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.
99
datasets available to search
ShareScore release 0.9.0
Dataset results
99 results for “scale selection”
Data from: Natural selection drives emergent genetic homogeneity in a century-scale experiment with barley
Open the record for dataset details and reuse information.
Data from: Temporal scale of habitat selection for large carnivores: Balancing energetics, risk and finding prey
Open the record for dataset details and reuse information.
Data from: How characteristic is the species characteristic selection scale?
The importance of framing investigations of organism-environment relationships to interpret patterns at relevant spatial scales is increasingly recognized. However, most research related to environmental relationships is single-scaled, implicitly or explicitly assuming that a 'species characteristic selection scale' exists. We tested the premise that a single characteristic scale exists to understand species-environment relationships within species by asking 1) what are the characteristic scales of species' relationships with environmental predictors, and 2) is within-species, cross-predictor consistency in characteristic scales a general phenomenon. Nebraska, USA. 2016 Birds We used data from 86 species at >500 locations to build hierarchical N-mixture models relating species abundance to landcover variables. By incorporating Bayesian latent indicator scale selection, we identified the spatial scales that best explain species-environment relationships with each landcover predictor. We quantify the extent of cross-predictor consistency in characteristic scales, and contrast this to the expectation given a single species' characteristic scale. We found no evidence for a characteristic spatial scale explaining all abundance-environment relationships within species, rather we found substantial variation in scale-dependence across multiple environmental attributes. Furthermore, 33% of species displayed evidence of multiple important scales within environmental attributes. Within species there is little evidence for a single characteristic scale of environmental relationships and considerable variation in species' scale–dependencies. Because species may respond to multiple environmental attributes at different spatial scales, or single environmental attributes at multiple scales, we caution against any unoptimized single-scale studies. Our results demonstrate that until a framework is developed to predict the scales at which species respond to environmental characteristics, multi-scale investigations must be performed to identify and account for multiscale dependencies. Natural selection acting on species' response to distinct environmental attributes, rather than natural selection acting on species' perception of spatial scales per se, may have shaped patterns of scale-dependency and is an area ripe for investigation.
Short-chain cello-oligosaccharides: Intensification and scale-up of their enzymatic production and selective growth promotion among probiotic bacteria
<p>We provide here the underlying data of the scientific publication "Short-chain cello-oligosaccharides: Intensification and scale-up of their enzymatic production and selective growth promotion among probiotic bacteria". Please find the abstract below:</p> <p>Short-chain cello-oligosaccharides (COS; degree of polymerization, DP≤6) are promising water-soluble dietary fibers. An efficient approach to their bottom-up synthesis is from sucrose and glucose using glycoside phosphorylases. Here, we show intensification and scale up (20 mL; gram scale) of COS production to 93 g/L product and in 82 mol % yield from sucrose (0.5 M). The COS were comprised of DP 3 (33 wt %), DP 4 (34 wt %), DP 5 (24 wt %) and DP 6 (9 wt %) and involved minimum loss (≤10 mol %) to insoluble fractions. After isolation (≥95% purity; ≥90% yield), the COS were examined for growth promotion of probiotic strains. Benchmarked against inulin, trans-galacto-oligosaccharides and cellobiose, COS showed up to 4.1-fold stimulation of cell density for <em>Clostridium butyricum</em>, <em>Lactococcus lactis</em> subsp.<em>lactis</em>, <em>Lactobacillus paracasei</em> subsp. <em>paracasei</em> and <em>Lb. rhamnosus</em> but were less efficient with <em>Bifidobacterium</em> sp. This study shows the COS as selectively functional carbohydrates with prebiotic potential and demonstrates their efficient enzymatic production.</p>
Data from: Fecundity selection on ornamental plumage colour differs between ages and sexes and varies over small spatial scales
Avian plumage colours are some of the most conspicuous sexual ornaments, and yet standardized selection gradients for plumage colour have rarely been quantified. We examined patterns of fecundity selection on plumage colour in blue tits (Cyanistes caeruleus L.). When not accounting for environmental heterogeneity, we detected relatively few cases of selection. We found significant disruptive selection on adult male crown colour and yearling female chest colour and marginally nonsignificant positive linear selection on adult female crown colour. We discovered no new significant selection gradients with canonical rotation of the matrix of nonlinear selection. Next, using a long-term data set, we identified territory-level environmental variables that predicted fecundity to determine whether these variables influenced patterns of plumage selection. The first of these variables, the density of oaks within 50 m of the nest, influenced selection gradients only for yearling males. The second variable, an inverse function of nesting density, interacted with a subset of plumage selection gradients for yearling males and adult females, although the strength and direction of selection did not vary predictably with population density across these analyses. Overall, fecundity selection on plumage colour in blue tits appeared rare and inconsistent among sexes and age classes.
Data from: Drift versus selection as drivers of phenotypic divergence at small spatial scales: the case of Belgjarskógur threespine stickleback
Divergence in phenotypic traits is facilitated by a combination of natural selection, phenotypic plasticity, gene flow and genetic drift, whereby the role of drift is expected to be particularly important in small and isolated populations. Separating the components of phenotypic divergence is notoriously difficult, particularly for multivariate phenotypes. Here we assessed phenotypic divergence of threespine stickleback (Gasterosteus aculeatus) across 19 semi-interconnected ponds within a small geographic region (~7.5 km2) using multivariate comparisons of phenotypic divergence (PST) neutral genetic (FST) and environmental (EST) variation. We found phenotypic divergence across the ponds in a suite of functionally relevant phenotypic traits, including feeding, defense and swimming traits and body shape (geometric morphometric). Comparisons of PSTs with FSTs suggest that phenotypic divergence is predominantly driven by neutral or stabilizing selection, whereas phenotypic divergence in defensive traits is in accordance with divergent selection. Comparisons of population pairwise PSTs with ESTs suggest that phenotypic divergence in swimming traits is correlated with prey availability, whereas there were no clear associations between phenotypic divergence and environmental difference in the other phenotypic groups. Overall, our results suggest that phenotypic divergence of these small populations at small geographic scales is largely driven by neutral processes (gene flow, drift), although environmental determinants (natural selection or phenotypic plasticity) may play a role.
Data from: Selection outweighs drift at a fine scale: lack of MHC differentiation within a family living lizard across geographically close but disconnected rocky outcrops
The highly polymorphic genes of the major histocompatibility complex (MHC) are involved in disease resistance, mate choice, and kin recognition. Therefore, they are widely used markers for investigating adaptive variation. Although selection is the key driver, gene flow and genetic drift also influence adaptive genetic variation, sometimes in opposing ways and with consequences for adaptive potential. To further understand the processes that generate MHC variation, it is helpful to compare variation at the MHC with that at neutral genetic loci. Differences in MHC and neutral genetic variation are useful for inferring the relative influence of selection, gene flow and drift on MHC variation. To date, such investigations have usually been undertaken at a broad spatial scale. Yet, evolutionary and ecological processes can occur at a fine spatial scale, particularly in small or fragmented populations. We investigated spatial patterns of MHC variation among three geographically close, naturally discrete, sampling sites of Egernia stokesii, an Australian lizard. The MHC of E. stokesii has recently been characterised and there is evidence for historical selection on the MHC. We found E. stokesii MHC weakly differentiated among sites compared to microsatellites, suggesting selection, acting similarly at each site, has outweighed any effects of low gene flow or of genetic drift on E. stokesii MHC variation. Our findings demonstrate the strength of selection in shaping patterns of MHC variation or consistency at a fine spatial scale.
Data from: Genomic signatures of fine‐scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis, and immune defence‐related genes
Elucidating the genetic basis of adaptation to the local environment can improve our understanding of how the diversity of life has evolved. In this study we used a dense SNP array to identify candidate loci potentially underlying fine-scale local adaptation within a large Atlantic salmon (Salmo salar) population. By combining outlier, gene–environment association, and haplotype homozygosity analyses, we identified multiple regions of the genome with strong evidence for diversifying selection. Several of these candidate regions had previously been identified in other studies, demonstrating that the same loci could be adaptively important in Atlantic salmon at sub-drainage, regional and continental scales. Notably, we identified signals consistent with local selection around genes associated with variation in sexual maturation, energy homeostasis, and immune defence. These included the large-effect age-at-maturity gene vgll3, the known obesity gene mc4r, and major histocompatibility complex II. Most strikingly, we confirmed a genomic region on Ssa09 that was extremely differentiated among subpopulations, and that is also a candidate for local selection over the global range of Atlantic salmon. This region co-localized with a haplotype strongly associated with spawning ecotype in sockeye salmon (Oncorhynchus nerka), with circumstantial evidence that the same gene (six6) may be the selective target in both cases. The phenotypic effect of this region in Atlantic salmon remains cryptic, although allelic variation is related to upstream catchment area and co-varies with timing of the return spawning migration. Our results further inform management of Atlantic salmon and open multiple avenues for future research.
Data from: Environment-dependent variation in selection on life history across small spatial scales
Variation in life-history traits is ubiquitous, even though genetic variation is thought to be depleted by selection. One potential mechanism for the maintenance of trait variation is spatially-variable selection. We explored spatial variation in selection in the field for a colonial marine invertebrate that shows phenotypic differences across a depth gradient of only three meters. Our analysis included life-history traits relating to module size, colony growth and phenology. Directional selection on colony growth varied in strength across depths, while module size was under directional selection at one depth but not the other. Differences in selection may explain some of the observed phenotypic differentiation among depths for one trait but not another: instead, selection should actually erode the differences observed for this trait. Our results suggest selection is not acting alone to maintain trait variation within and across environments in this system.
Data from: How sexual and natural selection shape sexual size dimorphism: evidence from multiple evolutionary scales
1. Sexual size dimorphism (SSD) is pervasive across taxa and reflects differences in the effects of sexual and natural selection on body size between the sexes. However, disentangling the complex eco-evolutionary interactions between these two mechanisms remains a major challenge for biologists. 2. Here, we combine macro-evolutionary (between-species), local evolutionary (between-population) and fine-scale evolutionary (within-population) patterns of SSD to explore how sexual and natural selection interact and shape the evolution of SSD in Australian agamid lizards. Australian agamid lizards show substantial variation in SSD, ecological traits and species density making them an ideal study system to address this question. 3. At the between-species level, population density, ecological generalism and mean species size significantly predict SSD variation, however, only ecological generalism was found to significantly explain variation in larger than average male-biased SSD. At the population level, density positively correlated with SSD in native habitats, but not city park habitats. Last, agonistic behaviour acted as the primary driver of SSD at the within-population level. 4. Our results indicate how sexual and natural selection can interact at different evolutionary scales, and show the importance of considering both selective mechanisms when investigating patterns of SSD.
Data from: The relationship between dN/dS and scaled selection coefficients
Numerous computational methods exist to assess the mode and strength of natural selection in protein-coding sequences, yet how distinct methods relate to one another remains largely unknown. Here, we elucidate the relationship between two widely-used phylogenetic modeling frameworks: dN/dS models and mutation-selection (MutSel) models. We derive a mathematical relationship between dN/dS and scaled selection coefficients, the focal parameters of MutSel models, and use this relationship to gain deeper insight into the behaviors, limitations, and applicabilities of these two modeling frameworks. We prove that, if all synonymous changes are neutral, standard MutSel models correspond to dN/dS < 1. However, if synonymous codons differ in fitness, dN/dS can take on arbitrarily high values even if all selection is purifying. Thus, the MutSel modeling framework cannot necessarily accommodate positive, diversifying selection, while dN/dS cannot distinguish between purifying selection on synonymous codons and positive selection on amino acids. We further propose a new benchmarking strategy of dN/dS inferences against MutSel simulations and demonstrate that the widely-used Goldman-Yang-style dN/dS models yield substantially biased dN/dS estimates on realistic sequence data. By contrast, the less frequently used Muse-Gaut-style models display much less bias. Strikingly, the least-biased and most-precise dN/dS estimates are never found in the models with the best fit to the data, measured through both AIC and BIC scores. Thus, selecting models based on goodness-of-fit criteria can yield poor parameter estimates if the models considered do not precisely correspond to the underlying mechanism that generated the data. In conclusion, establishing mathematical links among modeling frameworks represents a novel, powerful strategy to pinpoint previously unrecognized model limitations and strengths.
Data from: Density-dependent habitat selection of spawning Chinook salmon: broad scale evidence and implications
1. An extensive body of theory suggests that density-dependent habitat selection drives many fundamental ecological processes. The ideal free distribution and the ideal despotic distribution make contrasting predictions about the effect of total population size on relative abundances among habitats. Empirical assessment of these habitat selection models is uncommon because data must be collected over large temporal and spatial scales. 2. I ask whether fluctuation in Chinook salmon (Oncorhynchus tshawytscha) spawner population size through time leads to different relative densities over space. 3. Twenty six years of monitoring data on spawning Chinook salmon across the entire coast of Oregon, USA, were used to evaluate models that make contrasting statements about the interactions of a latent population abundance parameter with physical habitat characteristics. 4. There is strong information-theoretic support for models that include terms that allow the spatial variation in density to change as population size changes through time. Analysis of the best model reveals nonlinear isodars, which suggests a "despotic" or "preemptive" distribution of individuals across habitats, indicating that dominant or early arriving individuals exclude others from breeding sites. 5. This finding has implications for genetic dynamics, population dynamics, and conservation metrics of these highly valued fish. The novel application of modeling techniques used here to assess mechanisms of habitat selection from observational data can be used in the emerging field of eco-evolutionary dynamics.
Data from: Applications of random forest feature selection for fine-scale genetic population assignment
Genetic population assignment used to inform wildlife management and conservation efforts requires panels of highly informative genetic markers and sensitive assignment tests. We explored the utility of machine-learning algorithms (random forest, regularized random forest, and guided regularized random forest) compared with FST ranking for selection of single nucleotide polymorphisms (SNP) for fine-scale population assignment. We applied these methods to an unpublished SNP dataset for Atlantic salmon (Salmo salar) and a published SNP data set for Alaskan Chinook salmon (Oncorhynchus tshawytscha). In each species, we identified the minimum panel size required to obtain a self-assignment accuracy of at least 90% using each method to create panels of 50-700 markers Panels of SNPs identified using random forest-based methods performed up to 7.8 and 11.2 percentage points better than FST-selected panels of similar size for the Atlantic salmon and Chinook salmon data, respectively. Self-assignment accuracy ≥90% was obtained with panels of 670 and 384 SNPs for each dataset, respectively, a level of accuracy never reached for these species using FST-selected panels. Our results demonstrate a role for machine-learning approaches in marker selection across large genomic datasets to improve assignment for management and conservation of exploited populations.
Data from: Ecological segregation in a small mammal hybrid zone: habitat-specific mating opportunities and selection against hybrids restrict gene flow on a fine spatial scale
The degree to which closely related species interbreed is determined by a complex interaction of ecological, behavioral, and genetic factors. We examine the degree of interbreeding between two woodrat species, Neotoma bryanti and N. lepida, at a sharp ecological transition. We identify the ecological association of each genotypic class, assess the opportunity for mating between these groups, and test whether they have similar patterns of year-to-year persistence on our study site. We find that 13% of individuals have a hybrid signature but that the two parental populations and backcrosses are highly segregated by habitat type and use. Also, we find that adult hybrids are comparable to parental types in terms of year-to-year persistence on our site but that, among juveniles, significantly fewer hybrids reach adulthood on site compared to their purebred counterparts. Our analyses show that this hybrid zone is maintained by occasional nonassortative mating coupled with hybrid fertility, but that these factors are balanced by lower apparent survival of juvenile hybrids and habitat-based preference or selection that limits heterospecific mating while promoting backcrossing to habitat-specific genotypes. This system presents a novel example of the role that sharp resource gradients play in reproductive isolation and the potential for genetic introgression.
Data from: The population genomic signature of environmental selection in the widespread insect-pollinated tree species Frangula alnus at different geographical scales
The evaluation of the molecular signatures of selection in species lacking an available closely related reference genome remains challenging, yet it may provide valuable fundamental insights into the capacity of populations to respond to environmental cues. We screened 25 native populations of the tree species Frangula alnus subsp. alnus (Rhamnaceae), covering three different geographical scales, for 183 annotated single-nucleotide polymorphisms (SNPs). Standard population genomic outlier screens were combined with individual-based and multivariate landscape genomic approaches to examine the strength of selection relative to neutral processes in shaping genomic variation, and to identify the main environmental agents driving selection. Our results demonstrate a more distinct signature of selection with increasing geographical distance, as indicated by the proportion of SNPs (i) showing exceptional patterns of genetic diversity and differentiation (outliers) and (ii) associated with climate. Both temperature and precipitation have an important role as selective agents in shaping adaptive genomic differentiation in F. alnus subsp. alnus, although their relative importance differed among spatial scales. At the 'intermediate' and 'regional' scales, where limited genetic clustering and high population diversity were observed, some indications of natural selection may suggest a major role for gene flow in safeguarding adaptability. High genetic diversity at loci under selection in particular, indicated considerable adaptive potential, which may nevertheless be compromised by the combined effects of climate change and habitat fragmentation.
FIGURES 13–18. Sulawesi Onthophagus species, dorsal forebody. 13, O. bisscrutator, holotype male from Toraut. 14, O. scrutator, male from Moramo. 15, O. bongkudai, holotype male from Moajat 16, paratype female. 17, O. sangirensis, male from Toraut.18, O. sangirensis, female from Tangkoko. Scale lines approximately 1 in Sulawesi Onthophagus: seven new species in select groups (Coleoptera: Scarabaeidae: Scarabaeinae)
FIGURES 13–18. Sulawesi Onthophagus species, dorsal forebody. 13, O. bisscrutator, holotype male from Toraut. 14, O. scrutator, male from Moramo. 15, O. bongkudai, holotype male from Moajat 16, paratype female. 17, O. sangirensis, male from Toraut.18, O. sangirensis, female from Tangkoko. Scale lines approximately 1 mm.
FIGURES 25–30. Sulawesi Onthophagus species, dorsal forebody. 25, O. sopu, holotype male from Sopu. 26, O. sopu, paratype male from Sopu. 27, O. manguliensis, male from Mangoli. 28, O. annulopunctatus, paratype male from Mogogonipa. 29, O. hollowayi, holotype male from Dumoga. 30, O. seseba, holotype male from Batui. Scale lines approximately 1 in Sulawesi Onthophagus: seven new species in select groups (Coleoptera: Scarabaeidae: Scarabaeinae)
FIGURES 25–30. Sulawesi Onthophagus species, dorsal forebody. 25, O. sopu, holotype male from Sopu. 26, O. sopu, paratype male from Sopu. 27, O. manguliensis, male from Mangoli. 28, O. annulopunctatus, paratype male from Mogogonipa. 29, O. hollowayi, holotype male from Dumoga. 30, O. seseba, holotype male from Batui. Scale lines approximately 1 mm.
Selection in the city: Rapid and fine scale evolution of urban eastern water dragons
<p>Oceanic archipelagos have long been treated as a petri dish for studies of evolutionary and ecological processes. Like archipelagos, cities exhibit similar patterns and processes, such as the rapid phenotypic divergence of a species between urban and non-urban environments. However, on a local scale, cities can be highly heterogenous, where geographically close populations can experience dramatically different environmental conditions. Nevertheless, we are yet to understand the evolutionary and ecological implications for populations spread across a heterogenous cityscape. To address this, we compared neutral genetic divergence to quantitative trait divergence within three native riparian and four city park populations of an iconic urban adapter, the eastern water dragon. We demonstrated that selection is likely acting to drive divergence of snout-vent length and jaw width across native riparian populations that are geographically isolated and across city park populations that are geographically close yet isolated by urbanisation. City park populations as close as 0.9 kms exhibited signs of selection driven divergence to the same extent as native riparian populations isolated by up to 114.5 kms. These findings suggest that local adaptation may be occurring over exceptionally small geographic and temporal scales within a single metropolis, demonstrating that city parks can act as archipelagos for the study of rapid evolution.</p>
Millennial-Scale Microbiome Analysis Reveals Ancient Antimicrobial Resistance Conserved Despite Modern Selection Pressures
<p>This dataset contains metadata and profiled antibiotic resistance genes from ancient metagenome permafrost.</p>
Data from: Fine-scale genetic structure in a wild bird population: the role of limited dispersal and environmentally-based selection as causal factors
Individuals are typically not randomly distributed in space; consequently ecological and evolutionary theory depends heavily on understanding the spatial structure of populations. The central challenge of landscape genetics is therefore to link spatial heterogeneity of environments to population genetic structure. Here, we employ multivariate spatial analyses to identify environmentally induced genetic structures in a single breeding population of 1174 great tits Parus major genotyped at 4701 single-nucleotide polymorphism (SNP) loci. Despite the small spatial scale of the study relative to natal dispersal we found multiple axes of genetic structure. We built distance-based Moran's eigenvector maps to identify axes of pure spatial variation, which we used for spatial correction of regressions between SNPs and various external traits known to be related to fitness components (avian malaria infection risk, local density of conspecifics, oak tree density and altitude). We found clear evidence of fine-scale genetic structure, with 21, 7 and 9 significant SNPs respectively associated with infection risk by two species of avian malaria (Plasmodium circumflexum and P. relictum) and local conspecific density. Such fine-scale genetic structure relative to dispersal capabilities suggests ecological and evolutionary mechanisms maintain within-population genetic diversity in this population with the potential to drive micro-evolutionary change.
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.