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Large scale simulation of pressure induced phase-field fracture propagation using Utopia
<p>Utopia is an open-source C++ library for parallel non-linear multilevel solution strategies. Utopia provides the advantages of high-level programming interfaces while at same time a framework to access low level data-structures without breaking code encapsulation. Complex numerical procedures can be expressed with few lines of code, and evaluated by different implementations, libraries, or computing hardware. In this paper we investigate the parallel performance of our implementation of the recursive multilevel trust-region (RMTR) method based on the Utopia library. RMTR is a globally convergent multilevel solution strategy designed to solve non-convex constrained minimization problems. In particular, we solve pressure induced phase-field fracture propagation in large and complex fracture networks. Solving such problems is deemed challenging even for a few fractures, however, here we are considering realistic and idealized networks with up to 1000 fractures.</p>
Meeting radiation dosimetry capacity requirements of population-scale exposures by geostatistical sampling
<p>This is the data repository for the PLOS ONE Manuscript: "Meeting radiation dosimetry capacity requirements of population-scale exposures by geostatistical sampling". This repository contains the following data:</p> <p>1. "State-and-Subdivision-Boundary-Files.Edited-for-ArcMap-10.4.KML-Format.zip":</p> <p>This file contains modified U.S. state and sub-division boundary files [in KML format], which can be imported into ArcMap using its KMLtoLayer function. These files have been modified to prevent sub-division naming issues that we encountered when importing boundary data into ArcMap: A) State sub-divisions with identical names are considered a single sub-division by ArcMap (corrected by adding a letter after each sub-division of the same name, i.e. CenterA, CenterB, etc), and; B) ArcMap would only identify the sub-division by its first word if sub-division name contained spaces (corrected by converting all spaces into dashes). </p> <p>2. "HPAC-Plumes.Processed.zip" and "HPAC-Plumes.Unprocessed.zip":</p> <p>These files contain HPAC plume coordinate (WGS1984) and dose (in cGy) values for all scenarios discussed in the manuscript. We provide "processed" and "unprocessed" HPAC plume data files. The "unprocessed" HPAC plume data is provided in its original XML format, which cannot be imported into ArcMap directly. The "processed" HPAC plumes are provided in tab-delimited X,Y,Z format (Latitude, Longitude, and Dose). We have also added a "0 cGy" contour in the "processed" plumes (surrounding the HPAC plume), as the presence of unirradiated data points adjacent to the plume was found to be crucial for accurate kriging, since these points served as boundaries for kriging.</p> <p>3. "Final-Derived-Plumes.Data-Points.zip":</p> <p>This file contains geostatistically-derived plume coordinate (WGS1984) and dose (in cGy) values for all scenarios discussed in the manuscript. Data is in comma-delimited format (Latitude, Longitude, and Dose). Data points consist of a set of initial coordinates generated at random locations within each Census sub-division using the ArcMap tool, ‘CreateRandomPoints_management’, and subsequent points generated by densification (the geostatistical procedure that targets and localizes an additional small cohort of irradiated individuals to mitigate uncertainty in environmental measurements). These data points were assigned radiation level values corresponding to the adjacent outer HPAC contour by a script comparing each sample with its location within the HPAC plume of the same scenario.</p> <p>4. “Intermediate-Derived-Plumes.Data-Points.zip”</p> <p>This archive contains coordinate data (WGS1984) and dose values (in cGy) for all intermediary steps of plume development (using our geostatistical method) for all scenarios. Like (3), the data is comma-delimited (Latitude, Longitude, and Dose), and were assigned radiation level values by a script comparing sampling locations with the location of the HPAC plume of the same scenario. Scenario replicate folders contains text files for each iteration step of the plume derivation process, including a file containing just the initial random sampling (“Iteration-1”), a file containing initial sampling and sampling locations selected by the first densification step (“Iteration-2”), a file containing initial sampling and sampling locations selected by the first and second densification steps (“Iteration-3”), and so on.</p> <p>This archive also contains a Table (“Progression-of-New-Densification-Selected-Sampling-Locations-For-All-Scenarios.xslx”) which provides a categorical breakdown of how many unique densification-selected sampling locations occur within the irradiated region (i.e. overlap the HPAC plume) for each iteration of all scenario replicates. The fraction of irradiated to unirradiated sampling locations varies among each scenario and individual replicates for the same scenario. Our analysis shows that these results depend on the population densities and exact topography of the HPAC plume which is different among each scenario.</p> <p>5. "Geostatistical-Sampling-Project.All-Scripts.zip"</p> <p>This archive contains all programs required for this project. This includes Python scripts meant to be run within the ArcMap software environment (for random point generation and data extraction), and Perl scripts used to process HPAC and U.S. State and Sub-division boundary files, and to assign radiation values to sample locations based on a modified HPAC plume. A java program, “CompareReplicates.jar”, compares the overlapping areas between a pair of polygons that overlap one other using the ArcMap software environment, and requires access to the ArcGIS Runtime SDK (<a href="https://developers.arcgis.com/arcgis-runtime/">https://developers.arcgis.com/arcgis-runtime/</a>).</p>
Dataset used in the paper: "Scaling laws and dynamics of hashtags on Twitter"
<p>This dataset was used in the manuscript "Scaling laws and dynamics of hashtags on Twitter"..</p> <p>The Twitter data was obtained from a sample of 10% of all public tweets, provided by the Twitter streaming application programming interface. We extracted the hashtags from each tweet and counted how many times they were used in different time intervals. Time intervals of three different lengths were used: days, hours, and minutes. The tweets were published between November 1st 2015 and November 30th 2016, but not all time intervals between these dates are available.</p> <p>The <strong>four files</strong> in this dataset correspond each to one folder (collected using tar). Each folder contains compressed .csv files (compressed using gzip). The content of the .csv files in each folder are:</p> <p><em><strong>hashtags_frequency_day.tar</strong></em><br> Counts of hashtags in each day. The name of each file in the folder indicates the date (GMT). The entries in each file are the hashtag and the count in the interval.<br> <br> <em><strong>hashtags_frequency_hour.tar</strong></em><br> Counts of hashtags in each hour. The name of each file in the folder indicates the date (GMT). The entries in each file are the hashtag and the count in the interval.<br> <br> <em><strong>hashtags_frequency_minutes.tar</strong></em><br> Counts of hashtags in each minute. The name of each file in the folder indicates the date (GMT, only a fraction of all days is available). The entries in each file are the hashtag and the count in the interval.<br> <br> <em><strong>number_of_tweets.tar</strong></em><br> Counts of the number of tweets in each minute. The name of each file in the folder indicates the day. The entries in each file are the minute in the day (GMT) and count of tweets in our dataset.</p>
Fig. 1. Philonthus neoniger Solodovnikov, nom. nov. Holotype. Habitus. Scale bar 1 in Xanthopygoides niger Cameron, 1951 (Xanthopygina) belongs to the genus Philonthus Stephens, 1829 (Philonthina): systematic and nomenclatural changes for the African Staphylinini (Coleoptera, Staphylinidae, Staphylininae, Staphylinini)
Fig. 1. Philonthus neoniger Solodovnikov, nom. nov. Holotype. Habitus. Scale bar 1 mm.
Fig. 4 in New scale insects (Homoptera: Coccinea) from the Cape Floristic Region
Fig. 4. Cryptinglisia millari Gavrilov-Zimin sp. nov., adult female, holotype.
Fig. 5 in New scale insects (Homoptera: Coccinea) from the Cape Floristic Region
Fig. 5. Cryptinglisia millari Gavrilov-Zimin sp. nov., adult females in life.
Fig. 2 in New scale insects (Homoptera: Coccinea) from the Cape Floristic Region
Fig. 2. Coccidohystrix daedalea Gavrilov-Zimin sp. nov., adult female, holotype.
Fig. 3 in New scale insects (Homoptera: Coccinea) from the Cape Floristic Region
Fig. 3. Mirococcopsis ptilura Gavrilov-Zimin sp. nov., adult female (holotype) and primolarva (L1).
Large-scale comparison of bibliographic data sources: Scopus, Web of Science, Dimensions, Crossref, and Microsoft Academic
<p>This data set contains supplementary material for the paper 'Large-scale comparison of bibliographic data sources: Scopus, Web of Science, Dimensions, Crossref, and Microsoft Academic' by Martijn Visser, Nees Jan van Eck, and Ludo Waltman. The data set provides the statistics presented in the figures in the paper.</p>
Data from: Quantifying natural disturbances using a large-scale dendrochronological reconstruction to guide forest management
Estimates of historical disturbance patterns are essential to guide forest management aimed at ensuring the sustainability of ecosystem functions and biodiversity. However, quantitative estimates of various disturbance characteristics required in management applications are rare in longer-term historical studies. Thus, our objectives were to: (1) quantify past disturbance severity, patch size, and stand proportion disturbed, and (2) test for temporal and sub-regional differences in these characteristics. We developed a comprehensive dendrochronological method to evaluate an approximately two-century-long disturbance record in the remaining Central and Eastern European primary mountain spruce forests, where wind and bark beetles are the predominant disturbance agents. We used an unprecedented large-scale nested design dataset of 541 plots located within 44 stands and 6 sub-regions. To quantify individual disturbance events, we used tree-ring proxies, which were aggregated at plot and stand levels by smoothing and detecting peaks in their distributions. The spatial aggregation of disturbance events was used to estimate patch sizes. Data exhibited continuous gradients from low- to high-severity and small- to large-size disturbance events. In addition to the importance of small disturbance events, moderate-scale (25-75% of the stand disturbed, >10 ha patch size) and moderate-severity (25-75% of canopy disturbed) events were also common. Moderate disturbances represented more than 50% of the total disturbed area and their rotation periods ranged from one to several hundred years, which is within the lifespan of local tree species. Disturbance severities differed among sub-regions, whereas the stand proportion disturbed varied significantly over time. This indicates partially independent variations among disturbance characteristics. Our quantitative estimates of disturbance severity, patch size, stand proportion disturbed, and associated rotation periods provide rigorous baseline data for future ecological research, decisions within biodiversity conservation, and silviculture intended to maintain native biodiversity and ecosystem functions. These results highlight a need for sufficiently large and adequately connected networks of strict reserves, more complex silvicultural treatments that emulate the natural disturbance spectrum in harvest rotation times, sizes, and intensities, and higher levels of tree and structural legacy retention.
Data from: Attack and aggregation of a major squash pest: parsing the role of plant chemistry and beetle pheromones across spatial scales
<p>1. Successful management of insect crop pests requires an understanding of the cues and spatial scales at which they function to affect rates of attack of preferred and non-preferred host plants. A long-standing conceptual framework in insect-plant ecology posits that there is hierarchical structure spanning host location, acceptance, and attack that could be exploited for integrated pest management.</p> <p>2. We investigated how plant- and insect-derived chemical cues affect successive decisions of host choice in aggregating insects, and tested predictions in the Cucurbita pepo - Acalymma vittatum system. Acalymma vittatum is an aggregating specialist beetle pest that strongly prefers zucchini (C. p. pepo) to summer squash (C. p. ovifera), two independent domesticates of C. pepo. We hypothesized that subspecies-specific plant traits, especially volatile cues, interact with the male-produced aggregation pheromone to amplify beetle preference for C. p. pepo.</p> <p>3. Differential beetle attack of C. pepo subspecies in the field is not determined by plant traits that affect host finding or differential aggregation due to pheromones: across two years, beetles had strong density-dependent attraction to both subspecies when male beetles were feeding, and no interactions between plant volatiles and the male-produced pheromone were detected. In absence of male pheromone emission, beetles were equally unattracted to plants with or without beetle feeding.</p> <p>4. In contrast, plant traits that mediate insect acceptance appear to underlie differences in preference. At a local scale, beetles did not accept and emigrated from C. p. ovifera compared to C. p. pepo. Distinct volatile emissions were observed between subspecies, but further work is needed to identify if these volatiles promote emigration.</p> <p>5. Synthesis and applications: By dissecting pest preference during successive host choice decisions, we isolated a trait with implications for pest management. Beetles on cucurbits can be managed by employing cultivars with differential susceptibility (e.g. trap cropping), and the mechanistic knowledge presented here informs best practices and limitations for on-farm applications. More broadly, pest management in diversified cropping systems can be enhanced through understanding how plant preference gradients affect herbivore movement and behavior, and plant breeders can target traits to reduce herbivory in such systems.</p>
Extended data for Manuscript: Precision medicine implementation and research-practice partnerships: implications of measurement scale differential item functioning (DIF)
<p>This is the extended data for the manuscript submitted to F1000 Research titled:</p> <p>Precision medicine implementation and research-practice partnerships: implications of measurement scale differential item functioning (DIF).</p> <p>File 1 is the redacted survey responses from a card sort exercise carried out to find out how the study participants sorted and ranked various measures of factors thought to influence precision medicine implementation at health systems level.</p> <p>File 2 consists of the study package as described in the article</p>
Extended Data: Structure-dependence of the atomic-scale mechanisms of Pt electrooxidation and dissolution
<p><strong>Abstract:</strong></p> <p>Platinum dissolution and restructuring due to surface oxidation are primary degradation mechanisms that limit the lifetime of Pt-based electrocatalysts for electrochemical energy conversion. Here, we studied well-defined Pt(100) and Pt(111) electrode surfaces by in situ high-energy surface X-ray diffraction, on-line inductively coupled plasma mass spectrometry, and density functional theory calculations, to elucidate the atomic-scale mechanisms of these processes. The locations of the extracted Pt atoms after Pt(100) oxidation reveal distinct differences from the Pt(111) case, which explains the different surface stability. The evolution of a specific stripe oxide structure on Pt(100) produces unstable surface atoms which are prone to dissolution and restructuring, leading to one order of magnitude higher dissolution rates.</p> <p><strong>Contents of this repository:</strong></p> <p><strong>1. SXRD data:</strong></p> <p>The experiments for the acquisition of the raw SXRD data were performed at the the European Synchrotron Radiation Facility, Grenoble, France at the beamlines ID31 and ID03. We thank H. Isern and T. Dufrane for the help during the SXRD experiments.</p> <ul> <li>tomo_tomo.spec is the file with the X-ray diffraction metadata for the CTR scans. It is a plain text file.</li> <li>Each HESXRD dataset is saved in a folder, which denotes the potential (e.g. 1V0.zip). The png-image files are previews of the corresponding dataset. The individual raw cbf files can be opened by pyMCA or silx. From python, the images can be accessed using the fabio library.</li> <li>calibration.zip contains the pyFAI calibration files and a list with indexed Bragg reflections for the UB matrix calculation</li> <li>CTRs_parameters.zip contains the averaged CTR structure factors used for the structual analysis as well as files with the atomic coordinates of the refined structural model.</li> <li>steps.zip contains the full datasets from the potential step experiments in Fig. 1e.</li> </ul> <p><strong>2. DFT:</strong></p> <ul> <li>CONTCARs.zip contains the atomic coordinates of the optimized computational models.</li> </ul> <p> </p> <p> </p>
Data from: Spatial scale, neighbouring plants and variation in plant volatiles interactively determine the strength of host-parasitoid relationships
Species-specific responses to the environment can moderate the strength of interactions between plants, herbivores and parasitoids. However, the ways in which characteristics of plants, such as genotypic variation in herbivore induced volatiles (HIPVs) that attract parasitoids, affect trophic interactions in different contexts of plant patch size and plant neighbourhood is not well understood. We conducted a factorial field experiment with white cabbage (<i>Brassica oleracea</i>) accessions that differ in the attractiveness of their HIPVs for parasitoids, in the context of different patch sizes and presence or absence of surrounding <i>Brassica nigra</i> plants. Parasitism rates of experimentally introduced <i>Pieris brassicae</i> caterpillars and the presence of naturally occurring <i>Pieris</i> spp. caterpillars in the plots were assessed throughout the growing season. The abundance of <i>Pieris</i> caterpillars was neither affected by cabbage accession nor plot size. Later in the season, when <i>B. nigra</i> plants had senesced, fewer caterpillars were found on cabbage plants in plots with a <i>B. nigra</i> border. Parasitism rates fluctuated over the season, and were not affected by plot size. However, the <i>B. nigra</i> border negatively affected parasitism rates on the accession that is less attractive to the parasitoid <i>Cotesia glomerata</i>, but not on the more attractive accession. Our results show that plant variation in HIPVs can differentially influence herbivores and parasitoids depending on characteristics of the surrounding vegetation context. These findings underscore the importance of considering the interaction between focal plant traits and neighbourhood context to reliably predict trophic cascades.
Data from: A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways
Background: Teak, a member of the Lamiaceae family, produces one of the most expensive hardwoods in the world. High demand coupled with deforestation have caused a decrease in natural teak forests, and future supplies will be reliant on teak plantations. Hence, selection of teak tree varieties for clonal propagation with superior growth performance is of great importance, and access to high-quality genetic and genomic resources can accelerate the selection process by identifying genes underlying desired traits. Findings: To facilitate teak research and variety improvement, we generated a highly contiguous, chromosomal-scale genome assembly using high-coverage PacBio long reads coupled with high-throughput chromatin conformation capture. Of the 18 teak chromosomes, we generated 17 near-complete pseudomolecules with one chromosome present as two chromosome arm scaffolds. Genome annotation yielded 31,168 genes encoding 46,826 gene models, of which, 39,930 and 41,155 had Pfam domain and expression evidence, respectively. We identified 14 clusters of tandem-duplicated terpene synthases (TPSs), genes central to the biosynthesis of terpenes which are involved in plant defense and pollinator attraction. Transcriptome analysis revealed 10 TPSs highly expressed in woody tissues, of which, 8 were in tandem, revealing the importance of resolving tandemly duplicated genes and the quality of the assembly and annotation. We also validated the enzymatic activity of four TPSs to demonstrate the function of key TPSs. Conclusions: In summary, this high-quality chromosomal-scale assembly and functional annotation of the teak genome will facilitate the discovery of candidate genes related to traits critical for sustainable production of teak and for anti-insecticidal natural products.
Data from: Consistent scaling of inbreeding depression in space and time in a house sparrow metapopulation
<p>Inbreeding may increase the extinction risk of small populations. Yet, studies using modern genomic tools to investigate inbreeding depression in nature have been limited to single populations, and little is known about the dynamics of inbreeding depression in subdivided populations over time. Natural populations often experience different environmental conditions and differ in demographic history and genetic composition; characteristics that can affect the severity of inbreeding depression. We utilised extensive long-term data on more than 3100 individuals from eight islands in an insular house sparrow metapopulation to examine the generality of inbreeding effects. Using genomic<sub> </sub>estimates of realised inbreeding, we discovered that inbred individuals had lower survival probabilities and produced fewer recruiting offspring than non-inbred individuals. Inbreeding depression, measured as the decline in fitness related traits per unit inbreeding, did not vary appreciably among populations or with time. As a consequence, populations with more resident inbreeding (due to their demographic history) paid a higher total fitness cost, evidenced by a larger variance in fitness explained by inbreeding within these populations. Our results are in contrast to the idea that effects of inbreeding generally depend on ecological factors and genetic differences among populations, and expand the understanding of inbreeding depression in natural subdivided populations.</p>
Data from: Foundation species promote local adaptation and fine-scale distribution of herbaceous plants
<p><span><span><span>1) Interactions among neighbors can alter demography and traits of commingled species via adaptation or plasticity in phenotypic expression and understanding these two mechanisms in diverse communities is important for determining the ecological and evolutionary consequences of plant–plant interactions. </span></span></span></p> <p><span><span><span>2) We reciprocally transplanted perennial species (<i>Arenaria armerina</i> and <i>Festuca indigesta</i>) among patches of two foundation shrub species and open ground to assess whether origin microsite (defined as the spatially distinct abiotic and biotic conditions associated with the two shrubs and open ground) determines germination, recruitment and growth that, in turn, promotes fine-scale distribution of species among microsites. In addition, we tested the effect of origin microsite on traits, competitive ability, drought tolerance and outlier loci to assess whether origin microsite conditions drove differences in traits, strategies and adaptive loci.</span></span></span></p> <p><span><span><span>3) Germination was consistently greater for seeds planted back into their origin microsite relative to seeds sourced from foreign microsites, although this effect was weakened for recruitment. Plant growth was best in open sites regardless of origin microsite. In the greenhouse, <i>A.</i> <i>armerina</i> had conserved traits within origin microsite but distinct trait values among microsite conditions, specifically for plants originating from the most productive microsite (e.g. sufficient light and high nutrients and water availability). <i>Festuca indigesta</i> had conserved trait responses among microsites while within microsite, individuals had significant trait plasticity to different environmental conditions. The combined field and greenhouse results suggest that fine-scale distributions are supported by local adaptation among microsites of <i>A.</i> <i>armerina </i>and phenotypic plasticity of <i>F.</i> <i>indigesta</i>.</span></span></span></p> <p><span><span><span><i>Synthesis </i>Adaptation or plasticity in phenotypic expression have different implications for demographic rate and persistence of species in changing environments. Local adaptation to neighbors suggests that reductions in foundation species diversity could concomitantly lead to reduced genetic diversity of commingled species while a plastic response indicates a more robust and broad response to changing climatic and biotic conditions.</span></span></span></p>
Data for: Landscape scale variation in the hydrologic niche of California coast redwood
<p>Topoclimatic diversity within forest landscapes can underlie variation in water availability, which may correspond to patterns in habitat suitability of tree species with differing hydrologic niches. However, the trade-off between the collection of data at a fine grain size over large spatial extents has limited comprehensive analyses of landscape scale variation in habitat suitability. We present a fine scale analysis of the roles of topographic gradients in moisture availability, soil water storage, and fog frequency in the spatial pattern of habitat suitability for coast redwood (<i>Sequoia sempervirens</i>), at 10 m resolution across 34,800 hectares and three landscapes spanning approximately one-third of redwood's latitudinal range. A new 10 m resolution presence-absence map derived from airborne imaging spectroscopy was used to characterize current redwood distributions in three landscapes. Access to belowground moisture was assessed through four measures calculated from a high-resolution LiDAR digital elevation model, soil water storage was mapped from the USDA Soil Survey Geographic Database, and fog frequency was calculated from MODIS cloud cover data. Access to belowground moisture and fog predicted variation in suitability as redwood habitat from 22–75% and predicted redwood presence and absence at 10 m resolution with 63–74% accuracy. Across all three landscapes, redwood density consistently decreased with increasing interpolated height above a stream (IHAS), but the role of other predictors varied among the sites. Our results challenge previous assumptions that redwood habitat suitability within much coarser resolutions (800 m x 800 m) can be described by a single value. The elevated habitat suitability of sites close to streams suggests that these sites should be evaluated for their potential to become microrefugia within landscapes that may become climatically unsuitable for redwoods at a regional scale. </p>
Climate more important than soils for predicting forest biomass at the continental scale
<p>Above-ground biomass in forests is critical to the global carbon cycle as it stores and sequesters carbon from the atmosphere. Climate change will disrupt the carbon cycle hence understanding how climate and other abiotic variables determine forest biomass at broad spatial scales is important for validating and constraining Earth System models and predicting the impacts of climate change on forest carbon stores. We examined the importance of climate and soil variables to explaining above-ground biomass distribution across the Australian continent using publicly available biomass data from 3130 mature forest sites, in 6 broad ecoregions, encompassing tropical, subtropical, and temperate biomes. We used the Random Forest algorithm to test the explanatory power of 14 abiotic variables (8 climate, 6 soil) and to identify the best-performing models based on climate-only, soil-only, and climate plus soil. The best performing models explained ~50% of the variation (climate-only: <i>R<sup>2</sup></i> = 0.47 ± 0.04, and climate plus soils: <i>R<sup>2</sup></i> = 0.49 ± 0.04). Mean temperature of the driest quarter was the most important climate variable, and bulk density was the most important soil variable. Climate variables were consistently more important than soil variables in combined models, and model predictive performance was not substantively improved by the inclusion of soil variables. This result was also achieved when the analysis was repeated at the ecoregion scale. Predicted forest above-ground biomass ranged from 18 to 1066 Mg ha<sup>-1</sup>, often under-predicting measured above-ground biomass, which ranged from 7 to 1500 Mg ha<sup>-1</sup>. This suggested that other non-climate, non-edaphic variables impose a substantial influence on forest above-ground biomass, particularly in the high biomass range. We conclude that climate is a strong predictor of above-ground biomass at broad spatial scales and across large environmental gradients, yet to predict forest above-ground biomass distribution under future climates, other non-climatic factors must also be identified.</p>
Data from: Multi-scale spatial genetic structure within and between populations of wild cherry trees in nuclear genotypes and chloroplast haplotypes
Spatial genetic structure (SGS) of plants mainly depends on the effective population size and gene dispersal. Maternally inherited loci are expected to have higher genetic differentiation between populations and more intensive SGS within populations than biparentally inherited loci because of smaller effective population sizes and fewer opportunities of gene dispersal in the maternally inherited loci. We investigated biparentally inherited nuclear genotypes and maternally inherited chloroplast haplotypes of microsatellites in 17 tree populations of three wild cherry species under different conditions of tree distribution and seed dispersal. As expected, inter-population genetic differentiation was 6–9 times higher in chloroplast haplotypes than in nuclear genotypes. This difference indicated that pollen flow 4–7 times exceeded seed flow between populations. However, no difference between nuclear and chloroplast loci was detected in within-population SGS intensity due to their substantial variation among the populations. The SGS intensity tended to increase as trees became more aggregated, suggesting that tree aggregation biased pollen and seed dispersal distances toward shorter. The loss of effective seed dispersers, Asian black bears, did not affect the SGS intensity probably because of mitigation of the bear loss by other vertebrate dispersers and too few tree generations after the bear loss to alter SGS. The findings suggest that SGS is more variable in smaller spatial scales due to various ecological factors in local populations.
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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.