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29 results for “Continental-scale”
Data for: "Continental-scale patterns in diel flight timing of high-altitude migratory insects"
<p>This dataset contains the proportional migratory insect intensity and traffic data used in Haest <em>et al.</em> (2024) to quantify patterns in diel flight periodicity of migratory insects between 50-500m above ground level during March-October 2021 using a network of seventeen vertical-looking radars across Europe. Please see the Materials and Methods section in Haest <em>et al.</em> (2024) for more details on the dataset. </p>
Geochemical, physicochemical, and genomic data from a continental-scale survey of microbial diversity in Antarctic soils (2003-2023)
This data package offers comprehensive insights into Antarctic soil microbial diversity and composition. From 2003 to 2023, a total of 186 samples were collected from diverse locations spanning the Antarctic Peninsula to East Antarctica, representing a wide range of environmental gradients and climatic conditions. Soils were stored at -20°C to preserve their integrity for downstream analyses. This data package integrates cultivation-independent sequencing of prokaryotic and fungal communities alongside a robust cultivation-dependent culture collection to enable direct comparisons across microbial diversity assessment methods. Accompanying geochemical, physicochemical, and environmental parameters provide critical context for biogeographical analyses, offering a valuable resource for studying microbial adaptations and community dynamics in extreme Antarctic environments.
Using RS-DAT to study continental-scale phenology at high-spatial resolution
This repository includes the notebooks employed to calculate and analyze a gridded phenological model, as computed from a set of daily meteorological variables.
Fine-grain predictions are key to accurately represent continental-scale biodiversity patterns
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Data from: the great tit HapMap project: a continental-scale analysis of genomic variation in a songbird
<p>A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (<em>Parus major</em>) HapMap project. We screened <em>ca</em> 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude - almost the entire geographic range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugiam, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear "islands of differentiation", even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (F<sub>ST</sub>), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics.</p>
Termite trait data from: Continental-scale shifts in termite diversity and nesting and feeding strategies
<p>Typically, termites are treated as a single guild, which ignores important internal diversity, including diverse feeding and nesting traits. These termite traits are crucial for both ecosystem-level fluxes and trophic webs, with implications for vertebrate species. Despite their ecological importance, the large-scale distribution of termite feeding and nesting traits and the relationship with termite diversity is largely unknown. We investigated whether functional diversity, species richness, and feeding (wood, litter, grass, dung) and nesting trait (aboveground mound, belowground nest, inside tree or outside tree nest) distributions of termites were climatically control. To address this gap, we assembled a continental-scale database of termite traits and occurrence in Australia and modelled termite nesting and feeding traits in response to macroclimate. Functional richness and evenness increased primarily with temperature. Australia showed multiple hotspots of termite diversity with each hotspot showing a distinct guild composition. The large-scale distribution of nesting traits showed that aboveground nesting species were the most common nesting guild in the dry and wet tropics while belowground nesting dominated in seasonally cold arid environments, demonstrating a strong climatic control on nesting strategy. Given their large biomass and many interactions with other species, the macro-ecology of termite traits may be especially important in predicting shifts in other species' distributions at continental and global scales.</p>
Continental-scale associations of Arabidopsis thaliana phyllosphere members with host genotype and drought
<p><strong><span>Plants are colonized by distinct pathogenic and commensal microbiomes across different regions of the globe, but the factors driving their geographic variation are largely unknown. Using 16S rDNA and shotgun sequencing, we characterized the associations of the <em>Arabidopsis thaliana</em> leaf microbiome with host genetics and climate variables from 267 populations in the species’ native range across Europe. Comparing the distribution of the 575 major bacterial amplicon variants (phylotypes), we discovered that microbiome composition in <em>A. thaliana</em> segregates along a latitudinal gradient. The latitudinal clines in microbiome composition are predicted by metrics of drought, but also by the spatial genetics of the host. To validate the relative effects of drought and host genotype we conducted a common garden field study, finding 10% of the core bacteria to be affected directly by drought, and 20% to be affected by host genetic associations with drought. These data provide a valuable resource for the plant microbiome field, with the identified associations suggesting that drought can directly and indirectly shape genetic variation in A. thaliana via the leaf microbiome.</span></strong></p>
Convergent genomic signatures of local adaptation across a continental-scale environmental gradient
<p><span>Convergent local adaptation offers a glimpse into the role of constraint and stochasticity in adaptive evolution, in particular the extent to which similar genetic mechanisms drive adaptation to common selective forces. Here, we investigated the genomics of local adaptation in two non-sister woodpeckers that are co-distributed across an entire continent and exhibit remarkably convergent patterns of geographic variation. We sequenced the genomes of 140 individuals of Downy (<em>Dryobates</em> <em>pubescens</em>) and Hairy (<em>D</em>. <em>villosus</em>) woodpeckers and employed a suite of genomic approaches to identify loci under selection. We showed evidence that convergent genes have been targeted by selection in response to shared environmental pressures, such as temperature and precipitation. Among candidates, we found multiple genes putatively linked to key phenotypic adaptations to climate, including differences in body size (e.g., <em>IGFPB</em>) and plumage (e.g., <em>MREG</em>). These results are consistent with genetic constraints limiting the pathways of adaptation to broad climatic gradients, even after genetic backgrounds diverge.</span></p>
Termite trait data from: Continental-scale shifts in termite diversity and nesting and feeding strategies
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Convergent genomic signatures of local adaptation across a continental-scale environmental gradient
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Data from: the great tit HapMap project: a continental-scale analysis of genomic variation in a songbird
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Continental-scale shift in foraging habitat use by a highly nomadic species following Australia’s Black Summer megafires
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Continental-scale genomic analysis suggests shared post-admixture adaptation in the Americas - Z scores tables
<p><strong>Zscores20Pop. </strong>20pop dataset Z scores by SNP in the three ancestries (A. Africa B. Europe C. America).</p> <p><strong>Zscores1090Ind.</strong> 1090Ind dataset Z scores by SNP in the three ancestries (A. Africa B. Europe C. America).</p>
Data from: Continental-scale patterns reveal potential for warming-induced shifts in cattle diet
In North America, it has been shown that cattle in warmer, drier grasslands have lower quality diets than those cattle grazing cooler, wetter grasslands, which suggests warming will increase nutritional stress and reduce weight gain. Yet, little is known about how the plant species that comprise cattle diets change across these gradients and whether these shifts in dietary quality coincide with shifts in dietary composition, i.e. the relative abundance of different plant species consumed by cattle. To quantify geographic patterns in dietary composition, we analyzed the dietary composition and dietary quality of unsupplemented cattle from 289 sites across the central US by sequence-based analyses of plant DNA isolated from cattle fecal samples. Overall, assuming that the percentage of reads for a species in a sample corresponds to the percentage of protein derived from the species, only 45% of the protein intake for cattle was derived from grasses. Within the Great Plains, northern cattle relied more on grasses than southern cattle, which derived a greater proportion of their protein from herbaceous and woody eudicots. Eastern cattle were also more likely to consume a unique assemblage of plant species than western cattle. High dietary protein was not strongly tied to consumption of any specific plant species, which suggests that efforts to promote individual plant species may not easily remedy protein deficiencies. A few plant species were consistently associated with lower quality diets. For example, the diets of cattle with high amounts of Elymus or Hesperostipa were more likely to have lower crude protein concentrations than diets with less of these grasses. Overall, our analyses suggest that climatic warming will increase the reliance of cattle on eudicots as protein concentrations of grasses decline. Monitoring cattle diet with this DNA-based sequencing approach can be an effective tool for quantifying cattle diet to better increase animal performance and guide mitigation strategies to changing climates.
Data from: A generalizable energetics-based model of avian migration to facilitate continental-scale waterbird conservation
Conserving migratory birds is made especially difficult because of movement among spatially disparate locations across the annual cycle. In light of challenges presented by the scale and ecology of migratory birds, successful conservation requires integrating objectives, management, and monitoring across scales, from local management units to ecoregional and flyway administrative boundaries. We present an integrated approach using a spatially explicit energetic-based mechanistic bird migration model useful to conservation decision-making across disparate scales and locations. This model moves a Mallard-like bird (Anas platyrhynchos), through spring and fall migration as a function of caloric gains and losses across a continental-scale energy landscape. We predicted with this model that fall migration, where birds moved from breeding to wintering habitat, took a mean of 27.5 d of flight with a mean seasonal survivorship of 90.5% (95% CI = 89.2%, 91.9%), whereas spring migration took a mean of 23.5 d of flight with mean seasonal survivorship of 93.6% (95% CI = 92.5%, 94.7%). Sensitivity analyses suggested that survival during migration was sensitive to flight speed, flight cost, the amount of energy the animal could carry, and the spatial pattern of energy availability, but generally insensitive to total energy availability per se. Nevertheless, continental patterns in the bird-use days occurred principally in relation to wetland cover and agricultural habitat in the fall. Bird-use days were highest in both spring and fall in the Mississippi Alluvial Valley and along the coast and near-shore environments of South Carolina. Spatial sensitivity analyses suggested that locations nearer to migratory endpoints were less important to survivorship; for instance, removing energy from a 1036 km2 stopover site at a time from the Atlantic Flyway suggested coastal areas between New Jersey and North Carolina, including the Chesapeake Bay and the North Carolina piedmont, are essential locations for efficient migration and increasing survivorship during spring migration but not locations in Ontario and Massachusetts. This sort of spatially explicit information may allow decision-makers to prioritize their conservation actions toward locations most influential to migratory success. Thus, this mechanistic model of avian migration provides a decision-analytic medium integrating the potential consequences of local actions to flyway-scale phenomena.
Data from: Citizen science reveals unexpected continental-scale evolutionary change in a model organism
Organisms provide some of the most sensitive indicators of climate change and evolutionary responses are becoming apparent in species with short generation times. Large datasets on genetic polymorphism that can provide an historical benchmark against which to test for recent evolutionary responses are very rare, but an exception is found in the brown-lipped banded snail (Cepaea nemoralis). This species is sensitive to its thermal environment and exhibits several polymorphisms of shell colour and banding pattern affecting shell albedo in the majority of populations within its native range in Europe. We tested for evolutionary changes in shell albedo that might have been driven by the warming of the climate in Europe over the last half century by compiling an historical dataset for 6,515 native populations of C. nemoralis and comparing this with new data on nearly 3,000 populations. The new data were sampled mainly in 2009 through the Evolution MegaLab, a citizen science project that engaged thousands of volunteers in 15 countries throughout Europe in the biggest such exercise ever undertaken. A known geographic cline in the frequency of the colour phenotype with the highest albedo (yellow) was shown to have persisted and a difference in colour frequency between woodland and more open habitats was confirmed, but there was no general increase in the frequency of yellow shells. This may have been because snails adapted to a warming climate through behavioural thermoregulation. By contrast, we detected an unexpected decrease in the frequency of Unbanded shells and an increase in the Mid-banded morph. Neither of these evolutionary changes appears to be a direct response to climate change, indicating that the influence of other selective agents, possibly related to changing predation pressure and habitat change with effects on micro-climate.
Data from: Continental-scale biogeographic variation: provinces versus gradients in the Upper Ordovician of Laurentia
Although provinces are widely used to delimit large-scale variations in biotic composition, it is unknown to what extent such variations simply reflect large-scale gradients, much as has been shown at smaller scales for communities. We examine here whether four previously described Middle and Late Ordovician provinces on Laurentia are best described as distinct provinces or as biotic gradients through a combination of the Paleobiology Database and new field data. Both data sets indicate considerable overlap in faunal composition, with spatial patterns in Jaccard similarity, quantified Jaccard similarity, and nonmetric multidimensional scaling ordination structure that correspond to variations in substrate type, specifically from carbonate-dominated strata in western Laurentia to mixed carbonate–siliciclastic strata in the midcontinent to siliciclastic-dominated rocks in easternmost Laurentia. Because sampling was limited to shallow-subtidal settings, this gradient cannot be attributed to variations in water depth. Likewise, geographic distance accounts for only a quarter of the variation in faunal composition. This cross-continent faunal gradient increases in strength into the early Late Ordovician, and appears to represent increased siliciclastic influx into eastern Laurentia during the Taconic orogeny. These results raise the question of whether biogeographic provinces may be in general better interpreted and analyzed as biotic gradients rather than as discrete entities.
Data from: Continental-scale patterns of pathogen prevalence: a case study on the corncrake
Pathogen infections can represent a substantial threat to wild populations, especially those already limited in size. To determine how much variation in the pathogens observed among fragmented populations is caused by ecological factors, one needs to examine systems where host genetic diversity is consistent among the populations, thus controlling for any potentially confounding genetic effects. Here, we report geographic variation in haemosporidian infection among European populations of corncrake. This species now occurs in fragmented populations, but there is little genetic structure and equally high levels of genetic diversity among these populations. We observed a longitudinal gradient of prevalence from western to Eastern Europe negatively correlated with national agricultural yield, but positively correlated with corncrake census population sizes when only the most widespread lineage is considered. This likely reveals a possible impact of local agriculture intensity, which reduced host population densities in Western Europe and, potentially, insect vector abundance, thus reducing the transmission of pathogens. We conclude that in the corncrake system, where metapopulation dynamics resulted in variations in local census population sizes, but not in the genetic impoverishment of these populations, anthropogenic activity has led to a reduction in host populations and pathogen prevalence.
Obtaining Continental-Scale, High-Resolution 2-d Ionospheric Flows and Application to Meso-Scale Flow Science
<p>The SuperDARN 2-d velocity vectors using the spherical elementary current systems (SECS) technique. The file names show UT. Each file contains magnetic latitude and longitude, geographic latitude and longitude, northward and eastward velocity in magnetic, northward and eastward velocity in geographic, and the number of echoes in each grid. AACGM is used as the magnetic coordinates.</p>
A robust estimate of continental-scale terrestrial carbon sinks using GOSAT XCO2 retrievals
<p>The dataset contains monthly terrestrial ecosystem carbon fluxes (NEE) for 51 terrestrial regions from 2011-2014. We used simulations from 12 terrestrial biosphere models (TBMs) as the prior carbon fluxes, therefore the posterior carbon fluxes correspond to the 12 TBMs.</p>
ScienceDex guides
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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.