Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
3,100
datasets available to search
ShareScore release 0.9.0
Dataset results
3,100 results for “recent”
Unprecedented failure of the Northeastern Indian Monsoon and recent water scarcity
<p>Dataset used in the publication on "<strong>Unprecedented failure of the Northeastern Indian Monsoon and recent water scarcity" submitted in GRL.</strong></p>
Under the radar: genetic assessment of Rio Grande Shiner (Notropis jemezanus) and Speckled Chub (Macrhybopsis aestivalis), two Rio Grande basin endemic cyprinids that have experienced recent range contractions
<p>The Rio Grande drainage of the southwestern United States and Mexico has undergone intense anthropogenic alteration by water diversions, extraction and associated habitat changes. These alterations have disproportionately impacted the pelagic broadcast spawning guild of minnows (pelagophils). Several Rio Grande endemic pelagophils, including the co-occurring Rio Grande Shiner (<i>Notropis jemezanus</i>) and Speckled Chub (<i>Macrhybopsis aestivalis</i>), have experienced dramatic recent range-wide declines yet have slipped under the radar of conservation efforts. The status of <i>N. jemezanus </i>and <i>M. aestivalis </i>in the Rio Grande and Pecos River was evaluated and standing genetic variation were characterized. Genetic evidence indicates that populations of both species found in the Rio Grande and Pecos River are genetically distinct. Additionally, 159 outlier loci were identified in <i>M. aestivalis </i>suggesting possible local adaptation in the Rio Grande and Pecos River populations. Though range-wide genetic data are limited, <i>N. jemezanus </i>populations in both rivers harbor considerable genetic diversity. Mitochondrial data from both taxa are consistent with a history of secondary contact between formerly isolated populations with deeply divergent haplotypes found within the Rio Grande and Pecos River populations of <i>N. jemezanus </i>and within the Rio Grande population of <i>M. aestivalis.</i> Extensive survey efforts in the lower Rio Grande and its tributaries in Texas document significant range contraction and near extirpation of <i>N. jemezanus </i>from this part of the basin; highlighting the need for immediate action to protect the species. </p>
Limited genetic parallelism underlies recent, repeated incipient speciation in geographically proximate populations of an Arctic fish (Salvelinus alpinus)
<p>The genetic underpinnings of incipient speciation, including the genomic mechanisms which contribute to morphological and ecological differentiation and reproductive isolation, remain poorly understood. The repeated evolution of consistently, phenotypically distinct morphs of Arctic Charr (<i>Salvelinus alpinus</i>) within the Quaternary period offer an ideal model to study the repeatability of evolution at the genomic level. Sympatric morphs of Arctic Charr are found across this species' circumpolar distribution. However, the specific genetic mechanisms driving this morph differentiation are largely unknown despite the cultural and economic importance of the anadromous morph. We used a newly designed 87k SNP chip to investigate the character and consistency of the genomic differences among sympatric morphs within three recently deglaciated and geographically proximate lakes in Labrador, Canada. We found genetically distinct small and large morph Arctic Charr in all three lakes consistent with resident and anadromous morphs, respectively. A degree of reproductive isolation among sympatric morphs is likely given genome-wide distributions of outlier SNPs and high genome-wide <i>F</i><sub>ST</sub>s. Across all lakes, outlier SNPs were largely non-overlapping suggesting a lack of genetic parallelism driving morph differentiation. Alternatively, several genes and paralogous copies of the same gene consistently differentiated morphs across multiple lakes suggesting their importance to the manifestation of morphs. Our results confirm the utility of Arctic Charr as a model for investigating the predictability of evolution and support the importance of both genetic parallelism and non-parallelism to the incipient speciation of Arctic Charr morphs.</p>
Weak founder effects but significant spatial genetic imprint of recent contraction and expansion of European beech populations.
Understanding the ecological and evolutionary processes occurring during species range shifts is important in the current context of global change. Here, we investigate the interplay between recent expansion, gene flow and genetic drift, and their consequences for genetic diversity and structure at landscape and local scales in European beech (Fagus sylvatica L.) On Mont Ventoux, South-Eastern France, we located beech forest refugia at the time of the most recent population minimum, approximately 150 years ago, and sampled 71 populations (2042 trees) in both refugia and expanding populations over an area of 15,000 ha. We inferred patterns of gene flow and genetic structure using 12 microsatellite markers. We identified six plots as originating from planting, rather than natural establishment, mostly from local genetic material. Comparing genetic diversity and structure in refugia versus recent populations did not support the existence of founder effects: heterozygosity (He = 0.667) and allelic richness (Ar = 4.298) were similar, and FST was low (0.031 overall). Still, significant spatial evidence of colonization was detected, with He increasing along the expansion front, while genetic differentiation from the entire pool (βWT) decreased. Isolation by distance was found in refugia but not in recently expanding populations. Our study indicates that beech capacities for colonization and gene flow were sufficient to preserve genetic diversity despite recent forest contraction and expansion. Because beech has long distance pollen and seed dispersal, these results illustrate a 'best case scenario' for the maintenance of high genetic diversity and adaptive potential under climate-change related range change.
Does recent fire activity impact fire-related traits of Pinus halepensis Mill. and Pinus sylvestris L. in the French Mediterranean area?
<p>Data used for analyses in the paper by Romero B. and Ganteaume A., published in Annals of Forest Science in 2020.</p> <p>PS : <em>Pinus sylvestris</em></p> <p>PH : <em>Pinus halepensis</em></p>
Recent extinctions among Little Spotted Kiwi (Apteryx owenii) and the origin of extant populations
<p>Little Spotted Kiwi (LSK; <i>Apteryx owenii</i>) have the lowest genetic diversity of five currently recognised kiwi species apparently due to a bottleneck when at most five individuals were translocated to Kapiti Island in 1912. Ancient DNA analyses show that LSK also had the lowest genetic diversity of kiwi species historically, possibly due to population bottlenecks during Pleistocene glaciation. We compare genetic diversity between LSK from Kapiti Island (extant), D'Urville Island (extinct) and the South Island of mainland New Zealand (extinct) at 495 bp of the mitochondrial control region (mtDNA) and 15 nuclear microsatellite loci (nDNA). Despite higher sample sizes in extant (<i>n</i> = 31 mtDNA, 97 nDNA) than recently extinct (<i>n</i> = 10 mtDNA, 9 nDNA) populations, extant LSK have at least 78% fewer mtDNA haplotypes and 52% fewer microsatellite alleles than recently extinct LSK. Extant LSK were strongly divergent from historical LSK for both mtDNA and nDNA (<i>F<sub>ST</sub></i> = 0.237 to 0.480), but showed greatest similarity with historical samples from Fiordland near the putative source population of Kapiti founders. Microsatellite data suggest that Kapiti LSK could have arisen from as few as three birds and our mtDNA data show that at least two of the founders were female. Our results indicate that substantial genetic diversity has been lost with the recent extinctions of remnant populations. Locating and protecting any last surviving individuals in presumed extinct populations will require intensive conservation efforts, but could also provide an invaluable source of genetic diversity for the species.</p>
Monitoring recent changes in the Beaufort Sea coast using very high resolution remote sensing
<p>Arctic permafrost coasts are major carbon (Schuur et al., 2015) and mercury pools (Schuster et al., 2018). They represent about 34% of the Earth’s coastline, with long sections affected by high erosion rates (Fritz et al, 2017), increasingly threatening coastal communities. Year-round reduction in Arctic sea ice is forecasted and by the end of the 21st century, models indicate a decrease in sea ice area from 43 to 94% in September and from 8 to 34% in February (IPCC, 2014). An increase of the sea-ice free season leads to a longer exposure of coasts to wave action. Further, climate warming is also expected to modify the contribution of terrestrial erosion (Fritz et al., 2015, Ramage et al., 2018, Irrgang et al., 2018). Within the project EU Horizon2020 project NUNATARYUK, we are updating the mapping of the Arctic coast, with the Canadian Beaufort coast as a case-study. The surveying methodology includes: i. a high resolution update of the coastline mapping and change rates using Pleiades (CNES) satellite acquisitions from 2018, ii. a survey using RTK-UAV aerial imagery of long-term monitoring sites from the Canada-US border to King Point, and iii. the experimental use of TerraSAR-X staring spotlight scenes and PAZ at key sites to monitor intraseasonal dynamics of cliff edge retreat. This research is funded by the EC H2020 Project NUNATARYUK. Support on remote sensing imagery access by the WMO Polar Space Task Group.</p>
Phylogenetic diversity and environment form assembly rules for Arctic diatom genera – a study on recent and ancient sedimentary DNA
<p><span><b>Aim</b></span></p> <p><span>This study investigates taxonomic and phylogenetic diversity in diatom genera to evaluate assembly rules for eukaryotic microbes across the Siberian treeline. We first analysed how phylogenetic distance relates to taxonomic richness and turnover. Second, we used relatedness indices to evaluate if environmental filtering or competition influences the assemblies in space and through time. Third, we used distance-based ordination to test which environmental variables shape diatom turnover.</span></p> <p><span><b>Location</b></span></p> <p><span>Yakutia and Taymyria, Russia: we sampled 78 surface sediments and a sediment core, extending to 7000 years before present, to capture the forest–tundra transition in space and time, respectively. </span></p> <p><span><b>Taxon</b></span></p> <p><span>Arctic freshwater diatoms.</span></p> <p><span><b>Methods</b></span></p> <p><span>We applied metabarcoding to retrieve diatom diversity from surface and core sedimentary DNA. The taxonomic assignment binned sequence types (lineages) into genera and created taxonomic (abundance of lineages within different genera) and phylogenetic datasets (phylogenetic distances of lineages within different genera).</span></p> <p><span><b>Results</b></span></p> <p><span>Contrary to our expectations, we find a unimodal relationship between phylogenetic distance and richness in diatom genera. We discern a positive relationship between phylogenetic distance and taxonomic turnover in spatially and temporally distributed diatom genera. Further, we reveal positive relatedness indices in diatom genera across the spatial environmental gradient and predominantly in time-slices at a single location, with very few exceptions assuming effects of competition. Distance-based ordination of taxonomic and phylogenetic turnover indicates that lake environment variables, like HCO<sub>3</sub><sup>–</sup> and water depth, largely explain diatom turnover. </span></p> <p><span><b>Main conclusion</b></span></p> <p>Phylogenetic and abiotic assembly rules are important in understanding the regional assembly of diatom genera across lakes in the Siberian treeline ecotone. Using a space–time approach we are able to exclude the influence of geography and elucidate that lake environmental variables primarily shape the assemblies. We conclude that some diatom genera have greater capabilities to adapt to environmental changes, whereas others will be putatively replaced or lost due to the displacement of the Arctic tundra biome under recent global warming.</p>
Extreme variation in testes size in an insect is linked to recent mating activity
<p>Ample sperm production is essential for successful male reproduction in many species. The amount of sperm a male can produce is typically constrained by the size of his testes, which can be energetically expensive to grow and maintain. Whilst the economics of ejaculate allocation has been the focus of much theoretical and empirical literature, relatively little attention has been paid to individual adult variation and plasticity at the source of sperm production, the testes themselves. We experimentally address this issue using the insect <em>Narnia femorata </em>Stål (Hemiptera: Coreidae). We established the metabolic cost of testicular tissue, then quantified variation in individual testes mass in response to multiple mate quality and quantity treatments. We uncovered extreme variation across individuals and considerable short-term effects of mating activity on testes dry mass. Importantly, the observed variation in testes mass was associated with notable fitness consequences; females paired with males with larger testes had greater hatching success. Overall, pairing with a female resulted in a 11% reduction in dry testes mass. Despite this apparent considerable mating investment, we found no evidence of strategic allocation to higher quality females or longer-term changes in testes mass. The dynamic nature of testes mass and its metabolic cost is vital to consider in the context of re-mating rates, polyandry benefits and general mating system dynamics both in this species and more broadly.</p>
Data from: Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events
• Studies of the macroevolutionary legacy of polyploidy are limited by an incomplete sampling of these events across the tree of life. To better locate and understand these events, we need comprehensive taxonomic sampling as well as homology inference methods that accurately reconstruct the frequency and location of gene duplications. • We assembled a dataset of transcriptomes and genomes from 169 species in Caryophyllales, of which 43 were newly generated for this study, representing one of the densest sampled genomic-scale datasets available. We carried out phylogenomic analyses using a modified phylome strategy to reconstruct the species tree. We mapped phylogenetic distribution of polyploidy events by both tree-based and distance-based methods, and explicitly tested scenarios for allopolyploidy. • We identified twenty-six ancient and more recent polyploidy events distributed throughout Caryophyllales. Two of these events were inferred to be allopolyploidy. • Through dense phylogenomic sampling, we show the propensity of polyploidy throughout the evolutionary history of Caryophyllales. We also provide a framework for utilizing transcriptome data to detect allopolyploidy, which is important as it may have different macro-evolutionary implications compared to autopolyploidy.
The impact of the Pull of the Recent in extant elasmobranchs
<p><span><span><span><span><span><span><span><span><span><span><span>Modern elasmobranchs have a long evolutionary history and an abundant fossil record. Many fossil taxa have living representatives. However, the representation of extant taxa in the fossil record is unknown. To begin to understand the geological history of extant elasmobranchs, here we assess the quality of their fossil record. We do so by assessing the Pull of the Recent (herein, POR). The POR can bias the fossil record because the rather complete record of living taxa allows palaeontologists tobridge time bins where fossils are absent. We assessed the impact of the POR by quantifying the proportion of extant elasmobranchs that have a fossil record, but do not occur in the last 5 million years. We found that the POR does not affect orders and families, but it does affect 24% of elasmobranch genera. Although modest, the impact of the POR in extant elasmobranch genera is higher than that found in other taxa. Overall, the geological history of elasmobranchs contradicts the usual assumption that the fossil record becomes worse backwards in time. This is the case across geographical regions and tooth size, further suggesting that sampling intensity and outcrop availability can help explain the POR effect on sharks and rays.</span></span></span></span></span></span></span></span></span></span></span></p>
Genetic analyses reveal population structure and recent decline in leopards (Panthera pardus fusca) across Indian subcontinent
<p><span><span><b><i>Background </i></b></span></span></p> <p><span><span>Large carnivores maintain the stability and functioning of ecosystems. Currently, many carnivore species face declining population sizes due to natural and anthropogenic pressures. The leopard, <i>Panthera pardus</i>, is probably the most widely distributed and highly adaptable large felid globally, still persisting in most of its historic range. However, we lack subspecies-level data on country or regional scale on population trends, as ecological monitoring approaches are difficult to apply on such wide-ranging species. We used genetic data from leopards sampled across the Indian subcontinent to investigate population structure and patterns of demographic decline. </span></span></p> <p><span><span><b><i>Methods </i></b></span></span></p> <p><span><span>We collected faecal samples from the Terai-Arc landscape of north India and identified 56 unique individuals using a panel of 13 microsatellite markers. We merged this data with already available 143 leopard individuals and assessed genetic structure at country scale. Subsequently, we investigated the demographic history of each identified subpopulations and compared genetic decline analyses with countrywide local extinction probabilities. </span></span></p> <p><span><span><b><i>Results </i></b></span></span></p> <p><span><span>Our genetic analyses revealed four distinct subpopulations corresponding to Western Ghats, Deccan Plateau-Semi Arid, Shivalik and Terai region of the north Indian landscape, each with high genetic variation. Coalescent simulations with microsatellite loci revealed a possibly human-induced 75-90% population decline between ∼120-200 years ago across India. Population-specific estimates of genetic decline are in concordance with ecological estimates of local extinction probabilities in these subpopulations obtained from occupancy modeling of the historic and current distribution of leopards in India. </span></span></p> <p><span><span><b><i>Conclusions </i></b></span></span></p> <p><span><span>Our results confirm the population decline of a widely distributed, adaptable large carnivore. We re-iterate the relevance of indirect genetic methods for such species in conjunction with occupancy assessment and recommend that detailed, landscape-level ecological studies on leopard populations are critical to future conservation efforts. Our approaches and inference are relevant to other widely distributed, seemingly unaffected carnivores such as the leopard.</span></span></p>
Lags in phenological acclimation of mountain grasslands after recent warming
<p>1. In the current biodiversity crisis, one of the crucial questions is how quickly plant communities can acclimate to climate warming and longer growing seasons to buffer the impairment of community functioning. Answering this question is pivotal especially for mountain grasslands that experience harsh conditions but provide important ecosystem services to people.</p> <p>2. We conducted a reciprocal transplant experiment along an elevation gradient (1920 m vs. 2450 m) in the French Alps to test the ability of plant species and communities to acclimate to warming and cooling. For three years, we measured weekly the timing of phenological events (e.g. start of flowering or greening) and the length of phenological stages linked to demographic performance (e.g. lengths of flowering or greening periods).</p> <p>3. We found that warming (and cooling) changed the timing of phenological events strongly enough to result in complete acclimation for graminoids, for communities in early and mid-season, but not at all for forbs. For example, warming resulted in later greening of communities and delayed all phenophases of graminoids. Lengths of phenological stages did not respond strongly enough to climate change to acclimate completely, except for graminoids. For example, warming led to an acclimation lag in the community's yearly productivity and had a strong negative impact on flowering of forbs. Overall, when there was an acclimation failure, responses to cooling were mostly symmetric and confirmed slow acclimation in mountain grasslands.</p> <p>4. Synthesis. Our study highlights that phenological plasticity cannot prevent impairment of community functioning under climate warming in the short-term. The failures to acclimate after three years of warming signals that species and communities underperform and are probably at high risk of being replaced by locally better-adapted plants.</p>
High frequency of X4/DM-tropic viruses in PBMC samples from HIV-1 recently infected blood donors by massively parallel sequencing: the REDS II Study
<p>Here is a sub-library of the <em>env</em> V3 massively parallel sequencing proviral data generated (by Illumina MiSeq platform) during the early phase of HIV-1 infection in a group of first-time blood donors. Only paired-end reads that encompass the complete V3 region from each dataset were extracted, uploaded and considered for the analysis to avoid artificial generation of <em>in silico</em> chimeras through assembly and to evade inflating the diversity estimates of the V3 region</p>
Cranial CT Scan, Astrocytoma patient after recent tumor removal surgery
<p>A cranial CT scan from a patient with an astrocytoma brain tumor surgically removed August 19, 2014. Scan taken November 19, 2014. Patient: Steven Keating. Patient age: 26 at time of scan. Open access (CC0) with approval from patient. More information available on patient at www.stevenkeating.info.</p>
LIST OF RECENT EARTHQUAKES THAT POSSIBLY HAD SURFACE RUPTURE
<p>The Excel spreadsheet and its accompanying text file list all the shallow (<35 km) M6+ earthquakes that have occurred on-land in the period 2000-2016. These are of a size and type of earthquake that may have produced surface faulting. So in updating the SURE database, we need to ensure that we know whether each of these 134 earthquakes produced surface rupture, and how much. At this point it looks like there are published papers about surface faulting for 20 of these earthquakes. For the rest, we don't know if there was surface rupture or not. I suggest we ask for volunteers from the countries that contain these 114 undocumented earthquakes, and ask them if surface rupture was looked for, and if so, if it was found and what parameters were measured. These volunteers would come from the SURFACE project, or be new paleoseismologists who would like to become involved.</p>
FIGURE 46 in A description of two new species of the genus Erenna (Siphonophora: Physonectae: Erennidae), with notes on recently collected specimens of other Erenna species
FIGURE 46. Erenna sirena sp. nov. Nematocysts on cnidoband. Scale bars A., B. 25 µm; C. 50 µm.
Surveillance of recent HIV infections in Germany between 2008 and 2014
<p>The data file contains the raw data of an analysis in the scope of the surveillance of recent HIV infections in Germany, run by the Robert Koch Institute, Berlin, Germany. The data covers anonymous sociodemographic data and BED-CEIA test results from newly diagnosed HIV cases in Germany.</p>
Figure 1. from New data on recently described rodent species Paulina's Limestone Rat Saxatilomys paulinae Musser, Smith, Robinson & Lunde, 2005 (Mammalia: Rodentia) - Biodiversity Data Journal 3: e4961 (19 May 2015) https://doi.org/10.3897/BDJ.3.e4961
Figure 1. - Living specimen of Saxatilomyspaulinae from Quang Binh province (the nose is wounded by trapping).
Figure 4. from New data on recently described rodent species Paulina's Limestone Rat Saxatilomys paulinae Musser, Smith, Robinson & Lunde, 2005 (Mammalia: Rodentia) - Biodiversity Data Journal 3: e4961 (19 May 2015) https://doi.org/10.3897/BDJ.3.e4961
Figure 4. - Location of survey areas (the red commune names) and locality where specimens of Saxatilomyspaulinae were collected.
ScienceDex guides
Understand access before you commit
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.