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355 results for “collapses”
From seed dispersal service to reproductive collapse: density-dependent outcome of a palm-mammal interaction
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Data from: Micronuclear collapse from oxidative damage
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Native biodiversity collapse in the Eastern Mediterranean
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Principles Governing Establishment versus Collapse of HIV-1 Cellular Spread
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Data and code for: Sea level rise causes shorebird population collapse before habitat drowns
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Data from: Decadal-scale time series highlight the role of chronic disturbances in driving ecosystem collapse in the Anthropocene
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Effect of pore collapse and grain crushing on the frequency dependence of elastic wave velocities in a porous sandstone
<p>Dataset for the article "Effect of pore collapse and grain crushing on the frequency dependence of elastic wave velocities in a porous sandstone"<br> by Sun, C., Borgomano, J.V.M., Fortin J., Wang, S.</p> <p> </p> <p>Please refer to the ReadMe file or to kang2008ping2008@163.com for more details.</p>
Data from: The ecology of the collapse of Rapa Nui society
<p>Collapses of food producer societies are recurrent events in prehistory and have triggered a growing concern for identifying the underlying causes of convergences/divergences across cultures around the world. One of the most studied and used as a paradigmatic case is the population collapse of the Rapa Nui society. Here, we test different hypotheses about by developing explicit population dynamic models that integrate feedbacks between climatic, demographic and ecological factors that underpinned the socio-cultural trajectory of these people. We evaluate our model outputs against a reconstruction of past population size based on archaeological radiocarbon dates from the island. The resulting estimated demographic declines of the Rapa Nui people are linked to the long-term effects of climate change on the island's carrying capacity, and in turn on the "per capita food supply".</p>
Population collapse in viviparid gastropods of the Lake Victoria ecoregion started before the Last Glacial Maximum
<p>For the purpose of reproducibility, we here provide the datasets and R script supporting the analyses of the paper "Population collapse in viviparid gastropods of the Lake Victoria ecoregion started before the Last Glacial Maximum" by Van Bocxlaer et al. This paper has been accepted for publication in Molecular Ecology on 31 July 2020. In this study, we examine the population structure of the clade of <i>Bellamya</i> gastropods that occupies the Lake Victoria ecoregion with the aim to relate past environmental change with demography and diversification dynamics. The here provided datasets include 1) an alignment of a fragment of the gene cytochrome <i>c</i> oxidase subunit 1 for 60 specimens; 2) genotype data for 321 individuals from 39 localities for 15 microsatellite loci (total dataset); 3) a regrouped genotype dataset (282 specimens from 21 localities for 15 microsatellite loci), which was used for some analyses in our study. Analyses were performed with various programs as reported in our paper. Here we provide input and result files (33 files in total) for these analyses, complemented with an R script that readily allows reproducing the majority of our inquiries.</p>
Diversification or collapse of self-incompatibility haplotypes as a rescue process
In angiosperm self-incompatibility systems, pollen with an allele matching the pollen recipient at the self-incompatibility locus is rejected. Extreme allelic polymorphism is maintained by frequency-dependent selection favoring rare alleles. However, two challenges result in a "chicken-egg"problem for the spread of a new allele (a tightly linked haplotype in this case) under the widespread "collaborative non-self recognition" mechanism. A novel pollen-function mutation alone would merely grant compatibility with a nonexistent style-function allele: a neutral change at best. A novel pistil-function mutation alone could only be fertilized by pollen with a nonexistent pollen-function allele: a deleterious change that would eliminate all seed set. However, a pistil-function mutation complementary to a previously neutral pollen mutation may spread if it restores self-incompatibility to a self-compatible intermediate. We show that novel haplotypes can also drive elimination of existing ones with fewer siring opportunities. We calculate relative probabilities of increase and collapse in haplotype number given the initial collection of incompatibility haplotypes and the population gene conversion rate. Expansion in haplotype number is possible when population gene conversion rate is large, but large contractions are likely otherwise. A Markov chain model derived from these expansion and collapse probabilities generates a stable haplotype number distribution in the realistic range of 10--40 under plausible parameters. However, smaller populations might lose many haplotypes beyond those lost by chance during bottlenecks.
Caldera collapse vs inherited structures: a database of laboratory experiments
<p>This dataset presents the results of four experimental series of analogue models performed to investigate the role of inherited structures during caldera collapse. Our experimental series tested the role of one/two inherited discontinuities variously located with respect to an analogue magma chamber. Models have been analysed quantitatively by means of (i) photogrammetric Digital Elevation Model reconstruction and (ii) Digital Particle Image Velocimetry (DPIV) techniques. In this dataset, we show the row data supporting modelling results.</p>
Vertical stratification collapses under seasonal shifts in climate
<p><b>Aim: </b>Tropical forests are vertically complex, and offer unique niche opportunities in the form of climate-, habitat-, and resource-gradients from ground to canopy. Rainforest species organize within this vertical spatial gradient and recent macro-ecological research suggests that the highest levels of vertical stratification occur in structurally complex and climatically stable tropical rainforests. Yet, patterns of verticality are typically derived across latitude, linking annual precipitation regimes to canopy utilization and vertical stratification of communities in space. However, although the tropics are not thermally variable, they do have strong seasonality in rainfall—a temporal component that is missed in macro-scale studies. We hypothesise that verticality of ecological communities responds to seasonality in climate, particularly rainfall.</p> <p><b>Location: </b>Sierra Llorona, Colón Province, Panama.</p> <p><b>Taxon: </b>Amphibians.</p> <p><b>Methods: </b>We performed 121 ground-to-canopy surveys across the wet and dry seasons for amphibians. We calculated species specific and community wide vertical height and abundance shifts between seasons, and separately test the importance of vertical height and season on the vertical distribution of species. </p> <p><b>Results: </b>Our results show a clear downward shift of 5 m in height in amphibian communities from the wet season to dry season. We also observe significant changes in species composition across vertical strata in both seasons, driven by nestedness in the dry season (loss of species over height), and genuine turnover in the wet season (loss and addition of species over height).</p> <p><b>Main Conclusions: </b>The exploitation of canopy microhabitats and resources in the wet season resulted in complex patterns of stratification, whereas drying flattened the distribution and simplified the composition of arboreal communities. As such, pattern and process in the vertical dimension is not static in time but rather exists as a dichotomy with inverse patterns between wet and dry seasons. Complex, multidimensional distributions of diverse rainforest communities can be simplified by climatic constraints—an important consideration as anthropogenic climate change increases the magnitude of seasonal swings in temperature and precipitation.</p>
Measuring the distance and mass of galactic core-collapse supernovae using neutrinos
<p>This is the dataset and analysis scripts for the manuscript "Measuring the distance and mass of galactic core-collapse supernovae using neutrinos" (submitted to PRL, arXiv link to follow). </p>
Data from: Predator-induced collapse of niche structure and coexistence on islands
Biological invasions represent both a pressing environmental challenge and an opportunity to investigate fundamental ecological processes, such as the role of top predators in regulating species diversity and food-web structure. In whole-ecosystem manipulations of small Caribbean islands where brown anole lizards (Anolis sagrei) were the native top predator, we experimentally staged invasions by competitors (green anoles, A. smaragdinus) and/or novel top predators (curly-tailed lizards, Leiocephalus carinatus). We show that curly-tails destabilized coexistence of competing prey species, contrary to the classic idea of keystone predation. Fear-driven avoidance of predators collapsed the spatial and dietary niche structure that otherwise stabilized coexistence, intensifying interspecific competition within predator-free refuges and contributing to green-anole population extinctions. Moreover, whereas adding either green anoles or curly-tails lengthened food chains, adding both species reversed this effect, in part because apex predators were trophic omnivores. Our results underscore the importance of top-down control in community ecology, but show that its outcomes hinge on prey behavior, spatial structure, and omnivory. Diversity-enhancing effects of top predators cannot be assumed, and non-consumptive effects of predation risk may be a widespread constraint on species coexistence.
Data from: Oxygen limitations on marine animal distributions and the collapse of epibenthic community structure during shoaling hypoxia
Deoxygenation in the global ocean is predicted to induce ecosystem-wide changes. Analysis of multidecadal oxygen time-series projects the northeast Pacific to be a current and future hot spot of oxygen loss. However, the response of marine communities to deoxygenation is unresolved due to the lack of applicable data on component species. We repeated the same benthic transect (n = 10, between 45 and 190 m depths) over 8 years in a seasonally hypoxic fjord using remotely operated vehicles equipped with oxygen sensors to establish the lower oxygen levels at which 26 common epibenthic species can occur in the wild. By timing our surveys to shoaling hypoxia events, we show that fish and crustacean populations persist even in severe hypoxia (<0.5 mL L−1) with no mortality effects but that migration of mobile species occurs. Consequently, the immediate response to hypoxia expansion is the collapse of community structure; normally partitioned distributions of resident species coalesced and localized densities increased. After oxygen renewal and formation of steep oxygen gradients, former ranges re-established. High frequency data from the nearby VENUS subsea observatory show the average oxygen level at our site declined by ~0.05 mL L−1 year−1 over the period of our study. The increased annual duration of the hypoxic (<1.4 mL L−1) and severely hypoxic periods appears to reflect the oxygen dynamics demonstrated in offshore source waters and the adjacent Strait of Georgia. Should the current trajectory of oxygen loss continue, community homogenization and reduced suitable habitat may become the dominant state of epibenthic systems in the northeast Pacific. In situ oxygen occurrences were not congruent with lethal and sublethal hypoxia thresholds calculated across the literature for major taxonomic groups indicating that research biases toward laboratory studies on Atlantic species are not globally applicable. Region-specific hypoxia thresholds are necessary to predict future impacts of deoxygenation on marine biodiversity.
Collapse of dispersal trait diversity across a long-term chronosequence reveals a strong negative impact of frugivore extinctions on forest resilience
<p><span><b>1. </b></span><span>Understanding how seed dispersal disruption may alter plant community diversity and dynamics over a large temporal scale remains a challenge. Here, we use a long-term chronosequence to compare changes in the richness and composition of different dispersal trait assemblages in communities established before and after human colonisation in the Mascarene archipelago.</span></p> <p><span><b>2. </b></span><span>Our study was located on Réunion on the slopes of the Piton de la Fournaise, one of the most active volcanoes worldwide. We analysed 151 vegetation surveys on lava flows dated between 1401-AD and 1956-AD and in tropical rainforests established on older substrata. We defined five classes of substratum age, according to the well-known chronology of native frugivore defaunation: "old substrata" and </span>[1401, 1665[ when frugivores were abundant and diverse <span>before permanent human settlement</span>; [1665, 1800[ when large-bodied frugivore populations were strongly reduced; [1800, 1900[ when large-bodied frugivores went extinct and small-bodied frugivores were still abundant; [1900, 1956] <span>decline in the population of small-bodied frugivores. Based on dispersal traits, we categorised 146 native woody species as anemochorous, small fleshy-fruited or large fleshy-fruited, i.e. plant of which fruit could not theoretically be dispersed by extant frugivores.</span></p> <p><span><b>3. </b></span><span>Changes in dispersal trait diversity strongly correlated with the chronology of defaunation. Species-rich communities settled before human colonisation were strongly dominated by fleshy-fruited species. </span>L<span>arge fleshy-fruited plants in the oldest communities </span>settled after human colonisation <span>declined markedly and almost disappeared after 1800. The richness of small fleshy-fruited plants decreased less rapidly across the chronosequence, with medium levels on </span>[1665, 1800[ and [1800, 1900[ <span>lava flows and low levels on </span>[1900, 1956] lava flows<span>. Conversely, the richness of anemochorous plants remained unchanged. Communities settled before human colonisation had a similar composition. Fleshy-fruited assemblages showed strong species loss across the chronosequence, while anemochorous assemblages showed strong species turnover, which was probably due to lower dispersal limitation.</span></p> <p><span><b>4. Synthesis. </b></span><span>Our results provide the first insights into the tremendous impact that frugivore extinction has on plant colonisation dynamics over 300 years. The dramatic loss of fleshy-fruited plant diversity on historical lava flows highlights the irreplaceable dispersal role played by frugivores, especially large-bodied species. The conservation of </span>plant-animal mutualistic interactions<span> is invaluable and refaunation efforts need to be undertaken in areas where frugivores have been extirpated.</span></p>
Data from: Immanent conditions determine imminent collapses: nutrient regimes define the resilience of macroalgal communities
Predicting where state-changing thresholds lie can be inherently complex in ecosystems characterized by nonlinear dynamics. Unpacking the mechanisms underlying these transitions can help considerably reduce this unpredictability. We used empirical observations, field and laboratory experiments, and mathematical models to examine how differences in nutrient regimes mediate the capacity of macrophyte communities to sustain sea urchin grazing. In relatively nutrient-rich conditions, macrophyte systems were more resilient to grazing, shifting to barrens beyond 1 800 g m−2 (urchin biomass), more than twice the threshold of nutrient-poor conditions. The mechanisms driving these differences are linked to how nutrients mediate urchin foraging and algal growth: controlled experiments showed that low-nutrient regimes trigger compensatory feeding and reduce plant growth, mechanisms supported by our consumer–resource model. These mechanisms act together to halve macrophyte community resilience. Our study demonstrates that by mediating the underlying drivers, inherent conditions can strongly influence the buffer capacity of nonlinear systems.
Data from: Strong population structure deduced from genetics, otolith chemistry and parasite abundances explains vulnerability to localised fishery collapse in a large Sciaenid fish, Protonibea diacanthus
As pressure on coastal marine resources is increasing globally, the need to quantitatively assess vulnerable fish stocks is crucial in order to avoid the ecological consequences of stock depletions. Species of Sciaenidae (croakers, drums) are important components of tropical and temperate fisheries and are especially vulnerable to exploitation. The black-spotted croaker, Protonibea diacanthus, is the only large sciaenid in coastal waters of northern Australia where it is targeted by commercial, recreational and indigenous fishers due to its food value and predictable aggregating behaviour. Localised declines in the abundance of this species have been observed, highlighting the urgent requirement by managers for information on fine and broad-scale population connectivity. This study examined the population structure of P. diacanthus across northwestern Australia using three complementary methods: genetic variation in microsatellite markers, otolith elemental composition and parasite assemblage composition. The genetic analyses demonstrated that there were at least five genetically distinct populations across the study region, with gene flow most likely restricted by inshore biogeographic barriers such as the Dampier Peninsula. The otolith chemistry and parasite analyses also revealed strong spatial variation among locations within broad-scale regions, suggesting fine-scale location fidelity within the lifetimes of individual fish. The complementarity of the three techniques elucidated patterns of connectivity over a range of spatial and temporal scales. We conclude that fisheries stock assessments and management are required at fine scales (100's km) to account for the restricted exchange among populations (stocks) and to prevent localised extirpations of this species. Realistic management arrangements may involve the successive closure and opening of fishing areas to reduce fishing pressure.
Data from: Diversity change during the rise of tetrapods and the impact of the 'Carboniferous rainforest collapse'
The Carboniferous and early Permian were critical intervals in the diversification of early four-limbed vertebrates (tetrapods), yet the major patterns of diversity and biogeography during this time remain unresolved. Previous estimates suggest that global tetrapod diversity rose continuously across this interval and that habitat fragmentation following the 'Carboniferous rainforest collapse' (CRC) drove increased endemism among communities. However, previous work failed to adequately account for spatial and temporal biases in sampling. Here, we reassess early tetrapod diversity and biogeography with a new global species-level dataset using sampling standardization and network biogeography methods. Our results support a tight relationship between observed richness and sampling, particularly during the Carboniferous. We found that subsampled species richness initially increased into the late Carboniferous, then decreased substantially across the Carboniferous/Permian boundary before slowly recovering in the early Permian. Our analysis of biogeography does not support the hypothesis that the CRC drove endemism; instead, we found evidence for increased cosmopolitanism in the early Permian. While a changing environment may have played a role in reducing diversity in the earliest Permian, our results suggest that the CRC was followed by increased global connectivity between communities, possibly reflecting both reduced barriers to dispersal and the diversification of amniotes.
Data from: Resource exploitation collapses the home range of an apex predator
<p>Optimizing energy acquisition and expenditure is a fundamental trade-off for consumers, strikingly reflected in how mobile organisms use space. Several studies have established that home range size decreases as resource density increases, but the balance of costs and benefits associated with exploiting a given resource density is unclear. We evaluate how the ability of consumers to exploit their resources through movement (termed "resource exploitation") interacts with resource density to influence home range size. We then contrast two hypotheses to evaluate how resource exploitation influences home range size across a vast gradient of productivity and density of human-created linear features (roads and seismic lines) that are known to facilitate animal movements. Under the Diffusion Facilitation Hypothesis, linear features are predicted to lead to more diffuse space use and larger home ranges. Under the Exploitation Efficiency Hypothesis, linear features are predicted to increase foraging efficiency, resulting in less space being required to meet energetic demands and therefore smaller home ranges. Using GPS telemetry data from 142 wolves (<i>Canis lupus</i>) distributed over more than 500,000 km<sup>2</sup>, we found that wolf home range size was influenced by the interaction between resource density and exploitation efficiency. Home range size decreased as linear feature density increased, supporting the Exploitation Efficiency Hypothesis. However, the effect of linear features on home range size diminished in more productive areas, suggesting that exploitation efficiency is of greater importance when resource density is low. These results suggest that smaller home ranges will occur where both linear feature density and primary productivity are higher, thereby increasing regional wolf density.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.