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932 results for “Long term data”
Data from: A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability
Although ancient DNA from sediments (sedaDNA) has been used to investigate past ecosystems, the approach has never been directly compared to the traditional methods of pollen and macrofossil analysis. We conducted a comparative survey of 18 ancient permafrost samples spanning the Late Pleistocene (46–12.5 thousand years ago), from the Taymyr Peninsula in northern Siberia. The results show that pollen, macrofossils and sedaDNA are complementary rather than overlapping, and in combination reveal more detailed information on plant palaeocommunities than can be achieved by each individual approach. SedaDNA and macrofossils share greater overlap in plant identifications than with pollen, suggesting that sedaDNA is local in origin. These two proxies also permit identification to lower taxonomic levels than pollen, enabling investigation of temporal changes in species composition and the determination of indicator species to describe environmental changes. Combining data from all three proxies, reveals an area continually dominated by a mosaic vegetation of tundra-steppe, pioneer and wet-indicator plants. Such vegetational stability is unexpected, given the severe climate changes taking place in the northern hemisphere during this time, with changes in average annual temperatures of > 22ºC. This may explain the abundance of ice-age mammals such as horse and bison in Taymyr Peninsula during the Pleistocene, and why it acted as a refugium for the last mainland woolly mammoth. Our finding reveals the benefits of combining sedaDNA, pollen and macrofossil for palaeovegetational reconstruction and add to the increasing evidence suggesting large areas of the northern hemisphere remained ecologically stable during the Late Pleistocene.
Data from: Host resistance, population structure and the long-term persistence of bubonic plague: contributions of a modelling approach in the Malagasy focus
Although bubonic plague is an endemic zoonosis in many countries around the world, the factors responsible for the persistence of this highly virulent disease remain poorly known. Classically, the endemic persistence of plague is suspected to be due to the coexistence of plague resistant and plague susceptible rodents in natural foci, and/or to a metapopulation structure of reservoirs. Here, we test separately the effect of each of these factors on the long-term persistence of plague. We analyse the dynamics and equilibria of a model of plague propagation, consistent with plague ecology in Madagascar, a major focus where this disease is endemic since the 1920s in central highlands. By combining deterministic and stochastic analyses of this model, and including sensitivity analyses, we show that (i) endemicity is favoured by intermediate host population sizes, (ii) in large host populations, the presence of resistant rats is sufficient to explain long-term persistence of plague, and (iii) the metapopulation structure of susceptible host populations alone can also account for plague endemicity, thanks to both subdivision and the subsequent reduction in the size of subpopulations, and extinction-recolonization dynamics of the disease. In the light of these results, we suggest scenarios to explain the localized presence of plague in Madagascar.
Data from: Reduced tillage, but not organic matter input, increased nematode diversity and food web stability in European long-term field experiments
Soil nematode communities and food web indices can inform about the complexity, nutrient flows and decomposition pathways of soil food webs, reflecting soil quality. Relative abundance of nematode feeding and life-history groups are used for calculating food web indices, i.e. maturity index (MI), enrichment index (EI), structure index (SI) and channel index (CI). Molecular methods to study nematode communities potentially offer advantages compared to traditional methods in terms of resolution, throughput, cost and time. In spite of such advantages, molecular data have not often been adopted so far to assess the effects of soil management on nematode communities and to calculate these food web indices. Here, we used high-throughput amplicon sequencing to investigate the effects of tillage (conventional vs reduced) and organic matter addition (low vs high) on nematode communities and food web indices in ten European long-term field experiments and we assessed the relationship between nematode communities and soil parameters. We found that nematode communities were more strongly affected by tillage than by organic matter addition. Compared to conventional tillage, reduced tillage increased nematode diversity (23% higher Shannon diversity index), nematode community stability (12% higher MI), structure (24% higher SI), and the fungal decomposition channel (59% higher CI), and also the number of herbivorous nematodes (70% higher). Total and labile organic carbon, available K and microbial parameters explained nematode community structure. Our findings show that nematode communities are sensitive indicators of soil quality and that molecular profiling of nematode communities has the potential to reveal the effects of soil management on soil quality.
Data from: Ant mutualism increases long-term growth and survival of a common Amazonian tree
How ecological context shapes mutualistic relationships remains poorly understood. We combined long-term tree census data with ant censuses in a permanent 25-ha Amazonian forest dynamics plot to evaluate the effect of the mutualistic ant Myrmelachista schumanni (Formicinae) on the growth and survival of the common Amazonian tree Duroia hirsuta (Rubiaceae), considering its interactions with tree growth, population structure, and habitat. We found that the mutualist ant more than doubled tree relative growth rates and increased odds of survival. However, host tree size and density of conspecific neighbors modified the effect of the ant. Smaller trees hosting the mutualist ant consistently grew faster when surrounded by higher densities of conspecifics, suggesting that the benefit to the tree outweighs any negative effects of high conspecific densities. Moreover, our findings suggest that the benefit afforded by the ant diminishes with plant age and also depends on the density of conspecific neighbors. We provide the first long-term large-scale evidence of how mutualism affects the population biology of an Amazonian tree species.
Data from: Exploring the temporal variability of a food web using long-term biomonitoring data
Ecological communities are constantly being reshaped in the face of environmental change and anthropogenic pressures. Yet, how food webs change over time remains poorly understood. Food web science is characterized by a trade-off between complexity (in terms of the number of species and feeding links) and dynamics. Topological analysis can use complex, highly resolved empirical food web models to explore the architecture of feeding interactions but is limited to a static view, whereas ecosystem models can be dynamic but use highly aggregated food webs. Here, we explore the temporal dynamics of a highly resolved empirical food web over a time period of 18 years, using the German Bight fish and benthic epifauna community as our case study. We relied on long-term monitoring ecosystem surveys (from 1998 to 2015) to build a metaweb, i.e. the meta food web containing all species recorded over the time span of our study. We then combined time series of species abundances with topological network analysis to construct annual food web snapshots. We developed a new approach, "node-weighted" food web metrics by including species abundances to represent the temporal dynamics of food web structure, focusing on generality and vulnerability. Our results suggest that structural food web properties change through time; however, binary food web structural properties may not be as temporally variable as the underlying changes in species composition. Further, the node-weighted metrics enabled us to detect that food web structure was influenced by changes in species composition during the first half of the time series and more strongly by changes in species dominance during the second half. Our results demonstrate how ecosystem surveys can be used to monitor temporal changes in food web structure, which are important ecosystem indicators for building marine management and conservation plans.
Data from: Long-term stasis and short-term divergence in the phenotypes of microsnails on oceanic islands
Phenotypic divergence is often unrelated to genotypic divergence. An extreme example is rapid phenotypic differentiation despite genetic similarity. Another extreme is morphological stasis despite substantial genetic divergence. These opposite patterns have been viewed as reflecting opposite properties of the lineages. In this study, phenotypic radiation accompanied by both rapid divergence and long-term conservatism is documented in the inferred molecular phylogeny of the micro land snails Cavernacmella (Assimineidae) on the Ogasawara Islands. The populations of Cavernacmella on the Sekimon limestone outcrop of Hahajima Island showed marked divergence in shell morphology. Within this area, one lineage diversified into types with elongated turret shells, conical shells and flat disc-like shells without substantial genetic differentiation. Additionally, a co-occurring species with these types developed a much larger shell size. Moreover, a lineage adapted to live inside caves in this area. In contrast, populations in the other areas exhibited no morphological differences despite high genetic divergence among populations. Accordingly, the phenotypic evolution of Cavernacmella in Ogasawara is characterized by a pattern of long-term stasis and periodic bursts of change. This pattern suggests that even lineages with phenotypic conservatism could shift to an alternative state allowing rapid phenotypic divergence.
Data Processing for a Small-Scale Long-Term Coastal Ocean Observing System Near Mobile Bay, Alabama: A Geoscience Papers of the Future (GPF) Data Set
<p>The Dauphin Island Sea Lab (DISL) has been operating a permanent moored oceanographic station at 30 05.410'N, 88 12.694'W, 25 km southwest of the entrance to Mobile Bay, Alabama, since 2004. It collects hydrographic and current velocity data.</p> <p>This set of data files was collected between 27 Jan and 18 May 2011. It includes the raw data at initial download from the instruments, several intermediate processing steps, and final processed files ready for initial scientific analysis.</p> <p>The files have been prepared as supplementary material for a Geoscience Paper of the Future (GPF) in prep for publication at Earth and Space Science, as part of the OntoSoft GPF Initiative.</p> <p> </p>
Data Processing for a Small-Scale Long-Term Coastal Ocean Observing System Near Mobile Bay, Alabama: A Geoscience Papers of the Future (GPF) Workflow Diagram
<p>The Dauphin Island Sea Lab (DISL) has been operating a permanent moored oceanographic station at 30 05.410'N, 88 12.694'W, 25 km southwest of the entrance to Mobile Bay, Alabama, since 2004. It collects hydrographic and current velocity data.</p> <p>This diagram shows the processing steps for data from the instruments at this mooring, from initial download to initial scientific analysis. The accompanying text explains how to apply the workflow to the example dataset (10.5281/zenodo.18943) using the provided software (10.5281/zenodo.32741). </p> <p>The files have been prepared as supplementary material for a Geoscience Paper of the Future (GPF) in prep for publication at Earth and Space Science, as part of the OntoSoft GPF Initiative.</p>
Data_PlosOne_Too many is too bad: Long-term net negative effects of high density ungulate populations on a dominant Mediterranean shrub
<p>Dataset for Plos One Publication (2016): Too many is too bad: Long-term net negative effects of high density ungulate populations on a dominant Mediterranean shrub</p>
Long-term demographic data on the red-cockaded woodpecker
<p>In cooperative breeding systems, inclusive fitness theory predicts that non-breeding helpers more closely related to the breeders should be more willing to provide costly alloparental care, and thus have more impact on breeder fitness. In the red-cockaded woodpecker (<em>Dryobates borealis</em>), most helpers are the breeders' earlier offspring, but helpers do vary within groups in both relatedness to the breeders (some even being unrelated) and sex, and it can be difficult to parse their separate impacts on breeder fitness. Moreover, most support for inclusive fitness theory has been positive associations between relatedness and behavior, rather than actual fitness consequences. We used functional linear models to evaluate the per capita effects of helpers of different relatedness on eight breeder fitness components measured for up to 41 years at three sites. In support of inclusive fitness theory, helpers more related to the breeding pair made greater contributions to six fitness components. However, male helpers made equal contributions to increasing pre-fledging survival regardless of relatedness. These findings suggest that both inclusive fitness benefits and other, direct benefits may underlie helping behaviors in the red-cockaded woodpecker. Our results also demonstrate the application of an underused statistical approach to disentangle a complex ecological phenomenon.</p>
Data Source file for manuscript: Within-host genetic diversity of extended-spectrum beta-lactamase-producing Enterobacterales in long-term colonized patients
<p>ABSTRACT</p><p>Infections caused by extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (ESBL-PE) are associated with excess morbidity and mortality. Despite recognition of this immediate impact on human health, essential aspects of their molecular epidemiology remain under-investigated. This includes knowledge on the potential of a particular strain to persist in a host, mutational events during colonization, and the genetic diversity in individual patients over time. To investigate long-term genetic diversity of colonizing and infecting ESBL-producing <i>Klebsiella pneumoniae </i>species complex and ESBL-<i>Escherichia coli</i> in individual patients over time, we conducted performed a ten-year longitudinal retrospective study and extracted clinical and microbiological data from electronic health records. In this investigation, 76 ESBL-<i>K. pneumoniae</i> species complex and 284 ESBL-<i>E. coli</i> isolates were recovered from 19 and 61 patients. Strain persistence was detected in all patients colonized with ESBL-<i>K. pneumoniae </i>species complex, and 83.6% of patients colonized with ES BL-<i>E. coli</i>. Antimicrobial resistance genes, plasmid replicons, and whole ESBL-plasmids were shared between isolates regardless of chromosomal relatedness. Our study suggests that patients colonized with ESBL-producers may act as durable reservoirs for ongoing transmission of ESBLs, and that they are at a prolonged risk of recurrent infection with colonizing strains.</p><p>DATA SOURCE FILE</p><p>In this Data Source file, you will find access to the raw data, metadata and results obtained during the study: "Within-host genetic diversity of extended-spectrum beta-lactamase-producing Enterobacterales in long-term colonized patients". Data is organized following the structure of Figures/Tables of the manuscript and Supplementary Material. Additional figures not included in the main manuscript nor in the Supplementary Material are also available.</p><p>All sequencing and sample data from this study can be accessed at the NCBI database under the BioProject number PRJNA910977: <a href="http://dataview.ncbi.nlm.nih.gov/object/PRJNA910977">http://dataview.ncbi.nlm.nih.gov/object/PRJNA910977. </a>No new software was developed during this study. Standard bioinformatics software was used and the commands used can be accessed at the Supplementary Information file.</p>
Data from: Long-term aquarium records delineate the synchronized spawning strategy of Acropora corals
<p>Coral mass spawning, where corals synchronically release their gametes over several days following full moon, is one of the most spectacular reproduction events in the world. However, despite decades of studies, environmental drivers of the synchronous spawning remain controversial, partly because long-term systematic characterisations of the reproduction activities are challenging in the field. In this study, the authors take an advantage of 15-years-long spawning records of <em>Acropora</em> corals from aquarium tanks to successfully identify key environmental factors to determine coral spawning timing. The study demonstrates the great potential of the aquarium system in shaping our understanding of coral reproduction behaviour.</p>
Field data of soil greenhouse gas fluxes from SOMMIT long-term experiments
<p>This is a database of field data of soil greenhouse gas fluxes and ancillary data from long-term experiments (LTEs) that participated in the task 1 of the work package 3 from SOMMIT. As of November 2024 (V 1.0) six LTEs have contributed with data: "ACBB Estrées-Mons, France", "Rutzendorf_17, Austria", "Maintainance of organic orchards, Italy", "Fagna, Italy", "ULBF-Ljubljana, Slovenia" and "Grabow 2, Poland". All LTEs are referenced according to the LTE Index from <a href="https://doi.org/10.5281/zenodo.7598122" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.7598122</a>. The data includes soil greenhouse gas fluxes (N2O, CO2 and CH4) under different management practices, as well as ancillary data that might be useful to explain the observed fluxes. The database includes metadata on how soil greenhouse flux data and ancillary data were collected. Individual soil gas flux estimates are also expressed in CO2 equivalents [mg CO2-eq m-2 h-1], thereby providing a dataset on the contribution of soil CO2, N2O and CH4 fluxes to the soil global warming potential. This product is part of the EJP SOIL internal project SOMMIT, and serves as deliverables WP3.2 and WP3.3.</p>
Supplementary Data and Codes for "Machine Learning Based Long-term Water Quality in the Turbid Pearl River Estuary, China"
<p>The file "Ma_AGUSupplementary.xlsx" contains the in situ data used to develop the ANN model.</p> <p>The files "example_Chla.zip" and "example_TSS.zip" contain codes for retrieving the concentration of Chl-a and TSS on the sea surface of the Pearl River Estuary.</p> <p> </p>
Insights into short and long-term crop-foraging strategies in a chacma baboon (Papio ursinus) from GPS and accelerometer data
<p>Crop-foraging by animals is a leading cause of human-wildlife 'conflict' globally, affecting farmers and resulting in the death of many animals in retaliation, including primates. Despite significant research into crop-foraging by primates, relatively little is understood about the behaviour and movements of primates in and around crop fields, largely due to the limitations of traditional observational methods. Crop-foraging by primates in large scale agriculture has also received little attention. We used GPS and accelerometer bio-loggers, along with environmental data, to gain an understanding of the spatial and temporal patterns of activity for a female in a crop-foraging baboon group in and around commercial farms in South Africa over one year. Crop fields were avoided for most of the year, suggesting that fields are perceived as a high-risk habitat. When field visits did occur, this was generally when plant primary productivity was low, suggesting that crops were a 'fallback food'. All recorded field visits were at or before 15:00. Activity was significantly higher in crop fields than in the landscape in general, evidence that crop-foraging is an energetically costly strategy and that fields are perceived as a risky habitat. In contrast, activity was significantly lower within 100m of the field edge than in the rest of the landscape, suggesting that baboons wait near the field edge to assess risks before crop-foraging. Together this understanding of the spatiotemporal dynamics of crop-foraging can help to inform crop protection strategies and reduce conflict between humans and baboons in South Africa.</p>
Data for: The long-term impacts of deer herbivory in determining temperate forest stand and canopy structural complexity
<p>1. Ungulates place immense consumptive pressure on forest vegetation globally, leaving legacies of reduced biodiversity and simplified vegetative structure. However, what remains unresolved is whether browse-induced changes occurring early in succession ultimately manifest themselves in the developed forest canopy. Understanding the development and persistence of these legacies is critical as canopy structure is an important determinant of forest ecosystem functions like carbon sequestration and wildlife habitat.</p> <p>2. We measured how white-tailed deer (Odocoileus virginianus) browse during stand initiation affected canopy structure, tree species richness, diversity, stem density, and basal area on Pennsylvania's Allegheny Plateau using a portable canopy LiDAR system. We capitalized on an historic deer enclosure experiment where forests were subjected to four deer densities (4, 8, 15, and 25 deer/km2) for ten years following stand initiation.</p> <p>3. Deer browsing impacts on the forest canopy are apparent nearly four decades since stand initiation. The highest deer density treatment experienced a significant reduction in tree species diversity, density, and basal area with stands becoming dominated by black cherry (Prunus serotina). Reductions in overstory diversity and tree density resulted in a more open canopy with low leaf area and high horizontal leaf variability. Canopies were tallest at the lowest and highest deer densities.</p> <p><i>4. Synthesis and Applications</i>: Using a portable canopy LiDAR system and a former deer enclosure experiment, we show that high deer browsing pressure during stand initiation can have a decades-long impact on stand and canopy structure. High deer densities led to stands with lower species diversity and tree density, which resulted in canopies that were taller and less dense. Managers should consider the lasting legacy of ungulate herbivory on canopy structure, as canopy structure influences several important management goals, such as forest carbon sequestration, maintenance of diverse understory communities, and creation of wildlife habitat.</p>
Data from: Population collapse of habitat-forming species in the Mediterranean: a long-term study of gorgonian populations affected by recurrent marine heatwaves
<p><span><span><span><span><span><span><span><span><span><span><span>Understanding the resilience of temperate reefs to climate change requires exploring the recovery capacity of their habitat-forming species from recurrent marine heatwaves (MHWs). Here, we show that, in a Mediterranean highly enforced Marine Protected Area established more than 40 years ago, habitat-forming octocoral populations that were firstly affected by a severe MHW in 2003 have not recovered after 15 years. Contrarily, they have followed collapse trajectories that have brought them to the brink of local ecological extinction. Since 2003, impacted populations of the red gorgonian <i>Paramuricea clavata</i> (Risso, 1826) and the red coral <i>Corallium rubrum</i> (Linnaeus, 1758) have followed different trends in terms of size structure, but a similar progressive reduction in density and biomass. Concurrently, recurrent MHWs were observed in the area during the 2003-2018 study period, which may have hindered populations recovery. The studied octocorals play a unique habitat-forming role in the coralligenous assemblages (i.e., reefs endemic to the Mediterranean Sea home to approximately 10% of its species). Therefore, our results underpin the great risk that recurrent MHWs pose for the long-term integrity and functioning of these emblematic temperate reefs.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: A shift from phenol to silica-based leaf defenses during long-term soil and ecosystem development
<p>The resource availability hypothesis predicts that plants adapted to infertile soils have high levels of anti-herbivore leaf defenses. This hypothesis has been mostly explored for secondary metabolites such as phenolics, while it remains underexplored for silica-based defenses. We determined leaf concentrations of total phenols and silicon (Si) in plants growing along the 2-million-year Jurien Bay chronosequence, exhibiting an extreme gradient of soil fertility. We found that nitrogen (N) limitation on young soils led to a greater expression of phenol-based defenses, whereas old, phosphorus (P)-impoverished soils favored silica-based defenses. Both defense types were negatively correlated at the community and individual species level. Our results suggest a tradeoff among these two leaf defense strategies based on the strength and type of nutrient limitation, thereby opening up new perspectives for the resource availability hypothesis and plant defense research. This study also highlights the importance of silica-based defenses under low P supply.</p>
Biological experimental raw data from: The Incubascope : A simple, compact and large field of view microscope for long-term
<p>Optical imaging has rapidly evolved in the last decades. Sophisticated microscopes allowing optical sectioning for 3D imaging or sub-diffraction resolution are available. Due to price and maintenance issues, these microscopes are often shared between users in facilities. Consequently, long term access is often prohibited and does not allow to monitor slowly evolving biological systems or to validate new models like organoids. Preliminary coarse long-term data that do not require do acquisition of terabytes of high-resolution images are important as a first step. By contrast with expansive all-in-one commercialized stations standard microscopes equipped with incubator stages offer a more cost-effective solution despite imperfect long run atmosphere and temperature control. Here, we present the Incubascope, a custom-made compact microscope that fits into a table-top incubator. It is cheap and simple to implement user-friendly and yet provides high imaging performances. The system has a field of view of 5.5×8 mm2, a 3 µm resolution, a 10 frames/second acquisition rate, and is controlled with a Python-based graphical interface. We exemplify the capabilities of the Incubascope on biological applications such as the hatching of Artemia salina eggs, the growth of the slime mold Physarum polycephalum and of encapsulated spheroids of mammalian cells.</p>
Data from: Harvest and density-dependent predation drive long-term population decline in a northern ungulate
<p><span>The relative effect of top-down versus bottom-up forces in regulating and limiting wildlife populations is an important theme in ecology. Untangling these effects is critical for a basic understanding of trophic dynamics and effective management. We examined the drivers of moose (<em>Alces alces</em>) population growth by integrating two independent sources of observations within a hierarchical Bayesian population model. This analysis used one of the largest existing spatiotemporal datasets on ungulate population dynamics globally. We documented a 20% population decline over the period examined. Moose population growth was negatively density-dependent. Although the mechanisms producing density-dependent suppression of population growth could not be determined, the relatively low densities at which moose populations were documented suggests it could be due primarily to density-dependent predation. Predation </span>primarily limited population growth, except at low density, where it was regulating. <span>Harvest appeared to be largely </span>additive<span> and contributed to population declines.</span> Our results, highlight how <span>population dynamics are context dependent and vary strongly across gradients in climate, forest type, and predator abundance. These results help clarify long-standing questions in population ecology and highlight the complex relationships between natural and human-caused mortality in driving ungulate population dynamics. </span></p>
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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.