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549 results for “species extinction”
Competition increases risk of species extinction during extreme warming
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Data from: Niche width predicts extinction from climate change and vulnerability of tropical species
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First demographic insights reveal high extinction risk of an endemic raptor species: the Reunion harrier
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Caucasian treasure: genomics sheds light on the evolution of half-extinct Sevan trout, Salmo ischchan, species flock
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Data from: Intraspecific haplotype diversity in Cherleria sedoides L. (Caryophyllaceae) is best explained by chloroplast capture from an extinct species
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Data from: Loss of animal seed dispersal increases extinction risk in a tropical tree species due to pervasive negative density dependence across life stages
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Data from: Body size and extinction risk in terrestrial mammals above the species level
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Fig. 2 in Conservation status and bio-ecology of Brycon orbignyanus (Characiformes: Bryconidae), an endemic fish species from the Paraná River basin (Brazil) threatened with extinction
Fig. 2. Abundance (captures per unit of effort – CPUE) of Brycon orbignyanus observed in the Upper Paraná River floodplain in different years (1986 to 1988, 1992 to 1994 and 2000 to 2010) and subsystems (Paraná, Baía and Ivinhema).
Fig. 4 in Conservation status and bio-ecology of Brycon orbignyanus (Characiformes: Bryconidae), an endemic fish species from the Paraná River basin (Brazil) threatened with extinction
Fig. 4. Ontogenetic variations in the diet of Brycon orbignyanus in the Upper Paraná River floodplain. FI = fish; AI = aquatic invertebrates; TI = terrestrial invertebrates; TP = terrestrial plants; AP = aquatic plants.
Fig. 1 in Conservation status and bio-ecology of Brycon orbignyanus (Characiformes: Bryconidae), an endemic fish species from the Paraná River basin (Brazil) threatened with extinction
Fig. 1. The locations of reservoirs from which the Brycon orbignyanus occurrence was evaluated and sites sampled throughout the Upper Paraná River floodplain (the Paraná, Baía and Ivinhema River subsystems).
Fig. 3 in Conservation status and bio-ecology of Brycon orbignyanus (Characiformes: Bryconidae), an endemic fish species from the Paraná River basin (Brazil) threatened with extinction
Fig. 3. Relationships between YOY abundance (CPUE) of Brycon orbignyanus and hydrological attributes observed in the Paraná and Ivinhema subsystems. a. Interrupted flood duration (days) (> 4.5 m Paraná River and> 2.75 m Ivinhema River), b. Uninterrupted flood duration (days).
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
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: Amphibian species' traits, evolutionary history, and environment predict Batrachochytrium dendrobatidis infection patterns, but not extinction risk
The fungal pathogen Batrachochytrium dendrobatidis (Bd) has emerged as a major agent of amphibian extinction, requiring conservation intervention for many susceptible species. Identifying susceptible species is challenging, but many aspects of species' biology are predicted to influence the evolution of host resistance, tolerance, or avoidance strategies towards disease. In turn, we may expect species exhibiting these distinct strategies to differ in their ability to survive epizootic disease outbreaks. Here we test for phylogenetic and trait-based patterns of Bd infection risk and infection intensity among 302 amphibian species by compiling a global dataset of Bd infection surveys across 95 sites. We then use best-fit models that associate traits, taxonomy, and environment with Bd infection risk and intensity to predict host disease mitigation strategies (tolerance, resistance, avoidance) for 122 Neotropical amphibian species that experienced epizootic Bd outbreaks, and noted species' persistence or extinction from these events. Aspects of amphibian species' life history, habitat use, and climatic niche were consistently linked to variation in Bd infection patterns across sites around the world. However, predicted Bd infection risk and intensity based on site environment and species traits did not reveal a consistent pattern between the predicted host disease mitigation strategy and extinction outcome. This suggests that either tolerant or resistant species may have no advantage in ameliorating disease during epizootic events, or that other factors drive the persistence of amphibian populations during chytridiomycosis outbreaks. These results suggest that using a trait-based approach may allow us to identify species with resistance or tolerance to endemic Bd infections, but that this approach may be insufficient to ultimately identify species at risk of extinction from epizootics.
Data from: Testosterone in ancient hair from an extinct species
Testosterone is a key regulator in vertebrate development, physiology, and behaviour. Whereas technology allows extraction of a wealth of genetic information from extant as well as extinct species, complimentary information on steroid hormone levels may add a social, sexual, and environmental context. Hair shafts have been previously used to sequence DNA from >50,000 14C years old Siberian woolly mammoths (Mammuthus primigenius). Hair-testing has also been used to measure endogenous steroids in multiple extant species. Here we use small quantities of woolly mammoth hair samples to measure testosterone, and a genomics-based approach to determine sex, in permafrost-preserved mammoths dated to circa 10-60 thousand 14C years. Our validated method opens up exciting opportunities to measure multiple steroids in keratinized tissues from extinct populations of mammals. This may be specifically applied to investigating life histories, including the extinct Quaternary megafauna populations whose remains are preserved in the permafrost throughout the northern hemisphere.
Data from: Color polymorphism influences species' range and extinction risk
Polymorphisms in a population are expected to increase growth rate and stability of the population, leading to the expansion of geographic distribution and mitigation of extinction risk of a species. However, the generality of such ecological consequences of color polymorphism remains uncertain. Here, via a comparative approach, we assessed whether color polymorphisms influence climatic niche breadth and extinction risk in some groups of damselflies, butterflies, and vertebrates. The climatic niche breadth was greater and extinction risk was lower in polymorphic species than in monomorphic species in all taxa analyzed. The results suggest that color polymorphism facilitates range expansion and species persistence.
Data from: A multi-state dynamic occupancy model to estimate local colonization-extinction rates and patterns of co-occurrence between two or more interacting species
1. Although ecology is rife with theory that explores how multiple species co-occur through space and time, the field lacks robust statistical models to parameterize this theory with empirical data, particularly when species are detected imperfectly and data are collected as a time-series. 2. We address this need by developing an occupancy model that estimates local colonization and extinction rates for two or more interacting species when data are collected across multiple sampling occasions. This model estimates how community composition at a site may change across sampling occasions by assuming the latent occupancy state is a categorical random variable. We used a multinomial-logit model to parameterize species-specific parameters and pairwise interactions between species, both of which can be made a function of covariates. These transition probabilities between community states can then be converted to occupancy or co-occurrence probabilities to determine how community composition varies along an environmental gradient or through time. 3. As an example, we estimate patterns of co-occurrence between coyote (Canis latrans), Virginia opossum (Didelphis virginiana), and raccoon (Procyon lotor) in Chicago, Illinois, USA with data from a multi-year camera trapping study. Models with pairwise interactions between species greatly out performed models that assumed independence between species. Opossum and raccoon, for example, were far less likely to go extinct in habitat patches where coyotes were present. 4. Community composition at a site depends on species interactions and the local environment. Our model can separate such effects by estimating the underlying processes that define species occurrence patterns. As a result, our model can more explicitly quantify a wide range of ecological dynamics and therefore be used to empirically test ecological theory, such as estimating priority effects at a site or turnover rates between species, both of which can be made to vary as a function of covariates.
FIGURE 2 in A new and presumably extinct species of Ptychochromoides (Teleostei: Perciformes: Cichlidae) from central Madagascar
FIGURE 2. Ptychochromoides itasy, holotype, UMMZ 243393, immature female, 123.2 mm SL; Madagascar.
FIGURE 3 in A new and presumably extinct species of Ptychochromoides (Teleostei: Perciformes: Cichlidae) from central Madagascar
FIGURE 3. Ptychochromoides itasy, paratype, AMNH 233643, immature male, 106.3 mm SL; Madagascar.
FIGURE 1 in A taxonomic revision of Atelopus pachydermus, and description of two new (extinct?) species of Atelopus from Ecuador (Anura: Bufonidae)
FIGURE 1. Holotype of Atelopus pachydermus (KM 1013/1356). Male, SVL = 52.9 mm.
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.