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94 results for “local environments”
Scripts and files for "Small-scale population divergence is driven by local larval environment in a temperate amphibian"
<p>Genomic variation within and among populations is shaped by the interplay between natural selection and the effects of genetic drift and gene flow. Adaptive divergence can be found in small scale natural systems even when population sizes are small and the potential for gene flow is high, suggesting that local environments exert selection pressures strong enough to counteract the opposing effects of drift and gene flow. Here, we investigated genomic differentiation in nine moor frog (<i>Rana arvalis</i>) populations in a small-scale network of local wetlands using 16 707 ddRAD-seq SNPs, relating levels of differentiation with local environments as well as with properties of the surrounding landscape. We characterized population structure and differentiation, and partitioned the effects of geographic distance, local larval environment and landscape features on total genomic variation. We also conducted gene-environment association studies using univariate and multivariate approaches. We found small-scale population structure corresponding to 6-8 clusters. Local larval environment was the most influential component explaining 2.3% of the total genetic variation followed by landscape features (1.8%) and geographic distance (0.8%), indicative of isolation-by-environment, -by-landscape and -by-distance, respectively. We identified 1000 potential candidate SNPs putatively under divergent selection mediated by the local larval environment. The candidate SNPs were involved in, among other biological functions, immune system function and development. Our results suggest that small scale environmental differences can exert selection pressures strong enough to counteract homogenizing effects of gene flow and drift in this small-scale system leading to observable population differentiation.</p>
Data Set htwddKogRob-InfDynSim for Localization in Highly Crowded Environments
<p>This data set presents a major challenge for robot localization in highly crowded environments. The total distance travelled over all runs is 113.3 km. 50 dynamic obstacles (see htwddKogRob-InfDynSim_dynObstacles.png) were inserted into the map (see htwddKogRob-InfDynSim.png | 1px <span class="math-tex">\(\widehat{=}\)</span> 0.1m).</p> <p>The work was first presented in:</p> <ul> <li>A Fuzzy-based Adaptive Environment Model for Indoor Robot Localization</li> <li>Authors: Frank Bahrmann, Sven Hellbach, Hans-Joachim Böhme</li> <li>Date of Publication: 2016/10/6</li> <li>Conference: Telehealth and Assistive Technology / 847: Intelligent Systems and Robotics</li> <li>Publisher: ACTA Press</li> </ul> <p>Additionally, we present a video with the proposed algorithm and an insight of this dataset under:</p> <ul> <li>youtube.com/AugustDerSmarte</li> <li>https://www.youtube.com/watch?v=26NBFN_XeQg</li> </ul> <p><strong>Instructions for use</strong></p> <p>The zip archives contain ascii files, which hold the log files of the robot observations and robot poses. Since this data set was recorded in a simulated environment, the logfiles include both a changed starting position and a ground-truth pose. For further information, please refer to the header of the logfile. To simplify the parsing of the files, you can use these two Java snippets:</p> <p> </p> <p><strong>Laser Range Measurements:</strong></p> <pre><code class="language-java"> List<Double> ranges = new ArrayList<>(numOfLaserRays); List<Error> errors = new ArrayList<>(numOfLaserRays); String s = line.substring(4); String delimiter = "()"; StringTokenizer tokenizer = new StringTokenizer(s, delimiter); while(tokenizer.hasMoreElements()){ String[] arr = tokenizer.nextToken().split(";"); boolean usable = (arr[0].equals("0")?false:true); double range = Double.parseDouble(arr[1]); ranges.add(range); errors.add(usable?Error.OKAY:Error.INVALID_MEASUREMENT); }</code></pre> <p><strong>Poses:</strong></p> <pre><code class="language-java"> String poseString = line.split(":")[2]; String[] elements = poseString.substring(1, poseString.length()-1).split(";"); double x = Double.parseDouble(elements[0]); double y = Double.parseDouble(elements[1]); double phi = Double.parseDouble(elements[2]);</code></pre> <p> </p>
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: Adaptation of diploid and tetraploid Chamerion angustifolium to elevation but not local environment
Polyploid organisms often have different geographic ranges than their diploid relatives. However, it is unclear whether this divergence is maintained by adaptation or results from historical differences in colonization. Here we conducted a reciprocal transplant experiment with diploid and autotetraploid Chamerion angustifolium to test for adaptation at the ploidy and population level. In the Rocky Mountains, pure diploid populations occur at high elevations and pure autotetraploid populations occur at low elevations with mixed-ploidy populations between. We planted 3134 seedlings in 2004 and 3890 juveniles (bolting) in 2005 among nine plots, three in each of the diploid, mixed-ploidy and tetraploid zones, and monitored survival until 2008. For both seedlings and juvenile plants, elevation significantly influenced survival. The juvenile plants also showed a significant ploidy by elevation interaction, indicating that diploids and tetraploids survived best at their native elevations. In contrast, we found no evidence of local adaptation to plot within elevation. This suggests that the current distribution of diploids and tetraploids across elevations is the result of adaptation and that genome duplication may have facilitated the invasion of lower elevation habitats by limiting the movement of maladapted alleles from diploid populations at higher elevations.
Data from: Adaptation to local climate in a multi-trait space: evidence from silver fir (Abies alba Mill.) populations across a heterogeneous environment
Heterogeneous environments, such as mountainous landscapes, create spatially varying selection pressure that potentially affects several traits simultaneously across different life stages, yet little is known about the general patterns and drivers of adaptation in such complex settings. We studied silver fir (Abies alba Mill.) populations across Switzerland and characterized their mountainous landscape using downscaled historical climate data. We sampled 387 trees from 19 populations and genotyped them at 374 single-nucleotide polymorphisms (SNPs) to estimate their demographic distances. Seedling morphology, growth and phenology traits were recorded in a common garden, and a proxy for water use efficiency was estimated for adult trees. We tested whether populations have more strongly diverged at quantitative traits than expected based on genetic drift alone in a multi-trait framework, and identified potential environmental drivers of selection. We found two main responses to selection: (i) populations from warmer and more thermally stable locations have evolved towards a taller stature, and (ii) the growth timing of populations evolved towards two extreme strategies, "start early and grow slowly" or "start late and grow fast", driven by precipitation seasonality. Populations following the "start early and grow slowly" strategy had higher water use efficiency and came from inner Alpine valleys characterized by pronounced summer droughts. Our results suggest that contrasting adaptive life-history strategies exist in silver fir across different life stages (seedling to adult), and that some of the characterized populations may provide suitable seed sources for tree growth under future climatic conditions.
Data from: Nest size is predicted by female identity and the local environment in the blue tit, but is not related to genetic or foster mother's nest size
The potential for animals to respond to changing climates has sparked interest in intraspecific variation in avian nest structure since this may influence nest microclimate and protect eggs and offspring from inclement weather. However, there have been relatively few large-scale attempts to examine variation in nests or the determinates of individual variation in nest structure within populations. Using a set of mostly pre-registered analyses, we studied potential predictors of variation in the size of a large sample (803) of blue tit (Cyanistes caeruleus) nests across three breeding seasons at Wytham Woods, UK. Whilst our pre-registered analyses found that individual females built very similar nests across years, there was no evidence in follow-up (post hoc) analyses that their nest size correlated to that of their genetic mother or, in a cross-fostering experiment, to the nest where they were reared. In further pre-registered analyses, spatial environmental variability explained nest size variability at relatively broad spatial scales, and especially strongly at the scale of individual nestboxes. Our study indicates that nest structure is a characteristic of individuals, but is not strongly heritable, indicating that it will not respond rapidly to selection. Explaining the within-individual and within-location repeatability we observed requires further study.
Data from: Spore germination determines yeast inbreeding according to fitness in the local environment
Gene combinations conferring local fitness may be destroyed by mating with individuals that are adapted to a different environment. This form of outbreeding depression provides an evolutionary incentive for self-fertilization. We show that the yeast Saccharomyces paradoxus tends to self-fertilize when it is well adapted to its local environment but tends to outcross when it is poorly adapted. This behavior could preserve combinations of genes when they are beneficial and break them up when they are not, thereby helping adaptation. Haploid spores must germinate before mating, and we found that fitter spores had higher rates of germination across a 24-hour period, increasing the probability that they mate with germinated spores from the same meiotic tetrad. The ability of yeast spores to detect local conditions before germinating and mating suggests the novel possibility that these gametes directly sense their own adaptation and plastically adjust their breeding strategy accordingly.
A dataset for RSSI based outdoor localization using LoRaWAN in a harbor as a harsh and industrial environment
<p>Enabling precise device localization is a critical requirement for the future of industry. Leveraging signal features for location determination has emerged as a leading approach and good alternative for Global Navigation Satellite Systems (GNSS) because of their limitations (low accuracy for indoor environments, expensive chips, and high energy consumption). On this basis, to provide localization for IoT in an industry with a harsh environment, the adopted wireless networks should have a long range coverage area. LoRaWAN is one of the most common communication networks that can provide large coverage with low power consumption and low implementation cost. Between various signal features that can be used for localization, Received Signal Strength (RSS) received more attention because of their low-cost deployment. But, RSS is highly dependent and sensitive to environmental changes, such as temperature, humidity, and background noise. This sensitivity becomes more intensive in an industrial environment with a harsh and dynamic environment. In order to evaluate the environmental effects on RSS in the harsh and highly dynamic industry, we present a comprehensive repository of LoRaWAN Received Signal Strength Indicator (RSSI) measurements, collected in a harbor as a testbed featuring three LoRaWAN gateways and one mobile end node. During the data collecting process, the mobile device obtains its location via a GPS and transmits it as the LoRaWAN message. In addition, to provide more insight of the effect of dynamic environment on the RSSI, two end nodes are implemented in fixed locations. These end nodes transmit messages with fixed time intervals including their unique id. The collected dataset includes RSSI and SNR measurements recorded by multiple gateways for each transmitted packet by fixed or mobile end nodes, and timestamp. This dataset enables the development and evaluation of RSSI-based localization and allows researchers to explore the challenges and opportunities associated with localization in dynamic IoT deployments.</p>
Regional and local environment drive biogeographic patterns in intertidal microorganisms
<p><span>Aim:</span><span> Understanding large-scale spatial distribution patterns is not only a central goal of ecology but is also essential for conservation planning. Nevertheless, the biogeographical patterns of diversity and composition remain unclear for microorganisms and the role of various factors in structuring their assemblages is still poorly known. Here, we tested whether the diversity and community structure of ciliates are driven by both local environmental and regional dispersal-related processes.</span></p> <p><span>Location:</span><span> Coasts of China.</span></p> <p><span>Taxon:</span><span> Benthic ciliates.</span></p> <p><span>Results:</span><span> We found that local environmental factors including BI, salinity and MPS were more important in shaping ciliate alpha diversity than latitude. However, the Shannon alpha diversity index decreased with latitude, perhaps due to anthropogenic disturbances. DistLM analysis emphasized regional processes in shaping community structure. Both NMDS and PERMANOVA supported a clear separation among the three clusters matching with the ecoregional delineations suggested for macroorganisms. We also note that community trait composition was partially explained by a local factor, i.e. the maximum spring tide range of beaches.</span></p> <p><span>Main conclusions:</span><span> Ciliate communities were driven by both local environmental and regional factors. We suggest that these biogeographic patterns may have stemmed from large-scale environmental filtering related to the outflow of Yangtze River, rather than from dispersal limitation or historical events. The current study provides a new understanding of the biogeographic patterns and underlying mechanisms of marine microorganisms, thus helping improve their management and conservation in the face of future global change.</span></p>
Data from: Correlation of shell phenotype and local environment suggests a role for natural selection in the evolution of Placostylus snails
The giant edible Placostylus snails of New Caledonia occur across a wide range of environmental conditions, from the dry southwest to the wetter central and northeastern regions. In large, slow-moving animals such as Placostylus, speciation could be assumed to be largely driven by allopatry and genetic drift as opposed to natural selection. We examined variation in shell morphology using geometric morphometrics and genetic structure within two species of Placostylus (P. fibratus, P. porphyrostomus), to determine the drivers of diversity in this group. Despite the current patchy distribution of snails on New Caledonia, both mtDNA and nuclear SNP data sets (>3000 loci) showed weak admixing between populations and species. Shell morphology was concordant with the genetic clusters we identified and had a strong relationship with local environment. The genetic data, in contrast to the morphological data, did not show concordance with climatic conditions, suggesting the snails are not limited in their ability to adapt to different environments. In sympatry, P. fibratus and P. porphyrostomus maintained genetic and morphological differences, suggesting a genetic basis of phenotypic variation. Convergence of shell shape was observed in two adjacent populations that are genetically isolated but experience similar habitat and climatic conditions. Conversely, some populations in contrasting environments were morphologically distinct although genetically indistinguishable. We infer that morphological divergence in the Placostylus snails of New Caledonia is mediated by adaptation to the local environment.
Safe trajectories from local information for coverage control in non-convex environments
<h2>Description</h2> <p>This dataset contains 3-channels grid-based representations of local information individually retrieved by robots in a team, tasked with a coverage control operation. Data collection was performed running 50 episodes of a coverage control mission with a team of 16 robots controlled by a theoretically proven safe expert controller.</p> <h3>Features</h3> <p>Features encode local information in a 3-channels <em>64 x 64</em> image, corresponding to the discretized sensing region of the robot. The first channel encodes the local likelihood density, the second one the position of team-mates, and the third channel contains the position of obstacles and boundaries. </p> <p><em>imgs{i}.npy</em> files contain data collected over each episode in the form of a [<em>S, N, C, W,</em> W] <em>numpy </em>array, where S is the number of steps of that episode, N is the number of robots, C = 3 is the number of channels, and W = 64 is the size of the image. </p> <h3>Labels</h3> <p>Labels contain the 2D velocity calculated by the expert controller, which is theoretically proven to guarantee collision avoidance. </p> <p><em>vels{i}.npy </em>files contain data collected over each episode in the form of a [<em>S, N, 2</em>] <em>numpy</em> array, associated to the corresponding feature.</p> <p> </p> <h2>Training and Testing</h2> <p>Code for training and testing a CNN-based model mapping local information to 2D velocity is available at <a href="https://github.com/ARSControl/cnn_coverage.git">https://github.com/ARSControl/cnn_coverage.git</a>.</p> <p> </p> <h2>Contact Information</h2> <p>If you are interested in any further information, please contact <a href="mailto:mattia.catellani@unimore.it">mattia.catellani@unimore.it</a>.</p> <p> </p>
Data from: Short-term microbial effects of a large-scale mine-tailing storage facility collapse on the local natural environment
We investigated the impacts of the Mount Polley tailings impoundment failure on chemical, physical, and microbial properties of substrates within the affected watershed, comprised of 70 hectares of riparian wetlands and 40 km of stream and lake shore. We established a biomonitoring network in October of 2014, two months following the disturbance, and evaluated riparian and wetland substrates for microbial community composition and function via 16S and full metagenome sequencing. A total of 234 samples were collected from substrates at 3 depths and 1,650,752 sequences were recorded in a geodatabase framework. These data revealed a wealth of information regarding watershed-scale distribution of microbial community members, as well as community composition, structure, and response to disturbance. Substrates associated with the impact zone were distinct chemically as indicated by elevated pH, nitrate, and sulphate. The microbial community exhibited elevated metabolic capacity for selenate and sulfate reduction and an abundance of chemolithoautotrophs in the Thiobacillus thiophilus/T. denitrificans/T. thioparus clade that may contribute to nitrate attenuation within the affected watershed. The most impacted area (a 6km stream connecting two lakes) exhibited 30% lower microbial diversity relative to the remaining sites. The tailings impoundment failure at Mount Polley Mine has provided a unique opportunity to evaluate functional and compositional diversity soon after a major catastrophic disturbance to assess metabolic potential for ecosystem recovery.
Use climatic space-for-time substitutions with care: not only climate, but also local environment affect performance of the key forest species bilberry along elevation gradient
<p><span>An urgent aim of ecology is to understand how key species relate to climatic and environmental variation, to better predict their prospects under future climate change. The abundant dwarf shrub bilberry (<em>Vaccinium myrtillus</em> L.) has caught particular interest due to its uphill expansion into alpine areas. Species' performance under changing climate has been widely studied using the climatic space-for-time approach along elevation gradients, but potentially confounding, local environmental variables that vary along elevation gradients have rarely been considered. In this study, performed in ten sites along an elevation gradient (200–875 m) in W Norway, we recorded species composition and bilberry performance, both vegetative (ramet size and cover) and reproductive (berry and seed production) properties, over one to four years. We disentangled effects of local environmental variables and between-year, climatic variation (precipitation and temperature), and identified shared and unique contributions of these variables by variation partitioning. We found bilberry ramet size, cover, and berry production to peak at intermediate elevations, whereas seed production increased upwards. The peaks were less pronounced in extreme (dry or cold) summers than in normal summers. Local environmental variables explained much variation in ramet size and cover, less in berry production, and showed no relation to seed production. Climatic variables explained more of the variation in berry and seed production than in ramet size and cover, with temperature relating to vegetative performance, and precipitation to reproductive performance. Bilberry's clonal growth and effective reproduction probably explain why the species persists in the forest and at the same time invades alpine areas. Our findings raise concerns about the appropriateness of the climatic space-for-time approach. We recommend including both climatic and local environmental variables in studies of variation along elevation gradients, and conclude that variation partitioning can be a useful supplement to other methods for analysing variation in plant performance. </span></p>
Intrinsic traits, social context, local environment, and home range size and fidelity data from a field study of sleepy lizards, 2009 - 2017
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Context dependence of local adaptation to abiotic and biotic environments: a quantitative and qualitative synthesis
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Data from: AFLPs and mitochondrial haplotypes reveal local adaptation to extreme thermal environments in a freshwater gastropod
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Self-organising cicada choruses respond to the local sound and light environment
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Regional and local environment drive biogeographic patterns in intertidal microorganisms
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Data from: Reciprocally-transplanted lizards along an elevational gradient match light-environment use of local lizards via phenotypic plasticity
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Data from: Localization of QTL for diapause and other photoperiodically regulated life-history traits important in adaptation to seasonally varying environments
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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.