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954 results for “survival data”
Data from: Topography in tropical forests enhances growth and survival differences within and among species via water availability and biotic interactions
<p class="Cuerpo">Topography is associated with variation in soil water, biogeochemical properties and climate, which drive diversity by filtering species and promoting niche differences. However, the potential for topography to promote fitness differences and diversity among tree species and populations remains poorly tested in tropical rainforests, especially at small spatial scales in everwet climates.</p> <p class="Cuerpo">We reciprocally transplanted tree seedlings between ridge and riparian sites and manipulated neighbour abundance and water availability to assess growth and survival differences both among species and between populations within species in response to changes in biotic interactions and soil water gradients associated with topographic heterogeneity.</p> <p class="Cuerpo">Seedling growth rates were higher on the ridge, but probability of survival was lower on the ridge than the riparian site. Topography also altered growth and survival responses to water availability such that seedlings in the inundated soils in the riparian site had the lowest growth and survival but increased rapidly with moderate soil drying. By contrast, growth and survival on the ridge were generally unresponsive to drying, although severe drought on the ridge reinforced differences among species in growth rates and probability of survival.</p> <p class="Cuerpo">The patterns of growth and survival within species did not provide evidence of local adaptation between seedlings from lowland and upslope origins. However, within species, topographic seed-origin determined the response of seedling growth and survival to increasing neighbour abundance, indicative of divergent selective pressures between individuals growing in different topographic environments.</p> <p class="Cuerpo">Combined, these results suggest that topographic heterogeneity promotes tropical forest diversity both at the species level via environmental filtering due to water availability and at the population level via functional responses to the density of neighbouring vegetation.</p>
Data from: Season rather than habitat affects lynx survival and risk of mortality in the human-dominated landscape of southern Sweden
<p><span><span><span><span><span><span><span><span><span><span><span>Landscapes are mosaics of habitat associated with different risks and resources, including human activities, which can affect individual survival in wildlife. Different relationships between habitat characteristics and human-caused and natural mortality can result in attractive sinks. We used individual-based data from 97 Eurasian lynx (<i>Lynx lynx</i>) monitored for 160 exposure years to link adult survival and the risk of mortality to home range habitat characteristics in the human-dominated landscape of southern Sweden. Human-caused mortality dominated mortality causes (24 out of 37 deaths). We did not detect any strong effects of habitat characteristics explaining the variation in mortality risk in lynx. Although the density of roe deer affects several aspects of lynx ecology, we could not detect any effects of roe deer density on lynx survival, probably because roe deer density was sufficiently high in our study area. Instead, there was a high seasonal variation in mortality lynx. Mortality was highest during the hunting season for lynx (February 16 – March 31), as well as during autumn and winter, probably because lynx poaching occurred opportunistically during the hunting season for moose and roe deer. We did not find any indication that human activity created attractive sinks for lynx, since there was no contrasting pattern between human-caused and natural mortality in terms of habitat characteristics. One explanation for the limited influence of the home range characteristics may be that lynx in our study died from multiple causes (natural causes 35%, legal hunting 27 %, poaching 22 % and vehicle collisions 16 %). Therefore, it is less likely that one or a few habitat characteristics could explain the risk of mortality at the home range scale. There is strong evidence that lynx can coexist with humans in multi-use and human-dominated landscapes, even without large protected areas, if the management regimes are favourable.</span></span></span></span></span></span></span></span></span></span></span></p> <p> </p>
Data from: Cascading effects of pre-adult survival on sexual selection
<p>Sexual selection influences broad-scale patterns of biodiversity. While a large body of research has investigated the effect of mate competition on sexual selection, less work has examined how pre-adult life history influences sexual selection. We used a mathematical framework to explore the influence of pre-adult survival on sexual selection. Our model suggests that pre-adult male mortality will affect the strength of sexual selection when a fixed number of adult males have an advantageous mate-acquisition trait. When a fixed number of males have an advantageous mate-acquisition trait, sexual selection is expected to increase when pre-adult mortality is relatively low. In contrast, if a fixed proportion (rather than number) of adult males have a mate-acquisition trait, pre-adult male mortality is not expected to affect the strength of sexual selection. Further, if the advantageous mating trait affects pre-adult survival, natural and sexual selection can interact to influence the overall selection on the mating trait. Given that pre-adult mortality is often shaped by natural selection, our results highlight conditions under which natural selection can have cascading effects on sexual selection.</p>
Data from: Metabolomic and transcriptomic responses of ticks during recovery from cold shock reveal mechanisms of survival
<p>Ticks are blood-feeding ectoparasites but spend most of their life off-host where they may have to tolerate low winter temperatures. Rapid cold-hardening (RCH) is a process commonly used by arthropods, including ticks, to improve survival of acute low temperature exposure. However, little is known about the underlying mechanisms in ticks associated with RCH, cold shock, and recovery from these stresses. In the present study, we investigated the extent to which RCH influences gene expression and metabolism during recovery from cold stress in Dermacentor variabilis, the American dog tick, using a combined transcriptomics and metabolomics approach. Following recovery from RCH, 1,860 genes were differentially expressed in ticks, whereas only 99 genes responded during recovery to direct cold shock. Recovery from RCH resulted in an upregulation of various pathways associated with ion binding, transport, metabolism, and cellular structures seen in the response of other arthropods to cold. The accumulation of various metabolites, including several amino acids and betaine, corresponded to transcriptional shifts in the pathways associated with these molecules, suggesting congruent metabolome and transcriptome changes. Ticks receiving exogenous betaine and valine demonstrated enhanced cold tolerance, suggesting cryoprotective effects of these metabolites. Overall, many of the responses during recovery from cold shock in ticks were similar to those observed in other arthropods, but several adjustments may be distinct from other currently examined taxa.</p>
Pinniped comparative survival data
<p>Survival rates are a central component of life-history strategies of large vertebrate species. However, comparative studies seldom investigate interspecific variation in survival rates with respect to other life-history traits, especially for males. The lack of such studies could be due to the challenges associated with obtaining reliable datasets, incorporating information on the 0-1 probability scale, or dealing with several types of measurement error in life-history traits, which can be a computationally intensive process that is often absent in comparative studies. We present a quantitative approach using Bayesian phylogenetically controlled regression with the flexibility to incorporate uncertainty in estimated survival rates and quantitative life-history traits while considering genetic similarity among species and uncertainty in relatedness. As with any comparative analysis, our approach makes several assumptions regarding the generalizability and comparability of empirical data from separate studies. Our model is versatile in that it can be applied to any species group of interest and include any life-history traits as covariates. We used an unbiased simulation framework to provide "proof of concept" for our model and applied a slightly richer model to a real-data example for pinnipeds. Pinnipeds are an excellent taxonomic group for comparative analysis, but survival rate data are scarce. Our work elucidates the challenges associated with addressing important questions related to broader ecological life-history patterns and how survival-reproduction tradeoffs might shape evolutionary histories of extant taxa. Specifically, we underscore the importance of having high-quality estimates of age-specific survival rates and information on other life-history traits that reasonably characterize a species for accurately comparing across species.</p>
Data from: Simulated winter warming negatively impacts survival of Antarctica's only endemic insect
<p>Antarctic winters are challenging for terrestrial invertebrates, and species that live there have specialized adaptations to conserve energy and protect against cold injury in the winter. However, rapidly occurring climate change in these regions will increase the unpredictability of winter conditions, and there is currently a dearth of knowledge on how the highly adapted invertebrates of Antarctica will respond to changes in winter temperatures.</p> <p>We evaluated the response of larvae of the Antarctic midge, <em>Belgica antarctica</em>, to simulated winters at three ecologically relevant mean temperature scenarios: Warm (-1 °C), Normal (-3 °C) and Cold (-5 °C). Within each scenario, larvae were placed into three distinct habitat types in which they are commonly observed (decaying organic matter, living moss, and <em>Prasiola crispa algae</em>). Following the simulated overwintering period, a range of physiological outcomes were measured, namely survival, locomotor activity, tissue damage, energy store levels and molecular stress responses.</p> <p>Survival, energy stores and locomotor activity were significantly lower following the Warm overwintering environment than at lower temperatures, but tissue damage and heat shock protein expression (a proxy for protein damage) did not significantly differ between the three temperatures. Survival was also significantly lower in larvae overwintered in <em>Prasiola crispa</em> algae, although the underlying mechanism is unclear. Heat shock proteins were expressed least in larvae overwintering in living moss, suggesting it is less stressful to overwinter in this substrate, perhaps due to a more defined structure affording less direct contact with ice.</p> <p>Our results demonstrate that a realistic 2 °C increase in winter microhabitat temperature reduces survival and causes energy deficits that have implications for subsequent development and reproduction. While our Warm winter scenario was close to the range of observed overwintering temperatures for this species, warmer winters are expected to become more common in response to climate change. Conversely, if climate change reduces the length of winter, some of the negative consequences of winter warming may be attenuated, so it will be important to consider this factor in future studies. Nonetheless, our results indicate that winter warming could negatively impact cold-adapted insects like the Antarctic midge.</p>
Raw Data Survival, Development and Reproduction of Gonipterus platensis on Eucalyptus genotypes
<p>Data used in the paper "The survival, development, and reproduction of <em>Gonipterus platensis </em>(Coleoptera: Curculionidae) on the main <em>Eucalyptus </em>(Myrtaceae) genotypes planted in Brazil"</p>
data for the manuscript entitled Survival probability of atmospheric new particles: closure between theory and measurements from 1.4 to 100 nm
<p>data for figures.</p> <p>Please contact runlong.cai@helsinki.fi if needed</p>
Raw data - Macronutrient balance has opposing effects on cognition and survival in honey bees
<p>This file contains the dataset used in the paper "Macronutrient balance has opposing effects on cognition and survival in honey bees"</p>
Supporting data for: Planted conifer seedling survival in a post-wildfire landscape in New Mexico: From experimental planting to predictive probabilistic surfaces
<p>Across the southwestern United States, high-severity wildfire is causing increasingly large patches of tree mortality, removing the seed sources required for the natural regeneration of these formerly conifer-dominated landscapes. Planting tree seedlings can accelerate succession and restore the ecosystem services that pre-wildfire forests provided, but in the semi-arid southwestern US, the survival of planted conifer seedlings is typically low. We present data on a seedling planting experiment within the footprint of the 2011 Las Conchas Fire in northern New Mexico, using microclimate variables and site-level topographic indices to determine which factors influence seedling survival of four conifer tree species. We then extrapolate these findings to the wider landscape for the most commonly planted species, producing a spatial projection of probabilistic seedling survival as a function of both site- and landscape-scale factors, using readily available topographic data. Both sets of analyses highlight the importance of landscape heterogeneity, quantifiable using topographic indices, in shaping microclimatic environments and affecting seedling survival in a predictable manner. Our results demonstrate that using these methods to guide future plantings may increase conifer tree seedling survival in high-severity post-wildfire landscapes.</p>
Supporting Information: DATA and CODE. Contrasted impacts of weather conditions in species sensitive to both survival and fecundity: a montane bird case study.
<p>This folder contains the R code (file “Rock_partridge_IPM.r “) of the integrated population model (IPM) used to study the population dynamics of the rock partridge in the French Alps, along with associated data (file “jags.data”). The integrated population model allowed us to model survival and breeding success (split in several steps) simultaneously. Data were collected by the French Office for Biodiversity (OFB) and the Observatory of mountain galliformes (OGM: <a href="https://www.observatoire-galliformes-montagne.com/">https://www.observatoire-galliformes-montagne.com/</a>). The “Read.me” file provides a detailed description of the different datasets. We also included values of the covariates used to study the influence of weather variation on survival and breeding success (files “covariates_survival”, “covariates_brood_size” and “covariates_brood_size_per_site”).</p>
Raw data article "Surviving adversity: exploring the presence of Lunularia cruciata (L.) Dum. on metal-polluted mining waste"
<p>This is the raw data of the article "Surviving adversity: exploring the presence of Lunularia cruciata (L.) Dum. on metal-polluted mining waste".</p>
Data and Codes for Publication: "Sexually Dimorphic Computational Histopathological Signatures Prognostic of Overall Survival in High-Grade Gliomas via Deep Learning"
<p><strong>Data</strong></p> <p>The patches and the associated tumor segmentation labels (expert-vetted) from our analysis are available in Patches.pytable file.<br><br><strong>Codes<br><br></strong>The codes for training tumor segmentation models and conducting survival analysis are available in the following files</p> <ul> <li>ResNet-train: Code to train Resnet18 model for Tumor Segmentation</li> <li>Tumor_Segmentation: Code to segment tumor regions from WSI using ResNet18 model</li> <li>ResNet_Cox_train: Code to train ResNet-Cox model in 5 folds cross-validation setting</li> <li>Evaluate_ResNetCox: Code to evaluate ResNet-Cox model</li> </ul>
Data from: Endocrine phenotype, reproductive success and survival in the great tit, Parus major
A central goal in evolutionary ecology is to characterize and identify selection patterns on the optimal phenotype in different environments. Physiological traits, such as hormonal responses, provide important mechanisms by which individuals can adapt to fluctuating environmental conditions. It is therefore expected that selection shapes hormonal traits, but the strength and the direction of selection on plastic hormonal signals are still under investigation. Here, we determined whether, and in which way, selection is acting on the hormones corticosterone and prolactin by characterizing endocrine phenotypes and their relationship with fitness in free-living great tits, Parus major. We quantified variation in circulating concentrations of baseline and stress-induced corticosterone and in prolactin during the prebreeding (March) and the breeding season (May) for two consecutive years, and correlated these with reproductive success (yearly fledgling number) and overwinter survival in female and male individuals. In both years, individuals with high baseline corticosterone concentrations in March had the highest yearly fledgling numbers; while in May, individuals with low baseline corticosterone had the highest yearly reproductive success. Likewise, individuals that displayed strong seasonal plasticity in baseline corticosterone concentrations (high in March and low in May) had the highest reproductive success in each year. Prolactin concentrations were not related to reproductive success, but were positively correlated to the proximity to lay. Between-year plasticity in stress-induced corticosterone concentrations of males was related to yearly variation in food abundance, but not to overall reproductive success. These findings suggest that seasonally alternating directional selection is operating on baseline corticosterone concentrations in both sexes. The observed between-year consistency in selection patterns indicates that a one-time hormone sample in a given season can allow the prediction of individual fitness.
Data from: Leukocyte profiles are associated with longevity and survival, but not migratory effort: a comparative analysis of shorebirds
1. Assessment of leukocyte profiles has become an increasingly popular tool in the fields of ecology and ecophysiology. The ratio of heterophils to lymphocytes (H/L ratio) is of special utility, as it reflects physiological adaptation of an organism to cope either with an infection through injury (via heterophils) or a communicable disease (via lymphocytes). Thus, elevated H/L ratios may constitute an adaptation to risky environments (i.e. associated with high risk of injury). While intra-population variation in avian H/L ratio has been extensively studied, we are aware of no studies that linked this trait to life-history components at the inter-specific level. 2. We measured H/L ratio in over 400 shorebirds from 19 species during their autumn migration through Central Europe. Phylogenetically informed comparative methods were used to test whether H/L ratio was related to: i) annual survival and lifespan; ii) migratory effort, as measured with total migration distance and migratory energy reserves; and iii) confounding variables such as body size or breeding latitude. 3. A relatively strong phylogenetic signal and spatial phylogenetic autocorrelation indicated that most diversification in shorebird H/L ratios occurred relatively early in radiation of this group. 4. Comparative analysis gave strong support for the negative associations of H/L ratio with residual lifespan and annual survival. In contrast, we found no support for the effect of migratory behaviour on H/L ratios, suggesting that leukocyte profiles in shorebirds may not constitute an important physiological adaptation for long-distance migration. 5. Our study provided the first comparative evidence for a link between H/L ratios and important life-history traits in birds. Strong negative associations with annual survival and residual lifespan indicate that leukocyte profiles may form an adaptive basis for life-history strategies in birds.
Data from: Increased male bias in eider ducks can be explained by sex-specific survival of prime-age breeders
In contrast to theoretical predictions of even adult sex ratios, males are dominating in many bird populations. Such bias among adults may be critical to population growth and viability. Nevertheless, demographic mechanisms for biased adult sex ratios are still poorly understood. Here, we examined potential demographic mechanisms for the recent dramatic shift from a slight female bias among adult eider ducks (Somateria mollissima) to a male bias (about 65% males) in the Baltic Sea, where the species is currently declining. We analysed a nine-year dataset on offspring sex ratio at hatching based on molecularly sexed ducklings of individually known mothers. Moreover, using demographic data from long-term individual-based capture-recapture records, we investigated how sex-specific survival at different ages after fledgling can modify the adult sex ratio. More specifically, we constructed a stochastic two-sex matrix population model and simulated scenarios of different survival probabilities for males and females. We found that sex ratio at hatching was slightly female-biased (52.8%) and therefore unlikely to explain the observed male bias among adult birds. Our stochastic simulations with higher survival for males than for females revealed that despite a slight female bias at hatching, study populations shifted to a male-biased adult sex ratio (> 60% males) in a few decades. This shift that was driven by prime reproductive-age individuals (≥5-year-old), with sex-specific survival of younger age classes playing a minor role. Hence, different age classes contributed disproportionally to population dynamics. We argue that an alternative explanation for the observed male dominance among adults - sex-biased dispersal - can be considered redundant and is unlikely, given the ecology of the species. The present study highlights the importance of considering population structure and age-specific vital rates when assessing population dynamics and management targets.
Data from: Effect of light-level geolocators on apparent survival of two highly aerial swift species
Light-level geolocators are currently widely used to track the migration of small-sized birds, but their potentially detrimental effects on survival of highly aerial species have been poorly investigated so far. We recorded capture-recapture histories of 283 common swifts Apus apus and 107 pallid swifts Apus pallidus breeding in 14 colonies in Italy, Spain, Sweden and Switzerland that were deployed with 10 different types of geolocators ('geolocator birds'), and compared their survival with that of, respectively, 215 common and 101 pallid swifts not equipped with geolocators ('control birds'). We performed both traditional GLMM using return rate as a proxy for survival and mark-recapture models to estimate survival while accounting for recapture probability. In all the analyses, geolocator birds showed reduced apparent survival compared to controls. The extent of the negative effect on survival differed between the species but the direction of the difference between species was opposite in either type of analysis. Geolocator weight was always lower 3% of body mass or less, and did not affect survival per se. Geolocators with a light-stalk, which is used in some geolocator models to reduce light sensor shading by feathers, decreased apparent survival more than models without light-stalk. Apparent survival of geolocator birds significantly varied among sites, being much higher in northern Europe. Despite in our analyses we could only partly account for variable recapture probabilities among sites and for inter-annual variability in survival, our results generally showed that equipping swifts with geolocators decreased their survival prospects, but also that the magnitude of this effect may depend on species-specific traits. These conclusions are in line with those of other studies on aerial foragers. We suggest that future studies tracking the movements of aerial insectivorous birds should use devices designed to minimize drag.
Data from: Specific alleles at immune genes, rather than genome-wide heterozygosity, are related to immunity and survival in the critically endangered Attwater's prairie-chicken
The negative effects of inbreeding on fitness are serious concerns for populations of endangered species. Reduced fitness has been associated with lower genome-wide heterozygosity and immune gene diversity in the wild; however, it is rare that both types of genetic measures are included in the same study. Thus, it is often unclear whether the variation in fitness is due to the general effects of inbreeding, immunity-related genes or both. Here, we tested whether genome-wide heterozygosity (20 990 SNPs) and diversity at nine immune genes were better predictors of two measures of fitness (immune response and survival) in the endangered Attwater's prairie-chicken (Tympanuchus cupido attwateri). We found that postrelease survival of captive-bred birds was related to alleles of the innate (Toll-like receptors, TLRs) and adaptive (major histocompatibility complex, MHC) immune systems, but not to genome-wide heterozygosity. Likewise, we found that the immune response at the time of release was related to TLR and MHC alleles, and not to genome-wide heterozygosity. Overall, this study demonstrates that immune genes may serve as important genetic markers when monitoring fitness in inbred populations and that in some populations specific functional genes may be better predictors of fitness than genome-wide heterozygosity.
Data from: Introgression threatens the survival of the critically endangered freshwater crayfish Cherax tenuimanus (Decapoda : Parastacidae) in the wild
Hybridization and genetic introgression following the introduction of exotic species can pose a significant threat to the survival of geographically restricted species. A remnant population of the critically endangered freshwater crayfish Cherax tenuimanus in the upper reaches of the Margaret River in southwestern Australia is under threat following the introduction and spread of its congener Cherax cainii. Here, we examine the extent of hybridization and introgression between the two species using twelve polymorphic microsatellite loci. Our study reveals there are three times more C. cainii than C. tenuimanus at our study site in the upper reaches of the Margaret River. There is also evidence of hybridization and introgression between C. tenuimanus and C. cainii at this site, with F1, F2 and backcrossed individuals identified. While interbreeding was confirmed in this study, our simulations suggest that the levels of introgression are much lower than would be expected under random mating, indicating partial reproductive barriers exist. Nevertheless, it is apparent that hybridization and introgression with C. cainii pose a serious threat to C. tenuimanus and their survival in the wild will require active adaptive management and continued genetic monitoring to evaluate management effectiveness.
Data from: Survival estimates strongly depend on capture-recapture designs in a disturbed environment inducing dispersal
Capture‐Recapture (CR) approaches are extensively used to estimate demographic parameters. Their robustness relies on the selection of suitable statistical models, but also on the sampling design and effort deployed in the field. In colonial or territorial species showing breeding site fidelity, recurrent local perturbations, such as predation‐induced breeding failure, may lead individuals to disperse locally or regionally. This might induce heterogeneity in individual CR histories and biases in demographic parameter estimates. Here, we assessed the effect of buffer areas and multi‐site designs on annual survival estimate accuracy and precision. First, using simulated data with and without a multi‐site design, we compared survival estimates for different scenarios involving contrasted local and regional dispersal. Then, using data from a local multi‐site long‐term monitoring survey carried out in a colony of black‐legged kittiwakes, we tested the homogeneity of individual CR histories and compared survival estimates from three datasets including one or several breeding cliffs with or without buffer areas. Results from simulations highlighted that a single‐site design consistently led to underestimated or less precise survival values compared to a multi‐site design. Similarly, a multi‐site design allowed detecting significant temporal trends while a single‐site one did not. In the field‐based study, adding buffer areas reduced individual heterogeneity, but all three datasets suffered from strong trap‐dependence possibly due to individual breeding success affecting nest‐site fidelity. Implementing a multi‐site design significantly improved the accuracy and precision of annual survival estimates, regardless of CR models applied. Adapting the spatial scale of sampling design to the local environment and species behaviour is essential to provide robust parameters of key relevance for population monitoring and management. We show that implementing buffer areas and/or multi‐site designs may be especially beneficial for long‐lived species facing regular local perturbation events leading to local dispersal.
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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.