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495 results for “spatial scale”
Data and code from: Traits and phylogenies modulate the environmental responses of wood-inhabiting fungal communities across spatial scales
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Limited seed dispersal shapes fine-scale spatial genetic structure in a Neotropical dioecious large-seeded palm
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Data from: Philopatry influences the genetic population structure of the blacktip shark (Carcharhinus limbatus) at multiple spatial scales
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Community patch‐dynamics governs direct and indirect nutrient recycling by aggregated animals across spatial scales
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Detecting phylogenetic signal and adaptation in papionin cranial shape by decomposing variation at different spatial scales
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Unraveling the cavity-nesting network at large spatial scales: The biogeographic role of woodpeckers as ecosystem engineers
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Multiple spatial scales affect direct and indirect interactions between a non-native and a native species
Plant–plant interactions influence community assembly and species responses to environmental change. However, species interactions are complex phenomena influenced by context and scale. We conducted a one-year replacement experiment between two grasses in subtropical grasslands (native Axonopus fissifolius and non-native Paspalum notatum) in central Florida, USA. We evaluated interactions between these species at three ecological scales, ‘pairwise interactions’, ‘patch’ (33 cm x 33 cm) and ‘plot’ (1m x 3m), and along a gradient (15 levels) of increasing non-native and decreasing native plot groundcover within enclosures in semi-native pastures. We transplanted 18 individuals of each species per plot (18 × 30 plots = 1080 plants in total) in a 2×2 design intersecting direct pairwise interactions (additional transplanted neighbor: absent/present) with recipient patch type (Axonopus fissifolius/Paspalum notatum). Leaf length, leaf number and plant biomass were measured at the beginning and the end of the experiment along with soil nutrients and pH at patch level. Over 92% of the transplants survived. We observed an interactive effect between patch type (non-native vs. native dominated) and plant abundance at plot level on plant performance, suggesting that indirect effects at larger spatial scales can influence effects at smaller scales. Surprisingly, both species exhibited enhanced performance with increasing abundance of the non-native species at plot level. We discuss several mechanisms explaining these indirect effects including Paspalum notatum induced changes in soil pH, soil feedbacks from the soil microbial community, preconditioning effects of the native species on the recipient soil, and positive density dependence effects after transplantation.
Data from: Genetic structure at three spatial scales is consistent with limited philopatry in Ricord's Rock Iguanas (Cyclura ricordii)
Cyclura ricordii is an endemic iguana from Hispaniola Island and is threatened on the IUCN Red List. The main threats are predation by introduced mammals, habitat destruction, and hunting pressure. The present study focused on two nesting sites from Pedernales Province in the Dominican Republic. The hypothesis that natal philopatry influences dispersal and nest site selection was tested. Monitoring and sampling took place in 2012 and 2013. Polymorphic markers were used to evaluate whether natal philopatry limits dispersal at multiple spatial scales. Ripley's K revealed that nests were significantly clustered at multiple scales, when both nesting sites were considered and within each nesting site. This suggests a patchy, non-random distribution of nests within nest sites. Hierarchical AMOVA revealed that nest site aggregations did not explain a significant portion of genetic variation within nesting sites. However, a small but positive correlation between geographic and genetic distance was detected using a Mantel's test. Hence, the relationship between geographic distance and genetic distance among hatchlings within nest sites, while detectable, was not strong enough to have a marked effect on fine scale genetic structure. Spatial and genetic data combined determined that the nesting sites included nesting females from multiple locations, and the hypothesis of 'natal philopatry', was not supported because females nesting in the same cluster were no more closely related to each other than to other females from the same nesting site. These findings imply that nesting aggregations are more likely associated with cryptic habitat variables contributing to optimal nesting conditions.
Data from: Multiple scales of spatial heterogeneity control soil respiration responses to precipitation across a dryland rainfall gradient
<p><i>Aims –</i> Soil respiration (R<sub>s</sub>) is a major pathway for releasing fixed carbon back to the atmosphere. However, controls over R<sub>s</sub> are poorly understood in arid and hyper-arid systems where microbial activity is frequently constrained by moisture. We addressed key uncertainties in R<sub>s</sub>: 1) How do short-term rainfall pulses affect R<sub>s</sub> at sites that differ in long-term precipitation inputs?, 2) how do R<sub>s</sub> responses to short and long-term rainfall differ across soil surfaces?, and 3) how are R<sub>s</sub> responses affected by local-scale attributes?</p> <p><i>Methods – </i>We measured R<sub>s</sub> responses to rainfall pulses over a 48 h period. Working across a climate gradient, we compared R<sub>s </sub>responses on two contrasting soil surfaces which both had two vegetation/soil morphology patch types that differed in organic matter inputs and accumulation.</p> <p><i>Results – </i>Rates of R<sub>s </sub>were low, but highly responsive to rainfall pulses. Stimulation of R<sub>s </sub>by rainfall was generally greater in areas with higher annual rainfall. However, patterns for R<sub>s </sub>responses to rainfall differed greatly on the two soil surfaces and among patch types.</p> <p><i>Conclusions – </i>The strong role of patch type and soil surface in controlling R<sub>s</sub> points to the need to carefully consider small-scale spatial and temporal variation when interpreting dryland biogeochemical fluxes.</p>
Data from: Specialization and niche overlap across spatial scales: revealing ecological factors shaping species richness and coexistence in Australian songbirds
1. Ecological specialization enables the partitioning of resources and thus can facilitate the coexistence of species and promote higher species richness. Specialization and niche partitioning are expected to exert a decisive influence on local spatial scales, while species richness at regional scales should be shaped mostly by historical factors and abiotic conditions. Moreover, specialization is expected to be particularly important in communities that are exceptionally species rich for their environmental conditions. Concurrently, niche overlap in these communities should be minimized to enable species coexistence. 2. We tested these hypotheses by studying specialization-richness relationship and niche overlap in assemblages of 298 species of songbirds (Passeriformes) across Australia. We used local (2-6 ha) to regional (bioregions) spatial scales, and detailed data on habitat, diet, and foraging behaviour (method, substrate, and stratum). 3. We expected the richness-specialization relationship to be particularly strong i) on local spatial scales and ii) in communities exceptionally species rich for given environmental conditions (approximated by moisture and vegetation complexity). We also expected iii) low niche overlap in assemblages with specialized species. 4. Only the third prediction was partly supported. First, while the specialization and species richness were often positively related, the strength and the direction of the relationship changed between traits and across spatial scales. The strength of the specialization-richness relationship was consistently positive only in foraging stratum, and it increased towards smaller spatial scales only in case of habitat and diet. Simultaneously, species in local communities demonstrated high overlap in habitat and diet. Second, we did not find particularly strong specialization-richness relationships in exceptionally species rich communities. Third, we found the expected negative relationship between specialization and overlap in foraging stratum and substrate (in local communities), suggesting that species partition ecological space locally in terms of where they find food. 5. Our expectations were only weakly supported. Specialization on foraging stratum was probably important in facilitating species co-existence. Conversely, although species were often specialized on habitat and diet, high overlap in these traits did not preclude their local coexistence. Overall, specialization and overlap in foraging traits were more important for species coexistence than habitat or diet.
Data from: Spatial scaling of beta diversity in the shallow marine fossil record
Beta diversity quantifies the spatial structuring of ecological communities and is a fundamental partition of biodiversity, central to understanding many macroecological phenomena in modern biology and paleobiology. Despite its common application in ecology, studies of beta diversity in the fossil record are limited, particularly at regional spatial scales that are important for understanding macroevolutionary processes. The spatial scaling of beta diversity in the fossil record is poorly understood, but has significant implications due to temporal variation in the spatial distribution of fossil collections and the large spatio-temporal scales typically employed. Here we test the spatial scaling of several common measures of beta diversity using the Cenozoic shallow marine molluscan fossil record of New Zealand, and derive a spatially standardized time series of beta diversity. To measure spatial scaling we use and compare grid cell occupancy based on an equal-area grid and summed minimum spanning tree length, both based on reconstructed paleocoordinates of fossil collections. We find that beta diversity is spatially dependent at local to regional scales, regardless of the metric or spatial scaling utilised, and that spatial standardization significantly changes apparent temporal trends of beta diversity and, therefore, inferences about processes driving diversity change.
Data from: Helianthus maximiliani and species fine-scale spatial pattern affect diversity interactions in reconstructed tallgrass prairies
1. Biodiversity and Ecosystem Function analyses aim to explain how individual species and their interactions affect ecosystem function. With this study we asked in what ways do species interact, are these interactions affected by species planting pattern, and are initial (planted) proportions or previous year (realized) proportions a better reference point for characterizing grassland diversity effects? 2. We addressed these questions with experimental communities compiled from a pool of 16 tallgrass prairie species. We planted all species in monocultures and mixtures that varied in their species richness, evenness, and spatial pattern. We recorded species-specific biomass production over three growing seasons and fitted Diversity-Interactions (DI) models to annual plot biomass yields. 3. In the establishment season, all species interacted equally to form the diversity effect. In years 2 and 3, each species contributed a unique additive coefficient to its interaction with every other species to form the diversity effect. These interactions were affected by H. maximiliani and the species planting pattern. Models based on species planted proportions better-fit annual plot yields than models based on species previous contributions to plot biomass. 4. Outcomes suggest that efforts to plant tallgrass prairies to maximize diversity effects should focus on the specific species present and in what arrangement they are planted. Furthermore, for particularly diverse grasslands, the effort of collecting annual species biomass data may not be necessary when quantifying diversity effects with Diversity-Interactions models.
Spatial scaling properties of coral reef benthic communities
<p>The spatial structure of ecological communities on tropical coral reefs across seascapes and geographies have historically been poorly understood. Here we addressed this for the first time using spatially expansive and thematically resolved benthic community data collected around five uninhabited central Pacific oceanic islands, spanning 6° latitude and 17° longitude. Using towed-diver digital image surveys over ~140 linear km of shallow (8 – 20 m depth) tropical reef, we highlight the autocorrelated nature of coral reef seascapes. Benthic functional groups and hard coral morphologies displayed significant spatial clustering (positive autocorrelation) up to kilometre-scales around all islands, in some instances dominating entire sections of coastline. The scale and strength of these autocorrelation patterns showed differences across geographies, but patterns were more similar between islands in closer proximity and of a similar size. For example, crustose coralline algae (CCA) were clustered up to scales of 0.3 km at neighbouring Howland and Baker Islands and macroalgae were spatially clustered at scales up to ~3 km at both neighbouring Kingman Reef and Palmyra Atoll. Of all the functional groups, macroalgae had the highest levels of spatial clustering across geographies at the finest resolution of our data (100 m). There were several cases where the upper scale at which benthic community members showed evidence of spatial clustering correlated highly with the upper scales at which concurrent gradients in physical environmental drivers were spatially clustered. These correlations were stronger for surface wave energy than subsurface temperature (regardless of benthic group) and turf algae and CCA had the closest alignments in scale with wave energy across functional groups and geographies. Our findings suggest such physical drivers not only limit or promote the abundance of various benthic competitors on coral reefs, but also play a key role in governing their spatial scaling properties across seascapes.</p>
Diurnal timing of nonmigratory movement by birds: the importance of foraging spatial scales
Timing of activity can reveal an organism's efforts to optimize foraging either by minimizing energy loss through passive movement or by maximizing energetic gain through foraging. Here, we assess whether signals of either of these strategies are detectable in the timing of activity of daily, local movements by birds. We compare the similarities of timing of movement activity among species using six temporal variables: start of activity relative to sunrise, end of activity relative to sunset, relative speed at midday, number of movement bouts, bout duration, and proportion of active daytime hours. We test for the influence of flight mode and foraging habitat on the timing of movement activity across avian guilds. We used 64570 days of GPS movement data collected between 2002 and 2019 for local (non-migratory) movements of 991 birds from 49 species, representing 14 orders. Dissimilarity among daily activity patterns was best explained by flight mode. Terrestrial soaring birds began activity later and stopped activity earlier than pelagic soaring or flapping birds. Broad-scale foraging habitat explained less of the clustering patterns because of divergent timing of active periods of pelagic surface and diving foragers. Among pelagic birds, surface foragers were active throughout the day while diving foragers matched their active hours more closely to daylight hours. Pelagic surface foragers also had the greatest daily foraging distances, which was consistent with their daytime activity patterns. This study demonstrates that flight mode and foraging habitat influence temporal patterns of daily movement activity of birds.
What drives temporal stability of biomass production? Testing the roles of species diversity, dominance, asynchrony and spatial scale in annual plant communities
<p><span><b><span>Aims:</span></b><span> Primary biomass production is a fundamental process for ecosystem functioning. Yet, little is known on the mechanisms driving temporal stability of biomass production in annual plant communities, particularly in communities </span>subjected to highly variable environments and undergoing temporal changes in species composition.<span> We aimed to disentangle </span>the relative importance of biomass production, species <span>diversity, dominance and asynchrony of species fluctuations as drivers of biomass stability in Mediterranean and semiarid annual plant communities. </span></span></p> <p><span><b><span>Location:</span></b><span> Mediterranean (</span><span>N31<sup>o</sup>42'; E35<sup>o</sup>03') and Semiarid (N31<sup>o</sup>23'; E34<sup>o</sup>54') sites, Israel.</span></span></p> <p><span><b><span>Methods:</span></b><span> Aboveground biomass and species abundance were monitored in 15 plots of 250m<sup>2</sup> per site during eight consecutive years. Relationships between stability drivers and community stability were studied at the regional (between-sites) and local (within-sites) spatial scales.</span></span></p> <p><span><b><span>Results:</span></b><span> Community biomass stability (temporal mean/SD) increased from the Semiarid to the Mediterranean site concomitantly with higher </span>biomass production, richness, and evenness, but was not associated with changes in species synchrony. Differences in stability between sites were due to opposite effects of site conditions on the mean and SD of community biomass, leading to higher stability in the Mediterranean site. Within sites, species asynchrony was the key driver of stability at the local spatial-scale. Richness and biomass production affected stability indirectly through asynchrony, but in different ways at each site. At the Mediterranean site, these factors had indirect negative effects on stability by reducing asynchrony, but did not rescind a positive effect of asynchrony on community stability. At the Semiarid site, biomass production had indirect positive effects on stability through asynchrony, while richness had no effect on asynchrony and stability. Stability was not driven by species evenness in either site. </span></p> <p><span><b><span>Conclusions: </span></b>Our study provides new insights into the complex control of biomass stability in the dynamics of <span>Mediterranean and semiarid annual plant communities, with d</span>ifferent mechanisms driving stability across the regional <i>vs.</i> local spatial scales. </span></p>
Data from: Genetic assessment of population structure and connectivity in the threatened Mediterranean coral Astroides calycularis (Scleractinia, Dendrophylliidae) at different spatial scales
Understanding dispersal patterns, population structure and connectivity among populations is helpful in the management and conservation of threatened species. Molecular markers are useful tools as indirect estimators of these characteristics. In this study we assess the population genetic structure of the endemic Mediterranean coral Astroides calycularis in the Alboran Sea at local and regional scales, and at three localities outside of this basin. Bayesian clustering methods, traditional F-statistics and Dest statistics were used to determine the patterns of genetic structure. Likelihood and coalescence approaches were used to infer migration patterns and effective population sizes. The results obtained reveal a high level of connectivity among localities separated by as much as one kilometer and moderate levels of genetic differentiation among more distant localities, somewhat corresponding with a stepping-stone model of gene flow and connectivity. These data suggest that connectivity among populations of this coral is mainly driven by the biology of the species, with low dispersal abilities; in addition, hydrodynamic processes, oceanographic fronts and the distribution of rocky substrate along the coastline may influence larval dispersal.
Data from: Genetic structure across broad spatial and temporal scales: Rocky Mountain tailed frogs (Ascaphus montanus; Anura: Ascaphidae) in the inland temperate rainforest
Contemporary and historical processes interact to structure genetic variation, however discerning between these can be difficult. Here, we analyze range-wide variation at 13 microsatellite loci in 2098 Rocky Mountain tailed frogs, Ascaphus montanus, collected from 117 streams across the species distribution in the Inland Northwest (INW) and interpret that variation in light of historical phylogeography, contemporary landscape genetics, and the reconstructed paleodistribution of the species. Further, we project species distribution models (SDMs) to predict future changes in the range as a function of changing climate. Genetic structure has a strong spatial signature that is precisely congruent with a deep (~1.8 MY) phylogeographic split in mtDNA when we partition populations into 2 clusters (K = 2), and is congruent with refugia areas inferred from our paleorange reconstructions. There is a hierarchical pattern of geographic structure as we permit additional clusters, with populations clustering following mountain ranges. Nevertheless, genetic diversity is the highest in populations at the center of the range and is attenuated in populations closer to the range edges. Similarly, geographic distance is the single best predictor of pairwise genetic differentiation, but connectivity also is an important predictor. At intermediate and local geographic scales, deviations from isolation-by-distance are more apparent, at least in the northern portion of the distribution. These results indicate that both historical and landscape factors are contributing to the genetic structure and diversity of tailed frogs in the Inland Northwest.
Data from: Fecundity selection on ornamental plumage colour differs between ages and sexes and varies over small spatial scales
Avian plumage colours are some of the most conspicuous sexual ornaments, and yet standardized selection gradients for plumage colour have rarely been quantified. We examined patterns of fecundity selection on plumage colour in blue tits (Cyanistes caeruleus L.). When not accounting for environmental heterogeneity, we detected relatively few cases of selection. We found significant disruptive selection on adult male crown colour and yearling female chest colour and marginally nonsignificant positive linear selection on adult female crown colour. We discovered no new significant selection gradients with canonical rotation of the matrix of nonlinear selection. Next, using a long-term data set, we identified territory-level environmental variables that predicted fecundity to determine whether these variables influenced patterns of plumage selection. The first of these variables, the density of oaks within 50 m of the nest, influenced selection gradients only for yearling males. The second variable, an inverse function of nesting density, interacted with a subset of plumage selection gradients for yearling males and adult females, although the strength and direction of selection did not vary predictably with population density across these analyses. Overall, fecundity selection on plumage colour in blue tits appeared rare and inconsistent among sexes and age classes.
Data from: Geographic isolation and larval dispersal shape seascape genetic patterns differently according to spatial scale
Genetic variation, as a basis of evolutionary change, allows species to adapt and persist in different climates and environments. Yet, a comprehensive assessment of the drivers of genetic variation at different spatial scales is still missing in marine ecosystems. Here, we investigated the influence of environment, geographic isolation, and larval dispersal on the variation in allele frequencies, using an extensive spatial sampling (47 locations) of the striped red mullet (Mullus surmuletus) in the Mediterranean Sea. Univariate multiple regressions were used to test the influence of environment (salinity and temperature), geographic isolation, and larval dispersal on Single Nucleotide Polymorphisms (SNPs) allele frequencies. We used Moran's Eigenvector Maps (db-MEMs) and Asymmetric Eigenvector Maps (AEMs) to decompose geographic and dispersal distances in predictors representing different spatial scales. We found that salinity and temperature had only a weak effect on the variation in allele frequencies. Our results revealed the predominance of geographic isolation to explain variation in allele frequencies at large spatial scale (> 1,000km) while larval dispersal was the major predictor at smaller spatial scale (< 1,000km). Our findings stress the importance of including spatial scales to understand the drivers of spatial genetic variation. We suggest that larval dispersal allows to maintain gene flows at small to intermediate scale, while at broad scale, genetic variation may be mostly shaped by adult mobility, demographic history or multi-generational stepping stone dispersal. These findings bring out important spatial scale considerations to account for in the design of a protected areas network that would efficiently enhance protection and persistence capacity of marine species.
Data from: Drift versus selection as drivers of phenotypic divergence at small spatial scales: the case of Belgjarskógur threespine stickleback
Divergence in phenotypic traits is facilitated by a combination of natural selection, phenotypic plasticity, gene flow and genetic drift, whereby the role of drift is expected to be particularly important in small and isolated populations. Separating the components of phenotypic divergence is notoriously difficult, particularly for multivariate phenotypes. Here we assessed phenotypic divergence of threespine stickleback (Gasterosteus aculeatus) across 19 semi-interconnected ponds within a small geographic region (~7.5 km2) using multivariate comparisons of phenotypic divergence (PST) neutral genetic (FST) and environmental (EST) variation. We found phenotypic divergence across the ponds in a suite of functionally relevant phenotypic traits, including feeding, defense and swimming traits and body shape (geometric morphometric). Comparisons of PSTs with FSTs suggest that phenotypic divergence is predominantly driven by neutral or stabilizing selection, whereas phenotypic divergence in defensive traits is in accordance with divergent selection. Comparisons of population pairwise PSTs with ESTs suggest that phenotypic divergence in swimming traits is correlated with prey availability, whereas there were no clear associations between phenotypic divergence and environmental difference in the other phenotypic groups. Overall, our results suggest that phenotypic divergence of these small populations at small geographic scales is largely driven by neutral processes (gene flow, drift), although environmental determinants (natural selection or phenotypic plasticity) may play a role.
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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.