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3,139 results for “fits”
Data for: Multi-generational fitness effects of natural immigration indicate strong heterosis and epistatic breakdown in a wild bird population
<p><span>The fitness of immigrants and their descendants produced within recipient populations fundamentally underpins the genetic </span><span>and population dynamic</span><span> consequences of immigration. </span><span>I</span><span>mmigrants can </span><span>in principle </span><span>induce contrasting genetic effects on fitness across generations, reflecting multi-faceted additive, dominance, and epistatic effects. Y</span><span>et, full multi-generational and sex-specific fitness effects of regular immigration have not been quantified within naturally structured systems, precluding inference on underlying genetic architectures </span><span>and population outcomes</span><span>. We used four decades of song sparrow </span><span>(<em>Melospiza melodia</em>)</span> <span>life-history and pedigree data to quantify fitness of natural immigrants, natives, and their F1, F2, and backcross descendants, and test for evidence of non-additive genetic effects. Values of key fitness components (including adult lifetime reproductive success and zygote survival) of F1 offspring of immigrant-native matings substantially exceeded their parent mean, indicating strong heterosis. Meanwhile, F2 offspring of F1-F1 matings had notably low values, indicating surprisingly strong epistatic breakdown. Further, magnitudes of effects varied among fitness components, and</span> <span>differed between female</span><span>s</span><span> and male</span><span>s</span><span> descendants. These results demonstrate that strong non-additive genetic effects on fitness can arise within </span><span>weakly </span><span>structured </span><span>and fragmented </span><span>populations </span><span>experiencing </span><span>frequent </span><span>natural </span><span>immigration. </span><span>Such effects will substantially affect the net </span><span>degree of effective gene flow and resulting local genetic introgression and adaptation.</span></p>
Fitness benefits of alternated chick provisioning in cooperatively breeding carrion crows
<p>In most bird species, parents raise offspring cooperatively. In some cases, this cooperation extends to helpers-at-the-nest who assist the breeders with a range of tasks. While cooperative food provisioning might merely arise incidentally, as a result of the efforts of carers that act independently from each other, recent studies suggest that birds may coordinate by taking turns in visiting the nest. However, evidence that such coordination emerges because individuals actively respond to each other's behaviour is controversial, and the potential benefits of carers' alternation remain unknown. We addressed this knowledge gap by analysing a multi-year dataset for cooperatively breeding carrion crows, <em>Corvus corone</em>, comprising 8,693 nest visits across 50 groups. Our results reveal that turn taking does occur in this species and that all group members, regardless of their sex and social role (breeder/helper), tend to alternate at the nest with other carers rather than to make repeat visits. Importantly, we found that the body mass of nestlings increased significantly with the degree of carers' alternation, possibly because well-coordinated groups provided food at more regular intervals. Using earlier monitoring data, the observed increase in body mass is predicted to substantially boost post-fledging survival rates. Our analyses demonstrate that alternation in nestling provisioning has measurable fitness benefits in this study system. This raises the possibility that cooperatively breeding carrion crows, as well as other bird species with similarly coordinated brood provisioning, exhibit specialized behavioural strategies that enable effective alternation.</p>
Data associated to the paper "Phase diagram detection via Gaussian fitting of number probability distribution"
<p>We investigate the number probability density function that characterizes subportions of a quantum many-body system with globally conserved number of particles. We put forward a linear fitting protocol capable of mapping out the ground-state phase diagram of the rich one-dimensional extended Bose-Hubbard model: The results are quantitatively comparable with more sophisticated traditional and machine learning techniques. We argue that the studied quantity should be considered among the most informative bipartite properties, being moreover readily accessible in atomic gases experiments.<br><br>The dataset contains the entanglement spectra of several configurations of the extended Bose-Hubbard model ground state for different systems' sizes. </p>
Consistent traffic noise impacts few fitness-related traits in a field cricket
<p>Anthropogenic habitat change is occurring rapidly, and organisms can respond through within-generation responses that improve the match between their phenotype and the novel conditions they encounter. But, plastic responses can be adaptive or maladaptive and are most likely to be adaptive only when contemporary conditions reasonably mimic something experienced historically to which a response has already evolved. Noise pollution is a ubiquitous anthropogenic stressor that accompanies expanding urbanization. We tested whether the amplitude of traffic noise influences a suite of fitness-related traits (e.g. survival, life history, reproductive investment, immunity) and whether that depends on the life stage at which the noise is experienced (juvenile or adult). Our treatments mimic the conditions experienced by animals living in urban roadside environments with variable vehicle types, but continuous movement of traffic. We used the Pacific field cricket, an acoustically communicating insect that was previously shown to experience some negative behavioral and life history responses to very loud, variable traffic noise, as a model system. </p>
Toward greater realism in inclusive fitness models: the case of caste fate conflict in insect societies
<p>In the field of social evolution, inclusive fitness theory has been successful in making a wide range of qualitative predictions on expected patterns of cooperation and conflict. Nevertheless, outside of sex ratio theory, inclusive fitness models that make accurate quantitative predictions remain relatively rare. Past models dealing with caste fate conflict in insect societies, for example, successfully predicted that if female larvae can control their own caste fate, an excess should opt to selfishly develop as queens. Available models, however, were unable to accurately predict levels of queen production observed in <em>Melipona</em> bees – a genus of stingless bees where caste is self-determined – as empirically observed levels of queen production are ca. two times lower than the theoretically predicted ones. Here, we show that this discrepancy can be resolved by explicitly deriving the colony-level cost of queen overproduction from a dynamic model of colony growth, requiring incorporation of parameters of colony growth and demography, such as the per-capita rate at which new brood cells are built and provisioned, the percentage of the queen's eggs that are female, costs linked with worker reproduction and worker mortality. Our revised model predicts queen overproduction to more severely impact colony productivity, resulting in an evolutionarily stable strategy (ESS) that is ca. half that of the original model, and is shown to accurately predict actual levels of queen overproduction observed in different <em>Melipona</em> species. Altogether, this shows how inclusive fitness models can provide accurate quantitative predictions, provided that costs and benefits are modelled in sufficient detail and are measured precisely.</p>
Main model fits and substitution rate predictions for: A quantitative genetic model of background selection in humans
<p>Across the human genome, there are large-scale fluctuations in genetic diversity caused by the indirect effects of selection. This can be thought of as a "linked selection signal" that reflects the impact of selection varying according to the placement of functional regions and recombination rates along the genome. Previous work has shown that negative selection against the steady influx of new deleterious mutations into conserved regions is the predominant mode of selection in humans. However, the theoretic model that underpins these results, classic Background Selection theory, is only applicable when new mutations are so deleterious that they cannot fix in the population. Here, we develop a statistical method based on a quantitative genetics view of the linked selection, which models the effects of weak draft created according to how polygenic additive fitness variance is distributed along the genome. We use a recent model that jointly predicts the equilibrium fitness variance and substitution rates due to both strong and weakly deleterious mutations, we estimate the distribution of fitness effects (DFE) and mutation rate across three human populations. While our model can accommodate weaker selection, we initially find evidence across three human populations of very strong selection against deleterious mutations consistent with previous work. However, the corollary predicted substitution rates for conserved regions are unreasonably low, and in disagreement with observed rates. We hypothesize this could be due to selected sites experiencing a further diminished population size due to selective interference. When we account for this in our method, we find evidence of weakly deleterious mutations in conserved regions which brings the predicted substitution rate into agreement with observations. However, these models lead to implausibly large mutation rate estimates. Overall, while our model of the genomic linked selection signal brings us a step towards uniting population and quantitative genetic selection models with the substitution process, our work suggests considerable uncertainty remains about the processes generating fitness variance in humans.</p>
Complex models of sequence evolution improve fit, but not gene tree discordance, for tetrapod mitogenomes
<p>Variation in gene tree estimates is widely observed in empirical phylogenomic data and is often assumed to be the result of biological processes. However, a recent study using tetrapod mitochondrial genomes to control for biological sources of variation due to their haploid, uniparentally inherited, and non-recombining nature found that levels of discordance among mitochondrial gene trees were comparable to those found in studies that assume only biological sources of variation. Additionally, they found that several of the models of sequence evolution chosen to infer gene trees were doing an inadequate job of fitting the sequence data. These results indicated that significant amounts of gene tree discordance in empirical data may be due to poor fit of sequence evolution models and that more complex and biologically realistic models may be needed. To test how the fit of sequence evolution models relates to gene tree discordance, we analyzed the same mitochondrial datasets as the previous study using two additional, more complex models of sequence evolution that each model a different biologically realistic aspect of the evolutionary process: a covarion model to incorporate heterotachy, and a model partitioned model to incorporate variable evolutionary patterns by codon position. Our results show that both additional models fit the data better than the models used in the previous study, with the covarion being consistently and strongly preferred as tree size increases. However, even these more preferred models still inferred highly discordant mitochondrial gene trees, thus deepening the mystery around what we label the "Mito-Phylo Paradox" and leading us to ask whether the observed variation could be biological after all.</p>
Code from: Fitness as the organismal performance measure guiding adaptive evolution
<p>A long-standing problem in evolutionary theory is to clarify in what sense (if any) natural selection cumulatively improves the design of organisms. Various concepts, such as fitness and inclusive fitness, have been proposed to resolve this problem. In addition, there have been attempts to replace the original problem with more tractable questions such as whether a given gene or trait is favoured by selection. Here we ask what theoretical properties the concept of fitness should possess to encapsulate the improvement criterion required to talk meaningfully about adaptive evolution. We argue that natural selection tends to shape phenotypes based on the causal properties of individuals and that this tendency is, therefore, best captured by a fitness concept that focuses on these properties. We highlight a fitness concept that meets this role under broad conditions but requires adjustments in our conceptual understanding of adaptive evolution. These adjustments combine elements of Dawkinsian gene selectionism and Egbert Leigh's "Parliament of Genes".</p>
When does antimicrobial resistance increase bacterial fitness? Effects of dosing, social interactions and frequency dependence on the benefits of AmpC β-lactamases in broth, biofilms and a gut infection model.
<p><span>One of the longstanding puzzles of antimicrobial resistance is why the frequency of resistance persists at intermediate levels.<span> </span>Theoretical explanations for the lack of fixation of resistance include cryptic costs of resistance or negative frequency-dependence but are seldom explored experimentally. <span> </span><em>β</em>-lactamases, which detoxify penicillin-related antibiotics, have well-characterized frequency-dependent dynamics driven by cheating and cooperation.<span> </span>However, bacterial physiology determines whether <em>β</em>-lactamases are cooperative and we know little about the sociality or fitness of <em>β</em>-lactamase producers in infections.<span> </span>Moreover, media-based experiments constrain how we measure fitness, and ignore important parameters such as infectivity and transmission among hosts.<span> </span>Here, we investigated the fitness effects of broad-spectrum AmpC <em>β</em>-lactamases in <em>Enterobacter cloacae</em> in broth, biofilms and gut infections in a model insect. <span> </span>We quantified frequency- and dose-dependent fitness using cefotaxime, a third-generation cephalosporin.<span> </span>We predicted that infection dynamics would be similar to those observed in biofilms, with social protection extending over a wide dose range.<span> </span>We found evidence for the sociality of <em>β</em>-lactamases in all contexts with negative frequency-dependent selection ensuring the persistence of wild-type bacteria although cooperation was less prevalent in biofilms, contrary to predictions.<span> </span>While competitive fitness in gut infections and broth had similar dynamics, incorporating infectivity into measurements of fitness in infections<em> </em>significantly affected conclusions. <span> </span>Resistant bacteria had reduced infectivity which limited the fitness benefits of resistance to infections challenged with low antibiotic doses and having low initial frequencies of resistance. <span> </span>The fitness of resistant bacteria in more physiologically tolerant states (in biofilms, in infections) could be constrained by the presence of wild-type bacteria, high antibiotic doses and limited availability of <em>β</em>-lactamases.<span> </span>One conclusion is that increased tolerance of <em>β</em> -lactams does not necessarily increase selection pressure for resistance.<span> </span>Overall, both cryptic fitness costs and frequency-dependence curtailed the fitness benefits of resistance in this study.<span> </span></span></p> <p><span> </span></p>
Concrete habitat: Impervious surface in nest vicinity is associated with avian fitness decline in two urban adapters
<p>The conversion of natural habitats to impervious surfaces in cities affects biotic and abiotic attributes of urban ecosystems. Detailed information on the gradual influence of impervious surfaces on reproductive success, however, is lacking. Using five years of nestbox-breeding great tit and blue tit breeding data collected across various habitat types within and outside a Central-Eastern European capital city, we quantified the impact of impervious surfaces on avian reproductive success. Impervious surfaces strongly and negatively covaried with the number of fledged young in both species: a 50% increase in impervious surface resulted in 2.93 (95% CI: -4.27; -1.58) fewer blue tit offspring fledging the nest, and 3.51 (95% CI: -4.79; -2.23) fewer great tit offspring fledging the nest, thus halving the reproductive output of two widespread urban species. These results provide benchmark values of avian productivity for ecologists and urban policy makers, and for the management of urban areas.</p>
Operating diagram of larvae hatching module, this installation was used to determine the optimum larvae load during the rearing process and provided additional space for rearing several thousand larvae. It consists of nine 20-litre tanks with a glass panel along the front. They are fitted with an inlet supplying filtrated water at a rate of 100 l/h and an individual air inlet. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of larvae hatching module, this installation was used to determine the optimum larvae load during the rearing process and provided additional space for rearing several thousand larvae. It consists of nine 20-litre tanks with a glass panel along the front. They are fitted with an inlet supplying filtrated water at a rate of 100 l/h and an individual air inlet.
Bottom of DR1 tank, the sides of the module are fitted with glass panels which allow natural light from a window to enter the tank, and the observer to view the behaviour of the broodstock. This device ensures easy viewing and checking of the broodstock, facilitates management of feeding and allows effective monitoring of reproduction. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Bottom of DR1 tank, the sides of the module are fitted with glass panels which allow natural light from a window to enter the tank, and the observer to view the behaviour of the broodstock. This device ensures easy viewing and checking of the broodstock, facilitates management of feeding and allows effective monitoring of reproduction.
Spectral model fitting for all 4XMM-DR11 for all sources
<p>Fitting products for all sources: this deliverable includes fits with a simple model (absorbed power law) to the pipeline count rates from emldetect to all detections in the 4XMM DR11 catalogue.</p>
F I G U R E 2 Fitted logistic curves with 95 in Circadian and seasonal flight activity differences between the sexes of the biocontrol agent Eadya daenerys (Hymenoptera: Braconidae) and the impact of host size on adult emergence
F I G U R E 2 Fitted logistic curves with 95% confidence intervals for the effect of Paropsisterna agricola beetle prepupal weight (mg) for three post-beetle prepupal outcomes (dead beetle prepupa, beetle or E. daenerys wasp).
Pre- and postnatal noise directly impairs avian development, with fitness consequences
<p><span>Noise pollution is expanding at an unprecedented rate and </span><span>is</span><span> increasingly associated with impaired reproduction and development across taxa. However, whether noise soundwaves are intrinsically harmful for developing young – or merely disturb parents – and the fitness consequences of early exposure </span><span>remains</span><span> unknown. Here, </span><span>by only manipulating the offspring</span><span>, we </span><span>show</span><span> that sole exposure to noise in early-life </span><span>in zebra finches </span><span>has fitness consequences, </span><span>and causes</span><span> embryonic death during exposure. </span><span>Exposure to </span><span>pre- and postnatal traffic noise cumulatively impaired nestling growth and physiology, and </span><span>aggravated telomere shortening </span><span>across life stages </span><span>until adulthood</span><span>. Consistent with a long-term somatic impact, early-life noise exposure, especially prenatally, decreased individual offspring production throughout adulthood. Our findings </span><span>suggest the </span><span>effects of noise pollution </span><span>are more pervasive </span><span>than previously realized.</span></p>
Data for fitting a statistical global burned area model for seamless integration into Dynamic Global Vegetation Models
<p>The dataset is a large R data.table object saved in RDS format. It contains global, monthly data spanning the period from 2002 to 2018, with a 0.5 degrees spatial resolution. The dataset is utilized to develop and validate statistical models for predicting global burnt areas resulting from wildfires.</p>
Demonstrations for imitation learning for the paper "Fitting parameters of linear dynamical systems to regularize forcing terms in Dynamical Movement Primitives"
<p>Demonstrations for the coathanger experiment in the paper "Fitting parameters of linear dynamical systems to regularize forcing terms in Dynamical Movement Primitives". https://elib.dlr.de/205110/</p>
Structural equation modeling reveals determinants of fitness in a cooperatively breeding bird
<p>Even in well-studied organisms, it is often challenging to uncover the social and environmental determinants of fitness. Typically, fitness is determined by a variety of factors that act in concert, thus forming complex networks of causal relationships. Moreover, even strong correlations between social and environmental conditions and fitness components may not be indicative of direct causal links, as the measured variables may be driven by unmeasured (or unmeasurable) causal factors. Standard statistical approaches, like multiple regression analyses, are not suited for disentangling such complex causal relationships. Here, we apply structural equation modeling (SEM), a technique that is specifically designed to reveal causal relationships between variables, and which also allows to include hypothetical causal factors. Therefore, SEM seems ideally suited for comparing alternative hypotheses on how fitness differences arise from differences in social and environmental factors. We apply SEM to a rich data set collected in a long-term study on the Seychelles warbler (Acrocephalus seychellensis), a bird species with facultatively cooperative breeding and a high rate of extra-group paternity. Our analysis reveals that the presence of helpers has a positive effect on the reproductive output of both female and male breeders. In contrast, per capita food availability does not affect reproductive output. Our analysis does not confirm earlier suggestions on other species that the presence of helpers has a negative effect on the reproductive output of male breeders. As such, both female and male breeders should tolerate helpers in their territories, irrespective of food availability.</p>
Are terrestrial biosphere models fit for simulating the global land carbon sink?
<p>This repository contains the data and code required for reproducing the results presented in the paper "Are terrestrial biosphere models fit for simulating the global land carbon sink?" by Seiler et al., 2021. The study evaluates an ensemble of terrestrial biosphere models (<a href="https://sites.exeter.ac.uk/trendy/">TRENDY</a>; v9; S3 simulations) against a wide range of reference data using the Automated Model Benchmarking R package (AMBER; version 1.1.1). The only requirement for reproducing our results is access to a Linux machine with <a href="https://docs.conda.io">conda</a>, an open-source package management system and environment management system, installed. Follow the steps described in the <em>readme</em> file to install AMBER and run the analysis. The repository also contains all output produced by our analysis. </p>
Impact of heat stress on the fitness outcomes of symbiotic infection in aphids: a meta-analysis
<p>This is the dataset for the article "<em><strong>Impact of heat stress on the fitness outcomes of symbiotic infection in aphids: a meta-analysis</strong></em>". </p> <p>Beneficial symbiosis shape their host eco-evolutionary responses. Here we show how the responses of insect-microbe associations may be modulated by rising temperatures. The outcome of the symbiotic association is therefore temperature-dependent, but also trait-dependent. We show the importance of better understanding the cost-benefits balance of insect-microbe associations faced with climate change.</p>
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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.