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2,441 results for “extinct”
Data from: Replaying evolution to test the cause of extinction of one ecotype in an experimentally evolved population
In a long-term evolution experiment with Escherichia coli, bacteria in one of twelve populations evolved the ability to consume citrate, a previously unexploited resource in a glucose-limited medium. This innovation led to the frequency-dependent coexistence of citrate-consuming (Cit+) and non-consuming (Cit–) ecotypes, with Cit−bacteria persisting on the exogenously supplied glucose as well as other carbon molecules released by the Cit+ bacteria. After more than 10,000 generations of coexistence, however, the Cit−lineage went extinct; cells with the Cit−phenotype dropped to levels below detection, and the Cit−clade could not be detected by molecular assays based on its unique genotype. We hypothesized that this extinction was a deterministic outcome of evolutionary change within the population, specifically the appearance of a more-fit Cit+ ecotype that competitively excluded the Cit−ecotype. We tested this hypothesis by re-evolving the population from a frozen population sample taken within 500 generations of the extinction and from another sample taken several thousand generations earlier, in each case for 500 generations and with 20-fold replication. To our surprise, the Cit−type did not go extinct in any of these replays, and Cit−cells also persisted in a single replicate that was propagated for 2,500 generations. Even more unexpectedly, we showed that the Cit−ecotype could reinvade the Cit+ population after its extinction. Taken together, these results indicate that the extinction of the Cit−ecotype was not a deterministic outcome driven by competitive exclusion by the Cit+ ecotype. The extinction also cannot be explained by demographic stochasticity alone, as the population size of the Cit−ecotype should have been many thousands of cells even during the daily transfer events. Instead, we infer that the extinction must have been caused by a rare chance event in which some aspect of the experimental conditions was inadvertently perturbed.
Data from: Morphological and biomechanical disparity of crocodile-line archosaurs following the end-Triassic extinction
Mesozoic crurotarsans exhibited diverse morphologies and feeding modes, representing considerable ecological diversity, yet macroevolutionary patterns remain unexplored. Here we employ a unique combination of morphological and biomechanical disparity metrics to quantify the ecological diversity and trophic radiations of Mesozoic crurotarsans, using the mandible as a morpho-functional proxy. We recover three major trends. First, the diverse assemblage of Late Triassic crurotarsans was morphologically and biomechanically disparate, implying high levels of ecological variation; but, following the end-Triassic extinction, disparity declined. Second, the Jurassic radiation of marine thalattosuchians resulted in very low morphological disparity but moderate variation in jaw biomechanics, highlighting a hydrodynamic constraint on mandibular form. Third, during the Cretaceous terrestrial radiations of neosuchians and notosuchians, mandibular morphological variation increased considerably. By the Late Cretaceous, crocodylomorphs evolved a range of morphologies equaling Late Triassic crurotarsans. In contrast, biomechanical disparity in the Cretaceous did not increase, essentially decoupling from morphology. This enigmatic result could be attributed to biomechanical evolution in other anatomical regions (e.g. cranium, dentition or postcranium), possibly releasing the mandible from selective pressures. Overall, our analyses reveal a complex relationship between morphological and biomechanical disparity in Mesozoic crurotarsans that culminated in specialized feeding ecologies and associated lifestyles.
Data from: Experimental demonstration of accelerated extinction in source-sink metapopulations
Population extinction is a fundamental ecological process which may be aggravated by the exchange of organisms between productive (source) and unproductive (sink) habitat patches. The extent to which such source-sink exchange affects extinction rates is unknown. We conducted an experiment in which metapopulation effects could be distinguished from source-sink effects in laboratory populations of Daphnia magna. Time-to-extinction in this experiment was maximized at intermediate levels of habitat fragmentation, which is consistent with a minority of theoretical models. These results provided a baseline for comparison with experimental treatments designed to detect effects of concentrating resources in source patches. These treatments showed that source-sink configurations increased population variability (the coefficient of variation in abundance) and extinction hazard compared with homogeneous environments. These results suggest that where environments are spatially heterogeneous, accurate assessments of extinction risk will require understanding the exchange of organisms among population sources and sinks. Such heterogeneity may be the norm rather than the exception because of both the intrinsic heterogeneity naturally exhibited by ecosystems and increasing habitat fragmentation by human activity.
Data from: Completeness of the eutherian mammal fossil record and implications for reconstructing mammal evolution through the Cretaceous/Paleogene mass extinction
There is a well-established discrepancy between paleontological and molecular data regarding the timing of the origin and diversification of placental mammals. Molecular estimates place interordinal diversification dates in the Cretaceous, whilst no unambiguous crown placental fossils have been found prior to the end-Cretaceous mass extinction. Here, the completeness of the eutherian fossil record through geological time is evaluated in order to assess the suggestion that a poor fossil record is largely responsible for the difference in estimates of placental origins. The completeness of fossil specimens was measured using the Character Completeness Metric, a metric that quantifies the completeness of fossil taxa as the percentage of phylogenetic characters that are available to be scored for any given taxon. Our dataset was comprised of 33 published cladistic matrices representing 445 genera, of which 333 were coded at the species-level. There was no significant difference in eutherian completeness across the Cretaceous/Palaeogene boundary. This suggests that the lack of placental mammal fossils in the Cretaceous is not due to a poor fossil record, but more likely represents a genuine absence of placental mammals in the Cretaceous. This result supports the 'explosive model' of early placental evolution, whereby placental mammals originated around the time of the Cretaceous/Palaeogene boundary and diversified soon after the event. No correlation was found between the completeness pattern observed in this study and those of previous completeness studies on birds and sauropodomorph dinosaurs, suggesting that different factors affect the preservation of these groups. No correlations were found with various isotope proxy measures, but Akaike Information Criterion analysis found that eutherian Character Completeness Metric scores were best explained by models involving the marine carbonate strontium isotope ratios (87Sr/86Sr), suggesting that the tectonic activity might play a role in controlling the completeness of the eutherian fossil record.
Data from: Spatially correlated extinctions select for less emigration but larger dispersal distances in the spider mite Tetranychus urticae
Dispersal is a central process to almost all species on earth, as it connects spatially structured populations and thereby increases population persistence. Dispersal is subject to (rapid) evolution and local patch extinctions are an important selective force in this context. In contrast to the randomly distributed local extinctions considered in most theoretical studies, habitat fragmentation or other anthropogenic interventions will lead to spatially correlated extinction patterns. Under such conditions natural selection is thought to lead to more long-distance dispersal, but this theoretical prediction has not yet been verified empirically. We test this hypothesis in experimental spatially structured populations of the spider mite Tetranychus urticae and supplement these empirical results with insights from an individual-based evolutionary model. We demonstrate that the spatial correlation of local extinctions changes the entire distribution of dispersal distances (dispersal kernel) and selects for overall less emigration but more long-distance dispersal.
Data from: Extinction, ecological opportunity, and the origins of global snake diversity
Snake diversity varies by at least two orders of magnitude among extant lineages, with numerous groups containing only one or two species, and several young clades exhibiting exceptional richness (>700 taxa). With a phylogeny containing all known families and subfamilies, we find that these patterns cannot be explained by background rates of speciation and extinction. The majority of diversity appears to derive from a radiation within the superfamily Colubroidea, potentially stemming from the colonization of new areas and the evolution of advanced venom-delivery systems. In contrast, negative relationships between clade age, clade size, and diversification rate suggest the potential for possible bias in estimated diversification rates, interpreted by some recent authors as support for ecologically-mediated limits on diversity. However, evidence from the fossil record indicates that numerous lineages were far more diverse in the past, and that extinction has had an important impact on extant diversity patterns. Thus, failure to adequately account for extinction appears to prevent both rate- and diversity-limited models from fully characterizing richness dynamics in snakes. We suggest that clade-level extinction may provide a key mechanism for explaining negative or hump-shaped relationships between clade age and diversity, and the prevalence of ancient, species-poor lineages in numerous groups.
Data from: Dental ontogeny in extinct synapsids reveals a complex evolutionary history of the mammalian tooth attachment system
The mammalian dentition is uniquely characterized by a combination of precise occlusion, permanent adult teeth, and a unique tooth attachment system. Unlike the ankylosed teeth in most reptiles, mammal teeth are supported by a ligamentous tissue that suspends each tooth in its socket, providing flexible and compliant tooth attachment that prolongs the life of each tooth and maintains occlusal relationships. Here we investigate dental ontogeny through histological examination of a wide range of extinct synapsid lineages to assess whether the ligamentous tooth attachment system is unique to mammals and to determine how it evolved. This study shows for the first time that the ligamentous tooth attachment system is not unique to crown mammals within Synapsida, having arisen in several non-mammalian therapsid clades as a result of neoteny and progenesis in dental ontogeny. Mammalian tooth attachment is here re-interpreted as a paedomorphic condition relative to the ancestral synapsid form of tooth attachment.
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 3 from: Tello F, Verdú JR, Rossini M, Zunino M (2021) Onthophagus pilauco sp. nov. (Coleoptera, Scarabaeidae): evidence of beetle extinction in the Pleistocene–Holocene transition in Chilean Northern Patagonia. ZooKeys 1043: 133-145. https://doi.org/10.3897/zookeys.1043.61706
Figure 3 Artistic reconstruction of Onthophagus pilauco sp. nov. and its palaeoenvironment (by Mauricio Alvarez).
Figure 1 from: Tello F, Verdú JR, Rossini M, Zunino M (2021) Onthophagus pilauco sp. nov. (Coleoptera, Scarabaeidae): evidence of beetle extinction in the Pleistocene–Holocene transition in Chilean Northern Patagonia. ZooKeys 1043: 133-145. https://doi.org/10.3897/zookeys.1043.61706
Figure 1 Type locality of Onthophagus pilauco sp. nov. A shaded elevation map shows Pilauco and Monte Verde sites. Representation of profile of a grid of the Pilauco site B symbol (star) indicates the layer in which Onthophagus pilauco sp. nov. was collected.
Figure 2 from: Tello F, Verdú JR, Rossini M, Zunino M (2021) Onthophagus pilauco sp. nov. (Coleoptera, Scarabaeidae): evidence of beetle extinction in the Pleistocene–Holocene transition in Chilean Northern Patagonia. ZooKeys 1043: 133-145. https://doi.org/10.3897/zookeys.1043.61706
Figure 2 Holotype of Onthophagus pilauco sp. nov. A dorsal B ventral and C frontal views D detail of the microsculpture.
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.
FIGURE 2 in Notes on the extinct family Protapioceridae, with description of a new species from China (Insecta: Diptera: Asiloidea)
FIGURE 2. Protapiocera convergens sp. nov. Body, photograph.
FIGURE 1 in Notes on the extinct family Protapioceridae, with description of a new species from China (Insecta: Diptera: Asiloidea)
FIGURE 1. Geographic position of the type locality of Protapiocera convergens sp. nov.
FIGURES 3–4 in Notes on the extinct family Protapioceridae, with description of a new species from China (Insecta: Diptera: Asiloidea)
FIGURES 3–4. Protapiocera convergens sp. nov. 3. Body, camera lucida drawing. 4. Antennae.
FIGURE 5 in Balantiocheilos ambusticauda, a new and possibly extinct species of cyprinid fish from Indochina (Cypriniformes: Cyprinidae)
FIGURE 5. Snout length (SNL) plotted against standard length for Balantiocheilos species.
FIGURE 8 in Anthropogenic extinction of Pacific land snails: A case study of Rurutu, French Polynesia, with description of eight new species of endodontids (Pulmonata)
FIGURE 8. Australdonta pakalolo sp. nov. A. Holotype; B. Paratype. Scale bars = 1 mm.
FIGURE 2 in A new extinct species of Snipe (Aves: Scolopacidae: Gallinago) from the West Indies
FIGURE 2. The Bahamian Archipelago, showing islands with fossils of Gallinago new sp.
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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.