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2,441 results for “extinct”
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: Quantitative analysis of the ecological dominance of benthic disaster taxa in the aftermath of the end-Permian mass extinction
The end-Permian mass extinction, the largest extinction of the Phanerozoic, led to a severe reduction in both taxonomic richness and ecological complexity of marine communities in its aftermath, eventually culminating in a dramatic ecological restructuring of communities. During the Early Triassic recovery interval, disaster taxa proliferated and numerically dominated many marine benthic invertebrate assemblages. These disaster taxa include the bivalve genera Claraia, Unionites, Eumorphotis and Promyalina, and the inarticulate brachiopod Lingularia. The exact nature and extent of their dominance remains uncertain. Here, a quantitative analysis of the dominance of these taxa within the fossil communities of Panthalassa and Tethys benthic realms is undertaken for the stages of the Early Triassic to examine temporal and regional changes in disaster taxon dominance as recovery progresses. Community dominance and disaster taxon abundance is markedly different between Panthalassic and Tethyan communities. In Panthalassa, community evenness is low in the Induan stage, but increases significantly in the Smithian and Spathian. This is coincident with a significant decrease in the relative abundance and occurrence frequency of the disaster taxa, most notably of low-oxygen affinity taxa Claraia and Lingularia. While the disaster taxa are present in post-Induan assemblages, other taxa, including two articulate brachiopod genera, outrank the disaster taxa in relative abundance. In the Tethys, assemblages are generally more even than contemporaneous Panthalassic assemblages. We observe an averaged trend towards more even communities with fewer disaster taxa in both Panthalassic and Tethyan assemblages over time.
Data from: Is specialization an evolutionary dead-end? Testing for differences in speciation, extinction and trait transition rates across diverse phylogenies of specialists and generalists.
Specialization has often been claimed to be an evolutionary dead end, with specialist lineages having a reduced capacity to persist or diversify. In a phylogenetic comparative framework, an evolutionary dead end may be detectable from the phylogenetic distribution of specialists, if specialists rarely give rise to large, diverse clades. Previous phylogenetic studies of the influence of specialization on macroevolutionary processes have demonstrated a range of patterns, including examples where specialists have both higher and lower diversification rates than generalists, as well as examples where the rates of evolutionary transitions from generalists to specialists are higher, lower or equal to transitions from specialists to generalists. Here, we wish to ask whether these varied answers are due to the differences in macroevolutionary processes in different clades, or partly due to differences in methodology. We analysed ten phylogenies containing multiple independent origins of specialization and quantified the phylogenetic distribution of specialists by applying a common set of metrics to all datasets. We compared the tip branch lengths of specialists to generalists, the size of specialist clades arising from each evolutionary origin of a specialized trait and whether specialists tend to be clustered or scattered on phylogenies. For each of these measures, we compared the observed values to expectations under null models of trait evolution and expected outcomes under alternative macroevolutionary scenarios. We found that specialization is sometimes an evolutionary dead end: in two of the ten case studies (pollinator-specific plants and host-specific flies), specialization is associated with a reduced rate of diversification or trait persistence. However, in the majority of studies, we could not distinguish the observed phylogenetic distribution of specialists from null models in which specialization has no effect on diversification or trait persistence.
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: Bayesian estimation of speciation and extinction from incomplete fossil occurrence data
The temporal dynamics of species diversity are shaped by variations in the rates of speciation and extinction, and there is a long history of inferring these rates using first and last appearances of taxa in the fossil record. Understanding diversity dynamics critically depends on unbiased estimates of the unobserved times of speciation and extinction for all lineages, but the inference of these parameters is challenging due to the complex nature of the available data. Here, we present a new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process based on the fossil record. The rates are allowed to vary through time independently of each other, and the probability of preservation and sampling is explicitly incorporated in the model to estimate the true lifespan of each lineage. We implement a Bayesian algorithm to assess the presence of rate shifts by exploring alternative diversification models. Tests on a range of simulated data sets reveal the accuracy and robustness of our approach against violations of the underlying assumptions and various degrees of data incompleteness. Finally, we demonstrate the application of our method with the diversification of the mammal family Rhinocerotidae and reveal a complex history of repeated and independent temporal shifts of both speciation and extinction rates, leading to the expansion and subsequent decline of the group. The estimated parameters of the birth-death process implemented here are directly comparable with those obtained from dated molecular phylogenies. Thus, our model represents a step towards integrating phylogenetic and fossil information to infer macroevolutionary processes.
Data from: Comparing the rates of speciation and extinction between phylogenetic trees
Over the past decade or so it has become increasingly popular to use reconstructed evolutionary trees to investigate questions about the rates of speciation and extinction. Although the methodology of this field has grown substantially in its sophistication in recent years, here I'll take a step back to present a very simple model that is designed to investigate the relatively straightforward question of whether the tempo of diversification (speciation and extinction) differs between two or more phylogenetic trees, without attempting to attribute a causal basis to this difference. It is a likelihood method, and I demonstrate that it generally shows type I error that is close to the nominal level. I also demonstrate that parameter estimates obtained with this approach are largely unbiased. Since this method can be used to compare trees of unknown relationship, it will be particularly well-suited to problems in which a difference in diversification rate between clades is suspected, but in which these clades are not particularly closely related. Since diversification methods can easily take into account an incomplete sampling fraction, but missing lineages are assumed to be missing at random, this method is also appropriate for cases in which we've hypothesized a difference in the process of diversification between two or more focal clades, but in which many un-sampled groups separate the few of interest. The method of this study is by no means an attempt to replace more sophisticated models in which, for instance, diversification depends on the state of an observed or unobserved discrete or continuous trait. Rather, my intention is to provide a complementary approach for circumstances in which a simpler hypothesis is warranted and of biological interest.
Data from: Mid-Cretaceous amber inclusions reveal morphogenesis of extinct rachis-dominated feathers
<p>We describe three-dimensionally preserved feathers in mid-Cretaceous Burmese amber that share macro-morphological similarities (e.g., proportionally wide rachis with a "medial stripe") with lithic, two-dimensionally preserved rachis-dominated feathers. These feathers in amber reveal a unique ventrally concave and dorsoventrally thin rachis, and a dorsal groove (sometimes pigmented) that we identify as the "medial stripe" visible in many rachis-dominated rectrices of Mesozoic birds. The distally pennaceous portion of these feathers shows differentiated proximal and distal barbules, the latter with hooklets forming interlocking barbs. Micro-CT scans and transverse sections demonstrate the absence of histodifferentiated cortex and medullary pith of the rachis and barb rami. The highly differentiated barbules combined with the lack of obvious histodifferentiation of the barb rami or rachis suggests that these feathers could have been formed without the full suite and developmental interplay of intermediate filament alpha keratins and corneous beta-proteins that is employed in the cornification process of modern feathers. This study thus highlights how the development of these feathers might have differed from that of their modern counterparts, namely in the morphogenesis of the ventral components of the rachis and barb rami. We suggest that the concave ventral surface of the rachis of these Cretaceous feathers is not homologous with the ventral groove of modern rachises. Our study of these Burmese feathers also confirms previous claims, based on two-dimensional fossils, that they correspond to an extinct morphotype and it cautions about the common practice of extrapolating developmental aspects (and mechanical attributes) of modern feathers to those of stem birds (and their dinosaurian outgroups) because the latter need not to have developed through identical pathways.</p>
Data from: Ecological correlates of extinction risk in Chinese amphibians
Aim: China is one of the countries with the richest amphibian biodiversity in the world. Among the 408 Chinese amphibians, 174 species are considered threatened according to the China Biodiversity Red List in 2015. However, to date, which species traits or extrinsic factors are correlated with extinction risk in Chinese amphibians is rarely examined in previous studies. The aims of this study were thus to identify the patterns and correlates of extinction risk in Chinese amphibians and to determine whether patterns and processes were similar between species with either small or large geographic distributions. Location: China. Methods: We obtained twelve species traits and four extrinsic factors that have been commonly linked to the extinction risk of amphibians. After phylogenetic correction, these factors were tested separately and in combination to identify their correlations with extinction risk in all Chinese amphibians, and in small-ranged and large-ranged species. Results: Geographic range size and elevational range were the most important predictors of extinction risk in all Chinese amphibians. Although extinction risk in small-ranged amphibians was predominantly determined by small elevational range, in large-ranged amphibians it was driven by geographic and elevational range sizes, body size, human exploitation index and adult microhabitat. Small-ranged amphibians had a higher percentage of threatened species than large-ranged species. However, the body size distributions were not statistically different between these two amphibian subgroups. Main conclusions: Our findings suggest that conservation priority should be given to species with small geographic and elevational ranges. Small-ranged and large-ranged amphibians should be conserved with different strategies because the factors influencing extinction risk differ between these two groups. In specific, the reduction of habitat loss should be a primary focus of management efforts for small-ranged species. Conservation efforts should also focus on preventing habitat loss and human overexploitation for the effective conservation of large-ranged amphibians.
Data from: The stratigraphy of mass extinction
Patterns of last occurrences of fossil species are often used to infer the tempo and timing of mass extinction, even though last occurrences generally precede the time of extinction. Numerical simulations with constant extinction demonstrate that last occurrences are not randomly distributed, but tend to cluster at subaerial unconformities, surfaces of forced regression, flooding surfaces and intervals of stratigraphical condensation, all of which occur in predictable stratigraphical positions. This clustering arises not only from hiatuses and non-deposition, but also from changes in water depth. Simulations with intervals of elevated extinction cause such clusters of last occurrences to be enhanced within and below the interval of extinction, suggesting that the timing and magnitude of extinctions in these instances could be misinterpreted. With the possible exception of the end-Cretaceous, mass extinctions in the fossil record are characterized by clusters of last occurrences at these sequence stratigraphical horizons. Although these clusters of last occurrences may represent brief pulses of elevated extinction, they are equally likely to form by stratigraphical processes during a protracted period (more than several hundred thousand years) of elevated extinction rate. Geochemical proxies of extinction causes are also affected similarly, suggesting that many local expressions of mass extinction should be re-evaluated for the timing of extinction and its relation to environmental change. We propose three tests for distinguishing pulses of extinction from clusters of last occurrences produced by stratigraphical processes.
Data from: The tree balance signature of mass extinction is erased by continued evolution in clades of constrained size with trait-dependent speciation
The kind and duration of phylogenetic topological "signatures" left in the wake of macroevolutionary events remain poorly understood. To this end, we examined a broad range of simulated phylogenies generated using trait-biased, heritable speciation probabilities and mass extinction that could be either random or selective on trait value, but also using background extinction and diversity-dependence to constrain clade sizes. In keeping with prior results, random mass extinction increased imbalance of clades that recovered to pre-extinction size, but was a relatively weak effect. Mass extinction that was selective on trait values tended to produce clades of similar or greater balance compared to random extinction or controls. Allowing evolution to continue past the point of clade-size recovery resulted in erosion and eventual erasure of this signal, with all treatments converging on similar values of imbalance, except for very intense extinction regimes targeted at taxa with high speciation rates. Return to a more balanced state with extended post-extinction evolution was also associated with loss of the previous phylogenetic root in most treatments. These results further demonstrate that while a mass extinction event can produce a recognizable phylogenetic signal, its effects become increasingly obscured the further an evolving clade gets from that event, with any sharp imbalance due to unrelated evolutionary factors.
Data from: Mating system affects population performance and extinction risk under environmental challenge
Failure of organisms to adapt to sudden environmental changes may lead to extinction. Mating system, by affecting fertility and the strength of sexual selection, may have a major impact on a population's chances to adapt and survive. Here, we use experimental evolution in bulb mites (Rhizoglyphus robini) to examine the effects of mating system on population performance under environmental change. We demonstrate that populations in which monogamy was enforced suffered a dramatic fitness decline when evolving at an increased temperature, whereas the negative effects of change in thermal environment were alleviated in polygamous populations. Strikingly, within 17 generations, all monogamous populations experiencing higher temperature went extinct, whereas all polygamous populations survived. Our results show that mating systems may have dramatic effects on the risk of extinction under environmental change.
Ancient mitogenomics clarifies radiation of extinct Mascarene giant tortoises (Cylindraspis spp.)
<p>The five extinct giant tortoises of the genus <i>Cylindraspis</i> belong to the most iconic species of the enigmatic fauna of the Mascarene Islands that went largely extinct after the discovery of the islands. To resolve the phylogeny and biogeography of <i>Cylindraspis</i>, we analysed a data set of 45 mitogenomes that includes all lineages of extant tortoises and eight near-complete sequences of all Mascarene species extracted from historic and subfossil material. <i>Cylindraspis </i>is an ancient lineage that diverged as early as the late Eocene. Diversification of <i>Cylindraspis</i> commenced in the mid-Oligocene, long before the formation of the Mascarene Islands. This rejects any notion suggesting that the group either arrived from nearby or distant continents over the course of the last millions of years or had even been translocated to the islands by humans. Instead, <i>Cylindraspis</i> likely originated on now submerged islands of the Réunion Hotspot and utilized these to island hop to reach the Mascarenes. The final diversification took place both before and after the arrival on the Mascarenes. With <i>Cylindraspis</i> a deeply divergent clade of tortoises became extinct that evolved long before the dodo or the Rodrigues solitaire, two other charismatic species of the lost Mascarene fauna.</p>
Data from: Total-evidence approach reveals an extinct lineage of Paederinae rove beetles from Cretaceous Burmese amber
The fossil record contains vital information about the evolution of lineages and is a source of data that cannot be reconciled in any other way than by the direct observation of morphologies. Total-evidence phylogenetic reconstruction is being increasingly used to assess the position of extinct taxa by incorporating morphological data from extinct and extant taxa together with molecular data from extant taxa in a united framework. Here we apply the method to two Cretaceous Burmese amber inclusions belonging to the rove beetle subfamily Paederinae. To perform the total evidence analysis, we constructed the first morphological matrix and the most comprehensive molecular dataset for the subfamily. Our analyses reveal an extinct lineage of Paederinae rove beetles with a suite of unique morphological characters, resulting in the description of a new genus: Diminudon gen. nov. and two new species: D. schomannae sp. nov. and D. kachinensis sp. nov. Simultaneously our analyses provide new insights into the evolution and classification of the entire subfamily. We also discuss the unusually small size of the newly described Paederinae, which may represent an additional case for miniaturization in the Cretaceous.
Data from: Age-dependent and lineage-dependent speciation and extinction in the imbalance of phylogenetic trees
It is known that phylogenetic trees are more imbalanced than expected from a birth–death model with constant rates of speciation and extinction, and also that imbalance can be better fit by allowing the rate of speciation to decrease as the age of the parent species increases. If imbalance is measured in more detail, at nodes within trees as a function of the number of species descended from the nodes, age-dependent models predict levels of imbalance comparable to real trees for small numbers of descendent species, but predicted imbalance approaches an asymptote not found in real trees as the number of descendent species becomes large. Age-dependence must therefore be complemented by another process such as inheritance of different rates along different lineages, which is known to predict insufficient imbalance at nodes with few descendent species, but can predict increasing imbalance with increasing numbers of descendent species.
Data from: Persistence of an extinction-prone predator-prey interaction through metapopulation dynamics
In theory, predator-prey pairs with extinction-prone local populations can persist through metapopulation dynamics, wherein local populations fluctuate asynchronously, occasionally providing dispersers that prevent permanent extinction in all patches. A few studies have shown that spatial structure can extend predator-prey persistence. However, no studies have unequivocally demonstrated the asynchrony among patches, low dispersal rates, and rescue effects that prove metapopulation dynamics extend persistence. We used a protist predator-prey pair to show that spatial subdivision lengthens persistence through metapopulation dynamics. The pair comprised the predaceous ciliate, Didinium nasutum, feeding on the bacterivorous ciliate, Colpidium cf. striatum. A replicated experiment assessed how habitat subdivision affects persistence. Undivided habitats were of four volumes: 30, 180, 270, and 750 mt. Subdivided microcosms, or ''arrays,'' were groups of nine or 25 linked 30-mL bottles (270 or 750 mt total volume). In arrays, predators and prey persisted for 130 d (602 prey and 437 predator generations), at which point the experiment ended. Predators went extinct in undivided microcosms of equivalent volumes within a mean of only 70 d. Predators persisted for a mean of just 19 d in isolated 30-mL bottles (equivalent to isolated patches of arrays). In a separate experiment, prey were driven extinct in four of 15 isolated 30-mL bottles, and persistence times of predators were broadly similar. We documented the following hallmarks of metapopulation dynamics: (1) asynchronous fluctuations in different subpopulations; (2) frequent local prey extinctions and recolonizations; (3) persistence of protists in arrays, despite extinction of isolated local populations; and (4) rescue effects in predator populations. Other experiments measured dispersal rates and the effects on local dynamics of immigrant predators and prey, and initial predator : prey ratios. Only a small fraction of protists dispersed within a generation, consistent with metapopulation dynamics. Immigration of predators increased the frequency of local extinctions of prey, and immigration of prey increased the persistence of both predators and prey. Higher initial predator:prey ratios decreased the persistence of prey in undivided volumes. Although the pair persisted regionally in arrays, data indicated that local extinctions of prey were common. In array patches, predator:prey ratios were higher and predator-prey cycles were shorter than in undivided volumes. Dispersal made local dynamics more prone to extinction, yet promoted regional persistence because the risk of extinction of distant subpopulations became independent.
Data from: Host population bottlenecks drive parasite extinction during antagonistic coevolution
Host-parasite interactions are often characterized by large fluctuations in host population size, and we investigated how such host bottlenecks affected coevolution between a bacterium and a virus. Previous theory suggests that host bottlenecks should provide parasites with an evolutionary advantage, but instead we found that phages were rapidly driven to extinction when coevolving with hosts exposed to large genetic bottlenecks. This was caused by the stochastic loss of sensitive bacteria, which are required for phage persistence and infectivity evolution. Our findings emphasize the importance of feedbacks between ecological and coevolutionary dynamics, and how this feedback can qualitatively alter coevolutionary dynamics.
Data from: Sexual selection protects against extinction
Reproduction through sex carries substantial costs, mainly because only half of sexual adults produce offspring. It has been theorized that these costs could be countered if sex allows sexual selection to clear the universal fitness constraint of mutation load. Under sexual selection, competition between (usually) males and mate choice by (usually) females create important intraspecific filters for reproductive success, so that only a subset of males gains paternity. If reproductive success under sexual selection is dependent on individual condition, which is contingent to mutation load, then sexually selected filtering through 'genic capture' could offset the costs of sex because it provides genetic benefits to populations. Here we test this theory experimentally by comparing whether populations with histories of strong versus weak sexual selection purge mutation load and resist extinction differently. After evolving replicate populations of the flour beetle Tribolium castaneum for 6 to 7 years under conditions that differed solely in the strengths of sexual selection, we revealed mutation load using inbreeding. Lineages from populations that had previously experienced strong sexual selection were resilient to extinction and maintained fitness under inbreeding, with some families continuing to survive after 20 generations of sib × sib mating. By contrast, lineages derived from populations that experienced weak or non-existent sexual selection showed rapid fitness declines under inbreeding, and all were extinct after generation 10. Multiple mutations across the genome with individually small effects can be difficult to clear, yet sum to a significant fitness load; our findings reveal that sexual selection reduces this load, improving population viability in the face of genetic stress.
Data from: Does morphological variation buffer against extinction? A test using veneroid bivalves from the Plio-Pleistocene of Florida
Although morphological variation is known to influence the evolutionary fates of species, the relationship between morphological variation and survivorship in the face of extinction-inducing perturbations is poorly understood. Here, we investigate this relationship for veneroid bivalves in association with the Plio-Pleistocene extinction in Florida. Fourteen pairs of related species were selected for analysis, with each pair including one species that survived the Plio-Pleistocene extinction and another that became extinct during the interval. Morphological landmark data were acquired for more than 1500 museum specimens, representing 19 localities that encompass four well-known Plio-Pleistocene units in the study region. Procrustes superimposition was applied to each sample, and overall multivariate variation was calculated as the mean squared partial Procrustes distance between specimens and their mean form. Morphological variation was calculated at three geographic scales for each species, and differences in variation between survivors and victims were examined within each species pair. Results indicate that species surviving the Plio-Pleistocene extinction were significantly more variable morphologically than victims. Greater morphological variation may promote survivorship by directly enhancing species adaptations to changing conditions or by permitting the occupation of a larger geographic range. Alternatively, high morphological variation and survivorship may both be mediated by a third variable, such as large geographic range.
Data from: Time-dependent speciation and extinction from phylogenies: a least squares approach
Molecular phylogenies contribute to the study of the patterns and processes of macroevolution even though past events (fossils) are not recorded in these data. In this paper, I consider the general time-dependent birth–death model in order to fit any model of temporal variation in speciation and extinction to phylogenies. I establish formulae to compute the expected cumulative distribution function of branching times for any model, and, building on previous published works, I derive maximum likelihood estimators. Some limitations of the likelihood approach are described, and a fitting procedure based on least squares is developed that alleviates the shortcomings of maximum likelihood in the present context. Parametric and nonparametric bootstrap procedures are developed to assess uncertainty in the parameter estimates, the latter version giving narrower confidence intervals and being faster to compute. I also present several general algorithms of tree simulation in continuous time. I illustrate the application of this approach with the analysis of simulated data sets, and two published phylogenies of primates (Catarrhinae) and lizards (Agamidae).
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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.
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