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.
9,882
datasets available to search
ShareScore release 0.9.0
Dataset results
9,882 results for “Scale”
Data from: Atoll-scale patterns in coral reef community structure: Human signatures on Ulithi Atoll, Micronesia
The dynamic relationship between reefs and the people who utilize them at a subsistence level is poorly understood. This paper characterizes atoll-scale patterns in shallow coral reef habitat and fish community structure, and correlates these with environmental characteristics and anthropogenic factors, critical to conservation efforts for the reefs and the people who depend on them. Hierarchical clustering analyses by site for benthic composition and fish community resulted in the same 3 major clusters: cluster 1–oceanic (close proximity to deep water) and uninhabited (low human impact); cluster 2–oceanic and inhabited (high human impact); and cluster 3–lagoonal (facing the inside of the lagoon) and inhabited (highest human impact). Distance from village, reef exposure to deep water and human population size had the greatest effect in predicting the fish and benthic community structure. Our study demonstrates a strong association between benthic and fish community structure and human use across the Ulithi Atoll (Yap State, Federated States of Micronesia) and confirms a pattern observed by local people that an 'opportunistic' scleractinian coral (Montipora sp.) is associated with more highly impacted reefs. Our findings suggest that small human populations (subsistence fishing) can nevertheless have considerable ecological impacts on reefs due, in part, to changes in fishing practices rather than overfishing per se, as well as larger global trends. Findings from this work can assist in building local capacity to manage reef resources across an atoll-wide scale, and illustrates the importance of anthropogenic impact even in small communities.
Data from: Morphology and genetics reveal an intriguing pattern of differentiation at a very small geographic scale in a bird species, the forest thrush Turdus lherminieri
Mobile organisms are expected to show population differentiation only over fairly large geographical distances. However, there is growing evidence of discrepancy between dispersal potential and realized gene flow. Here we report an intriguing pattern of differentiation at a very small spatial scale in the forest thrush (Turdus lherminieri), a bird species endemic to the Lesser Antilles. Analysis of 331 individuals from 17 sampling sites distributed over three islands revealed a clear morphological and genetic differentiation between these islands isolated by 40–50 km. More surprisingly, we found that the phenotypic divergence between the two geographic zones of the island of Guadeloupe was associated with a very strong genetic differentiation (Fst from 0.073–0.153), making this pattern a remarkable case in birds given the very small spatial scale considered. Molecular data (mitochondrial control region sequences and microsatellite genotypes) suggest that this strong differentiation could have occurred in situ, although alternative hypotheses cannot be fully discarded. This study suggests that the ongoing habitat fragmentation, especially in tropical forests, may have a deeper impact than previously thought on avian populations.
Data from: Functional outcomes of mutualistic network interactions: a community-scale study of frugivore gut passage on germination
1. Current understanding of mutualistic networks is grounded largely in data on interaction frequency, yet mutualistic network dynamics are also shaped by interaction quality—the functional outcomes of individual interactions on reproduction and survival. The difficulty of obtaining data on functional outcomes has resulted in limited understanding of functional variation among a network's pairwise species interactions, of the study designs that are necessary to capture major sources of functional variation, and of predictors of functional variation that may allow generalization across networks. 2. In this community-scale study, we targeted a key functional outcome in plant-frugivore networks: the impact of frugivore gut passage on seed germination. We used captive frugivore feeding trials and germination experiments in an island ecosystem, attaining species-level coverage across all extant native frugivores and the plants they consume to 1) assess sources of functional variation, 2) separate effects of pulp removal from those of scarification via gut passage, and 3) test trait-based correlates of gut passage effect sizes. 3. We found antagonistic seed predation effects of a frugivore previously assumed to be a seed disperser, highlighting the need to consider functional outcomes rather than interaction frequency alone. The other frugivores each exhibited similar impacts for individual plant species, with benefits primarily caused by pulp removal rather than scarification, supporting the use of animal functional groups in this context. In contrast, plant species varied widely in impacts of gut passage on germination. Species with smaller seeds and more frugivore partners had larger benefits of gut passage, showing promise for network metrics and functional traits to predict functional variation among plants. 4. Synthesis. Combining network and demographic approaches, we assessed the degree and sources of variation in a key functional outcome of plant-frugivore interactions across an entire network. Using a detailed study design, our work shows how simpler study designs can capture primary sources of functional variation and that functional traits and network metrics may allow generalization across networks. Efficiently measuring and generalizing sources of functional variation within mutualistic networks will strengthen our ability to model network dynamics and predict mutualist responses to global change.
Data from: Fine-scale genetic structure and helping decisions in a cooperatively breeding bird
In animal societies, characteristic demographic and dispersal patterns may lead to genetic structuring of populations, generating the potential for kin selection to operate. However, even in genetically structured populations, social interactions may still require kin discrimination for cooperative behaviour to be directed towards relatives. Here, we use molecular genetics and long-term field data to investigate genetic structure in an adult population of long-tailed tits Aegithalos caudatus, a cooperative breeder in which helping occurs within extended kin networks, and relate this to patterns of helping with respect to kinship. Spatial autocorrelation analyses reveal fine-scale genetic structure within our population, such that related adults of either sex are spatially clustered following natal dispersal, with relatedness among nearby males higher than that among nearby females, as predicted by observations of male-biased philopatry. This kin structure creates opportunities for failed breeders to gain indirect fitness benefits via redirected helping, but crucially, most close neighbours of failed breeders are unrelated and help is directed towards relatives more often than expected by indiscriminate helping. These findings are consistent with the effective kin discrimination mechanism known to exist in long-tailed tits, and support models identifying kin selection as the driver of cooperation.
Local and landscape scale variables shape insect diversity in an urban biodiversity hotspot.
<p>Local community structure is shaped by processes acting at local and landscape scales. The relative importance of drivers operating across different spatial scales are difficult to test without observations across regional or latitudinal gradients. Cities exhibit strong but predictable environmental gradients overlaying a mosaic of highly variable but repeated habitat types within a constrained area. Thus, cities present a unique opportunity to explore how both local and landscape factors influence local biotic communities. We used insect communities to examine the interactions among local environmental variables (such as temperature and relative humidity), local habitat characteristics (such as plant community composition), and broad-scale patterns of urbanization (including biophysical, human-built, and socio-economic variables) on local insect abundance, species richness, and species composition in Los Angeles, a hot, dry, near-desert city. After accounting for seasonal trends, insect species richness and abundance were highest in drier and hotter sites, but the magnitude of local environmental effects varied with the degree of urbanization. In contrast, insect species composition was best predicted by broad-scale urbanization trends, with the more native communities occurring in less urbanized sites and more cosmopolitan insects occurring in highly urbanized sites. However, insect species richness and abundance were >30% higher and insect composition was similar across sites that hosted either native or drought-tolerant plants, regardless of the degree of urbanization. These results demonstrate that urban insect biodiversity is a product of interacting mechanisms working at both local and landscape scales. However, local scale changes to urban habitats, such as cultivating plants that are adapted to the natural environment nearest the city, can positively impact urban biodiversity regardless of location.</p>
Data from: Resurrecting an extinct salmon evolutionarily significant unit: archived scales, historical DNA, and implications for restoration
Archival scales from 603 sockeye salmon (Oncorhynchus nerka), sampled from May to July 1924 in the lower Columbia River, were analyzed for genetic variability at 12 microsatellite loci, and compared to 17 present-day O. nerka populations—exhibiting either anadromous (sockeye salmon) or non-anadromous (kokanee) life histories—from throughout the Columbia River Basin, including areas upstream of impassable dams built subsequent to 1924. Statistical analyses identified four major genetic assemblages of sockeye salmon in the 1924 samples. Two of these putative historical groupings were found to be genetically similar to extant evolutionarily significant units (ESUs) in the Okanogan and Wenatchee rivers (pairwise FST = 0.004 and 0.002, respectively) and assignment tests were able to allocate 77% of the fish in these two historical groupings to the contemporary Okanogan River and Lake Wenatchee ESUs. A third historical genetic grouping was most closely aligned with contemporary sockeye salmon in Redfish Lake, Idaho, although the association was less robust (pairwise FST = 0.060). However, a fourth genetic grouping did not appear to be related to any contemporary sockeye salmon or kokanee population, assigned poorly to the O. nerka baseline, and had distinctive early return migration-timing suggesting that this group represented a putative historical ESU originating in headwater lakes in British Columbia that was likely extirpated sometime after 1924. The lack of a contemporary O. nerka population possessing the genetic legacy of this extinct ESU indicates that efforts to reestablish early-migrating sockeye salmon to the headwater lakes region of the Columbia River will be difficult.
Above- and below-ground biodiversity jointly regulate temperate forest multifunctionality along a local-scale environmental gradient
<p><span>1. Tree diversity has been shown to promote a broad range of ecosystem functions in forests. However, how important these effects are in driving ecosystem multifunctionality in natural forests, relative to other drivers, such as below-ground biodiversity (e.g., soil microbial diversity), community-level functional traits and environmental conditions, remains poorly understood. Here, we hypothesise that tree species or phylogenetic diversity, stand structure, functional traits and soil microbial diversity jointly regulate temperate forest multifunctionality along a local-scale environmental gradient.</span></p> <p><span>2. Using repeated census data from a 25-ha old-growth temperate forest, we first quantified eight ecosystem functions and properties related to above- and below-ground nutrient cycling. We then used these to estimate ecosystem multifunctionality using both an averaging and multiple thresholds (50, 75, and 95%) approaches. Finally, we used structural equation models to explore how different facets of tree (tree species, functional and phylogenetic diversity) and soil (bacteria, fungi, and nematode diversity) biodiversity influence ecosystem multifunctionality, as well as how these relationships are modulated by stand structural attributes and environmental conditions (topography and soil nutrients).</span></p> <p><span>3. Forest multifunctionality was positively related to stand structural complexity but negatively related to acquisitive traits (i.e. community-weighted mean of specific leaf area). Plant phylogenetic diversity had no significant direct effect on forest multifunctionality, but it had a significant indirect effect via increased stand structural complexity. The effect of soil microbial diversity on forest multifunctionality increased with increasing threshold levels of forest multifunctionality and outperformed tree diversity and environmental conditions at the highest threshold level (i.e. 95%). Forests on steep slopes had lower levels of ecosystem multifunctionality due to decreased stand structural complexity. Soil nutrients were responsible for regulating forest multifunctionality via plant trait composition and, to a lesser extent, via tree diversity, stand structure and soil microbial diversity.</span></p> <p><span>4. <i>Synthesis</i>: Plant phylogenetic diversity, stand structure and soil microbial diversity jointly regulated forest multifunctionality, and these effects were influenced by local-scale changes in environmental conditions. Soil microbial diversity was a key driver of highly multifunctional forests, whereas conservation of complex stand structure and conservative trait dominance could enhance mean values of multiple functions.</span></p> <p><span>1. Tree diversity has been shown to promote a broad range of ecosystem functions in forests. However, how important these effects are in driving ecosystem multifunctionality in natural forests, relative to other drivers, such as below-ground biodiversity (e.g., soil microbial diversity), community-level functional traits and environmental conditions, remains poorly understood. Here, we hypothesise that tree species or phylogenetic diversity, stand structure, functional traits and soil microbial diversity jointly regulate temperate forest multifunctionality along a local-scale environmental gradient.</span></p> <p><span>2. Using repeated census data from a 25-ha old-growth temperate forest, we first quantified eight ecosystem functions and properties related to above- and below-ground nutrient cycling. We then used these to estimate ecosystem multifunctionality using both an averaging and multiple thresholds (50, 75, and 95%) approaches. Finally, we used structural equation models to explore how different facets of tree (tree species, functional and phylogenetic diversity) and soil (bacteria, fungi, and nematode diversity) biodiversity influence ecosystem multifunctionality, as well as how these relationships are modulated by stand structural attributes and environmental conditions (topography and soil nutrients).</span></p> <p><span>3. Forest multifunctionality was positively related to stand structural complexity but negatively related to acquisitive traits (i.e. community-weighted mean of specific leaf area). Plant phylogenetic diversity had no significant direct effect on forest multifunctionality, but it had a significant indirect effect via increased stand structural complexity. The effect of soil microbial diversity on forest multifunctionality increased with increasing threshold levels of forest multifunctionality and outperformed tree diversity and environmental conditions at the highest threshold level (i.e. 95%). Forests on steep slopes had lower levels of ecosystem multifunctionality due to decreased stand structural complexity. Soil nutrients were responsible for regulating forest multifunctionality via plant trait composition and, to a lesser extent, via tree diversity, stand structure and soil microbial diversity.</span></p> <p><span>4. <i>Synthesis</i>: Plant phylogenetic diversity, stand structure and soil microbial diversity jointly regulated forest multifunctionality, and these effects were influenced by local-scale changes in environmental conditions. Soil microbial diversity was a key driver of highly multifunctional forests, whereas conservation of complex stand structure and conservative trait dominance could enhance mean values of multiple functions.</span></p> <p><span>1. Tree diversity has been shown to promote a broad range of ecosystem functions in forests. However, how important these effects are in driving ecosystem multifunctionality in natural forests, relative to other drivers, such as below-ground biodiversity (e.g., soil microbial diversity), community-level functional traits and environmental conditions, remains poorly understood. Here, we hypothesise that tree species or phylogenetic diversity, stand structure, functional traits and soil microbial diversity jointly regulate temperate forest multifunctionality along a local-scale environmental gradient.</span></p> <p><span>2. Using repeated census data from a 25-ha old-growth temperate forest, we first quantified eight ecosystem functions and properties related to above- and below-ground nutrient cycling. We then used these to estimate ecosystem multifunctionality using both an averaging and multiple thresholds (50, 75, and 95%) approaches. Finally, we used structural equation models to explore how different facets of tree (tree species, functional and phylogenetic diversity) and soil (bacteria, fungi, and nematode diversity) biodiversity influence ecosystem multifunctionality, as well as how these relationships are modulated by stand structural attributes and environmental conditions (topography and soil nutrients).</span></p> <p><span>3. Forest multifunctionality was positively related to stand structural complexity but negatively related to acquisitive traits (i.e. community-weighted mean of specific leaf area). Plant phylogenetic diversity had no significant direct effect on forest multifunctionality, but it had a significant indirect effect via increased stand structural complexity. The effect of soil microbial diversity on forest multifunctionality increased with increasing threshold levels of forest multifunctionality and outperformed tree diversity and environmental conditions at the highest threshold level (i.e. 95%). Forests on steep slopes had lower levels of ecosystem multifunctionality due to decreased stand structural complexity. Soil nutrients were responsible for regulating forest multifunctionality via plant trait composition and, to a lesser extent, via tree diversity, stand structure and soil microbial diversity.</span></p> <p><span>4. <i>Synthesis</i>: Plant phylogenetic diversity, stand structure and soil microbial diversity jointly regulated forest multifunctionality, and these effects were influenced by local-scale changes in environmental conditions. Soil microbial diversity was a key driver of highly multifunctional forests, whereas conservation of complex stand structure and conservative trait dominance could enhance mean values of multiple functions.</span></p>
Data from: A continental scale trophic cascade from wolves through coyotes to foxes
Top-down processes, via the direct and indirect effects of interspecific competitive killing (no consumption of the kill) or intraguild predation (consumption of the kill), can potentially influence the spatial distribution of terrestrial predators, but few studies have demonstrated the phenomenon at a continental scale. For example, in North America, grey wolves (Canis lupus) are known to kill coyotes (Canis latrans), and coyotes, in turn, may kill foxes (Vulpes spp.), but the spatial effects of these competitive interactions at large scales are unknown. Here, we analyse fur return data across eight jurisdictions in North America to test whether the presence or absence of wolves has caused a continent-wide shift in coyote and red fox (Vulpes vulpes) density. Our results support the existence of a continental scale cascade whereby coyotes outnumber red foxes in areas where wolves have been extirpated by humans, whereas red foxes outnumber coyotes in areas where wolves are present. However, for a distance of up to 200 km on the edge of wolf distribution, there is a transition zone where the effects of top-down control are weakened, possibly due to the rapid dispersal and reinvasion capabilities of coyotes into areas where wolves are sporadically distributed or at low densities. Our results have implications for understanding how the restoration of wolf populations across North America could potentially affect co-occurring predators and prey. We conclude that large carnivores may need to occupy large continuous areas to facilitate among-carnivore cascades and that studies of small areas may not be indicative of the effects of top-down mesopredator control.
Data from: Population genetic structure and its implications for adaptive variation in memory and the hippocampus on a continental scale in food-caching black-capped chickadees
Food-caching birds rely on stored food to survive the winter and spatial memory has been shown to be critical in successful cache recovery. Both spatial memory and the hippocampus, an area of the brain involved in spatial memory, exhibit significant geographic variation linked to climate-based environmental harshness and the potential reliance on food caches for survival. Such geographic variation has been suggested to have a heritable basis associated with differential selection. Here, we ask whether population genetic differentiation and potential isolation among multiple populations of food-caching black-capped chickadees is associated with differences in memory and hippocampal morphology by exploring population genetic structure within and among groups of populations that are divergent to different degrees in hippocampal morphology. Using mitochondrial DNA and 583 AFLP loci, we found that population divergence in hippocampal morphology is not significantly associated with neutral genetic divergence or geographic distance, but instead is significantly associated with differences in winter climate. These results are consistent with variation in a history of natural selection on memory and hippocampal morphology that creates and maintains differences in these traits regardless of population genetic structure and likely associated gene flow.
Data from: Short-term climate change manipulation effects do not scale up to long-term legacies: effects of an absent snow cover on boreal forest plants
1. Despite time lags and non-linearity in ecological processes, the majority of our knowledge about ecosystem responses to long-term changes in climate originates from relatively short-term experiments. 2. We utilized the longest ongoing snow removal experiment in the world and an additional set of new plots at the same location in northern Sweden to simultaneously measure the effects of long-term (11 winters) and short-term (1 winter) absence of snow cover on boreal forest understorey plants, including effects on root growth and phenology. 3. Short-term absence of snow reduced vascular plant cover in the understorey by 42%, reduced fine root biomass by 16%, reduced shoot growth by up to 53%, and induced tissue damage on two common dwarf shrubs. In the long-term manipulation, more substantial effects on understorey plant cover (92% reduced) and standing fine root biomass (39% reduced) were observed, whereas other response parameters, such as tissue damage, were observed less. Fine root growth was generally reduced, and its initiation delayed by c. 3 (short-term) to 6 weeks (long-term manipulation). 4. Synthesis We show that one extreme winter with a reduced snow cover can already induce ecologically significant alterations. We also show that long-term changes were smaller than suggested by an extrapolation of short-term manipulation results (using a constant proportional decline). In addition, some of those negative responses, such as frost damage and shoot growth, were even absolutely stronger in the short-term compared to the long-term manipulation. This suggests adaptation or survival of only those individuals that are able to cope with these extreme winter conditions, and that the short-term manipulation alone would over-predict long-term impacts. These results highlight both the ecological importance of snow cover in this boreal forest, and the value of combining short- and long-term experiments side by side in climate change research.
Data from: Scale-dependent responses of pollination and seed dispersal mutualisms in a habitat transformation scenario
Transformed habitats are the result of deliberate replacement of native species by an exotic monoculture, involving changes in biotic and abiotic conditions. Despite this, transformed habitats are becoming more common and constitute a major biodiversity change driver, little is known about the scale-dependent responses of plant-animal mutualisms. Aiming to test the multi-scale responses of pollination and seed dispersal in a habitat transformation scenario, we examined a gradient of native and transformed habitats at three spatial scales (0-50, 50-100, and 100-250 m), focused on a highly-specialized mutualistic system composed of a hemiparasitic mistletoe (Tristerix corymbosus) that is almost exclusively pollinated by a hummingbird (Sephanoides sephaniodes) and dispersed by an arboreal marsupial (Dromiciops gliroides). Even though mistletoes were found along the gradient, they were more abundant and more densely aggregated when the transformed habitat was dominant. Disperser and pollinator activity also increased as the transformed habitat become dominant, at the scale of 0-50 m and 50-100 m, respectively. Furthermore, crop size and disperser activity co-varied at broad and intermediate scales, whereas recruitment co-varied at intermediate and fine scales. Moreover, disperser activity and the number of seedlings were spatially associated, stressing D. gliroides' role in the recruitment of the mistletoe. Synthesis: This highly specialized mutualistic system seems to be responding positively to the habitat structure modifications associated with Eucalyptus plantations. However, the actual costs (e.g., reduced gene flow, increased herbivory) in these transformed habitats are yet to be assessed.
Data from: Variation in fine-scale genetic structure and local dispersal patterns between peripheral populations of a South American passerine bird
The distribution of suitable habitat influences natal and breeding dispersal at small spatial scales, resulting in strong micro-geographic genetic structure. Although environmental variation can promote inter-population differences in dispersal behavior and local spatial patterns, the effects of distinct ecological conditions on within-species variation in dispersal strategies and in fine-scale genetic structure remain poorly understood. We studied local dispersal and fine-scale genetic structure in the thorn-tailed rayadito (Aphrastura spinicauda), a South American bird that breeds along a wide latitudinal gradient. We combine capture-mark-recapture data from eight breeding seasons and molecular genetics to compare two peripheral populations with contrasting environments in Chile: Navarino Island, a continuous and low density habitat, and Fray Jorge National Park, a fragmented, densely populated and more stressful environment. Natal dispersal showed no sex bias in Navarino, but was female-biased in the more dense population in Fray Jorge. In the latter, male movements were restricted and some birds seemed to skip breeding in their first year, suggesting habitat saturation. Breeding dispersal was limited in both populations, with males being more philopatric than females. Spatial genetic autocorrelation analyses using 13 polymorphic microsatellite loci confirmed the observed dispersal patterns: a fine-scale genetic structure was only detectable for males in Fray Jorge for distances up to 450 m. Furthermore, two-dimensional autocorrelation analyses and estimates of genetic relatedness indicated that related males tended to be spatially clustered in this population. Our study shows evidence for context-dependent variation in natal dispersal and corresponding local genetic structure in peripheral populations of this bird. It seems likely that the costs of dispersal are higher in the fragmented and higher density environment in Fray Jorge, particularly for males. The observed differences in micro-geographic genetic structure for rayaditos might reflect the genetic consequences of population-specific responses to contrasting environmental pressures near the range limits of its distribution.
Data from: Grains of connectivity: analysis at multiple spatial scales in landscape genetics
Landscape genetic analyses are typically conducted at one spatial scale. Considering multiple scales may be essential for identifying landscape features influencing gene flow. We examined landscape connectivity for woodland caribou (Rangifer tarandus caribou) at multiple spatial scales using a new approach based on landscape graphs that creates a Voronoi tessellation of the landscape. To illustrate the potential of the method, we generated five resistance surfaces to explain how landscape pattern may influence gene flow across the range of this population. We tested each resistance surface using a raster at the spatial grain of available landscape data (200 m grid squares). We then used our method to produce up to 127 additional grains for each resistance surface. We applied a causal modelling framework with partial Mantel tests, where evidence of landscape resistance is tested against an alternative hypothesis of isolation-by-distance, and found statistically significant support for landscape resistance to gene flow in 89 of the 507 spatial grains examined. We found evidence that major roads as well as the cumulative effects of natural and anthropogenic disturbance may be contributing to the genetic structure. Using only the original grid surface yielded no evidence for landscape resistance to gene flow. Our results show that using multiple spatial grains can reveal landscape influences on genetic structure that may be overlooked with a single grain, and suggest that coarsening the grain of landcover data may be appropriate for highly-mobile species. We discuss how grains of connectivity and related analyses have potential landscape genetic applications in a broad range of systems.
Data from: Complementary responses of morphology and physiology enhance the stand-scale production of a model invasive species under elevated CO2 and nitrogen
1. Elevated atmospheric carbon dioxide (eCO2) concentrations and nitrogen (N) enrichment are known to enhance plant productivity and invasion. However, the implications of their interactive effects for plant productivity are not well understood, especially at the stand scale, presumably because morphological and physiological responses to these global change factors are rarely studied together in the field or assessed at the stand-level. 2. We first determined how leaf-level morphological and physiological traits responded to factorial combinations of ambient and elevated CO2 and N. We collected trait data from the model invasive species Phragmites australis (common reed) that were measured over three years in a long-term global change field experiment. We then combined the trait data and additional descriptions of P. australis canopies in a simulation model of carbon assimilation to determine how morphology and physiology contribute to P. australis' stand scale productivity. 3. At the leaf level, we found that light-saturated rates of photosynthesis were strongly stimulated by eCO2 (37%) and that this effect was enhanced by increasing salinity. N had a smaller effect (17% stimulation) on physiological responses than eCO2, but leaf morphological traits responded primarily to N; plant height increased by 27% and leaf area increased by 47%. 4. Stand scale simulations demonstrated that that morphological and physiological adjustments induced approximately additive responses when P. australis experienced both eCO2 and N enrichment. The simulations also indicated that morphological changes (which were primarily associated with canopy size) influenced stand scale carbon assimilation more than physiological changes. Moreover, 97% of the N response was due to changes in morphology, whereas 62% of the eCO2 response was caused by physiological shifts. 5. Our analysis indicates that morphological and physiological trait responses to elevated CO2 and nitrogen are likely to enhance the productivity of P. australis in complementary ways, potentially accelerating its invasion in North America. Furthermore, our data suggest that changes in morphological traits may have a greater influence on carbon gain than leaf-level physiology under near-future environmental conditions. Our study also highlights the importance of accounting for both morphological and physiological responses when attempting to infer global change responses from leaf-level data.
Modeling human migration across spatial scales in Colombia
<p><span><span><span><span><span><span><span><span><span><span><span>Human mobility, both short and long term, are important considerations in the study of numerous systems. Economic and technological advances have led to a more interconnected global community, further increasing the need for considerations of human mobility. While data on human mobility are better recorded in many developed countries, availability of such data remains limited in many low- and middle-income countries around the world, particularly at the fine temporal and spatial scales required by many applications. In this study, we used 5-year census-based internal migration microdata for 32 departments in Colombia (i.e., Admin-1 level) to develop a novel spatial interaction modeling approach for estimating migration, at a finer spatial scale, among the 1,122 municipalities in the country (i.e., Admin-2 level). Our modeling approach bridges a significant gap in the availability of migration data at administrative unit levels finer than those at which migration data are typically recorded. Due to the widespread availability of census-based migration microdata at the Admin-1 level, our modeling approach opens up for the possibilities of modeling migration patterns at Admin-2 and Admin-3 levels across many other countries where such data are currently lacking. </span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Polygamy and an absence of fine-scale structure in Dendroctonus ponderosae (Hopk.) (Coleoptera: Curcilionidae) confirmed using molecular markers
An understanding of mating systems and fine-scale spatial genetic structure is required to effectively manage forest pest species such as Dendroctonus ponderosae (mountain pine beetle). Here we used genome-wide single-nucleotide polymorphisms to assess the fine-scale genetic structure and mating system of D. ponderosae collected from a single stand in Alberta, Canada. Fine-scale spatial genetic structure was absent within the stand and the majority of genetic variation was best explained at the individual level. Relatedness estimates support previous reports of pre-emergence mating. Parentage assignment tests indicate that a polygamous mating system better explains the relationships among individuals within a gallery than the previously reported female monogamous/male polygynous system. Furthermore, there is some evidence to suggest that females may exploit the galleries of other females, at least under epidemic conditions. Our results suggest that current management models are likely to be effective across large geographic areas based on the absence of fine-scale genetic structure.
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: Patterns of local community composition are linked to large-scale diversification and dispersal of clades
At any location, a group of organisms may be represented by several clades. What determines which clades will dominate local communities in terms of their species richness? Here, this relatively neglected question is addressed by analyzing 166 local assemblages of snakes distributed globally. For most regions, local assemblages are dominated by clades with higher global-scale diversification rates and more frequent dispersal into each region, and not by clades that have been present in that region longer. This result contrasts with many other studies of local richness (in other organisms), which show strong impacts of regional colonization time on overall local species richness of clades. Furthermore, even though local assemblages are assembled independently on different continents, most regions have converged on similar patterns of proportional richness. Specifically, a few rapidly diversifying clades dominate most communities around the world. The high diversification rates of these clades are then linked to their high dispersal rates. Similar patterns may occur in many groups, such as plants, frogs, salamanders, birds, and mammals.
Data from: Evolutionary dynamics of quantitative variation in an adaptive trait at the regional scale: the case of zinc hyperaccumulation in Arabidopsis halleri
Metal hyperaccumulation in plants is an ecological trait whose biological significance remains debated, in particular because the selective pressures that govern its evolutionary dynamics are complex. One of the possible causes of quantitative variation in hyperaccumulation may be local adaptation to metalliferous soils. Here we explored the population genetic structure of Arabidopsis halleri at fourteen metalliferous and non-metalliferous sampling sites in Southern Poland. The results were integrated with a quantitative assessment of variation in zinc hyperaccumulation to trace local adaptation. We identified a clear hierarchical structure with two distinct genetic groups at the upper level of clustering. Interestingly, these groups corresponded to different geographic sub-regions, rather than to ecological types (i.e. metallicolous vs non-metallicolous). Also, approximate Bayesian computation analyses suggested that the current distribution of A. halleri in Southern Poland could be relictual as a result of habitat fragmentation caused by climatic shifts during the Holocene, rather than due to recent colonization of industrially polluted sites. In addition, we find evidence that some non-metallicolous lowland populations may have actually derived from metallicolous populations. Meanwhile, the distribution of quantitative variation in zinc hyperaccumulation did separate metallicolous and non-metallicolous accessions, indicating more recent adaptive evolution and diversifying selection between metalliferous and non-metalliferous habitats. This suggests that zinc hyperaccumulation evolves both ways – towards higher levels at non-metalliferous sites and lower levels at metalliferous sites. Our results open a new perspective on possible evolutionary relationships between A. halleri edaphic types that may inspire future genetic studies of quantitative variation in metal hyperaccumulation.
Data from: Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery
Individual assignment and genetic mixture analysis are commonly utilized in contemporary wildlife and fisheries management. Although microsatellite loci provide unparalleled numbers of alleles per locus, their use in assignment applications is increasingly limited. However, next-generation sequencing, in conjunction with novel bioinformatic tools allows large numbers of microsatellite loci to be simultaneously genotyped, presenting new opportunities for individual assignment and genetic mixture analysis. Here we scanned the published Atlantic salmon genome to identify 706 microsatellite loci, from which we developed a final panel of 101 microsatellites distributed across the genome (average 3.4 loci per chromosome). Using samples from 35 Atlantic salmon populations (n=1485 individuals) from coastal Labrador, Canada, a region characterized by low levels of differentiation in this species, this panel identified 844 alleles (average of 8.4 alleles per locus). Simulation-based evaluations of assignment and mixture identification accuracy revealed unprecedented resolution, clearly identifying 26 rivers or groups of rivers spanning 500 km of coastline. This baseline was used to examine the stock composition of 696 individuals harvested in the Labrador Atlantic salmon fishery and revealed that coastal fisheries largely targeted regional groups (<300km). This work suggests that the development and application of large sequenced microsatellite panels presents great potential for stock resolution in Atlantic salmon and more broadly in other exploited anadromous and marine species.
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.