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470 results for “dead”
Data from: Dead ant walking: a myrmecophilous beetle predator uses parasitoid host location cues to selectively prey on parasitized ants
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Data from: Priority effects of early successional insects influence late successional fungi in dead wood
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Data from: Dead before detection: addressing the effects of left truncation on survival estimation and ecological inference for neonates
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Data from: Living, dead, and absent trees - How do moth outbreaks shape small-scale patterns of soil organic matter stocks and dynamics at the Subarctic mountain birch treeline?
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Data from: Contests with deadly weapons: telson sparring in mantis shrimp (Stomatopoda)
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Phylogenetic analysis of the distribution of deadly amatoxins among the little brown mushrooms of the genus Galerina
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Data from: Digging their own macroevolutionary grave: Fossoriality as an evolutionary dead-end in snakes
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Data from: A quantitative framework for investigating risk of deadly collisions between marine wildlife and boats
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Data from: Pelagic zone is an evolutionary catalyst, but an ecological dead end, for North American minnows
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Peaceful coexistence between people and deadly wildlife: why are recreational users of the ocean so rarely bitten by sea snakes?
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Figure 5 in The five deadly sins of science publishing
Figure 5. Summary of the F1000Research open science publishing process.
Data from: Live, dead, and fossil mollusks in Florida freshwater springs and spring-fed rivers: taphonomic pathways and the formation of multi-sourced, time-averaged death assemblages
Taphonomic processes are informative about the magnitude and timing of paleoecological changes but remain poorly understood with respect to freshwater invertebrates in spring-fed rivers and streams. We compared taphonomic alteration among freshwater gastropods in live, dead (surficial shell accumulations), and fossil (late Pleistocene-early Holocene in situ sediments) assemblages from two Florida spring-fed systems, the Wakulla and Silver/Ocklawaha Rivers. We assessed taphonomy of two gastropod species: the native <i>Elimia floridensis</i> (n=2504) and introduced <i>Melanoides tuberculata</i> (n=168). We quantified seven taphonomic attributes (aperture condition, color, fragmentation, abrasion, juvenile spire condition, dissolution, and exterior luster) and combined those attributes into a total taphonomic score (TT). Fossil <i>E. floridensis</i> specimens exhibited the greatest degradation (highest TT scores), whereas live specimens of both species were least degraded. Specimens of <i>E. floridensis</i> from death assemblages were less altered than fossil specimens of the same species. Within death assemblages, specimens of <i>M. tuberculata</i> were significantly less altered than specimens of <i>E. floridensis</i>, but highly degraded specimens dominated in both species. Radiocarbon dates on fossils clustered between 9792 and 7087 cal. BP, whereas death assemblage ages ranged from 10,692 to 1173 cal. BP. Possible explanations for the observed taphonomic patterns include: (1) rapid taphonomic shell alteration, (2) prolonged near-surface exposure to moderate alteration rates, and/or (3) introduction of reworked fossil shells into surficial assemblages. Combined radiocarbon dates and taphonomic analyses suggest that all these processes may have played a role in death assemblage formation. In these fluvial settings, shell accumulations develop as a complex mixture of specimens derived from multiple sources and characterized by multi-millennial time averaging. These findings suggest that, when available, fossil assemblages may be more appropriate than death assemblages for assessing pre-industrial faunal associations and recent anthropogenic changes in freshwater ecosystems.
Data from: The quick are the dead: pheasants that are slow to reverse a learned association survive for longer in the wild
Cognitive abilities likely evolve through natural selection if they provide individuals with fitness benefits. A growing number of studies demonstrate a positive relationship between performance in psychometric tasks and (proxy) measures of fitness. We assayed the performance of 154 Common Pheasant Phasianus colchicus chicks on tests of acquisition and reversal learning, using a different set of chicks and different set of cue types (spatial location and colour) in each of two years and then followed their fates after release into the wild. Across all birds, individuals that were slow to reverse previously learned associations were more likely to survive to four months old. For heavy birds, individuals that rapidly acquired an association had improved survival to four months, whereas for light birds, slow acquirers were more likely to be alive. Slow reversers also exhibited less exploratory behaviour in assays when five weeks old. Fast acquirers visited more artificial feeders after release. By contrast to most other studies, we showed that apparently 'poor' cognitive performance (slow reversal speed suggesting low behavioural flexibility) correlates with fitness benefits in at least some circumstances. This correlation suggests a novel mechanism by which continued exaggeration of cognitive abilities may be constrained.
Data from: Neurospora and the dead-end hypothesis: genomic consequences of selfing in the model genus.
It is becoming increasingly evident that adoption of different reproductive strategies, such as sexual selfing and asexuality, greatly impacts genome evolution. In this study, we test theoretical predictions on genomic maladaptation of selfing lineages using empirical data from the model fungus Neurospora. We sequenced the genomes of four species representing distinct transitions to selfing within the history of the genus, as well as the transcriptome of one of these, and compared with available data from three outcrossing species. Our results provide evidence for a relaxation of purifying selection in protein-coding genes and for a reduced efficiency of transposable element silencing by Repeat Induced Point mutation. A reduction in adaptive evolution was also identified in the form of reduced codon usage bias in highly expressed genes of selfing Neurospora, but this result may be confounded by mutational bias. Potentially counteracting these negative effects, the nucleotide substitution rate and the spread of transposons is reduced in selfing species. We suggest that differences in substitution rate relate to the absence of the asexual pathway producing conidia in selfing Neurospora. Our results support the dead-end theory and show that Neurospora genomes bear signatures of both sexual and asexual reproductive mode.
Data from: Lateral gene transfer from the dead
In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer (LGT), however, this may not be the case, because the species lineage from which a gene was transferred may have gone extinct or not have been sampled. Because it is not feasible to specify or reconstruct the complete phylogeny of all species, we must describe the evolution of genes outside the represented phylogeny by modelling the speciation dynamics that gave rise to the complete phylogeny. We demonstrate that if the number of sampled species is small compared to the total number of existing species, the overwhelming majority of gene transfers involve speciation to, and evolution along extinct or unsampled lineages. We show that the evolution of genes along extinct or unsampled lineages can to good approximation be treated as those of independently evolving lineages described by a few global parameters. Using this result, we derive an algorithm to calculate the probability of a gene tree and recover the maximum likelihood reconciliation given the phylogeny of the sampled species. Examining 473 near universal gene families from 36 cyanobacteria, we find that nearly a third of transfer events − 28% – appear to have topological signatures of evolution along extinct species, but only approximately 6% of transfers trace their ancestry to before the common ancestor of the sampled cyanobacteria.
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: Impacts of dead-wood manipulation on the biodiversity of temperate and boreal forests - A systematic review
Dead wood (DW) provides critical habitat for thousands of species in forests, but its amount, quality and diversity have been heavily reduced by forestry. Therefore, interventions aiming to increase DW might be necessary to support its associated biodiversity, even in protected forests, which may be former production forests. Our aim was to synthesise the current state of knowledge drawn from replicated experimental studies into solid quantitative evidence of the effects of DW manipulation on forest biodiversity, with a focus on protected forests. We conducted a full systematic review of effects of DW manipulation on forest biodiversity in boreal and temperate regions. We included three intervention types: creation of DW from live trees at the site, addition of DW from outside the site, and prescribed burning. Outcomes included abundance and species richness of saproxylic insects, ground insects, wood‐inhabiting fungi, lichens, reptiles and cavity‐nesting birds. In total, we included 91 studies, 37 of which were used in meta‐analyses. Although meta‐analysis outcomes were heterogeneous, they showed that increasing the amount of DW ("DW enrichment") has positive effects on the abundance and richness of saproxylic insects and fungi. The positive effect on saproxylic pest insect abundance tended to be less than that on saproxylic insects in general. No significant effects were found for ground insects or cavity‐nesting birds. Although reviewed studies were mainly short‐term, our results support that management that increases DW amounts has the potential to increase the abundance of DW‐dependent species and, in most cases, also their species richness. Studies of burning showed positive effects on the abundance of saproxylic insects similar to those of other interventions, even though burning on average resulted in a smaller enrichment of DW amounts. Policy implications. The findings of the review suggest that manipulating dead wood can be an effective part of conservation management to support biodiversity in protected areas. The findings also indicate that the diversity of dead‐wood types is important, a mix of dead‐wood qualities should be favoured. Burning seems to be an effective method to increase biodiversity but to benefit cavity‐nesting birds, snag losses need to be minimised.
Data from: Why we are not dead 100 times over
The possibility of pervasive weak selection at tens or hundreds of millions of sites across the genome, suggested by recent studies of silent site DNA sequence variation and divergence, raises the problem of the survival of the population in the face of the large genetic load that may result. Two alternative resolutions of this problem are presented for populations where recombination is sufficiently frequent that different sites under selection evolve independently. One invokes weak stabilizing selection, of the magnitude compatible with abundant silent site variability. This can be shown to produce only a modest genetic load, due to the effectiveness of even weak stabilizing selection in keeping the trait mean close to the optimum. The other invokes soft selection, whereby individuals compete for a limiting resource whose abundance determines the absolute fitness of the population. Weak purifying selection at a large number of sites produces only a small variance in fitness among individuals within the population, due to the fact that most sites are fixed rather than polymorphic. Even when it produces a large genetic load, it is compatible with the observations when selection is soft. It may be very difficult to distinguish between these two possibilities.
Data from: Fear and lethality in snowshoe hares: the deadly effects of non-consumptive predation risk
Predators play a critical, top-down role in shaping ecosystems, driving prey population and community dynamics. Traditionally, studies of predator-prey interactions have focused on direct effects of predators, namely the killing of prey. More recently, the non-consumptive effects of predation risk are being appreciated; e.g., the Ecology of Fear. Prey responses to predation risk can be morphological, behavioural, and physiological, and are assumed to come at a cost to prey fitness. However, few studies have examined the relationship between predation risk and survival in wild animals. We tested the hypothesis that predation risk itself could reduce survival in wild-caught snowshoe hares. We exposed female snowshoe hares to a simulated predator (a trained dog) during gestation only, and measured adult survival and, in surviving females, their ability to successfully wean offspring. We show for the first time in a wild mammal that the risk of predation can itself be lethal. Predation risk reduced adult female survival by 30%, and had trans-generational effects, reducing offspring survival to weaning by over 85% - even though the period of risk ended at birth. As a consequence of these effects the predator-exposed group experienced a decrease in number, while the control group substantially increased. Challenges remain in determining the importance of risk-induced mortality in natural field settings; however, our findings show that non-lethal predator encounters can influence survival of both adults and offspring. Future work is needed to test these effects in free-living animals.
Data from: Eating down the food chain: generalism is not an evolutionary dead end for herbivores
The role of trophic specialisation in taxonomic diversification remains unclear. Plant specialists diversify faster than omnivores and animalivores, but at shorter macroevolutionary scales this pattern sometimes reverses. Here, we estimate the effect of diet diversification on speciation rates in noctilionoid bats, controlling for tree shape, rate heterogeneity and macroevolutionary regimes. We hypothesise that niche subdivision among herbivores positively relates to speciation rates, differing between macroevolutionary regimes. We found the rate at which new herbivorous lineages originate decreases as rates of diet evolution increase. Herbivores experience higher speciation rates, but generalist herbivores and predominantly herbivorous omnivores speciate faster than specialised herbivores, omnivores and animalivores. Generalised herbivory is not a dead end. We show that analysing ecological traits and diversification requires accounting for macroevolutionary regimes and within- and between-clade variation in evolutionary rates. Our approach overcomes the high false-positive rates of other methods and illuminates the roles of herbivory and specialisation in speciation.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.