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1,018 results for “paste”
Data from: The role of migration in the change of Northern Hemisphere vegetation for the past 50,000 years
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Data for: Wolverine density distribution reflects past persecution and current management in Scandinavia
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Supporting code and data to reproduce analysis for: Genomic signatures of past megafrugivore-mediated dispersal in Malagasy palms
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Temporal population structure, a genetic dating method for ancient Eurasian genomes from the past 10,000 years
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Dataset and R code: Genetic diversity of lion populations in Kenya: evaluating past management practices and recommendations for future conservation actions by Chege M et.al
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Supporting model data for Paleogeographic controls on the evolution of Late Cretaceous ocean circulation by Ladant, J.-B., et al. in Climate of the Past, doi:10.5194/cp-2019-157.
<p>The dataset is comprised of CCSM4 model variables required to reproduce the figures shown in the following manuscript:</p> <p>Ladant, J.-B., C. J. Poulsen, F. Fluteau, C. R. Tabor, K. G. MacLeod, E. E. Martin, S. J. Haynes and M. A. Rostami, Paleogeographic controls on the evolution of Late Cretaceous ocean circulation, Climate of the Past, doi:10.5194/cp-2019-157.</p>
Dataset for NMR quadrature echo and T1 saturation recovery pulse sequences underlying the publication 'On the quantification of solid phases in hydrated cement paste by 1H nuclear magnetic resonance relaxometry'
<p>This record comprises the datasets of combined 1H NMR quadrature echo and T1 saturation recovery pulse sequences underlying the publication “On the quantification of solid phases in hydrated cement paste by 1H nuclear magnetic resonance relaxometry” by Robert Schulte Holthausen & Peter J. McDonald, Cement and Concrete Research, https://doi.org/10.1016/j.cemconres.2020.106095.</p> <p><br> In this work different solid phases, important to cement paste hydration, are investigated with low-field bench top 1H nuclear magnetic resonance with a view to developing an alternate characterisation methodology that requires minimal invasive or destructive sample preparation.</p> <p><br> A combination of the well-established quadrature echo pulse sequence with variable pulse gap together with a T1 saturation recovery quadrature echo pulse sequence is used.</p>
Data from: The ghost of disturbance past: long-term effects of pulse disturbances on community biomass and composition
<p><span><span><span><span><span><span><span><span><span><span><span>Current global change is associated with an increase in disturbance frequency and intensity, with the potential to trigger population collapses and to cause permanent transitions to new ecosystem states. However, our understanding of ecosystem responses to disturbances is still incomplete. Specifically, there is a mismatch between the diversity of disturbance regimes experienced by ecosystems and the one-dimensional description of disturbances used in most studies on ecological stability. To fill this gap, we conducted a full factorial experiment on microbial communities, where we varied the frequency and intensity of disturbances affecting species mortality, resulting in twenty different disturbance regimes. We explored the <span><span>direct</span></span> and long-term effects of these disturbance regimes on community biomass. While most communities were able to recover biomass and composition states similar to undisturbed controls after a halt of the disturbances, we identified some disturbance thresholds that had long-lasting legacies on communities. <span><span>Using a model based on logistic growth, we identified qualitatively</span></span> the sets of disturbance frequency and intensity that had equivalent long-term <span><span>negative</span></span> impacts on experimental communities. Our results show that an increase in disturbance intensity is a bigger threat for biodiversity and biomass recovery than the occurrence of more frequent but less intense disturbances.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Modeling phylogenetic biome shifts on a planet with a past
<p>The spatial distribution of biomes has changed considerably over deep time, so the geographical opportunity for an evolutionary lineage to shift into a new biome may depend on how the availability and connectivity of biomes has varied temporally. To better understand how lineages shift between biomes in space and time, we developed a phylogenetic biome shift model in which each lineage shifts between biomes and disperses between regions at rates that depend on the lineage's biome affinity and location relative to the spatiotemporal distribution of biomes at any given time. To study the behavior of the biome shift model in an empirical setting, we developed a literature-based representation of paleobiome structure for three mesic forest biomes, six regions, and eight time strata, ranging from the Late Cretaceous (100 Ma) through the present. We then fitted the model to a time-calibrated phylogeny of 119 <em>Viburnum</em> species to compare how the results responded to various realistic or unrealistic assumptions about paleobiome structure. Ancestral biome estimates that account for paleobiome dynamics reconstructed a warm temperate (or tropical) origin of <em>Viburnum</em>, which is consistent with previous fossil-based estimates of ancestral biomes. Imposing unrealistic paleobiome distributions led to ancestral biome estimates that eliminated support for tropical origins, and instead inflated support for cold temperate ancestry throughout the warmer Paleocene and Eocene. The biome shift model we describe is applicable to the study of evolutionary systems beyond <em>Viburnum</em>, and the core mechanisms of our model are extensible to the design of richer phylogenetic models of historical biogeography and/or lineage diversification. We conclude that biome shift models that account for dynamic geographical opportunities are important for inferring ancestral biomes that are compatible with our understanding of Earth history.</p>
Data from: Global vegetation patterns of the past 140,000 years
<p>Aim Insight into global biome responses to climatic and other environmental changes is essential to address key questions about past and future impacts of such changes. By simulating global biome patterns 140 ka to present we aimed to address important questions about biome changes during this interval.<br> <br> Location Global.<br> <br> Taxon Plantae.<br> <br> Methods Using the LPJ-GUESS dynamic global vegetation model, we made 89 simulations driven using ice-core atmospheric CO2 concentrations, Earth's obliquity, and outputs from a pre-industrial and 88 palaeoclimate experiments run using HadCM3. Experiments were run for 81 time slices between 1 ka and 140 ka, seven 'hosing' experiments also being run, using a 1 Sv freshwater flux to the North Atlantic, for time slices corresponding to Heinrich Events H0 – H7. Using a rule-based approach, based on carbon mass and leaf area index of the LPJ-GUESS plant functional types, the biome was inferred for each grid cell. Biomes were mapped, and the extent and total vegetation biomass of each biome, and total global vegetation biomass, estimated.<br> <br> Results Substantial changes in biome extents and locations were found on all vegetated continents. Although the largest-magnitude changes were in Eurasia, important changes were seen in tropical latitudes and the Southern Hemisphere. Total global extent of most biomes varied on multi-millennial (orbital) time scales, although some (e.g. Tropical Raingreen Forest) responded principally to the ca. 100 kyr glacial–interglacial cycle and others (e.g. Temperate Broad-leaved Evergreen Forest) mainly to the ca. 20 kyr precession cycle. Many also responded to millennial contrasts between stadial ('hosing') and interstadial climates, with some (e.g. Tropical Evergreen Forest) showing stronger responses than to the multi-millennial changes.<br> <br> Main conclusions No two time slices had identical biome patterns. Even equivalent Holocene and last interglacial time slices, and the last and penultimate glacial maxima, showed important differences. Only a small proportion of global land area experienced no biome change since 140 ka; many places experienced multiple biome changes. These modelling experiments provided little evidence for long-term biome stability.</p>
Data from: Fluid preservation causes minimal reduction of parasite detectability in fish specimens: a new approach for reconstructing parasite communities of the past?
<ol> <li>Long-term datasets are needed to evaluate temporal patterns in wildlife disease burdens, but historical data on parasite abundance are extremely rare. For more than a century, natural history collections have been accumulating fluid-preserved specimens, which should contain the parasites infecting the host at the time of its preservation. However, before this unique data source can be exploited, we must identify the artefacts that are introduced by the preservation process. Here, we experimentally address whether the preservation process alters the degree to which metazoan parasites are detectable in fluid-preserved fish specimens when using visual parasite detection techniques.</li> <li>We randomly assigned fish of three species (<i>Gadus chalcogrammus, Thaleichthys pacificus, Parophrys vetulus</i>) to two treatments. In the first treatment, fish were preserved according to the standard procedures used in ichthyological collections. Immediately after the fluid-preservation process was complete, we performed parasitological dissection on those specimens. The second treatment was a control, in which fish were dissected without being subjected to the fluid-preservation process. We compared parasite abundance between the two treatments.</li> <li>Across 298 fish individuals and 59 host–parasite pairs, we found few differences between treatments, with 24 of 27 host–parasite pairs equally abundant between the two treatments. Of these, one pair was significantly more abundant in the preservation treatment than in the control group, and two pairs were significantly less abundant in the preservation treatment than in the control group.</li> <li>Our data suggest that the fluid-preservation process does not have a substantial effect on the detectability of metazoan parasites. This study addresses only the effects of the fixation and preservation process; long-term experiments are needed to address whether parasite detectability remains unchanged in the months, years, and decades of storage following preservation. If so, ecologists will be able to reconstruct novel, long-term datasets on parasite diversity and abundance over the past century or more using fluid-preserved specimens from natural history collections.</li> </ol>
Data and code for: Past and future extinctions shape the body size - fruit size relationship between palms and mammalian frugivores
<p>The dispersal of seeds by mammalian frugivores influences the structure and composition of plant communities, but most ecosystems have undergone defaunation over thousands of years, a process that continues today. Understanding how past defaunation has affected fruit-frugivore interactions will thus provide insights into how ecosystems may respond to future frugivore loss. By integrating palm and mammalian frugivore trait and occurrence data worldwide, we reveal a global positive relationship between fruit size and body size of frugivore assemblages. Global variation in fruit size is better explained by present-day frugivore assemblages compared to those of the Late Pleistocene (including extinct species), suggesting a substantial ecological and evolutionary reorganization after Pleistocene mammal extinctions. Interestingly, the reverse is true for the Neotropics where some large-fruited palm species may have persisted over thousands of years following extinction of their main seed dispersers. Simulations of frugivore extinction over the next 100 years suggest that changes in body size will require up to a 4% assemblage-level decrease in palm fruit sizes to maintain the current global frugivore body size - fruit size relationship. Absolute changes in assemblage-level means of palm fruit size were on average up to two-fold higher than observed species-level estimates of seed size change following defaunation. Overall, our results suggest that while some large-fruited palms may persist after the loss of their main dispersers, many palms may be unable to keep pace with future defaunation through evolutionary changes in fruit size alone. The burden of the impact of the extinction of seed dispersers will probably be disproportionately borne by large-fruited palms, possibly over thousands of years to come.</p>
Data from: Consequences of past and present harvest management in a declining flyway population of common eiders Somateria mollissima
<p>1. Harvested species population dynamics are shaped by the relative contribution of natural and harvest mortality. Natural mortality is usually not under management control, so managers must continuously adjust harvest rates to prevent overexploitation. Ideally, this requires regular assessment of the contribution of harvest to total mortality and how this affects population dynamics. 2. To assess the impact of hunting mortality on the dynamics of the rapidly declining Baltic/Wadden Sea population of common eiders Somateria mollissima we first estimated vital rates of ten study colonies over the period 1970–2015. By means of a multi-event capture-recovery model we then used the cause of death of recovered individuals to estimate proportions of adult females that died due to hunting or other causes. Finally, we adopted a stochastic matrix population modelling approach based on simulations to investigate the effect of past and present harvest regulations on changes in flyway population size and composition. 3. Results showed that even the complete ban on shooting females implemented in 2014 in Denmark, where most hunting takes place was not enough to stop the population decline given current levels of natural female mortality. Despite continued hunting of males our predictions suggest that the proportion of females will continue to decline unless natural mortality of the females is reduced. 4. Although levels of natural mortality must decrease to halt the decline of this population, we advocate that the current hunting ban on females is maintained while further investigations of factors causing increased levels of natural mortality among females are undertaken. 5. Synthesis and applications. At the flyway scale, continuous and accurate estimates of vital rates and the relative contribution of harvest versus other mortality causes are increasingly important as the population effect of adjusting harvest rates is most effectively evaluated within a model-based adaptive management framework.</p>
Back into the past: Resurveying random plots to track community changes in Italian coastal dunes
<p>This dataset includes two excel sheets. The first contains vegetation data ("species_data", a matrix of 668 plots x 213 species) and the second contains plant functional traits data ("traits_data") that were used to evaluate temporal changes in taxonomic and functional diversity of Mediterranean coastal dune habitats.</p> <p><span><span><span><span><span><span><span><span><span><span><span>As to the first sheet ("species_data"): vegetation data were collected at two points in time (Time 0, hereafter T<sub>0</sub>: 2002-2007, and Time 1, herafter T<sub>1</sub>: 2017-2018) in 334 randomly-sampled, georeferenced, standardized (4 m<sup>2</sup>) plots. Historical data used for the resurveying study were extracted from RanVegDunes (Sperandii et al. 2017). Details on the resurveying protocol can be found in Sperandii et al. (2019), but in short: resampling activities took place during the same months in which the original sampling was done, and plot positions were relocated using a GPS unit on which historical geographic coordinates were stored. Plots are located in coastal dune sites along the Tyrrhenian and Adriatic coasts of Central Italy, and belong to herbaceous communities classified into the following EU Habitats (sensu Annex I 92/43/EEC): upper beach (Habitat 1210), embryo dunes (Habitat 2110), shifting dunes (Habitat 2120), fixed dunes (Habitat 2210), and dune grasslands (Habitat 2230). A subset of plots could not be classified into an EU Habitat because they were highly disturbed or invaded by alien species ("NC-plots"). The matrix includes cover data, expressed as percentage (%) cover. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>As to the second sheet ("traits_data"): this sheet includes data on 3 plant functional traits, two of them quantitative (plant height, specific leaf area - SLA) and one qualitative (plant lifespan). Data for the quantitative traits represent species-level average trait values and were extracted from "TraitDunes", a database registered on the global platform TRY (Kattge et al., 2020). Functional trait data were collected in the same sites covered by the resurveying study. Functional trait data were originally measured on the most abundant species, and are available for a varying number of species depending on the trait.</span></span></span></span></span></span></span></span></span></span></span></p> <p>References:</p> <p>Kattge, J., Bönisch, G., Díaz, S., Lavorel, S., Prentice, I. C., Leadley, P., ... & Wirth, C. (2020). TRY plant trait database–enhanced coverage and open access. Global Change Biology.</p> <p>Sperandii, M.G., Prisco, I., Stanisci, A., & Acosta, A.T.R (2017). RanVegDunes-A random plot database of Italian coastal dunes. Phytocoenologia, 47(2), 231-232.</p> <p>Sperandii, M.G., Bazzichetto, M., Gatti, F., & Acosta, A.T.R. (2019). Back into the past: Resurveying random plots to track community changes in Italian coastal dunes. Ecological Indicators, 96, 572-578.</p>
Data from: Selection past impacts the strength of an aquatic trophic cascade
1. In complex food webs, interactions among species in different trophic levels can generate cascading indirect effects that couple top predators with primary producers, thereby affecting ecosystem functioning. Natural selection imposed by top predators on intermediate predators may play a role in shaping the strength of these trophic cascades, but this conjecture remains largely untested. 2. To determine the effects of natural selection on the strength of trophic cascades we conducted a two-part experiment in a four-level aquatic trophic system involving a top predator (fish), an intermediate predator (damselflies), herbivores (zooplankton), and primary producers (algae). We first quantified how predation by fish generated selection on damselfly activity levels after controlling for phenotypic plasticity. We then measured the indirect effects of this selection on primary production (phytoplankton biomass). In both experiments we varied the density of predators, allowing us to elucidate both trait-mediated and density-mediated indirect effects. 3. We found that as fish density increased, damselfly survivorship declined, which generated natural selection favoring less active damselflies. These results are robust after taking into account latent effects of plasticity in response to fish predator cues. The surviving damselflies likely foraged less, freeing herbivores from predation, which in turn reduced primary production. This selection driven trait-mediated indirect effect was only apparent at low damselfly densities, because the consumptive effect of damselflies at high densities overwhelmed the effects of past selection. 4. These results demonstrate that the past action of natural selection can affect the strength of a trophic cascade. Natural selection can therefore act as a mechanism coupling ecological dynamics across trophic levels, which ultimately influences ecosystem functioning.
Data from: Herbarium specimens reveal increasing herbivory over the past century
Predicting how ecological interactions will respond to global change is a major challenge. Plants and their associated insect herbivores compose much of macroscopic diversity, yet how their interactions have been altered by recent environmental change remains underexplored. To address this gap, we quantified herbivory on herbarium specimens of four plant species with records extending back 112 years. Our study focused on the northeastern US, where temperatures have increased rapidly over the last few decades. This region also represents a range of urban development, a form of global change that has shown variable effects on herbivores in the past studies. Herbarium specimens collected in the early 2000s were 23% more likely to be damaged by herbivores than those collected in the early 1900s. Herbivory was greater following warmer winters and at low latitudes, suggesting that climate warming may drive increasing insect damage over time. In contrast, human population densities were negatively associated with herbivore damage. To explore whether changes in insect occurrence or abundance might explain shifts in herbivory, we used insect observational records to build climate occupancy models for lepidopteran herbivores (butterflies and moths) of our focal plant species. These models show that higher winter temperatures were associated with higher probability of insect herbivore presence, while urbanization was associated with reduced probability of herbivore presence, supporting a link between insect herbivore occurrence and herbivory mediated through environment. Synthesis. Using a temporal record of plant herbivory that spans over a century, we show that both temperature and urbanization influence insect damage to plants, but in very different ways. Our results indicate that damage to plants by insect herbivores will likely continue to increase through time in the northeastern US as global temperatures rise, but that urbanization may disrupt local effects of winter warming on herbivory by excluding certain herbivores. These changes may scale to shape ecosystem processes that are driven by herbivory, including plant productivity.
Data from: Emergence patterns of novelty in European vegetation assemblages over the past 15,000 years
Plant communities are not stable over time and biological novelty is predicted to emerge due to climate change, the introduction of exotic species and land-use change. However, the rate at which this novelty may arise over longer time periods has so far received little attention. We reconstruct the emergence of novelty in Europe for a set of baseline conditions over the past 15 000 years to assess past rates of emergence and investigate underlying causes. The emergence of novelty is baseline specific and, during the early-Holocene, was mitigated by the rapid spread of plant taxa. Although novelty generally increases as a function of time, climate and human-induced landscape changes contributed to a non-linear post-glacial trajectory of novelty with jumps corresponding to periods of rapid changes. Emergence of novelty accelerated during the past 1000 years. Historical cultural landscapes experienced a faster novelty development due to the contribution from anthropogenic land-cover changes.
Figure 7 in To be or not to be a tibial comb: A discussion on the (past) use of tibial armature in tribal/subtribal organization in Cholevinae (Coleoptera: Leiodidae)
Figure 7. Apex of protibiae. (A-B) Ptomaphaminus chapmani (Peck), right leg (mirrored image), (A) ventral and (B) dorsal views; (C) Proptomaphaginus puertoricensis Peck, ventral view (used with permission and modified from fig. 19 in Perreau, 2000); (D-E) Eucatops sp., (D) dorsal (note the serrate nature of the external margin of the protibia in this species) and (E) ventral views; (F-H) Eucatops (Napocatops) giganteus Salgado, (F) lateral-external, (G) ventro-lateral-external, and (H) lateral-internal views. gp = 'gap' on the apical crown of spines around base of spur; is = inner spur; os = outer spur; the arrow shows the point where the spines stop circling the apical margin of the protibia and start to follow the external margin of the protibia, instead of making a complete apical crown; the rectangle highlights the presence of a series of small spines that extends from the internal portion of the apical crown of spines (to the left of the figure) towards the external comb of spines (to the right of the figure); the circle highlights the series of spines at the inner face of the protibia; the ellipse highlights the longitudinal row of strong spines along the outer margin of the protibia.
Figure 4 in To be or not to be a tibial comb: A discussion on the (past) use of tibial armature in tribal/subtribal organization in Cholevinae (Coleoptera: Leiodidae)
Figure 4. Apex of mesotibiae in Anemadini. (A-B) Anemadus italicus Zoia, (A) lateral-internal and (B) dorsal views; (C) Dissochaetus vanini Gnaspini, ventral view; (D-E) Eunemadus chilensis Portevin, (D) ventral and (E) lateral-external views. bg = 'body guard' seta; in = 'interstitial spines'; is = inner spur; os = outer spur; the ellipses highlight the longer spines on the dorsal portion of the apical crown of spines.
Figure 8 in To be or not to be a tibial comb: A discussion on the (past) use of tibial armature in tribal/subtribal organization in Cholevinae (Coleoptera: Leiodidae)
Figure 8. Apex of protibiae, Adelopsis leo Gnaspini, (A) dorsal, (B) ventral, and (C) frontal views. is = inner spur; os = outer spur.
ScienceDex guides
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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.