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3,139 results for “fitting”
Data from: Oxidative status and fitness components in the Seychelles warbler
Oxidative damage, caused by reactive oxygen species during aerobic respiration, is thought to be an important mediator of life-history trade-offs. To mitigate oxidative damage, antioxidant defence mechanisms are deployed, often at the cost of resource allocation to other body functions. Both reduced resource allocation to body functions and direct oxidative damage may decrease individual fitness, through reducing survival and/or reproductive output. The oxidative costs of reproduction have gained much attention recently, but few studies have investigated the long-term consequences of oxidative damage on survival and (future) reproductive output under natural conditions. Using a wild population of the cooperatively breeding Seychelles warbler (Acrocephalus sechellensis), we tested the prediction that high levels of reactive oxygen species, or high antioxidant investments to avoid oxidative damage, have fitness consequences because they reduce survival and/or reproductive output. We found that individuals with higher circulating non-enzymatic antioxidant capacity had a lower probability of surviving until the next year. However, neither current reproductive output, nor future reproductive output in the surviving individuals, was associated with circulating non-enzymatic antioxidant capacity or oxidative damage. The negative relationship between antioxidant capacity and survival that we observed concurs with the findings of an extensive comparative study on birds, however the mechanisms underlying this association remain to be resolved.
Data from: Effects of apical meristem mining on plant fitness, architecture and flowering phenology in Cirsium altissimum (Asteracaeae)
Premise of the study: Interactions that limit lifetime seed production have the potential to limit plant population sizes and drive adaptation through natural selection. Effects of insect herbivory to apical meristems (apical meristem mining) on lifetime seed production rarely have been quantified experimentally. We studied Cirsium altissimum (tall thistle), whose meristems are mined by Platyptilia carduidactyla (artichoke plume moth), to determine how apical damage affects plant maternal fitness and evaluate both direct and indirect mechanisms underlying these effects. Methods: In restored prairie, apical mining was manipulated on tall thistles by applying insecticide, water, or no spray to apical meristems. We quantified effects on lifetime seed production, plant architecture, and flowering phenology. Seed germinability and seedling mass were evaluated in a greenhouse. Key results: Apical meristem miners decreased lifetime seed production of C. altissimum, but not seed quality. Higher mortality rates of damaged plants contributed to reduced seed production. Apical damage reduced plant height and increased the proportion of blooming flower heads in axial positions on branches. Apical damage delayed flowering and shortened flowering duration. Conclusions: Apical meristem mining reduced plant maternal fitness. The shift in the identity of blooming flower heads from terminal to axial positions contributed to this reduction because axial heads are less fecund. Shorter, meristem-mined plants may have been more susceptible to competition, and this susceptibility may explain their higher mortality rates. The kinds of changes in architecture and phenology that resulted from apical damage to C. altissimum have been shown to affect floral visitation in other plant species.
Inbreeding reduces fitness of seed beetles under thermal stress
<p>Human-induced environmental change can influence populations both at the global level through climatic warming and at the local level through habitat fragmentation. As populations become more isolated, they can suffer from high levels of inbreeding which contributes to a reduction in fitness, termed inbreeding depression. However, it is still unclear if this increase in homozygosity also results in a corresponding increase in sensitivity to stressful conditions, which could intensify the already detrimental effects of environmental warming. Here, in a fully factorial design, we assessed the life-long impact of increased inbreeding load and elevated temperature on key life history traits in the seed beetle, <i>Callosobruchus maculatus</i>. We found that beetles raised at higher temperatures had far reduced fitness and survival than beetles from control temperatures. Importantly, these negative effects were exacerbated in inbred beetles as a result of increased inbreeding load, with further detrimental effects manifesting on individual eclosion probability and lifetime reproductive success. These results reveal the harmful impact that increasing temperature and likelihood of habitat fragmentation due to anthropogenetic changes in environmental conditions could have on populations of organisms worldwide.</p>
Data for: Sex pheromone signal and stability covary with fitness
<p>If sexual signals are costly, covariance between signal expression and fitness is expected. Signal-fitness covariance is important, because it can contribute to the maintenance of genetic variation in signals that are under natural or sexual selection. Chemical signals, such as female sex pheromones in moths, have traditionally been assumed to be species-recognition signals, but their relationship with fitness is unclear. Here we test whether chemical, conspecific mate finding signals covary with fitness in the moth <i>Heliothis subflexa</i>. Additionally, as moth signals are synthesized <i>de novo</i> every night, the maintenance of the signal can be costly. Therefore, we also hypothesized that fitness covaries with signal stability (i.e., lack of temporal intra-individual variation). We measured among- and within-individual variation in pheromone characteristics as well as fecundity, fertility, and life span in two independent groups that differed in the time in between two pheromone samples. In both groups, we found fitness to be correlated with pheromone amount, composition, and stability, supporting both our hypotheses. This study is the first to report a correlation between fitness and sex pheromone composition in moths, supporting evidence of condition-dependence and highlighting how signal-fitness covariance may contribute to heritable variation in chemical signals both among and within individuals.</p>
Data from: Alteration of (frequency-dependent) fitness in time-shift experiments reveals cryptic co-evolution and uncoordinated stasis in a virtual Jurassic Park
Digital evolution is a computer-based instantiation of Darwinian evolution in which short self-replicating computer programs compete, mutate, and evolve. It is an excellent experimental platform for addressing topics in both short-term and long-term evolution, such as whether co-evolving multispecies communities are dominated more by biotic or abiotic factors, and whether evolutionary stasis affects performance as well as ecological profile. We evolved model communities with ecological interdependence among community members, which were subjected to two principal types of mass extinction: a pulse extinction that killed randomly, and a selective press extinction involving an alteration of the abiotic environment to which the communities had to adapt. These treatments were applied at two different strengths (Strong and Weak), along with unperturbed Control experiments. We performed several kinds of competition experiments using simplified versions of these communities to see whether long-term stability that was implied previously by ecological and phylogenetic metrics was also reflected in terms of performance, i.e. whether fitness was static over long periods of time. Results from Control and Weak treatment communities revealed almost completely transitive evolution, while Strong treatment communities showed higher incidences of intransitivity, with pre-treatment ecotypes often able to displace some of their post-recovery successors. However, pre-treatment carryovers more often had lower fitness in mixed communities than in their own fully native conditions. Replacement and invasion experiments pitting single ecotypes against pre-treatment reference communities showed that many of the invading ecotypes could measurably alter the fitnesses of one or more residents, usually with depressive effects, and that the strength of these effects increased over time even in the most stable communities. However, invaders taken from Strong treatment communities often had little to no effect on resident performance. While we detected periods of time when the fitness of a particular evolving ecotype remained static, this stasis was not permanent and was uncoordinated, never affecting an entire community at once. Our results lend support to the fitness-deterioration interpretation of the Red Queen hypothesis, and highlight community context-dependence in determining fitness, the shaping of communities by both biotic factors and abiotic forcing, and the illusory nature of evolutionary stasis. Our results also demonstrate the potential of digital evolution studies to illuminate many aspects of evolution in interacting multispecies communities.
One size does not fit all: Tuning eDNA protocols for high and low turbidity water sampling
<p class="abstract_para">Findings from eDNA metabarcoding are strongly influenced by experimental approach, yet the effect of pre‐PCR sample processing on taxon detection and estimates of biodiversity across different water types is still poorly resolved. To fill this data gap, we investigated the impact of sampling effort, extraction method, and filter pore size on DNA yield, PCR inhibition, and 16S rDNA metabarcoding results for fishes in water samples collected from inshore turbid‐ and offshore clear‐water environments. The turbid‐water samples had high concentrations of suspended organic and/or inorganic material and yielded ~3.2× more DNA and exhibited high levels of PCR inhibition compared with the low‐turbidity, clear‐water samples. Importantly, there were no striking differences in the results of our metabarcoding experiments based on extraction method or filter pore size. While a small number of unique species of relatively low read count were detected in all turbid‐water treatments, most species were consistently detected across samples. Results for the clear‐water samples were strikingly different, with low DNA yield, high levels of variation across replicates, and a high number of non‐overlapping species across treatments. These findings indicate a patchy distribution of eDNA in offshore environments, which means higher volumes of water (≥ 2 L per replicate) must be filtered in habitats where target DNA is likely to be sparse. In semi‐closed systems such as estuaries, higher concentrations of target DNA are expected, and we found that either a 1.0 or 3.0 µm filter pore size was sufficient to capture standing diversity, while decreasing the risk of clogging. For economical DNA extraction and inhibitor removal, we recommend a combination of Omega Bio‐tek E.Z.N.A Tissue DNA kit followed by a PCR inhibitor removal step using the Zymo Kit. Finally, we emphasize that pilot studies should be undertaken whenever sampling in a new environment to identify which protocol is most appropriate.</p>
Data from: Uncertainty in geographic estimates of performance and fitness
1. Thermal performance curves (TPCs) have become key tools for predicting geographic distributions of performance by ectotherms. Such TPC-based predictions, however, may be sensitive to errors arising from diverse sources. 2. We analyzed potential errors that arise from common choices faced by biologists integrating TPCs with climate data by constructing case studies focusing on experimental sets of TPCs and simulating geographic patterns of mean performance. We first analyzed differences in geographic patterns of performance derived from two pairs of commonly used TPCs. Mean performance differed most (up to 30%) in regions with relatively constant mean temperatures similar to those at which the TPCs diverged the most. 3. We also analyzed the effects of thermal history by comparing geographic estimates derived from (1) a broad TPC based on short-term measurements of insect larvae (Manduca sexta) with a history of exposure to thermal variation versus (2) a narrow TPC based on long-term measurements of larvae held at constant temperatures. Estimated mean performance diverged by up to 40%, and differences were magnified in simulated future climates. 4. Finally, to quantify geographic error arising from statistical error in fitted TPCs, we propose and illustrate a bootstrapping technique for establishing 95% prediction intervals on mean performance at each location (pixel). 5. Collectively, our analyses indicate that error arising from several underappreciated sources can significantly affect the mean performance values derived from TPCs, and we suggest that the magnitudes of these errors should be estimated routinely in future studies.
Drought has negative consequences on aphid fitness and plant vigour: insights from a meta-analysis
<p>1. Aphids are abundant in natural and managed vegetation, supporting a diverse community of organisms and causing damage to agricultural crops. Due to a changing climate, periods of drought are anticipated to increase, and the potential consequences of this for aphid-plant interactions are unclear.</p> <p>2. Using a meta-analysis and synthesis approach, we aimed to advance understanding of how increased drought incidence will affect this ecologically and economically important insect group, and to characterise any potential underlying mechanisms. We used qualitative and quantitative synthesis techniques to determine whether drought stress has a negative, positive, or null effect on aphid fitness and examined these effects in relation to 1) aphid biology, 2) geographical region, 3) host plant biology.</p> <p>3. Across all studies, aphid fitness is typically reduced under drought. Subgroup analysis detected no difference in relation to aphid biology, geographical region, or the aphid-plant combination, indicating the negative effect of drought on aphids is potentially universal. Furthermore, drought stress had a negative impact on plant vigour and increased plant concentrations of defensive chemicals, suggesting the observed response of aphids is associated with reduced plant vigour and increased chemical defence in drought-stressed plants.</p> <p>4. We propose a conceptual model to predict drought effects on aphid fitness in relation to plant vigour and defence to stimulate further research.</p>
Bayesian Analysis of Quasar Lightcurves with a Running Optimal Average: PyROA Fits to COSMOGRAIL Data
<p>Available as .zip files are the data/results of using PyROA to fit to the COSMOGRAIL gravitationally lensed quasar data. In each .zip are the individual lightcurves for each image as a .dat file, a plot of the results, a corner plot of the sampled parameters and three pickle objects. These are samples.obj, samples_flat.obj and X_t.obj.</p> <ul> <li>The first of these, samples.obj, contains all the MCMC samples in an array with shape (Nsamples, Nwalkers, Ndim).</li> <li>The second, samples_flat.obj, contains the flattened samples, where the burn-in has been removed and is an array with shape (Nsamples_final, Ndim), where Nsamples_final is the number of samples with burn-in removed. This was used to generate the corner plot and obtain the best fit parameters.</li> <li>The last, X_t.obj, contains the driving lightcurve, X(t), as described in Donnan et al. 2021. This is an array of the form [t, X, X_errs], where X is the value of the driving lightcurve at time, t, with errors, X_errs.</li> </ul> <p>For objects with more than two images, folders where other images were the reference are included. The sigma parameter in the corner plot is the extra error added to the flux data which is labelled as <em>s<sub>i</sub></em> in the paper. The original data file downloaded from the COSMOGRAIL website is also included as a csv file.</p>
Data for manuscript:"Chronic exposure to sublethal levels of pesticides has significant effects on fitness and morphology in the ant, Cardiocondyla obscurior"
<p>All data used in analysis for manuscript "<strong>Chronic exposure to sublethal levels of pesticides has significant effects on fitness and morphology in the ant, <em>Cardiocondyla obscurior"</em></strong></p> <p> </p> <p> </p>
Fitness consequences of hybridization in a predominantly selfing species: insights into the role of dominance and epistatic incompatibilities
<p>Studying the consequences of hybridization on plant performance is insightful to understand the adaptive potential of populations, notably at local scales. Due to reduced effective recombination, predominantly selfing species are organized in highly homozygous multi-locus-genotypes (or lines) that accumulate genetic differentiation both among- and within-populations. This high level of homozygosity facilitates the dissection of the genetic basis of hybrid performance in highly selfing species, which gives insights into the mechanisms of reproductive isolation between lines. Here, we explored the fitness consequences of hybridization events between natural inbred lines of the predominantly selfing species Medicago truncatula, at both within- and among-populations scales. We found that hybridization has opposite effects pending on studied fitness proxies, with dry mass showing heterosis, and seed production showing outbreeding depression. Although we found significant patterns of heterosis and outbreeding depression, they did not differ significantly for within- compared to among-population crosses. Family-based analyses allowed us to determine that hybrid differentiation was mostly due to dominance and epistasis. Dominance and/or dominant epistatic interactions increased dry mass, while decreasing seed production, and recessive epistatic interactions mostly had a positive effect on both fitness proxies. Our results illustrate how genetic incompatibilities can accumulate at a very local scale among multi-locus-genotypes, and how non-additive genetic effects contributes to heterosis and outbreeding depression.</p>
Long-term changes in occurrence, relative abundance, and reproductive fitness of bat species in relation to arrival of White-nose Syndrome in West Virginia, USA
<p>White-nose syndrome (WNS) is a disease caused by the fungus Pseudogymnoascus destructans which has resulted in the deaths of millions of bats across eastern North America. To date, hibernacula counts have been the predominant means of tracking the spread and impact of this disease on bat populations. However, an understanding of the impacts of WNS on demographic parameters outside the winter season is critical to conservation and recovery of bat populations impacted by this disease. We used long-term monitoring data to examine WNS-related impacts to summer populations in West Virginia, where WNS has been documented since 2009. Using capture data from 290 mist-net sites surveyed from 2003–2019 on the Monongahela National Forest, we estimated temporal patterns in presence and relative abundance for each bat species. For species that exhibited a population-level response to WNS, we investigated post-WNS changes in adult female reproductive state and body mass. Myotis lucifugus (little brown bat), M. septentrionalis (northern long-eared bat), and Perimyotis subflavus (tri-colored bat) all showed significant decreases in presence and relative abundance during and following the introduction of WNS, while Eptesicus fuscus (big brown bat) and Lasiurus borealis (eastern red bat) responded positively during the WNS invasion. Probability of being reproductively active was not significantly different for any species, though a shift to earlier reproduction was estimated for E. fuscus and M. septentrionalis. For some species, body mass appeared to be influenced by the WNS invasion, but the response differed by species and reproductive state. Results suggest that continued long-term monitoring studies, additional research into impacts of this disease on the fitness of WNS survivors, and a focus on providing optimal non-wintering habitat may be valuable strategies for assessing and promoting recovery of WNS-affected bat populations.</p>
Figure 4 in Horn scaling relationships in three species of Bledius Leach 1819 (Insecta: Coleoptera: Staphylinidae) show no indication of fitting non-linear allometric models
Figure 4. Scaling relationship between log pronotum width and log horn length in Bledius tricornis (Herbst, 1784). The slope is 1.166 (SE = 0.093) and the linear model has an R2 of 0.78.
Figure 3 in Horn scaling relationships in three species of Bledius Leach 1819 (Insecta: Coleoptera: Staphylinidae) show no indication of fitting non-linear allometric models
Figure 3. Scaling relationship between log pronotum width and log horn length in Bledius frisius Lohse, 1978. The slope is 1.816 (SE = 0.136) and the linear model has an R2 of 0.78.
Figure 1 in Horn scaling relationships in three species of Bledius Leach 1819 (Insecta: Coleoptera: Staphylinidae) show no indication of fitting non-linear allometric models
Figure 1. (a) Bledius spectabilis Kraatz, 1857 schematic diagram of pronotal measurements taken and habitus. (b) Bledius spectabilis at Chesil Fleet, Dorset, UK (photograph by Steve Trewhella). HL = horn length; PW = pronotum width.
Figure 2 in Horn scaling relationships in three species of Bledius Leach 1819 (Insecta: Coleoptera: Staphylinidae) show no indication of fitting non-linear allometric models
Figure 2. Scaling relationship between log pronotum width and log horn length in Bledius spectabilis Kraatz, 1857. The slope is 1.447 (SE = 0.096) and the linear model has an R2 of 0.68.
Ecomorphological relationships and invasion history of non-native terrestrial bird species on O'ahu, Hawai'i suggests ecological fitting during community assembly
The widespread introduction of species has created novel communities in many areas of the world. Since introduced species tend to have generalized ecologies and often lack shared evolutionary history with other species in their communities, it would be expected that the relationship between form and function (i.e. ecomorphology) may change in novel communities. We tested this expectation in a subset of the novel bird community on O'ahu, Hawai'i. By relating foraging behavior observations to morphology obtained from live birds at four sites across the island, we found many relationships between species' morphology and foraging ecology that mirrored relationships found in the literature for native dominated bird communities. Both movement and certain foraging behaviors were related to a species' tarsus to wing ratio. Further, bill morphology was related to gleaning, frugivory, and flycatching behaviors. The commonness of significant ecomorphological relationships suggests that, within O'ahu's novel bird community, form is strongly related to function. We hypothesize that ecological fitting likely played a major role in the assembly of this novel community conserving the relationships between form and function found in many other bird communities. To further support this hypothesis, we used niche data from EltonTraits 1.0 to determine if the establishment of bird species introduced to O'ahu was related to the distinctiveness of their ecological niche from the incumbent community. Introduced species were more likely to establish on O'ahu if their diets were less similar to the bird species already present on the island. Our results support the idea that ecological fitting is an important mechanism in shaping ecological communities, especially in the Anthropocene, thereby influencing novel community assembly and functioning.
Data from: Integrating fitness components reveals that survival costs outweigh other benefits and costs of group living in two closely related species
Group living can be beneficial when individuals reproduce or survive better in the presence of others, but simultaneously there might be costs due to competition for resources. Positive and negative effects on various fitness components might thus counteract each other, so integration is essential to determine their overall effect. Here, we investigated how an integrated fitness measure (reproductive values; RV) based on six fitness components varied with group size among group members in cooperatively-breeding red-winged and superb fairy-wrens (Malurus elegans and M. cyaneus). Despite life historie differences between the species, patterns of RVs were similar, suggesting that the same behavioural mechanisms are important. Group living reduced RVs for dominant males, but for other group members this was only true in large groups. Decomposition analyses showed that our integrated fitness proxy was most strongly affected by group size effects on survival, which was amplified through carry-over effects between years. Our study shows that integrative consideration of fitness components and subsequent decomposition analysis provide much needed insights into the key behavioural mechanisms shaping the costs and benefits of group living. Such attribution is crucial if we are to synthesize the relative importance of the myriad group size costs and benefits currently reported in the literature.
Context dependent fitness costs of reproduction despite stable body mass costs in an Arctic herbivore
<p class="western">1. The cost of reproduction on demographic rates is often assumed to operate through changing body condition. Several studies have found that reproduction depresses body mass more if the current conditions are severe, such as high population densities or adverse weather, than under benign environmental conditions. However, few studies have investigated the association between the fitness and body mass costs of reproduction.</p> <p class="western">2. Using 25 years of individual-based capture-recapture data from Svalbard reindeer (<i>Rangifer tarandus platyrhynchus</i>), we built a novel Bayesian state-space model that jointly estimated inter-annual change in mass, annual reproductive success, and survival, while accounting for incomplete observations. The model allowed us to partition the differential effects of intrinsic and extrinsic factors on both non-reproductive mass change and the body mass cost of reproduction and to quantify their consequences on demographic rates.</p> <p class="western">3. Contrary to our expectation, the body mass cost of reproduction (mean = 5.8 kg) varied little between years (CV = 0.08) whereas the between-year variation in body mass changes, that were independent of the previous year's reproductive state, varied substantially (CV = 0.4) in relation to autumn temperature and the amount of rain-on-snow in winter. This mass loss led to a cost of reproduction on the next reproduction, which was amplified by the same environmental covariates, from a 10% reduction in reproductive success in benign years, to a 50% reduction in harsh years. The reproductive mass loss also resulted in a small reduction in survival.</p> <p class="western">4. Our results show how demographic costs of reproduction, driven by inter-annual fluctuations in individual body condition, result from the balance between body mass costs of reproduction and body mass changes that are independent of previous reproductive state. We illustrate how a strong context dependent fitness cost of reproduction can occur, despite a relatively fixed body mass cost of reproduction. This suggests that female reindeer display a very conservative energy allocation strategy, either aborting their reproductive attempt at an early stage or weaning at a relatively constant cost. Such a strategy might be common in species living in a highly stochastic food limited environment.</p>
Data for: Time at risk: Individual spatial behaviour drives effectiveness of marine protected areas and fitness
<p>The effectiveness of Marine Protected Areas (MPAs) depends on the mobility of the populations that are the target of protection, with sedentary species likely to spend more time under protection even within small MPAs. However, little is understood about how individual variation in mobility may influence the risk of crossing an MPA border, as well as the fitness costs associated with being exposed to spillover fisheries. Here we investigated the repeatability of spatial behaviour, its role in determining the probability of being at risk (i.e. exposed to the fishery) and the fitness consequences for the individuals. We acoustically tracked the movements and fate of 282 individuals of three fish species during 8 years in a southern Norwegian fjord. We found that for individuals with a home range centroid inside the MPA, the probability of being at risk outside the MPA increased rapidly with reduced distance from the home range centroid to MPA borders, particularly for individuals having larger and more dispersed home ranges. We also detected that the seasonal expansions of the home range are associated with increased time at risk. Last, we show that individuals spending more time at risk were also more likely to be harvested by the fishery operating outside the MPA. Our study provides clear links between individual fish behaviour, fisheries-induced selection, and the effectiveness of protected areas. These links highlight the importance of intraspecific trait variation for understanding the spatial dynamics of populations and emphasize the need to consider individual behaviour when designing and implementing MPAs.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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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.