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2,441 results for “extinct”
Data from: Cranial evolution in the extinct Rodrigues Island owl Otus murivorus (Strigidae), associated with unexpected ecological adaptations
<p>Island birds that were victim of anthropic extinctions were often more specialist species, having evolved their most distinctive features in isolation. Here we studied a fossil cranium of the 'giant' extinct scops owl <i>Otus murivorus</i> from Rodrigues Island (Mascarene Islands, southwestern Indian Ocean), to determine any potential unique characters. The fossil and extant strigids were imaged through x-ray microtomography, providing 3D views of external and internal (endocast, inner ear) cranial structures. Geometric morphometrics and analyses of traditional measurements yielded new information about the Rodrigues owl's evolution and ecology. <i>Otus murivorus </i>exhibits a 2-tier "lag behind" phenomenon for cranium and brain evolution, both being proportionately small relative to increased body size. It also had a much more developed olfactory bulb than congeners, indicating an unexpectedly developed olfactory sense, suggesting a partial food scavenging habit. In addition, <i>O. murivorus </i>had the eyes placed more laterally than <i>O. sunia</i>, the species from which it was derived, probably a side effect of a small brain; rather terrestrial habits; probably relatively fearless behavior; and a less vertical posture (head less upright) than other owls (this in part an allometric effect of size increase). These evolutionary features, added to gigantism and wing reduction, make the extinct Rodrigues owl's evolution remarkable, and with multiple causes.</p>
Recent extinctions among Little Spotted Kiwi (Apteryx owenii) and the origin of extant populations
<p>Little Spotted Kiwi (LSK; <i>Apteryx owenii</i>) have the lowest genetic diversity of five currently recognised kiwi species apparently due to a bottleneck when at most five individuals were translocated to Kapiti Island in 1912. Ancient DNA analyses show that LSK also had the lowest genetic diversity of kiwi species historically, possibly due to population bottlenecks during Pleistocene glaciation. We compare genetic diversity between LSK from Kapiti Island (extant), D'Urville Island (extinct) and the South Island of mainland New Zealand (extinct) at 495 bp of the mitochondrial control region (mtDNA) and 15 nuclear microsatellite loci (nDNA). Despite higher sample sizes in extant (<i>n</i> = 31 mtDNA, 97 nDNA) than recently extinct (<i>n</i> = 10 mtDNA, 9 nDNA) populations, extant LSK have at least 78% fewer mtDNA haplotypes and 52% fewer microsatellite alleles than recently extinct LSK. Extant LSK were strongly divergent from historical LSK for both mtDNA and nDNA (<i>F<sub>ST</sub></i> = 0.237 to 0.480), but showed greatest similarity with historical samples from Fiordland near the putative source population of Kapiti founders. Microsatellite data suggest that Kapiti LSK could have arisen from as few as three birds and our mtDNA data show that at least two of the founders were female. Our results indicate that substantial genetic diversity has been lost with the recent extinctions of remnant populations. Locating and protecting any last surviving individuals in presumed extinct populations will require intensive conservation efforts, but could also provide an invaluable source of genetic diversity for the species.</p>
Selective extinctions resulting from random habitat destruction lead to under‐estimates of local and regional biodiversity loss in a manipulative field experiment
<p>Land-use change is a significant cause of anthropogenic extinctions, which are likely to continue and accelerate as habitat conversion proceeds in most biomes. One way to understand the effects of habitat loss on biodiversity is through improved tools for predicting the number and identity of species losses in response to habitat loss. There are relatively few methods for predicting extinctions and even fewer opportunities for rigorously assessing the quality of these predictions. In this paper we address these issues by applying a new method based on rarefaction to predict species losses after random, but aggregated, habitat loss. We compare predictions from three rarefaction models, individual-based, sample-based, and spatially-clustered, to those derived from a commonly-used extinction estimation method, the Species-Area Relationship (SAR). We apply each method to a mesocosm experiment, in which we aim to predict species richness and extinctions of arthropods immediately following 50% habitat loss. While each model produced strikingly accurate predictions of species richness immediately after the habitat loss disturbance, each model significantly underestimated the number of extinctions occurring at both the local (within-mesocosm) and regional (treatment-wide) scales. Despite the stochastic nature of our small-scale, short-term, and randomly applied habitat loss experiment, we found surprisingly clear evidence for extinction selectivity, for example when abundant species with low extinction probabilities were extirpated following habitat loss. The important role played by selective extinction even in this contrived experimental system suggests that ecologically driven, trait-based extinctions play an equally important role to stochastic extinction, even when the disturbance itself has no clear selectivity. As a result, neutrally stochastic null models such as the SAR and rarefaction are likely to underestimate extinctions caused by habitat loss. Nevertheless, given the difficulty of predicting extinctions, null models provide useful benchmarks for conservation planning by providing minimum estimates and probabilities of species extinctions.</p>
Data archive for the peer-reviewed journal article "Detailed characterization of the CAPS single scattering albedo monitor (CAPS PMssa) as a field-deployable instrument for measuring aerosol light absorption with the extinction-minus-scattering method"
<p>Data archive accompanying the peer-reviewed journal article "Detailed characterization of the CAPS single scattering albedo monitor (CAPS PMssa) as a field-deployable instrument for measuring aerosol light absorption with the extinction-minus-scattering method". In 2020 this article was accepted for publication in the journal <em>Atmospheric Measurement Techniques</em>. Data are uploaded in the form of ascii text files, Igor Pro experiment files (.pxp), and Jupyter notebook files. In addition, a Jupyter notebook file is included containing an implementation of the error model used in the paper.</p>
The rescue effect and inference from isolation-extinction relationships
<p>The rescue effect in metapopulations hypothesizes that less isolated patches are unlikely to go extinct because recolonization may occur between breeding seasons ("recolonization rescue"), or immigrants may sufficiently bolster population size to prevent extinction altogether ("demographic rescue"). These mechanisms have rarely been demonstrated directly, and most evidence of the rescue effect is from relationships between isolation and extinction. We determined the frequency of recolonization rescue for metapopulations of black rails (<i>Laterallus jamaicensis</i>) and Virginia rails (<i>Rallus limicola</i>) from occupancy surveys conducted during and between breeding seasons, and assessed the reliability of inferences about the occurrence of rescue drawn from isolation-extinction relationships, including autologistic isolation measures that corrected for unsurveyed patches and imperfect detection. Recolonization rescue occurred at expected rates, but was elevated during periods of disturbance that resulted in nonequilibrium metapopulation dynamics. Inferences from extinction-isolation relationships were unreliable, particularly for autologistic measures and for the more vagile Virginia rail.</p>
Data from: When are extinctions simply bad luck? rarefaction as a framework for disentangling selective and stochastic extinctions
1. A key challenge in conservation biology is that not all species are equally likely to go extinct when faced with a disturbance. Traditionally, differences in species extinction risk are considered a form of extinction selectivity, a nanrondom process by which species' extinction risks are associated with their traits. While selectivity clearly contributes to varation in extinction among taxa, it is also clear that rare species are more likely to go extinct than are common species. While obvious, this law of extinction suggests that random chance, operating on species abundance, plays an important role in the extinction process. Unless ecologists and conservation biologists can disentangle random and nonrandom extinction processes, then the prediction and prevention of future extinctions will continue to be an elusive challenge. 2. We suggest that a modified version of a common null model procedure, rarefaction, can be used to disentangle the influence of stochastic species loss from selective nonrandom processes. To this end we applied a rarefaction based null model to three published data sets to characterize the influence of species rarity in driving biodiversity loss following three disturbance events: i) disease-associated bat declines; ii) disease-associated amphibian declines; and iii) habitat loss and invasive species-associated gastropod declines. For each case study, we used rarefaction to generate null expectations of stochastic biodiversity loss and species-specific extinction probabilities. 3. In each of our case studies we find evidence for random and nonrandom (selective) extinctions. Our findings highlight the importance of explicitly considering that some species extinctions are the result of stochastic processes, i.e., bad luck. 4. Policy Implications If there is a first law of extinction, it is that rare species are most likely than common species to go extinct. We suggest that taking this law into account in analyses of extinction risk is critical to the identification of selective extinctions. Our results suggest that rarefaction can be used to identify nonrandom decline, extirpation, and extinction events and provide an important baseline comparison point for future extinction analyses.12-Jul-2019
Data from: Climate change, extinction, and Sky Island biogeography in a montane lizard
Around the world, many species are confined to "Sky Islands," with different populations in isolated patches of montane habitat. How does this pattern arise? One scenario is that montane species were widespread in lowlands when climates were cooler, and were isolated by local extinction caused by warming conditions. This scenario implies that many montane species may be highly susceptible to anthropogenic warming. Here, we test this scenario in a montane lizard (Sceloporus jarrovii) from the Madrean Sky Islands of southeastern Arizona. We combined data from field surveys, climate, population genomics, and physiology. Overall, our results support the hypothesis that this species' current distribution is explained by local extinction caused by past climate change. However, our results for this species differ from simple expectations in several ways: (1) their absence at lower elevations is related to warm winter temperatures, not hot summer temperatures; (2) they appear to exclude a low-elevation congener from higher elevations, not the converse; (3) they are apparently absent from many climatically suitable but low mountain ranges, seemingly "pushed off the top" by climates even warmer than those today; (4) despite the potential for dispersal among ranges during recent glacial periods (~18,000 years ago), populations in different ranges diverged ~4.5–0.5 million years ago and remained largely distinct; and (5) body temperatures are inversely related to climatic temperatures among sites. These results may have implications for many other Sky Island systems. More broadly, we suggest that Sky Island species may be relevant for predicting responses to future warming.
Data from: Feeding capability in the extinct giant Siamogale melilutra and comparative mandibular biomechanics of living Lutrinae
At 50 kg in estimated weight, the extinct Siamogale melilutra is larger than all living otters, and ranks among the largest fossil otters. The biomechanical capability of S. melilutra jaws as related to their large size is unknown but crucial to reconstructing the species' potentially unique ecological niche. Here we compare the mandibular biomechanics of S. melilutra using engineering-based performance measures against ten extant otter biomechanical models. Despite a wide range of feeding preferences from durophagy to piscivory, living otter species exhibit a linear relationship between mandible stiffness and volume, as expected in isometric model scaling. In contrast, S. melilutra models exhibit a six-fold increase in stiffness from expected stiffness-volume relationships calculated from extant species models. Unlike stiffness, mechanical efficiency of biting is conserved among living otters and in S. melilutra. These findings indicate that although similar to living bunodont otters in morphology and biting efficiency, jaw strength in S. melilutra far surpasses molluscivores such as sea otters and Cape clawless otters, even after accounting for size. Therefore, Siamogale represents a feeding ecomorphology with no living analog, and its giant size and high mandibular strength confer shell-crushing capability matched only by other extinct molluscivores such as the marine bear Kolponomos.
Extinction dynamics under extreme conservation threat: The flora of St. Helena
<p><span><span><span><span><span><span><span><span><span><span><span>The flora of the island of St Helena provides an amplified system for the study of extinction by reason of the island's high endemism, small size, vulnerable biota, length of time of severe disturbance (since 1502) and severity of threats. Endemic plants have been eliminated from 96.5% of St Helena by habitat loss. There are eight recorded extinctions in the vascular flora since 1771 giving an extinction rate of 581 extinctions per million species per year (E/MSY). This is considerably higher than background extinction rates, variously estimated at 1 or 0.1 E/MSY. We have no information for plant extinctions prior to 1771 but applying the same extinction rate to the period 1502 to 1771 suggests that there may be around ten unrecorded historical extinctions. We use census data and population decline estimates to project likely extinction forward in time. The projected overall extinction rate for the next 200 years is somewhat higher at 625 E/MSY. However, our data predict an extinction crunch in the next 50 years with 4 species out of the remaining 48 likely to become extinct during this period. It is interesting that during a period when the native plant areas dropped to 3.5% of the original, the extinction rate appears to have remained shallowly linear with under 30% of the endemic flora becoming extinct.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Genetics at the verge of extinction: insights from the Iberian lynx
Population viability might become compromised by the loss of genetic diversity and the accumulation of inbreeding resulting from population decline and fragmentation. The Iberian lynx (Lynx pardinus) provides a paradigmatic example of a species at the verge of extinction and, because of the well-documented and different demographic histories of the two remaining populations (Doñana and Andújar), it provides the opportunity to evaluate the performance of analytical methods that are commonly applied to detect genetic signatures of demographic decline. We used mitochondrial sequences and a set of 36 microsatellite markers to evaluate the current genetic status of the species and to assess the genetic signatures of its past history. Mitochondrial diversity was extremely low with only two haplotypes, alternatively fixed in each population. Both remnant populations have low levels of genetic diversity at microsatellite markers, particularly the population from Doñana, which has been isolated and at small census sizes at least since the 1950s, and genetic differentiation between the two populations is high. Bayesian coalescent-based methods suggest an earlier decline starting hundreds of years ago, while heterozygosity-excess and M-ratio tests did not provide conclusive and consistent evidence for recent population size changes. Also, a model of gene-flow received overwhelming support over a model of pure drift. The discrepancies observed between some of our results and the known recent history of the species call for caution in the interpretation of the outcomes of some of these methods, especially when no information on previous demographic history is available. Overall, our results suggest that current genetic patterns in the Iberian lynx are mainly the result of its recent decline and fragmentation and alerts on possible genetic risks for its persistence. Conservation strategies should explicitly consider this threat and incorporate an integrated genetic management of captive, wild and reintroduced populations, including the genetic restoration of wild populations through translocations.
Data from: Why do bugs perish? range size and local vulnerability traits as surrogates of Odonata extinction risk
<p>Despite claims of an insect decline worldwide, our understanding of extinction risk in insects is incomplete. Using bionomic data of all odonate (603 dragonflies and damselflies) North American species, we assessed: a) regional extinction risk and whether this is related to local extirpation; b) whether these two patterns are similar altitudinally and latitudinally; and, c) areas of conservation concern. We used geographic range size as a predictor of regional extinction risk and body size, thermal limits and habitat association as predictors of local extirpation. We found that: a) greater regional extinction risk is related to narrow thermal limits, lotic habitat use and large body size (this in damselflies but not dragonflies); b) southern species are more climate-tolerant but with limited geographic range size than northern species; and, c) two priority areas for odonate conservation are the cold-temperate to sub-boreal Northeast USA and the Transversal Neo-Volcanic System. Our approach can be used to estimate insect extinction risk as it compensates for the lack of abundance data. </p>
Data from: Stratigraphic signatures of mass extinctions: ecological and sedimentary determinants
Stratigraphic patterns of last occurrences of fossil taxa (LOs) potentially fingerprint mass extinctions and delineate rates and geometries of those events. Although empirical studies of mass extinctions recognize that random sampling causes LOs to occur earlier than the time of extinction (Signor–Lipps effect), sequence-stratigraphic controls on the position of LOs are rarely considered. By tracing stratigraphic ranges of extant mollusc species preserved in the Holocene succession of the Po coastal plain (Italy), we demonstrated that, if mass extinction took place today, complex but entirely false extinction patterns would be recorded regionally due to shifts in local community composition and non-random variation in the abundance of skeletal remains, both controlled by relative sea-level changes. Consequently, rather than following an apparent gradual pattern expected from the Signor–Lipps effect, LOs concentrated within intervals of stratigraphic condensation and strong facies shifts mimicking sudden extinction pulses. Methods assuming uniform recovery potential of fossils falsely supported stepwise extinction patterns among studied species and systematically underestimated their stratigraphic ranges. Such effects of stratigraphic architecture, co-produced by ecological, sedimentary and taphonomic processes, can easily confound interpretations of the timing, duration, and selectivity of mass extinction events. Our results highlight the necessity of accounting for palaeoenvironmental and sequence-stratigraphic context when inferring extinction dynamics from the fossil record.
Data from: Anthropogenic extinction dominates Holocene declines of West Indian mammals
The extensive postglacial mammal losses in the West Indies provide an opportunity to evaluate extinction dynamics, but limited data have hindered our ability to test hypotheses. Here, we analyze the tempo and dynamics of extinction using a novel data set of faunal last-appearance dates and human first-appearance dates, demonstrating widespread overlap between humans and now-extinct native mammals. Humans arrived in four waves (Lithic, Archaic, Ceramic, and European), each associated with increased environmental impact. Large-bodied mammals and several bats were extinct by the Archaic, following protracted extinction dynamics perhaps reflecting habitat loss. Most small-bodied rodents and lipotyphlan insectivores survived the Ceramic, but extensive landscape transformation and the introduction of invasive mammals following European colonization caused further extinctions, leaving a threatened remnant fauna. Both large- and small-bodied nonvolant mammals disappeared, reflecting complex relationships between body size, ecology, and anthropogenic change. Extinct bats were generally larger species, paralleling declines from natural catastrophes.
Combined three-dimensional Milky Way extinction map
<p>This file contains the combined Milky-Way extinction map from Bovy, Rix, Green et al. (2015) (see the Appendix) in HDF5 format. The format is similar to that described here: http://argonaut.skymaps.info/usage, except that no samples are included (so only the /best_fit attribute and other supporting ones are included). This file is downloaded and read by the https://github.com/jobovy/mwdust code.</p>
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 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.
Environmentally driven extinction and opportunistic origination explain fern diversification patterns
<p>Datasets supporting "Contrasting drivers of originations and extinctions explain fern diversification patterns".</p>
Fig. 111 in An Anatomical And Phylogenetic Study Of The Osteology Of The Petrosal Of Extant And Extinct Artiodactylans (Mammalia) And Relatives
Fig. 111. Dorsomedial (cerebellar) views of left petrosal of †Mesonyx obtusidens (AMNH-VP 12643)
Fig. 106 in An Anatomical And Phylogenetic Study Of The Osteology Of The Petrosal Of Extant And Extinct Artiodactylans (Mammalia) And Relatives
Fig. 106. Dorsomedial (cerebellar) views of left petrosal of †Dissacus praenuntius (UM 75501)
Fig. 110 in An Anatomical And Phylogenetic Study Of The Osteology Of The Petrosal Of Extant And Extinct Artiodactylans (Mammalia) And Relatives
Fig. 110. Ventrolateral (tympanic) views of left petrosal of †Mesonyx obtusidens (AMNH-VP 12643)
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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.
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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.