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99 results for “scale-dependency”
Scale-dependent signatures of local adaptation in a widespread foundation tree species
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Scale-dependent environmental effects on phenotypic distributions in Heliconius butterflies
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Data from: Scale-dependent responses to environmental fluctuations in tropical tree species’ crown temperatures
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Scale-Dependence in Elk Habitat Selection for a Reintroduced Population in Wisconsin, USA.
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Data from: Scale-dependence of landscape heterogeneity effects on plant invasions
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Scale-dependent variation in leaf functional traits clarifies mechanisms of invasion
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Data from: Temporal scale-dependence of plant-pollinator networks
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Scale-dependent drivers of the phylogenetic structure and similarity of tree communities in northwestern Amazonia
<p><span><span><span><span><span><span><span><span><span><span><span><span>1. The extent to which historical dispersal, environmental features and geographic barriers shape the phylogenetic structure and turnover of tree communities in northwestern Amazonia at multiple spatial scales remains poorly understood. </span></span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><span>2. We used 85 floristically standardized 0.1-ha plots (DBH ³ 2.5 cm) distributed in three subregions of northwestern (NW) Amazonia across three main habitat types (floodplain, swamp, terra firme forests), to hypothesize that: i) historical dispersal overcome geographical barriers, which meant low local phylogenetic relatedness and low phylogenetic turnover. ii) Geographical barriers triggered dispersal limitation, causing high local and subregional phylogenetic clustering and high regional phylogenetic turnover. iii) Edaphic properties and flooding were negatively associated to stem size and determined the tree phylogenetic structure and turnover at local and regional scales in Amazon forests.</span></span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><span>3. We found that the extent to which environmental or evolutionary features shaped the phylogenetic structure and phylogenetic similarity of tree communities in NW Amazonia was scale dependent. Specifically, we show that the relative importance of environmental factors increases as spatial scale and species pool decreases. Further, we find that these results are generally robust for both adult and juvenile trees. </span></span></span></span></span></span></span></span></span></span></span></span></p> <p><i>Synthesis</i><span><span><span><span><span><span><span><span><span><span><span><span>: Our analysis at the regional (NW Amazon) scale lends support to the idea of Amazonian forests as a large metacommunity</span></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span><span> primarily structured by historical dispersal at large spatial scales with an increasing importance of environmental factors at finer spatial scales. The convergence of ancestral lineages across </span></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span><span>habitat types </span></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span><span>may have been due to the relatively recent formation of geographical barriers that promoted local isolation and allopatric speciation.</span></span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Functional diversity of phyllostomid bats in an urban-rural landscape: a scale-dependent analysis
<p>Urbanization is one of the most pervasive landscape transformational processes responsible for novel selection agents promoting functional community homogenization. Bats may persist in those human environments, but the mechanisms responsible for their adaptability and the spatial scales in which landscape imposes environmental filtering remain poorly studied in the Neotropics. We tested the hypothesis that landscape composition interacts with the spatial scale to affect the functional diversity of phyllostomids in an urban-rural gradient. Based on functional traits, we calculated indices of functional richness, divergence, evenness, community-weighted means of morphological traits, and classified species into functional groups. We evaluated the changes of those variables in response to forest, grassland, and urbanized areas at 0.5, 1.25 and, 2 km scales. The number of functional groups, functional richness, and functional evenness tended to be higher in areas far from cities and with higher forest cover, whereas functional divergence increased in more urbanized areas. Our results show that the mean value of wing loading in the assemblage was negatively associated to landscape transformation at several spatial scales. However, environmental filtering driven by grass cover was particularly robust at the 500 m scale, affecting big-sized species with long pointed wings. Retaining natural forest in cattle ranging systems at ~12 km<sup>2</sup> appears to favor bat abundance evenness among functional types in the urban-rural landscape. Recognizing the scale of the effect on phyllostomid functional responses appears to be a fundamental issue for elucidating the spatial extent to which phyllostomid conservation planning in urban-rural landscapes should be addressed.</p>
Data from: Scale-dependent variation in nitrogen cycling and soil fungal communities along gradients of forest composition and age in regenerating tropical dry forests
Rates of ecosystem nitrogen (N) cycling may be mediated by the presence of ectomycorrhizal fungi, which compete directly with free‐living microbes for N. In the regenerating tropical dry forests of Central America, the distribution of ectomycorrhizal trees is affected by succession and soil parent material, both of which may exert independent influence over soil N fluxes. In order to quantify these interacting controls, we used a scale‐explicit sampling strategy to examine soil N cycling at scales ranging from the microsite to ecosystem level. We measured fungal community composition, total and inorganic N pools, gross proteolytic rate, net N mineralization and microbial extracellular enzyme activity at multiple locations within 18 permanent plots that span dramatic gradients of soil N concentration, stand age and forest composition. The ratio of inorganic to organic N cycling was correlated with variation in fungal community structure, consistent with a strong influence of ectomycorrhiza on ecosystem‐scale N cycling. However, on average, > 61% of the variation in soil biogeochemistry occurred within plots, and the effects of forest composition were mediated by this local‐scale heterogeneity in total soil N concentrations. These cross‐scale interactions demonstrate the importance of a spatially explicit approach towards an understanding of controls on element cycling.
Data from: Scale-dependent foraging ecology of a marine top predator modelled using passive acoustic data
1. Understanding which environmental factors drive foraging preferences is critical for the development of effective management measures, but resource use patterns may emerge from processes that occur at different spatial and temporal scales. Direct observations of foraging are also especially challenging in marine predators, but passive acoustic techniques provide opportunities to study the behavior of echolocating species over a range of scales. 2. We used an extensive passive acoustic dataset to investigate the distribution and temporal dynamics of foraging in bottlenose dolphins using the Moray Firth (Scotland, UK). Echolocation buzzes were identified with a mixture model of detected echolocation inter-click intervals, and used as a proxy of foraging activity. A robust modelling approach accounting for autocorrelation in the data was then used to evaluate which environmental factors were associated with the observed dynamics at two different spatial and temporal scales. 3. At a broad scale, foraging varied seasonally, and was also affected by sea-bed slope and shelf-sea fronts. At a finer scale, we identified variation in seasonal use and local interactions with tidal processes. Foraging was best predicted at a daily scale, accounting for site-specificity in the shape of the estimated relationships. 4. This study demonstrates how passive acoustic data can be used to understand foraging ecology in echolocating species, and provides a robust analytical procedure for describing spatio-temporal patterns. Associations between foraging and environmental characteristics varied according to spatial and temporal scale, highlighting the need for a multi-scale approach. Our results indicate that dolphins respond to coarser-scale temporal dynamics, but have a detailed understanding of finer-scale spatial distribution of resources.
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: Scale-dependent shifts in the species composition of flower visitors with changing floral density
Responses of flower-visiting animals to floral density can alter interactions between plants, influencing a variety of biological processes, including plant population dynamics and the evolution of flowering phenology. Many studies have found effects of floral or plant density on pollinator visitation rates at patch scales, but little is known about responses of flower visitors to floral densities at larger scales. Here, I present data from an observational field study in which I measured the effects of floral density on visitation to the annual composite Holocarpha virgata at both patch (4 m(2)) and site (12.6 ha) spatial scales. The species composition of flower visitors changed with floral density, and did so in different ways at the two scales. At the site scale, average floral density within patches of H. virgata or within patches of all summer-flowering species combined had a significant positive effect on per-flowerhead visitation by the long-horned bee Melissodes lupina and no significant effects on visitation by any other taxa. At the patch scale, per-flowerhead visitation by honeybees significantly increased whereas visitation by M. lupina often decreased with increasing floral density. For both species, responses to patch-scale floral density were strongest when site-scale floral density was high. The scale-dependence of flower visitor responses to floral density and the interactions between site- and patch-scale effects of floral density observed in this study underscore the importance of improving our understanding of pollinators' responses to floral density at population scales.
Data from: Scale-dependent genetic structure of the Idaho giant salamander (Dicamptodon aterrimus) in stream networks
The network architecture of streams and rivers constrains evolutionary, demographic, and ecological processes of freshwater organisms. This consistent architecture also makes stream networks useful for testing general models of population genetic structure and the scaling of gene flow. We examined genetic structure and gene flow in the facultatively paedomorphic Idaho giant salamander, Dicamptodon aterrimus, in stream networks of Idaho and Montana, USA. We used microsatellite data to test population structure models by (1) examining hierarchical partitioning of genetic variation in stream networks and (2) testing for genetic isolation by distance along stream corridors versus overland pathways. Replicated sampling of streams within catchments within three river basins revealed that hierarchical scale had strong effects on genetic structure and gene flow. AMOVA identified significant structure at all hierarchical scales (among streams, among catchments, among basins), but divergence among catchments had the greatest structural influence. Isolation by distance was detected within catchments, and in-stream distance was a strong predictor of genetic divergence. Patterns of genetic divergence suggest that differentiation among streams within catchments was driven by limited migration, consistent with a stream hierarchy model of population structure. However, there was no evidence of migration among catchments within basins, or among basins, indicating that gene flow only counters the effects of genetic drift at smaller scales (within rather than among catchments). These results show the strong influence of stream networks on population structure and genetic divergence of a salamander, with contrasting effects at different hierarchical scales.
Data from: Testing scale-dependent effects of semi-natural habitats on farmland biodiversity
The effectiveness of conservation interventions for maximizing biodiversity benefits from agri-environment schemes (AESs) is expected to depend on the quantity of seminatural habitats in the surrounding landscape. To verify this hypothesis, we developed a hierarchical sampling design to assess the effects of field boundary type and cover of seminatural habitats in the landscape at two nested spatial scales. We sampled three types of field boundaries with increasing structural complexity (grass margin, simple hedgerow, complex hedgerow) in paired landscapes with the presence or absence of seminatural habitats (radius 0.5 km), that in turn, were nested within 15 areas with different proportions of seminatural habitats at a larger spatial scale (10 × 10 km). Overall, 90 field boundaries were sampled across a Mediterranean region (northeastern Italy). We considered species richness response across three different taxonomic groups: vascular plants, butterflies, and tachinid flies. No interactions between type of field boundary and surrounding landscape were found at either 0.5 and 10 km, indicating that the quality of field boundary had the same effect irrespective of the cover of seminatural habitats. At the local scale, extended-width grass margins yielded higher plant species richness, while hedgerows yielded higher species richness of butterflies and tachinids. At the 0.5-km landscape scale, the effect of the proportion of seminatural habitats was neutral for plants and tachinids, while butterflies were positively related to the proportion of forest. At the 10-km landscape scale, only butterflies responded positively to the proportion of seminatural habitats. Our study confirmed the importance of testing multiple scales when considering species from different taxa and with different mobility. We showed that the quality of field boundaries at the local scale was an important factor in enhancing farmland biodiversity. For butterflies, AESs should focus particular attention on preservation of forest patches in agricultural landscapes within 0.5 km, as well as the conservation of seminatural habitats at a wider landscape scale.
Data from: Scale-dependent home range optimality for a solitary omnivore
Spatial and temporal heterogeneity are fundamental mechanisms structuring home ranges. Under optimality, an individual should structure their space use economically to maximize fitness. We evaluated support for three hypotheses related to range optimality in American black bears (Ursus americanus), predicting (1) range location on a landscape will correspond with high vegetation productivity, (2) increasing forest fragmentation will result in larger ranges, and (3) increasing proportion of forest and/or mean vegetation productivity will result in smaller ranges. We used black bear radio telemetry data from Michigan (2009-2015), Missouri (2010-2016) and Mississippi (2008-2017), USA. Annual space use excluded winter, and we separated seasonal space use into spring, summer, and fall. We collected data from 143 bears (80 females, 63 males), resulting in 97 annual and 538 seasonal ranges. We used generalized linear mixed models to evaluate productivity (estimated through Normalized Difference Vegetation Index, NDVI) selection, and range size (km2) variation between individuals. At the annual scale, black bears consistently selected areas with greater vegetation productivity than the surrounding landscape; yet selection weakened and was more variable seasonally. Opposite to our prediction, we found that increasing fragmentation consistently resulted in smaller ranges; non-forested land covers and forest edges might provide greater abundance or more diverse foods for bears. Ranges with a greater proportion of forest were smaller, likely reflecting an increase in food and cover which could reduce movements, yet there was no support for more productive ranges also being smaller as expected from an area minimizing strategy. Black bears displayed a scale-dependent space use strategy: at larger spatial and temporal scales, productivity acted as the strongest limiting factor and energy maximizing was the dominant strategy, while an area minimizing strategy was exhibited seasonally. We revealed consistent, scale-dependent responses by black bears to environmental conditions, demonstrating the intrinsic plasticity of this adaptable omnivore.
Scale-dependent species-area relationship: niche-based versus stochastic processes in a typical subtropical forest
<p><span>Determining the patterns and drivers of the small-scale species-area relationship (SAR) is crucial for improving our understanding of community assembly and biodiversity patterns. Niche-based and stochastic processes are two principal categories of mechanisms potentially driving SARs. However, their relative importance has rarely been quantified rigorously owing to scale-dependence and the simplified niche volumes often used. </span></p> <p><span>In a fully mapped, 24-ha plot of a typical subtropical forest, we built the SARs and well-defined niche-hyper-volumes of a broad range of environmental variables at scales of 10 - 70 m (cell sizes). We then simulated passive sampling and partitioned the variances of the SAR slopes to disentangle the two contrasting mechanisms.</span></p> <p><span>We found that the small-scale SAR best followed a power-law relationship, consistent with large-scale SARs. The SAR slope declined with increasing scale; it was lower than expected under passive sampling at scales below 30 m and higher at larger scales. Environmental niches explained more (39%-64%) of the slope at larger scales, exceeding 50% at scales > 30 m, and these niches always captured the majority of the structured slopes. Environmental position (environmental mean values) effects were steady in absolute strength across scales and explained most (98%-68%) of the niche effect, but this proportion decreased with increasing scale. The effect of environmental heterogeneity increased with spatial scales, starting to rise at the 30 m scale after controlling for environmental position. Excluding soil properties from analyses strongly reduced these niche effects, highlighting the importance of soils for structuring the small-scale SAR. There was also substantial stochasticity in the SAR slopes, which was only partially explained by passive sampling.</span></p> <p><span>Synthesis: Our results show that the small-scale SAR in the studied subtropical forest follows a power-law, exhibits a scale shift in slope at 30 m, and is strongly shaped by niche effects that are dominated by environmental position relative to heterogeneity. However, soil heterogeneity controls the increase of niche effect and shift in the SAR slope with increasing spatial scales. Hence, edaphic factors can be responsible for scale-dependence in small-scale SARs, thereby linking small-scale and large-scale SARs. </span></p>
Supplementary material 1 from: Amatangelo KL, Stevens L, Wilcox DA, Jackson ST, Sax DF (2018) Provenance of invaders has scale-dependent impacts in a changing wetland ecosystem. NeoBiota 40: 51-72. https://doi.org/10.3897/neobiota.40.28914
Supplementary material 1 from: Amatangelo KL, Stevens L, Wilcox DA, Jackson ST, Sax DF (2018) Provenance of invaders has scale-dependent impacts in a changing wetland ecosystem. NeoBiota 40: 51-72. https://doi.org/10.3897/neobiota.40.28914
Data from: Scale-dependent effects of landscape variables on gene flow and population structure in bats
Aim: A common pattern in biogeography is the scale-dependent effect of environmental variables on the spatial distribution of species. We tested the role of climatic and land cover variables in structuring the distribution of genetic variation in the grey long-eared bat, Plecotus austriacus, across spatial scales. Although landscape genetics has been widely used to describe spatial patterns of gene flow in a variety of taxa, volant animals have generally been neglected because of their perceived high dispersal potential.Location: England and Europe. Methods: We used a multiscale integrated approach, combining population genetics with species distribution modelling and geographical information under a causal modelling framework, to identify landscape barriers to gene flow and their effect on population structure and conservation status. Genotyping involved 23 polymorphic microsatellites and 259 samples from across the species' range. Results: We identified distinct population structure shaped by geographical barriers and evidence of population fragmentation at the northern edge of the range. Habitat suitability (as captured by species distribution models, SDMs) was the most important landscape variable affecting genetic connectivity at the broad spatial scale, while at the fine scale, lowland unimproved grasslands, the main foraging habitat of P. austriacus, played a pivotal role in promoting genetic connectivity. Main conclusions: The importance of lowland unimproved grasslands in determining the biogeography and genetic connectivity in P. austriacus highlights the importance of their conservation as part of a wider landscape management for fragmented edge populations. This study illustrates the value of using SDMs in landscape genetics and highlights the need for multiscale approaches when studying genetic connectivity in volant animals or taxa with similar dispersal abilities.
Data from: Scale-dependent strategies for coexistence of mesocarnivores in human-dominated landscapes
Identifying factors influencing the distribution of, and interactions within carnivore communities is important for understanding how they are affected by human activities. Species differ in their ability to adapt to humans depending on their degree of specialization in habitat use and feeding habits. This results in asymmetric changes in the ecology of co-occurring species that can influence their interactions. We investigated whether human infrastructures and free-ranging domestic dogs (a species typically associated with humans) influenced the co-occurrence and habitat use of mesocarnivores in a landscape of high human population density in Maharashtra, India. We used 40 camera trap locations during 233 trapping nights and used Bayesian co-occurrence occupancy models to investigate the habitat use and coexistence of species at different spatial scales. Additionally, we investigated their temporal overlap in space use. Indian foxes altered their habitat use both spatially and temporally in order to avoid free-ranging domestic dogs and other larger competitors. The use of human infrastructure by jackals and jungle cats was limited by the presence of dogs. Our results illustrate how habitat use of smaller carnivore species change both spatially and temporally in order to avoid larger competitors. We also show that the presence of species associated with humans mediates the influence of human infrastructures on the habitat use of mesocarnivores. We highlight the importance of acknowledging the potential impact of urbanization not only on single species, but also on the interactions within the community.
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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.