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2,441 results for “extinct”
Data and analysis code for: Global protected areas seem insufficient to safeguard half of the world's mammals from human-induced extinction
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Data from: Mass extinctions alter extinction and origination dynamics with respect to body size
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Mitigating the extinction risk of globally threatened and endemic mountainous Orthoptera species: Parnassiana parnassica and Oropodisma parnassica
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Monitoring demography of resurrected populations of locally extinct and extant species to investigate drivers of species loss
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Environmental stochasticity increases extinction risk to a greater degree in pollination specialists than in generalists
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Data from: How density dependence, genetic erosion, and the extinction vortex impact evolutionary rescue
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Combined three-dimensional Milky Way extinction map (2019)
<p>This file contains an updated version of the combined Milky-Way extinction map from Bovy, Rix, Green et al. (2015) (see the Appendix) in HDF5 format. The component of the original dust map coming from Pan-STARRS data was updated to the Pan-STARRS dust map from Green et al. (2019). 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>
Data from: Ostracods from the end-Permian mass extinction in the Aras Valley section (Northwest Iran)
<p>The Aras Valley section (NW Iran) exposes a sedimentary succession that allows to study ostracod diversity patterns during/across the end-Permian mass extinction because of its ubiquitous fossil record. For the present study, 59 samples were investigated for their ostracod abundances, which ranged from 4 to 31500 specimens per 500 g. In 45 sample horizons, the ostracods were identified to the species-level. In total, 3,425 specimens were determined and 62 species were identified, of which one genus and ten species are described for the first time: <i>Fabalicypris</i> <i>veronicae </i>Gliwa, sp. nov., <i>Orthobairdia capuliformis</i> Gliwa, sp. nov., <i>Araxobairdia formosa</i> Gliwa, gen. et sp. nov., <i>Bairdiacypris kathleenae</i> Gliwa, sp. nov., <i>Eumiraculum mettei</i> Gliwa, sp. nov., <i>Liuzhinia julfensis </i>Gliwa, sp. nov., <i>Carinaknightina hofmanni</i> Gliwa, sp. nov., <i>Cavellina fosteri</i> Gliwa, sp. nov., <i>Cavellina hairapetiani</i> Gliwa, sp. nov. and <i>Hungaroleberis striatus</i> Forel, sp. nov. The assemblages show, at the end-Permian mass extinction event, a complete turnover from a low-diversity <i>Fabalicypris</i>-dominated pre-extinction community to a more diverse <i>Bairdiacypris</i>-dominated post-extinction community. The turnover coincides with the significant temperature increase that was previously recorded from NW Iranian sections. The low diversity in the horizon immediately below the extinction horizon indicates that environmental changes, such as thermal stress, may have had an impact on the ostracod assemblages prior to the extinction event. In comparison with other diverse ostracod assemblages from the Palaeotethyan realm, the ostracods of the Aras Valley section are not associated with microbialites.</p>
Data from: Upper Toarcian (Lower Jurassic) marine gastropods from the Cleveland Basin, England: systematics, palaeobiogeography and contribution to biotic recovery from the early Toarcian extinction event
<p>Here we describe a new late Toarcian (Lower Jurassic) marine gastropod fauna from rocks of the Cleveland Basin exposed on the North Yorkshire coast of England. The fossil assemblage comprises sixteen species, of which three are new: <i>Katosira</i>? <i>bicarinata</i> sp. nov., <i>Turritelloidea</i> <i>stepheni</i> sp. nov. and <i>Striactaenonina elegans</i> sp. nov. Four species are described in open nomenclature as <i>Tricarilda</i>? sp., <i>Jurilda</i> sp., <i>Cylindrobullina </i>sp. and <i>Cossmannina</i> sp. The other species have previously been described: <i>Coelodiscus minutus </i>(Schübler <i>in </i>Zieten), <i>Procerithium quadrilineatum </i>(Römer), <i>Pseudokatosira</i> <i>undulata</i> (Benz in von Zieten), <i>Palaeorissoina </i>aff.<i> acuminata</i><i> </i>(Gründel, 1999b), <i>Pietteia</i> <i>unicarinata</i> (Hudleston), <i>Globularia</i> cf. <i>canina</i> (Hudleston), <i>Striactaeonina</i> cf. <i>richterorum </i>Schulbert & Nützel, <i>Striactaenonina </i>aff.<i> tenuistriata </i>(Hudleston) and <i>Sulcoactaeon</i> <i>sedgvici </i>(Phillips). Most of these species are the earliest records of their respective genera and show palaeobiogeographical connections with contemporary gastropod associations from other regions of Europe and South America. The taxonomic composition of the late Toarcian Cleveland Basin gastropod assemblage differs substantially from the faunas of the late Pliensbachian and early Toarcian <i>Tenuicostatum</i> Zone, showing the strong effect of the early Toarcian mass extinction event on the marine gastropod communities in the basin. Only a few gastropod species are shared between the late Toarcian faunas and the much more diverse Aalenian gastropod faunas in the Cleveland Basin, suggesting there was a facies control on gastropod occurrences at that time. This is also a potential explanation for the taxonomic differences between the late Toarcian gastropod faunas in the Cleveland Basin and those in France, and Northern and Southern Germany.</p>
Data from: The origin of the legumes is a complex paleopolyploid phylogenomic tangle closely associated with the Cretaceous-Paleogene (K-Pg) mass extinction event
The consequences of the Cretaceous-Paleogene (K-Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic.
Data from: The latitudinal diversity gradient of tetrapods across the Permo-Triassic mass extinction and recovery interval
<p>The decline in species richness from the equator to the poles is referred to as the latitudinal diversity gradient (LDG). Higher equatorial diversity has been recognised for over 200 years, but the consistency of this pattern in deep time remains uncertain. Examination of spatial biodiversity patterns in the past across different global climate regimes and continental configurations can reveal how LDGs have varied over Earth history and potentially differentiate between suggested causal mechanisms. The Late Permian–Middle Triassic represents an ideal time interval for study, because it is characterised by large-scale volcanic episodes, extreme greenhouse temperatures, and the most severe mass extinction event in Earth history. We examined terrestrial and marine tetrapod spatial biodiversity patterns using a database of global tetrapod occurrences. Terrestrial tetrapods exhibit a bimodal richness distribution throughout the Late Permian–Middle Triassic, with peaks in the northern low latitudes and southern mid latitudes around 20-40°N and 60°S, respectively. Marine reptile fossils are known almost exclusively from the Northern Hemisphere in the Early and Middle Triassic, with highest diversity around 20°N. Reconstructed terrestrial LDGs contrast strongly with the generally unimodal gradients of today, potentially reflecting high global temperatures and prevailing Pangaean super-monsoonal climate system during the Permo-Triassic.</p>
A Hirnantian holdover from the late Ordovician mass extinction: phylogeny and biogeography of a new Anthracocrinid crinoid from Estonia
Relatively few Hirnantian (Late Ordovician) crinoids are known, and none have been previously described from the palaeocontinent of Baltica. This has impaired our ability to understand patterns of extinction and biogeographic dispersal surrounding the Late Ordovician mass extinction, which triggered a major turnover in crinoid faunas. Here, we describe <i>Tallinnicrinus toomae</i> gen. et sp. nov., an anthracocrinid diplobathrid from the Hirnantian of northern Estonia. <i>Tallinnicrinus</i> is the youngest member of the Anthracocrinidae and the first representative of the family to occur in Baltica. Morphologically, <i>Tallinnicrinus</i> is unusual in that the radial and basal plates are in a single circlet of ten plates, similar to the anthracocrinid <i>Rheocrinus</i> Haugh, 1979 from the Katian of Laurentia. Phylogenetic analysis further confirms a close relationship between <i>Tallinnicrinus</i> and Laurentian anthracocrinids, suggesting biogeographic dispersal of the lineage from Laurentia to Baltica during the late Katian or early Hirnantian. The occurrence of this new taxon establishes that the family Anthracocrinidae survived the first pulse of the Late Ordovician mass extinction. However, the lineage remained a "dead clade walking" as it failed to diversify in the wake of the end-Katian extinction and ultimately went extinct itself by the end of the Ordovician.
Code for individual-based simulations in "Environmental fluctuations can promote evolutionary rescue in high-extinction-risk scenarios"
<p>Substantial environmental change can force a population onto a path towards extinction, but under some conditions, adaptation by natural selection can rescue the population and allow it to persist. This process, known as evolutionary rescue, is believed to be less likely to occur with greater magnitudes of random environmental fluctuations because environmental variation decreases expected population size, increases variance in population size, and increases evolutionary lag. However, previous studies of evolutionary rescue in fluctuating environments have only considered scenarios in which evolutionary rescue was likely to occur. We extend these studies to assess how baseline extinction risk (which we manipulated via changes in the initial population size, degree of environmental change, or mutation rate) influences the effects of environmental variation on evolutionary rescue following an abrupt environmental change. Using a combination of analytical models and stochastic simulations, we show that autocorrelated environmental variation hinders evolutionary rescue in low-extinction-risk scenarios but facilitates rescue in high-risk scenarios. In these high-risk cases, the chance of a run of good years counteracts the otherwise negative effects of environmental variation on evolutionary demography. These findings can inform the development of effective conservation practices that consider evolutionary responses to abrupt environmental changes.</p>
Data and code for: Past and future extinctions shape the body size - fruit size relationship between palms and mammalian frugivores
<p>The dispersal of seeds by mammalian frugivores influences the structure and composition of plant communities, but most ecosystems have undergone defaunation over thousands of years, a process that continues today. Understanding how past defaunation has affected fruit-frugivore interactions will thus provide insights into how ecosystems may respond to future frugivore loss. By integrating palm and mammalian frugivore trait and occurrence data worldwide, we reveal a global positive relationship between fruit size and body size of frugivore assemblages. Global variation in fruit size is better explained by present-day frugivore assemblages compared to those of the Late Pleistocene (including extinct species), suggesting a substantial ecological and evolutionary reorganization after Pleistocene mammal extinctions. Interestingly, the reverse is true for the Neotropics where some large-fruited palm species may have persisted over thousands of years following extinction of their main seed dispersers. Simulations of frugivore extinction over the next 100 years suggest that changes in body size will require up to a 4% assemblage-level decrease in palm fruit sizes to maintain the current global frugivore body size - fruit size relationship. Absolute changes in assemblage-level means of palm fruit size were on average up to two-fold higher than observed species-level estimates of seed size change following defaunation. Overall, our results suggest that while some large-fruited palms may persist after the loss of their main dispersers, many palms may be unable to keep pace with future defaunation through evolutionary changes in fruit size alone. The burden of the impact of the extinction of seed dispersers will probably be disproportionately borne by large-fruited palms, possibly over thousands of years to come.</p>
Spatiophylogenetic modelling of extinction risk reveals evolutionary distinctiveness and brief flowering period as threats in a hotspot plant genus
Comparative models used to predict species threat status can help to identify diagnostic features of species at risk. Such models often combine variables measured at the species level with spatial variables, causing multiple statistical challenges, including phylogenetic and spatial non-independence. We present a novel Bayesian approach for modelling threat status that simultaneously deals with both forms of non-independence and estimates their relative contribution, and we apply the approach to modelling threat status in the Australian plant genus Hakea. We find that after phylogenetic and spatial effects are accounted for, species with greater evolutionary distinctiveness and a shorter annual flowering period are more likely to be threatened. The model allows us to combine information on evolutionary history, species biology, and spatial data, to calculate latent extinction risk (potential for non-threatened species to become threatened), estimate the most important drivers of risk for individual species, and map spatial patterns in the effects of different predictors on extinction risk. This could be of value for proactive conservation decision-making based on the early identification of species and regions of potential conservation concern.
How to build a dinosaur: musculoskeletal modelling and simulation of locomotor biomechanics in extinct animals
<p>The intersection of paleontology and biomechanics can be reciprocally illuminating, helping to improve paleobiological knowledge of extinct species and furthering our understanding of the generality of biomechanical principles derived from study of extant species. However, working with data gleaned primarily from the fossil record has its challenges. Building on decades of prior research, we outline and critically discuss a complete workflow for biomechanical analysis of extinct species, using locomotor biomechanics in the Triassic theropod dinosaur <em>Coelophysis </em>as a case study. We progress from the digital capture of fossil bone morphology to creating rigged skeletal models, to reconstructing musculature and soft tissue volumes, to the development of computational musculoskeletal models, and finally to the execution of biomechanical simulations. Using a three-dimensional musculoskeletal model comprising 33 muscles, a static inverse simulation of the mid-stance of running shows that <em>Coelophysis </em>probably used more upright (extended) hindlimb postures, and was likely capable of withstanding a vertical ground reaction force of magnitude more than 2.5 times body weight. We identify muscle force-generating capacity as a key source of uncertainty in the simulations, highlighting the need for more refined methods of estimating intrinsic muscle parameters such as fibre length. Our approach emphasizes the explicit application of quantitative techniques and physics-based principles, which helps maximize results robustness and reproducibility. Although we focus on one specific taxon and question, many of the techniques and philosophies explored here have much generality to them, so they can be applied in biomechanical investigation of other extinct organisms.</p>
Marine plankton show threshold extinction response to Neogene climate change
<p>Taxonomic occurrence datasets to accompany the article entitled "Marine plankton show threshold extinction response to Neogene climate change." Spreadsheets contain International Ocean Discovery Program (IODP) site information, sample names, depth in meters below the seafloor (mbsf), age (in millions of years), and the number of occurrences of each taxon per sample. For the eastern equatorial Pacific (EEP) dataset, ages were calculated using the astronomically-tuned model of Tian <em>et al.</em> (2018). Southern Ocean (SO) age information comes from the Neptune Sandbox Berlin (NSB) database (Renaudie <em>et al. </em>2020), with age model quality reported as: very good (VG), good (G), medium (M), or poor (P). Only species-level data associated with "very good" age models were analyzed in our study; however, here we provide all data at the species and genus level, with age models of any quality.</p>
Data from: Disproportionate extinction of South American mammals drove the asymmetry of the Great American Biotic Interchange
<p>Annotated R codes and datasets used in: Carrillo et al. 2020. Disproportionate extinction of South American mammals drove the asymmetry of the Great American Biotic Interchange. <em>Proc. Natl. Acad. Sci. U.S.A.</em></p>
Supplementary information for: The effects of geographic range size and abundance on extinction during a time of 'sluggish' evolution
<p>Geographic range size and abundance are important determinants of extinction risk in fossil and extant taxa. However, the relationship between these variables and extinction risk has not been tested extensively during evolutionarily 'quiescent' times of low extinction and speciation in the fossil record. Here we examine the influence of geographic range size and abundance on extinction risk during the late Paleozoic (Mississippian–Permian), a time of 'sluggish' evolution when global rates of origination and extinction were roughly half those of other Paleozoic intervals. Analyses used spatio-temporal occurrences for 164 brachiopod species from the North American midcontinent. We found abundance to be a better predictor of extinction risk than measures of geographic range size. Moreover, species exhibited reductions in abundance prior to their extinction, but did not display contractions in geographic range size. The weak relationship between geographic range size and extinction in this time and place may reflect the relative preponderance of larger-ranged taxa, combined with the physiographic conditions of the region that allowed for easy habitat tracking that dampened both extinction and speciation. These conditions led to a prolonged period (19 – 25 Myr) during which standard macroevolutionary rules did not apply.</p>
Data from: Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant subfossil koala lemur Megaladapis edwardsi
<p><span>No endemic Madagascar animal with body mass >10 kg survived a relatively recent wave of extinction on the island. From morphological and isotopic analyses of skeletal 'subfossil' remains we can reconstruct some of the biology and behavioral ecology of giant lemurs (primates; up to ~160 kg), elephant birds (up to ~860 kg), and other extraordinary Malagasy megafauna that survived well into the past millennium. Yet much about the evolutionary biology of these now extinct species remains unknown, along with persistent phylogenetic uncertainty in some cases. Thankfully, despite the challenges of DNA preservation in tropical and sub-tropical environments, technical advances have enabled the recovery of ancient DNA from some Malagasy subfossil specimens. Here we present a nuclear genome sequence (~2X coverage) for one of the largest extinct lemurs, the koala lemur <i>Megaladapis edwardsi </i>(~85kg). To support the testing of key phylogenetic and evolutionary hypotheses we also generated new high-coverage complete nuclear genomes for two extant lemur species, <i>Eulemur rufifrons</i> and <i>Lepilemur mustelinus</i>, and we aligned these sequences with previously published genomes for three other extant lemur species and 47 non-lemur vertebrates. Our phylogenetic results confirm that <i>Megaladapis</i> is most closely related to the extant Lemuridae (typified in our analysis by <i>E. rufifrons</i>) to the exclusion of <i>L. mustelinus</i>, which contradicts morphology-based phylogenies. Our evolutionary analyses identified significant convergent evolution between <i>M. edwardsi</i> and extant folivorous primates (colobine monkeys) and ungulate herbivores (horses) in genes encoding protein products that function in the biodegradation of plant toxins and nutrient absorption. These results suggest that koala lemurs were highly adapted to a leaf-based diet, which may also explain their convergent craniodental morphology with the small-bodied folivore <i>Lepilemur</i>.</span></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.