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154 results for “local structure”
Population structure and genetic variance among local populations of an non-native earthworm species in Minnesota, USA
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Human impacts on Great Lakes walleye Sander vitreus structure, diversity, and local adaptation
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Data from: Climate and local environment structure asynchrony and the stability of primary production in grasslands
<p><b>Aim</b>: Climate variability threatens to destabilize production in many ecosystems. Asynchronous species dynamics may buffer against such variability when decreased performance by some species is offset by increased performance of others. However, high climatic variability can eliminate species through stochastic extinctions or cause similar stress responses among species, reducing buffering. Local conditions, such as soil nutrients, can further alter production stability directly or by influencing asynchrony. We test these hypotheses using a globally distributed sampling experiment.</p> <p><b>Location</b>: Grasslands in North America, Europe and Australia.</p> <p><b>Time period</b>: Annual surveys over five-year intervals occurring between 2007 and 2014.</p> <p><b>Major taxa studied</b>: Herbaceous plants.</p> <p><b>Methods</b>: We annually sampled per-species cover and aboveground community biomass (net primary productivity; NPP), plus soil chemical properties, in twenty-nine grasslands. We tested how soil conditions, combined with precipitation and temperature variability, affect species richness, asynchrony and temporal stability of primary productivity. We used bivariate relationships and structural equation modeling to examine proximate and ultimate relationships.</p> <p><b>Results</b>: Climate variability strongly predicted asynchrony, whereas NPP stability was more related to soil conditions. Species richness was structured by both climate variability and soils, and in turn increased asynchrony. Temperature and precipitation variability caused a unimodal asynchrony response, with asynchrony lowest at low and high climate variability. Climate impacted stability indirectly through its effect on asynchrony, with stability increasing at higher asynchrony due to lower inter-annual NPP variability. Soil conditions had no detectable effect on asynchrony but increased stability by increasing mean NPP, especially when soil organic matter was high.</p> <p><b>Main Conclusions</b>: We found globally consistent evidence that climate modulates species asynchrony, but that the direct effect on stability is low relative to local soil conditions. Nonetheless, our observed unimodal responses to temperature and precipitation variability suggest asynchrony thresholds, beyond which there are detectable destabilizing impacts of climate on primary productivity.</p>
113Cd Solid-State NMR at 21.1 T Reveals the Local Structure and Passivation Mechanism of Cadmium in Hybrid and All-Inorganic Halide Perovskites
<p>Raw NMR data in Bruker Topspin format. Input and output files of the quantum mechanical calculations.</p>
Data from: Neighbour species richness and local structural variability modulate aboveground allocation patterns and crown morphology of individual trees
<p>Local neighbourhood interactions are considered a main driver for biodiversity–productivity relationships in forests. Yet, the structural responses of individual trees in species mixtures and their relation to crown complementarity remain poorly understood. Using a large‐scale forest experiment, we studied the impact of local tree species richness and structural variability on above‐ground wood volume allocation patterns and crown morphology. We applied terrestrial laser scanning to capture the three‐dimensional structure of trees and their temporal dynamics. We found that crown complementarity and crown plasticity increased with species richness. Trees growing in species‐rich neighbourhoods showed enhanced aboveground wood volume both in trunks and branches. Over time, neighbourhood diversity induced shifts in wood volume allocation in favour of branches, in particular for morphologically flexible species. Our results demonstrate that diversity‐mediated shifts in allocation pattern and crown morphology are a fundamental mechanism for crown complementarity and may be an important driver of overyielding.</p> <p> </p>
Data from: Effect of plant chemical variation and mutualistic ants on the local population genetic structure of an aphid herbivore
1.Plants exhibit impressive genetic and chemical diversity, not just between species but also within species, and the importance of plant intraspecific variation for structuring ecological communities is well known. When there is variation at the local population level, this can create a spatially‐heterogeneous habitat for specialized herbivores potentially leading to non‐random distribution of individuals across host‐plants. 2.Plant variation can affect herbivores directly and indirectly via a third species, resulting in variable herbivore growth rates across different host plants. Herbivores also exhibit within‐species variation, with some genotypes better adapted to some plant variants than others. 3.We genotyped aphids collected across two years from a field site containing ~200 patchily‐distributed host plants that exhibit high chemical diversity. The distribution of aphid genotypes, their ant mutualists, and other predators was assessed across the plants. 4.We present evidence that the local distribution of aphid (Metopeurum fuscoviride) genotypes across host‐plant individuals is associated with variation in the plant volatiles (chemotypes) and non‐volatile metabolites (metabotypes) of their host plant tansy (Tanacetum vulgare). Furthermore, these interactions in the field were influenced by plant‐host preferences of aphid‐mutualist ants. 5.Our results emphasize that plant intraspecific variation can structure ecological communities not only at the species level but also at the genetic level within species, and that this effect can be enhanced through indirect interactions with a third species.
Data from: Landscape heterogeneity and local adaptation define the spatial genetic structure of Pacific salmon in a pristine environment
Identifying the spatial distribution of genetic variation across the landscape is an essential step in informing species conservation. Comparison of closely related and geographically overlapping species can be particularly useful in cases where landscape may similarly influence genetic structure. Congruent patterns among species highlight the importance that landscape heterogeneity plays in determining genetic structure whereas contrasting patterns emphasize differences in species-specific ecology and life-history or the importance of species-specific adaptation to local environments. We examined the interacting roles of demography and adaptation in determining spatial genetic structure in two closely related and geographically overlapping species in a pristine environment. Using single nucleotide polymorphism (SNP) loci exhibiting both neutral and putative adaptive variation, we evaluated the genetic structure of sockeye salmon in the Copper River, Alaska; these data were compared to existing data for Chinook salmon from the same region. Overall, both species exhibited patterns of isolation by distance; the spatial distribution of populations largely determined the distribution of genetic variation across the landscape. Further, both species exhibited largely congruent patterns of within- and among-population genetic diversity, highlighting the role that landscape heterogeneity and historical processes play in determining spatial genetic structure. Potential adaptive differences among geographically proximate sockeye salmon populations were observed when high FST outlier SNPs were evaluated in a landscape genetics context. Results were evaluated in the context of conservation efforts with an emphasis on reproductive isolation, historical processes, and local adaptation.
Data from: Local coastal configuration rather than latitudinal gradient shape clonal diversity and genetic structure of Phymatolithon calcareum maerl beds in North European Atlantic
Maerl beds are one of the world's key coastal ecosystems and are threatened by human activities and global change. In this study, the genetic diversity and structure of one of the major European maerl-forming species, Phymatolithon calcareum, was studied using eight microsatellite markers. Two sampling scales (global: North East Atlantic and regional: Galicia) were investigated and fifteen maerl beds from Atlantic Europe were sampled. At the regional-scale the location of sites outside and within four estuaries allowed to test for the influence of coastal configuration on population connectivity and genetic diversity. Results suggested that clonal reproduction plays an important role in the population dynamics of P. calcareum maerl beds. Clonality was variable among populations, even within the same region. At the European scale, these differences in clonality cannot be explained by the geographic or latitudinal distribution of the populations studied. A significant genetic differentiation was found among almost all population pairs and a positive correlation between geographic and genetic distances showed the limited dispersal capacity of P. calcareum. Moreover, a very clear pattern of genetic structure was revealed at the regional scale between populations located within and at the mouth of the estuaries. Genetic differentiation among estuaries was less marked for the sites located in outer-zones compared to those located in the inner-zones. In addition, variation in level of clonality linked to seascape was also observed: populations situated in the outer-zones of the estuaries were less clonal than those in the inner-zones. Finally, populations from the same estuary generally shared one or several mutilocus genotypes.
Data from: Tick infestation of chicks in a seabird colony varies with local breeding synchrony, local nest density and habitat structure
Parasites are a major risk for group-living animals and seabirds are notoriously susceptible to ectoparasite infestations because they commonly nest in dense colonies. Ticks parasitize seabirds across all biogeographical regions and they can be particularly harmful to nestlings, but the ecological factors that affect their transmission to chicks are little studied and poorly understood. Here we show that abundance of tick larvae in blue-footed booby (Sula nebouxii) broods varies with local nest synchrony and density, and also with habitat structure: abundance increased with local breeding synchrony, was linearly and quadratically related to local nest density, and was highest toward the southern end of the study area which has suitable (boulder-rich) habitat for ticks. Also, with increasing chick age infestation first increased and then declined. The results of this study highlight how local physical and social environmental factors influence infestation of seabird nestlings by ticks.
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: Landscape composition has limited impact on local genetic structure in mountain clover, Trifolium montanum L.
Semi-dry grasslands in the European Alps have been increasingly fragmented over the last 150 years. Few studies have investigated the implications of landscape configuration for genetic structure and gene flow among remnant habitat patches. Conservation management of semi-dry grassland plants rarely accounts for possible effects of major landscape elements; such as forest patches, as barriers to gene flow and dispersal via seed and pollen, despite their potential importance for biodiversity conservation. Using 1,416 individuals from 61 sampling sites across two valleys in South-Eastern Switzerland and AFLP fingerprints we applied a spatial strip and a circle approach to determine the impact of different landscape elements on genetic differentiation in the semi-dry grassland herb Trifolium montanum (mountain clover). Overall genetic differentiation among sampling sites was low (overall FST = 0.044). Forest area had no effect on gene flow at the landscape scale but area of semi-dry grassland, the potential habitat of T. montanum, road area and altitude influenced genetic differentiation among sampling sites. The observed pattern of genetic differentiation suggests that a future increase in forest area, due to land use abandonment, at least in the short term, are unlikely to directly impact patterns of genetic variation in T. montanum.
Data from: From global to local genetic structuring in the red gorgonian Paramuricea clavata: the interplay between oceanographic conditions and limited larval dispersal
Defining the scale of connectivity among marine populations and identifying the barriers to gene flow are tasks of fundamental importance for understanding the genetic structure of populations and for the design of marine reserves. Here we investigated the population genetic structure at three spatial scales of the red gorgonian Paramuricea clavata (Cnidaria, Octocorallia) a key species dwelling in the coralligenous assemblages of the Mediterranean Sea. Colonies of P. clavata were collected from 39 locations across the Mediterranean Sea from Morocco to Turkey and analysed using microsatellite loci. Within three regions (Medes, Marseille and North Corsica) sampling was obtained from multiple locations and at different depths. Three different approaches (measures of genetic differentiation, Bayesian clustering and spatially explicit maximum-difference algorithm) were used to determine the pattern of genetic structure. We identified genetic breaks in the spatial distribution of genetic diversity which were concordant with oceanographic conditions in the Mediterranean Sea. We revealed a high level of genetic differentiation among populations and a pattern of isolation by distance across the studied area and within the three regions, underlining short effective larval dispersal in this species. We observed genetic differentiation among populations in the same locality dwelling at different depths which may be explained by local oceanographic conditions and which may allow a process of local adaptation of the populations to their environment. We discuss the implications of our results for the conservation of the species which is exposed to various threats.
FIGURE 1. Map showing collection localities for L in Morphological diversity and genetic structure within Lerista kalumburu Storr, 1976 (Squamata: Scincomorpha: Sphenomorphidae) — taxonomic implications
FIGURE 1. Map showing collection localities for L. kalumburu. Type locality (Kalumburu) in red, collection locality for twotoed specimens (Theda Station) in yellow. Locality lacking tissue sample (Doongan Station) indicated with hollow symbol. (Google © 2010; Image NASA © 2012 Cnes/Spot Image Data S10, NOAA, U.S. Navy, NGA, CEBCO).
Analysis of the Structure and Conduct of Watermelon Marketing in Ibarapa Central Local Government Area of Oyo State
<p><i>This study was carried out to analyze the structure and conduct of watermelon marketing in Ibarapa Central Local Government Area of Oyo State. Specific objectives of the study include to describe the socio-economic characteristics of watermelon marketers, examine the marketing margin and marketing efficiency of marketers in the study area. Multi-stage sampling technique was employed to select 95 marketers. Primary data were collected using a set of well-structured questionnaire. Data were analyzed using descriptive statistics, Gini coefficient model and marketing efficiency index. The result of the study shows that 57.9% of the marketers were male, 41.1% were married, Gini Coefficient result of 0.56 indicated a moderate concentration of watermelon marketers. Market Efficiency Index of 2.43 revealed a high level of efficiency in the market. Inadequate shed and price fluctuation were among the major constraints identified in the study area. It was therefore recommended that Local Government Authority in the area should as a matter of urgency construct sets of buildings to serve as store or shop which will be made available at affordable prices to the marketers.</i></p>
Replication package for the paper: Harnessing Test Call Structures for Improved Fault Localization Effectiveness
<p>This repository contains the replication package for the paper <strong>"Harnessing Test Call Structures for Improved Fault Localization Effectiveness"</strong>. The package includes the necessary scripts, data, and instructions to reproduce the results presented in the study, focusing on the effectiveness of Spectrum-Based Fault Localization (SBFL) using the Barinel algorithm.</p> <h3>Description of Folders and Files:</h3> <ul> <li><strong>algorithms/</strong>: Contains the SBFL algorithms implemented for this study. Note that only the Barinel algorithm was used in the presented results.</li> <li><strong>base/</strong>: Contains the scripts needed for calculating spectra for SBFL.</li> <li><strong>D4J/</strong>: Contains the Defects4J projects. These need to be unpacked using the appropriate scripts provided in this folder.</li> <li><strong>changeset.json</strong>: Contains metadata about changesets for the projects analyzed in this study.</li> <li><strong>main.py</strong>: The main script for calculating ranks and metrics for the selected projects and heuristics.</li> <li><strong>SBFL ranks.csv</strong>: Contains the SBFL ranks calculated from the analysis.</li> </ul> <h2>Requirements</h2> <p>To run the scripts, you will need:</p> <ul> <li><strong>Python 3.9</strong></li> <li><strong>Defects4J</strong>: The <code>D4J</code> folder should contain unpacked Defects4J projects. Please ensure you have followed the instructions in the <code>D4J</code> folder to unpack the projects accordingly.</li> <li><strong>Required Python packages</strong> (install using <code><a href="http://localhost:63343/markdownPreview/1636345610/markdown-preview-index-2076127249.html?_ijt=mqjd55qrfb1m1q15g8bm74pk1u#"></a>pip</code>): <code><a href="http://localhost:63343/markdownPreview/1636345610/markdown-preview-index-2076127249.html?_ijt=mqjd55qrfb1m1q15g8bm74pk1u#"></a>pip install -r requirements.txt</code></li> <li><strong>Prepare the Defects4J Projects</strong>: <ul> <li>Navigate to the <code>D4J</code> directory.</li> <li>Run the provided scripts to unpack the necessary Defects4J projects.</li> <li>Ensure that each project folder is structured properly to be used by the <code>main.py</code> script.</li> </ul> </li> </ul> <h2>Running the Main Script</h2> <p>The main analysis script is <code>main.py</code>, which calculates the SBFL ranks using the Barinel algorithm based on the selected heuristics.</p> <h3>Usage</h3> <p>To run the main script:</p> <div></div> <pre><code><a href="http://localhost:63343/markdownPreview/1636345610/markdown-preview-index-2076127249.html?_ijt=mqjd55qrfb1m1q15g8bm74pk1u#"></a>python main.py </code></pre> <h3>Parameters and Settings:</h3> <ul> <li><strong>Projects and Ranges</strong>: The projects are defined in the <code>projects</code> list, with their respective bug ranges in the <code>ranges</code> list. The script iterates over these projects and bug IDs to calculate SBFL ranks.</li> </ul> <h3>Outputs:</h3> <ul> <li>The script outputs the ranks and coverage metrics directly to the console. Results can be redirected or saved as needed.</li> <li>It uses the <code>Ranks.RankContainer</code> class to calculate and print the minimum suspiciousness ranks for the selected metrics.</li> </ul>
Landscape structure and local variables affect plant community
<p>The biodiversity in agricultural landscapes depends on land-use types, natural elements, and farming intensity. The Brazilian Cerrado is a biodiversity hotspot, however, the native vegetation loss rates have increased in the last years, leading several plant species to extinction risk. Here, we analyze the effects of local (soil fertility and litter amount) and landscape variables (patch shape, habitat amount, compositional heterogeneity, matrix dominance and connectivity) on alpha species richness and diversity, and basal area of different Cerrado vegetation types (savanna, forested savanna, and forest) using linear models and Akaike information criterion. We calculated landscape metrics at different spatial scales for 49 sampling sites in intensive farming landscapes. Woody plant diversity and richness were positively related to soil fertility and landscape compositional heterogeneity at 1500 m spatial scale. Plant richness was negatively related to the patch shape of remnants at 1000 m spatial scale. The effects of litter amount to explain the basal area varied between vegetation types. We found a positive effect in savanna and forested savanna and a negative effect in forest areas. Our findings suggest that the increase of monocultures lead to a decline on plant diversity in the studied landscapes. Also, local variables and the diversity of vegetation types need to be considered to design restoration actions in Cerrado. Sustainable intensification and biodiversity-friendly production systems may be alternatives to increase compositional heterogeneity, thus favoring plant diversity in Cerrado farming landscapes.</p>
Involvement of global coordinative structure in achieving the local pendulum swinging task
<p>Description:</p> <p>・This dataset contains the movement data (only vertical direction).</p> <p>・Each file name represents experimental conditions.</p> <p> - C: constrained, F: free(unconstrained)</p> <p> - AP: anti-phase, IP: in-phase</p> <p> - 90-150: BeatPerMinute</p> <p> </p> <p>abstract:</p> <p>In the literature on inter-limb coordination, the coordination among “focal” body parts (i.e., the two limbs) directly engaged in a pendulum swinging task has been studied by immobilizing other body parts to reduce “noise,” while putting aside questions of how one maintains posture while performing the task. However, in practical performance of musical instruments, for example, performers must coordinate different body parts in sync with the music while maintaining the whole body’s balance. This study demonstrates the effectiveness and necessity of understanding inter-limb coordination in whole-body coordination. Participants were asked to move two pendulums either in sync or alternatively with metronome beeps under two conditions: immobile (fixed forearms) and mobile (forearms not fixed). The explorative analyses focused on whether and how coordinative structures emerged and whether the degree of task achievement differed according to the phase mode, frequency, and mobility conditions. The motion similarity and phase difference between different parts and the pendulums showed that task-specific coordinative structures emerged in both immobile and mobile conditions. In the in-phase mobile condition, the emergent coordinative structure may have improved task achievement, shown by the phase difference between the left and right pendulums. These findings suggest that the global coordinative structure is involved in achieving the local pendulum swinging task.</p>
FIGURE. Coprolites preserved in an early Permian fern mesophyll. A, Gross morphology of a fragmentary fern frond, specimen PB23532. B, Basal part of a penultimate pinna showing sphenopteroid vegetative pinnules. C, Polished surface showing two sporangia with typical annulus structures (white arrowheads). D, SEM image showing an in situ trilete spore. E, The fertile pinnule which contains numerous coprolites along a transverse wound area. F, Enlargement showing coprolites filled with brown to black contents. G, SEM image of the same part in E. H, SEM image showing locally preserved epidermal cells and nearby coprolites. in Discovery of coprolites in an Early Permian fern mesophyll
FIGURE. Coprolites preserved in an early Permian fern mesophyll. A, Gross morphology of a fragmentary fern frond, specimen PB23532. B, Basal part of a penultimate pinna showing sphenopteroid vegetative pinnules. C, Polished surface showing two sporangia with typical annulus structures (white arrowheads). D, SEM image showing an in situ trilete spore. E, The fertile pinnule which contains numerous coprolites along a transverse wound area. F, Enlargement showing coprolites filled with brown to black contents. G, SEM image of the same part in E. H, SEM image showing locally preserved epidermal cells and nearby coprolites.
The relative influence of history, climate, topography and vegetation structure on local animal richness varies among taxa and spatial grains
<p>Understanding the spatial scales at which environmental factors drive species richness patterns is a major challenge in ecology. Due to the trade-off between spatial grain and extent, studies tend to focus on a single spatial scale, and the effects of multiple environmental variables operating across spatial scales on the pattern of local species richness have rarely been investigated.</p> <p>Here, we related variation in local species richness of ground beetles, landbirds, and small mammals to variation in vegetation structure and topography, regional climate, biome diversity, and glaciation history for 27 sites across the USA at two different spatial grains.</p> <p>We studied the relative influence of broad-scale (landscape) environmental conditions using variables estimated at the site level (climate, productivity, biome diversity, and glacial era ice cover) and fine-scale (local) environmental conditions using variables estimated at the plot level (topography and vegetation structure) to explain local species richness. We also examined whether plot-level factors scale up to drive continental scale richness patterns. We used Bayesian hierarchical models and quantified the amount of variance in observed richness that was explained by environmental factors at different spatial scales.</p> <p>For all three animal groups, our models explained much of the variation in local species richness (85-89%), but site-level variables explained a greater proportion of richness variance than plot-level variables. Temperature was the most important site-level predictor for explaining variance in landbirds and ground beetles richness. Some aspects of vegetation structure were the main plot-level predictors of landbird richness. Environmental predictors generally had poor explanatory power for small mammal richness, while glacial era ice cover was the most important site-level predictor.</p> <p>Relationships between plot-level factors and richness varied greatly among geographical regions and spatial grains, and most relationships did not hold when predictors were scaled up to continental scale. Our results suggest that the factors that determine richness may be highly dependent on spatial grain, geography, and animal group. We demonstrate that instead of artificially manipulating the resolution to study multi-scale effects, a hierarchical approach that uses fine grain data at broad extents could help solve the issue of scale selection in environment-richness studies. </p>
Local structure and density of liquid Fe-C-S alloys at Moon's core conditions
<p>This file includes the raw CAESAR and absorption data measured in each P-T condition and the Python codes for diffraction and absorption data analysis.</p> <p>Matlab codes for P-T calibration are also enclosed.</p>
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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.
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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.
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