thermodynamic sets include either a realistic heterogeneous environment or an environment that is homogenized outside clouds. It is important that homogenization also excludes subsiding shells surrounding cumulus clouds. The results show a small impact of the homogenization since the cloud field properties differ little between the master and slave thermodynamic sets. The physical explanation highlights the role of the subsiding shell shielding a shallow cumulus cloud from its environment."
Fig. 2. A in The Extent of Seed Predation by Bruchine Beetles (Coleoptera: Chrysomelidae: Bruchinae) in a Heterogeneous Landscape in Southeastern Brazil
Fig. 2. A dead Gibbobruchus individual (arrow) enclosed within a Bauhinia forficata seed.
Data for manuscript "Integrated microwave photonic notch filter using a heterogeneously integrated Brillouin and active-silicon photonic circuit"
<p>Experimental data and scripts to plot results for manuscript "Integrated microwave photonic notch filter using a heterogeneously integrated Brillouin and active-silicon photonic circuit"</p>
Developmental Basis of SHH Medulloblastoma Heterogeneity (mIHC Data)
Open the record for dataset details and reuse information.
Unveiling Heterogeneity in Individual Thresholds: Validation Using Urinary Prostaglandin D2 Metabolite in Food Allergy Reactions
Open the record for dataset details and reuse information.
Accurate Spatial Heterogeneity Dissection and Gene Regulation Interpretation for Spatial Transcriptomics using Dual Graph Contrastive Learning
Open the record for dataset details and reuse information.
Complex Isomerism Influencing the Texture Properties of Organometallic [Cu(salen)] Porous Polymers: Paramagnetic Solid-State NMR Characterization and Heterogeneous Catalysis
<p>Raw data from NMR experiments and numerical simulations.</p>
Joint identification of groundwater contamination source and heterogeneous hydrogeological parameters in LNAPL contaminated site based on deep convolutional encoder-decoder neural networks
Open the record for dataset details and reuse information.
Data from: Assessing urban-scale spatiotemporal heterogeneous metro station coverage using multi-source mobility data
Open the record for dataset details and reuse information.
How fern and fern allies respond to heterogeneous habitat
The Yuanjiang dry-hot valley features hot and dry climate, low vegetation and soil degradation. It had lush vegetation in the past, but has become degraded in recent decades. Understanding the interrelationship between species and the habitat is necessary to explain this change. In this study, a link between fern and fern allies - a group that is hypersensitive to environmental factors and their circumstances is constructed. Intensive transects and plots were designed to be proxies for extant fern and fern allies, and their habitats. Fifty years of meteorological records of precipitation and temperature along altitude and river running direction (latitudinal) were employed. Alpha and beta diversity are used to access diversity. Species_estimated, Singletons, Uniques, ACE, ICE, and Chao2, which associate to abundance and rarity, are subscribed to the correlation between fern and fern allies, and their ecosystem. Eight species, <i>Selaginella pseudopaleifera, Aleuritopteris squamosa, Adiantum malesianum, Pteris vittata, Davallia trichomanoides, Sinephropteris delavayi, Selaginella jugorum, </i>and<i> Lygodium japonicum </i>are used as indicators of a typical xeric and sun-drying habitat. The results indicate (1) accompanied by dramatically shrinking habitats, fern and fern allies are in very low diversity and abundance, whereas the rarity is relatively high; (2) for fern and fern allies, environmental factors are positive when altitude goes up; and (3) eight indicator species are latitudinally correlated with fern and fern allies along the river running direction.
Portfolio effect and asynchrony as drivers of stability in plant-pollinator communities along a gradient of landscape heterogeneity
<p>Understanding how pollination services can be maintained in increasingly anthropogenic landscapes is a current challenge for basic and applied ecology. The stability of plant-pollinator communities might increase in heterogeneous landscapes with a high diversity of species and alternative habitats, both through increased portfolio effect (property of communities to fluctuate less than the sum of its counterparts) and decreased synchrony (coincident changes in species abundance). However, how these drivers of stability (portfolio effect and synchrony) vary along land-use gradients remains largely unknown. Using independent samplings for plants, pollinators, and their interactions in Mediterranean communities along a gradient of landscape heterogeneity, we assessed the relationships between within-year stability and its drivers; and between the drivers of stability, landscape heterogeneity, and species diversity. Besides, we evaluated the relationships between the drivers of interaction stability and the structure of mutualistic networks (modularity, nestedness, connectance). Stability increased with larger portfolio effects and asynchronies. Interaction stability was positively related to pollinator stability, but not to plant stability. Landscape evenness increased the stability of plants, pollinators, and their interactions, through increased portfolio effects. However, for plants and pollinators, the landscape effect was detected at a smaller scale (1-km) than for interactions (2-km); and for pollinators and interactions, the effect was only evident from medium-to-high levels of landscape evenness. Temporal synchrony of species/pairwise interactions was an important driver of stability, tightly linked to species/interaction diversity. More asynchronous communities showed a larger portfolio effect and were also those with higher species evenness for all plants, pollinators, and their interactions; while synchrony was also weakly positively related to species richness for plants. Interestingly, more modular network structures conferred enhanced overall community stability, through higher portfolio effect and asynchrony. Preserving diverse communities within the heterogeneous Mediterranean landscapes helps maintain the stability of pollination services, both through increased asynchrony and portfolio effect.</p>
The impact of chlorine chemistry combined with heterogeneous N2O5 reactions on air quality in China
<p>This is the revised GEOS-Chem code for all sensitivity simulations in the paper.</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.