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.
2,441
datasets available to search
ShareScore release 0.9.0
Dataset results
2,441 results for “extinct”
Figures 5-9 from: Roháček J (2020) Protanthomyza grimaldii sp. nov., a further member of the extinct subfamily Protanthomyzinae (Diptera, Anthomyzidae) from Baltic amber. ZooKeys 973: 1-15. https://doi.org/10.3897/zookeys.973.51435
Figures 5-9 Protanthomyza grimaldii sp. nov., holotype male (Baltic amber) 5 head, left sublateral view 6 base of left wing 7 right mesopleuron, sternopleuron and pteropleuron, lateral view 8 abdomen and haltere, right lateral view 9 terminalia, right lateral view. Scale bars: 0.5 mm (5); 0.3 mm (6–8); 0.1 mm (9). For abbreviations see p. 4.
Figures 1- 2 from: Roháček J (2020) Protanthomyza grimaldii sp. nov., a further member of the extinct subfamily Protanthomyzinae (Diptera, Anthomyzidae) from Baltic amber. ZooKeys 973: 1-15. https://doi.org/10.3897/zookeys.973.51435
Figures 1- 2 Protanthomyza grimaldii sp. nov., holotype male (Baltic amber) 1 entire specimen, left laterodorsal view 2 ditto, right lateroventral view. Body length ca 2.6 mm. Photographs by J. Roháček.
Figure 3 from: Roháček J (2020) Protanthomyza grimaldii sp. nov., a further member of the extinct subfamily Protanthomyzinae (Diptera, Anthomyzidae) from Baltic amber. ZooKeys 973: 1-15. https://doi.org/10.3897/zookeys.973.51435
Figure 3 Protanthomyza grimaldii sp. nov., holotype male (Baltic amber). Head and thorax, left laterodorsal view. Photograph by J. Roháček.
Data from: Climate change-induced migration patterns and extinction risks of Theaceae species in China
Theaceae, an economically important angiosperm family, is widely distributed in tropical and subtropical forests in Asia. In China, Theaceae has particularly high abundances and endemism, comprising ~75% of the total genera and ~46% of the total species worldwide. Therefore, predicting the response of Theaceae species to climate change is vital. In this study, we collected distribution data for 200 wild Theaceae species in China, and predicted their distribution patterns under current and future climactic conditions by species distribution modeling (SDM). We revealed that Theaceae species richness is highest in southeastern China and on Hainan Island, reaching its highest value (137 species) in Fujian Province. According to the IUCN Red List criteria for assessing species threat levels under two dispersal assumptions (no dispersal and full dispersal), we evaluated the conservation status of all Theaceae species by calculating loss of suitable habitat under future climate scenarios. We predicted that nine additional species will become threatened due to climate change in the future; one species will be classified as critically endangered (CR), two as endangered (EN), and six as vulnerable (VU). Given their extinction risks associated with climate change, we recommended that these species be added to the Red List. Our investigation of migration patterns revealed regional differences in the number of emigrant, immigrant, and persistent species, indicating the need for targeted conservation strategies. Importantly, regions with high species turnover are located on the northern border of the entire Theaceae species distribution ranges owing to upwards migration; these regions are considered most sensitive to climate change and conservation planning should therefore be prioritized here. This study will contribute valuable information for reducing the negative impacts of climate change on Theaceae species, which will ultimately improve biodiversity conservation efficiency
Files to retrieve effective radius and extinction coefficient in liquid clouds from depolarization observations at two FOVs
<pre>Files needed to retrieve the effective radius and cloud extinction coefficient at 75 meters above liquid clouds, assumed as subadiabatic, using observations of \delta_in and delta_rat as explained in acp-2020-473. The FOVs considered are FOV_in=1.0 mrad and FOV_in=2.0 mrad. The files Input_alpha_75.txt and Input_r75.txt contain respectively the input values of the extinction and effective radius (at 75m above CB). 235 input values of alpha_75 and 122 values of r_75. The file Polynomial_coeff_r75_vs_depol_rat_all_cloud-bases.txt contains the coefficients of a ciubic polynom to compute the effective radius using observations of delta_rat. These set of 4 coefficients is provided for all 8 cloud base heights, having a size of 4x8. The files matrix_alpha_vs_depolin_and_r75_XXXX.txt, with XXXX the cloud base in meters (varying from 1000 to 5000 meters), provide each matrix of size 235x122 containing the value of the simulated integrated depolarizaiton ratio at the FOV in (i.e delta_in in acp-2020-473), for the given 235 input-values of alpha_75 (provided in the File Input_alpha_75.txt) and given 122 values of r_75 (provided in File Input_r75.txt). This matrix shall be used to determine alpha_75 after knowing r_75 and depol_in. </pre>
Extinction of herbivorous dinosaurs linked to Early Jurassic global warming event
<p><span>Sauropods, the giant long-necked dinosaurs, became the dominant group of large herbivores in terrestrial ecosystems after multiple related lineages became extinct towards the end of the Early Jurassic (190–174 Ma). The causes and precise timing of this key faunal change and as well as the origin of eusauropods (true sauropods) have remained ambiguous mainly due to the scarce dinosaurian fossil record of this time. The Cañadón Asfalto basin in Patagonia (Argentina) contains terrestrial sequences that document this critical interval of dinosaur evolution. Here we report a new dinosaur from this basin that is the oldest eusauropod known with a nearly complete skull and provide precise U-Pb radioisotopic dates that time the rise of eusauropods in Patagonia. We show eusauropod-dominance was established after a massive magmatic event impacting southern Gondwana (180–184 Ma) and coincided with severe perturbations to the climate and a drastic decrease in the floral diversity characterized by the rise of conifers with small scaly leaves. Floral and faunal changes from other regions suggest these were global changes that affected terrestrial ecosystems during the Toarcian warming of climate and formed part of a second-order mass extinction event.</span></p>
Reconstructing dietary ecology of extinct strepsirrhines (Primates, Mammalia) with new approaches for characterizing and analyzing tooth shape
<p>The morphological and ecological diversity of lemurs and lorisiformes once rivalled the rest of the primate order. Here, we assemble a dataset of 3D models representing the second mandibular molars of a wide range of extant and fossil strepsirrhines encompassing this diversity. We use these models to distill quantitative descriptors of tooth form and then analyze these data using new analytical methods. We employ a recently developed dental topography metric (ariaDNE), which is less sensitive to details of random error in 3D model quality than previously used metrics (e.g., DNE); Bayesian multinomial modelling with metrics designed to measure overfitting risk; and a tooth segmentation algorithm that allows the shapes of disaggregated tooth surface features to be quantified using dental topography metrics. This approach is successful at reclassifying extant strepsirrhine primates to known dietary ecology and indicates that the averaging of morphological information across the tooth surface does not interfere with the ability of dental topography metrics to predict dietary adaptation. When applied to extinct species, many subfossil lemurs and the most basal fossil strepsirrhines are predicted to have been primarily frugivorous or gummivorous. This supports an ecological contraction among the extant lemurs and the importance of frugivory in the origins of crown Strepsirrhini, potentially to avoid competition with more insectivorous and folivorous members of Paleogene Afro-Arabian primate faunas.</p>
Data from: Re-evaluation of the law of constant extinction for ruminants at different taxonomical scale
<p><span>The "law of constant extinction," proposed by Van Valen, states that long and short-lived taxa have equal chances of going extinct. This pattern of age-independent extinction was originally inferred using the fossil record of several different taxa and relied on survivorship curves built from the literal reading of the fossil record. Van Valen's seminal work was mostly done at higher taxonomic levels, hence its prevalence at the species level could not be directly inferred. The surprisingly few subsequent studies done at the species level have challenged the prevalence of age-independent extinction, but those have, for the most part, failed to explicitly incorporate inherent biases of the fossil record. Using a recent Bayesian framework that accounts for several of those biases, including the fact that very short-living lineages might never make to the record itself, we showed that Ruminantia species present age-dependent extinction, where extinction probability decreases with species age. An analysis at the genus level suggested age-independent extinction but further examination suggested that the pattern might be more complex than previously reported by Van Valen. Our results indicate that different taxonomic levels may present different extinction regimes, which could justify the development of new macroevolutionary theory and methods.</span></p>
Data from: Time to extinction in deteriorating environments
Habitat degradation and destruction are the predominant drivers of population extinction, but there is little theory to guide the analysis of population viability in deteriorating environments. To address this gap, we investigated extinction times in time-varying, demographically stochastic versions of the logistic model for population dynamics. A property of these models is the "extinction delay," a quantitative measure of the time lag in extinction created by species-specific extinction debt. For completeness, three models were constructed to represent the different demographic routes by which deterioration may affect population dynamics. Numerical analysis for two notional life histories indicated that the demographic response to environmental deterioration had a large effect on extinction delay, but a third analysis showed that the trajectory of the decline in carrying capacity ultimately characterized its magnitude. A concave decline in carrying capacity produced a large extinction delay while a small delay occurred with a convex decline. Furthermore, our results explore the non-monotonicity of extinction debt with respect to the speed of deterioration. A peak is present at low levels of deterioration, and the height of the peak and the asymptote of delay are affected by both life history parameterizations and the rate of change of the carrying capacity. The results suggest that population viability analyses must consider not only environmental deterioration, but also the effects of deterioration on the trajectory of the decline in carrying capacity.
Data from: A Bayesian approach for detecting the impact of mass-extinction events on molecular phylogenies when rates of lineage diversification may vary
The paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting the impact of mass-extinction events on molecular phylogenies, even in the presence of tree-wide diversification-rate variation and in the absence of additional information from the fossil record. Our approach is based on an episodic stochastic-branching process model in which rates of speciation and extinction are constant between events. We model three types of events: (i) instantaneous tree-wide shifts in speciation rate; (ii) instantaneous tree-wide shifts in extinction rate and (iii) instantaneous tree-wide mass-extinction events. Each type of event is modelled as an independent compound Poisson process (CPP), where the waiting times between events are exponentially distributed with event-specific rate parameters. The magnitude of each event is drawn from an event-specific prior distribution. Parameters of the model are then estimated in a Bayesian statistical framework using a reversible-jump Markov chain Monte Carlo algorithm. This Bayesian approach enables us to distinguish between tree-wide diversification-rate variation and mass-extinction events by specifying a biologically informed prior on the magnitude of mass-extinction events and empirical hyperpriors on the diversification-rate parameters. We demonstrate via simulation that this method has substantial power to detect the number of mass-extinction events and provides unbiased estimates of the timing of mass-extinction events, while exhibiting an appropriate (i.e. <5%) false-discovery rate, even when background diversification rates vary. Finally, we provide an empirical demonstration of this approach, which reveals that conifers experienced a major episode of mass extinction ≈23 Ma. This new approach – the CPP on Mass-Extinction Times (CoMET) model – provides an effective tool for detecting the impact of mass-extinction events on molecular phylogenies, even when the history of those groups includes temporal variation in diversification rates and when the fossil history of those groups is poorly known.
Data from: Interactions between demography, genetics, and landscape connectivity increase extinction probability for a small population of large carnivores in a major metropolitan area
The extinction vortex is a theoretical model describing the process by which extinction risk is elevated in small, isolated populations owing to interactions between environmental, demographic, and genetic factors. However, empirical demonstrations of these interactions have been elusive. We modelled the dynamics of a small mountain lion population isolated by anthropogenic barriers in greater Los Angeles, California, to evaluate the influence of demographic, genetic, and landscape factors on extinction probability. The population exhibited strong survival and reproduction, and the model predicted stable median population growth and a 15% probability of extinction over 50 years in the absence of inbreeding depression. However, our model also predicted the population will lose 40–57% of its heterozygosity in 50 years. When we reduced demographic parameters proportional to reductions documented in another wild population of mountain lions that experienced inbreeding depression, extinction probability rose to 99.7%. Simulating greater landscape connectivity by increasing immigration to greater than or equal to one migrant per generation appears sufficient to largely maintain genetic diversity and reduce extinction probability. We provide empirical support for the central tenet of the extinction vortex as interactions between genetics and demography greatly increased extinction probability relative to the risk from demographic and environmental stochasticity alone. Our modelling approach realistically integrates demographic and genetic data to provide a comprehensive assessment of factors threatening small populations.
Data from: Population extinctions can increase metapopulation persistence
Metapopulations persist when local populations are rapidly recolonized following local extinctions. Such persistence requires asynchrony; simultaneous crashes of all populations would leave no source of recolonization. We show theoretically and experimentally that catastrophic population extinctions themselves can promote metapopulation persistence, by preventing spatial synchrony and thus enhancing recolonization. We refer to this behaviour as the 'spatial hydra effect': as with the mythical hydra that grows two new heads when one is removed, extinctions can increase recolonization. The effect is robust, occurring in a wide range of theoretical models exhibiting cyclic or quasi-cyclic population dynamics. In a laboratory microcosm experiment using cyclic protist predator–prey metapopulations, catastrophic perturbations wiping out populations but leaving the patch otherwise unchanged increased metapopulation persistence when high dispersal rates would otherwise have led to spatially synchronous extinctions of all populations. We discuss several candidate examples of the spatial hydra effect in nature.
Data from: Sexual traits are sensitive to genetic stress and predict extinction risk in the stalk-eyed fly, Diasemopsis meigenii
The handicap principle predicts that sexual traits are more susceptible to inbreeding depression than nonsexual traits. However, this hypothesis has received little testing and results are inconsistent. We used 11 generations of full-sibling mating to test the effect of inbreeding on sexual and nonsexual traits in the stalk-eyed fly Diasemopsis meigenii. Consistent with the theoretical predictions, the male sexual trait (eyespan) decreased more than nonsexual traits (female eyespan and male wing length), even after controlling for body size variation. In addition, male eyespan was a reliable predictor of line extinction, unlike other nonsexual traits. After 11 generations, inbred lines were crossed to generate inbred and outbred families. All morphological traits were larger in outbred individuals than inbred individuals. This heterosis was greater in male eyespan than in male wing length, but not female eyespan. The elevated response in male eyespan to genetic stress mirrored the result found using environmental stress during larval development and suggests that common mechanisms underlie the patterns observed. Overall, these results support the hypothesis that male sexual traits suffer more from inbreeding depression than nonsexual traits and are in line with predictions based on the handicap principle.
Data from: Body length of bony fishes was not a selective factor during the biggest mass extinction of all time
The Permo-Triassic mass extinction devastated life on land and in the sea, but it is not clear why some species survived and others went extinct. One explanation is that lineage loss during mass extinctions is a random process in which luck determines which species survive. Alternatively, a phylogenetic signal in extinction may indicate a selection process operating on phenotypic traits. Large body size has often emerged as an extinction risk factor in studies of modern extinction risk, but this is not so commonly the case for mass extinctions in deep time. Here, we explore the evolution of non-teleostean Actinopterygii (bony fishes) from the Devonian to the present day, and we concentrate on the Permo-Triassic mass extinction. We apply a variety of time-scaling metrics to date the phylogeny, and show that diversity peaked in the latest Permian and declined severely during the Early Triassic. In line with previous evidence, we find the phylogenetic signal of extinction increases across the mass extinction boundary: extinction of species in the earliest Triassic is more clustered across phylogeny compared to the more randomly distributed extinction signal in the late Permian. However, body length plays no role in differential survival or extinction of taxa across the boundary. In the case of fishes, size did not determine which species survived and which went extinct, but phylogenetic signal indicates that the mass extinction was not a random field of bullets.
Data from: Quantifying age-dependent extinction from species phylogenies
Several ecological factors that could play into species extinction are expected to correlate with species age, i.e., time elapsed since the species arose by speciation. To date, however, statistical tools to incorporate species age into likelihood-based phylogenetic inference have been lacking. We present here a computational framework to quantify age-dependent extinction through maximum likelihood parameter estimation based on phylogenetic trees, assuming species lifetimes are gamma distributed. Testing on simulated trees shows that neglecting age dependence can lead to biased estimates of key macroevolutionary parameters. We then apply this method to two real data sets, namely a complete phylogeny of birds (class Aves) and a clade of self-compatible and -incompatible nightshades (Solanaceae), gaining initial insights into the extent to which age-dependent extinction may help explain macroevolutionary patterns. Our methods have been added to the R package TreePar.
Data from: Paleohistological estimation of bone growth rate in extinct archosaurs
The clade Archosauria contains two very different sister groups in terms of diversity (number of species) and disparity (phenotypic variation): Crurotarsi (taxa more closely related to crocodiles than to birds) and Ornithodira (pterosaurs and dinosaurs including birds). The extant species of Crurotarsi may constitute a biased sample of past biodiversity regarding growth patterns and metabolic rates. Bone histological characters can be conserved over hundreds of millions of years in the fossil record and potentially contain information about individual age at death, age at sexual maturity, bone growth rates, and basal metabolic rates of extinct vertebrates. Using a sample of extant amniotes, we have constructed a paleobiological model to estimate bone growth rate from bone histological traits. Cross-validation tests show that this model is reliable. We then used it to estimate bone growth rates in a sample of extinct archosaurs including Crurotarsi and Ornithodira. After testing for phylogenetic signal, optimization of femoral growth rates through squared change parsimony onto a time-calibrated tree of amniotes shows two divergent evolutionary trends: whereas bone growth rates increase from the last common ancestor of Ornithodira to extant birds, they decrease from the last common ancestor of Crurotarsi to extant crocodiles. However, we conclude, on the basis of recent evidence for unidirectional airflow in the lungs of alligators, that crocodiles may have retained the capacity of growing at high rates.
Data from: Multifaceted disparity approach reveals dinosaur herbivory flourished before the end-Cretaceous mass extinction
Understanding temporal patterns in biodiversity is an enduring question in paleontology. Compared to studies of taxonomic diversity, long-term perspectives on ecological diversity are rare, particularly in terrestrial systems. Yet ecological diversity is critical for the maintenance of biodiversity, particularly during times of major perturbations. Here, we explore the ecological diversity of Cretaceous herbivorous dinosaurs leading up to the K-Pg extinction, using dental and jaw morphological disparity as a proxy. We test the hypothesis that a decline in ecological diversity could have facilitated their rapid extinction 66 mya. We apply three disparity metrics that together capture different aspects of morphospace occupation, and show how this approach is key to understanding patterns of morphological evolution. We find no evidence of declining disparity in herbivorous dinosaurs as a whole – suggesting that dinosaur ecological diversity remained high during the last 10 million years of their existence. Clades show different disparity trends through the Cretaceous, but none except sauropods exhibits a long-term decline. Herbivorous dinosaurs show two disparity peaks characterised by different processes; in the Early Cretaceous by expansion in morphospace and in the Campanian by morphospace packing. These trends were only revealed by using a combination of disparity metrics, demonstrating how this approach can offer novel insights into macroevolutionary processes underlying patterns of disparity and ecological diversity.
Data from: Three types of rescue can avert extinction in a changing environment
Setting aside high-quality large areas of habitat to protect threatened populations is becoming increasingly difficult as humans fragment and degrade the environment. Biologists and managers therefore must determine the best way to shepherd small populations through the dual challenges of reductions in both the number of individuals and genetic variability. By bringing in additional individuals, threatened populations can be increased in size (demographic rescue) or provided with variation to facilitate adaptation and reduce inbreeding (genetic rescue). The relative strengths of demographic and genetic rescue for reducing extinction and increasing growth of threatened populations are untested, and which type of rescue is effective may vary with population size. Using the flour beetle (Tribolium castaneum) in a microcosm experiment, we disentangled the genetic and demographic components of rescue, and compared them with adaptation from standing genetic variation (evolutionary rescue in the strictest sense) using 244 experimental populations founded at either a smaller (50 individuals) or larger (150 individuals) size. Both types of rescue reduced extinction, and those effects were additive. Over the course of six generations, genetic rescue increased population sizes and intrinsic fitness substantially. Both large and small populations showed evidence of being able to adapt from standing genetic variation. Our results support the practice of genetic rescue in facilitating adaptation and reducing inbreeding depression, and suggest that demographic rescue alone may suffice in larger populations even if only moderately inbred individuals are available for addition.
Data from: Greenhouse biogeography: the relationship of geographic range to invasion and extinction in the Cretaceous Western Interior Seaway
Significant warming of Earth's climate in the near term seems increasingly likely. If significant enough, this climatic regime could, in the long term, come to resemble previous greenhouse intervals in earth history. Consequently, analysis of the fossil record during periods of extreme warmth may provide important lessons for species biology, including biogeography, in a much warmer world. To explore this issue, we analyzed the biogeographic response of 63 molluscan species to the long-term global warmth in the Late Cretaceous Western Interior Seaway (WIS) of North America, using Geographic Information Systems (GIS) to quantitatively measure changes in range size and distribution throughout this interval. We specifically considered the role that geographic range size played in mediating extinction resistance and invasion potential of these WIS species. We found no relationship between geographic range size and survivorship. However, endemic species with small range sizes were more likely to become invasive. Finally, mollusks did not experience a poleward shift in range out of the tropics during this warm regime. To the extent that these patterns are representative, and the WIS and taxa considered constitute a reasonable ancient analogue to a warmer future world, these results suggest that some biogeographic "rules" may not prevail under greenhouse conditions of long-term, equable warmth. They also suggest that other factors beyond geographic range size, including distinctive niche characteristics, may play quite important roles in species survival and invasion potential. This potentially complicates predictions regarding the future responses of extant species to long-term warming.
Data from: The effect of selection history on extinction risk during severe environmental change
Environments rarely remain the same over time, and populations are therefore frequently at risk of going extinct when changes are significant enough to reduce fitness. While many studies have investigated what attributes of the new environments and of the populations experiencing these changes will affect their probability of going extinct, limited work has been directed toward determining the role of population history on the probability of going extinct during severe environmental change. Here we compare the extinction risk of populations with a history of selection in a benign environment, to populations with a history of selection in one or two stressful environments. We exposed spores and lines of the green alga Chlamydomonas reinhardtii from these three different histories to a range of severe environmental changes. We found that the extinction risk was higher for populations with a history of selection in stressful environments compared to populations with a history of selection in a benign environment. This effect was not due to differences in initial population sizes. Finally, the rates of extinction were highly repeatable within histories, indicating strong historical contingency of extinction risk. Hence, information on the selection history of a population can be used to predict their probability of going extinct during environmental change.
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.