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3,139 results for “fits”
FLIGHTED: Inferring Fitness Landscapes from Noisy High-Throughput Experimental Data (Part 2)
<p>Data for FLIGHTED (Inferring Fitness Landscapes from Noisy High-Throughput Experimental Data). This data contains the TEV protease landscape and models trained on it. All other FLIGHTED data is in the other Zenodo repository (refer to the paper for details).</p> <p>The data is arranged in the following folders:</p> <ol> <li>TEV_Landscape: contains the TEV landscape (in flighted_fitnesses.csv) and splits thereof in Splits/. The main files for model training are flighted_fitnesses.csv and the files labeled one_vs_rest, two_vs_rest, and three_vs_rest. The files labeled three_vs_rest_control within Splits/ and the read count CSV files refer to further information about the read count in the landscape; see the Supplement for details. The dictionary files are the original raw data prior to processing with FLIGHTED.</li> <li>TEV_Models: contains models trained on the TEV landscape under the various splits. Each model folder contains hyperparameters, training history, and predictions on the test set which can be used to evaluate model performance. Raw model parameters are not provided for fine-tuned models due to size; contact us if you want them. The control_run/ refers to the run described in the supplement on just read counts.</li> </ol>
Reduced fitness under abiotic stress in F1 hybrids of Antirrhinum majus subspecies with divergent flower colors
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Data for: Living fast, dying young: anthropogenic habitat modification influences the fitness and life history traits of a cooperative breeder
<p>Datasets and scripts for the study: Living fast, dying young: anthropogenic habitat modification influences the fitness and life history traits of a cooperative breeder</p>
Database used to analyse body composition and physical fitness in children
<p>Descriptive characteristics for the entire sample and by age group, as well as differences between the<br>two age groups</p>
10 best fits for the dispersal speed distribution
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10 best fits of dispersal speed distribution for the split datasets
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Sequence and functional analyses of native plasmids from plant pathogenic Gammaproteobacteria: comparative genomics, conjugative mobilization and fitness effects
<p>These data tables are part of the Supplementary Material for Chapter I of the thesis titled <em>"Sequence and Functional Analyses of Native Plasmids from Plant-Pathogenic Gammaproteobacteria: Comparative Genomics, Conjugative Mobilization, and Fitness Effects."</em></p>
Supplementary Data: A global fit of non-relativistic effective dark matter operators including solar neutrinos
<p>The files within contain the data from <a href="https://gambitbsm.org/">GAMBIT</a> scans and the scripts to recreate the plots in Avis Kozar et al. "A global fit of non-relativistic effective dark matter operators including solar neutrinos" using <a href="https://www.python.org/">Python</a> and <a href="https://github.com/GambitBSM/pippi">pippi</a>.</p>
Density-by-diet interactions during larval development shape adult life-history trait expression and fitness in a polyphagous fly
<p><span>Habitat quality early in life determines individual fitness, with possible long-term evolutionary effects on groups and populations. In holometabolous insects, larval ecology plays a major role in determining the expression of traits in adulthood, but how ecological conditions during larval stage interact to shape adult life-history and fitness, particularly in non-model organisms, remains subject to scrutiny. Consequently, our knowledge of the interactive effects of ecological factors on insect development is limited. Here, using the polyphagous fly <i>Bactrocera tryoni</i>, we conducted a fully-factorial design where we manipulated larval density and larval diet (protein-rich, standard, and sugar-rich) to gain insights into how these ecological factors interact to modulate adult fitness. As expected, a protein-rich diet resulted in faster larval development, heavier and leaner adults that were more fecund compared with standard and sugar-rich diets, irrespective of larval density. Females from the protein-rich larval diet had overall higher reproductive rate (i.e., eggs per day) than females from other diets, and reproductive rate decreased linearly with density for females from the protein-rich but non-linearly for females from the standard and sugar-rich diets over time. Surprisingly, adult lipid reserve increased with larval density for adults from the sugar-rich diet (as opposed to decreasing, as in other diets), possibly due to a stress-response to an extremely adverse condition during development (i.e., high intraspecific competition and poor nutrition). Together, our results provide insights into how ecological factors early in life interact and shape the fate of individuals through life-stages in holometabolous insects. </span></p>
Relative traveltimes and amplitude ratios of seismic triplications for the four earthquakes in the southwestern Siberia and resulting best-fit LVL velocity models
<p>For details about the data, please see the published paper titled "A partial molten low-velocity layer atop the mantle transition zone beneath the western Junggar: implication for the formation of subduction-induced sub-slab mantle plume" in the journal G-Cubed.</p>
Data from: Proximity to parasites reduces host fitness independent of infection in a Drosophila-Macrocheles system
<p>We assayed the longevity and reproductive output of Drosophila nigrospiracula exposed or not exposed to ectoparasitic Macrocheles subbadius accross a mesh barrier. As such we measured the non-consumptive effects (extending the ecology of fear to host-parasite systems) of an ectoparasite on host fecundity and survival. We found that exposure to mites, without infection, caused flies to live shorter lives and produce fewer offspring.</p>
Discussions of the not-so-fit: how ableism limits diverse thought and investigative potential in evolutionary biology
<p>Evolutionary biology and many of its foundational concepts are grounded in a history of ableism and eugenics. The field has not made a concerted effort to divest our concepts and investigative tools from this fraught history and as a result, an ableist investigative lens has persisted into present-day evolutionary research, limiting the scope of research and harming the ability to communicate and synthesize knowledge about evolutionary processes. This failure to divest from our eugenicist and ableist history has harmed progress in evolutionary biology and allowed principles from evolutionary biology to continue to be weaponized against marginalized communities in the modern-day. To rectify this problem, scholars in evolutionary research must come to terms with how the history of the field has influenced their investigations and work to establish a new framework for defining and investigating concepts, such as selection and fitness.</p>
Transgenerational plasticity of dispersal-related traits in a ciliate: genotype-dependency and fitness consequences
<p>The data presented here are those used in the paper : CAYUELA H., JACOB S., SCHTICKZELLE N., VERDONCK R., PHILIPPE H., LAPORTE M., HUET M., BERNATCHEZ L., LEGRAND D. Transgenerational plasticity of dispersal-related traits in a ciliate: genotype-dependency and fitness consequences. Oikos. DOI: 10.1111/oik.08846</p> <p>Phenotypic plasticity, the ability of one genotype to produce different phenotypes in different environments, plays a central role in species' response to environmental changes. Transgenerational plasticity (TGP) allows the transmission of this environmentally-induced phenotypic variation across generations, and can influence adaptation. To date, the genetic control of TGP, its long-term stability, and its potential costs remain largely unknown, mostly because empirical demonstrations of TGP across many generations in several genetic backgrounds are scarce. In the paper of Cayuela et al., we examined how genotype determines the TGP of phenotypic traits related to dispersal, a fundamental process in ecology and evolution. We used an experimental approach in <i>Tetrahymena thermophila</i>, a ciliate model-species, to determine if and how phenotypic changes expressed following a dispersal treatment are inherited over multiple generations. The data include morphological and movement traits, dispersal rates, and cell growth data measured before and after dispersal trials. We considered different genotypes and different populations within each genotype.</p>
Fluctuating exposures to UV radiation and Erythromycin result in increased mean and variance in fitness in novel environments
<p>List of non-synonymous mutations identified in populations subjected to UV radiation and Erythromycin. Mutations identified in whole-population as well as in sub-populations resistant to either rifampicin or nalidixic acid are listed in separate files.</p>
Rosetta/VIRTIS-H water spectra and spectral fits
<p>This archive contains 204 figures which shows spectral fits to the S1 data set studied in the paper "The water Ortho-to-Para ratio in the coma of comet 67P/Churyumov-Gerasimenko" by Cheng et al. A&A, 2022.</p> <p>The figure names start with the VIRTIS-H observation number, followed by "MB" or "HB", which indicates which spectral domain is used for the fit.</p>
Data related to "Frozen-Density Embedding for including environmental effects in the Dirac-Kohn-Sham theory: an implementation based on density fitting and prototyping techniques"
<p>Geometries and data of several gold clusters embedded using an increasing number (5, 10, 20, 40 and 80) of water molecules.</p>
Sex-specific influence of communal breeding experience on parenting performance and fitness in a burying beetle
<p>Communal breeding, wherein multiple conspecific individuals live and reproduce together during a single breeding event, may generate immediate benefits in terms of defence and reproduction. However, the carry-over effects of events in communal breeding on individual behaviour and fitness remain less studied. We experimentally tested the immediate and carry-over effects of communal breeding on parenting performance and fitness in the burying beetle (<em><span>Nicrophorus vespilloides</span></em>). These beetles bury carcasses as food resource for their offspring and themselves, and provide extended care to the developing larvae on the buried carcass. We subjected individuals of varying sizes to communal (i.e. group-breeding) or non-communal breeding (i.e. pair-breeding) experience during their first breeding event, and subsequently to non-communal breeding during their second breeding event, and measured parental effort and reproductive success during both breeding events. In communal groups, large individuals became dominant and monopolized the carcass. At the first breeding attempt, large males in communal groups spent more time providing care than large males in non-communal groups, while such a difference was not observed for large females and small females or males in communal and non-communal groups. Reproductive success was similar for individuals that bred in communal and non-communal groups during their first reproductive event, indicating no significant immediate benefits of communal breeding in terms of reproduction. Compared to males that originated from non-communal groups, males from communal groups produced a similar number, but heavier larvae during their second breeding attempt, whereas such an effect was not observed for females. Our results provide evidence for sex-specific effects of communal breeding experience on parenting performance and fitness. Such observed sex differences in carry-over effects of communal breeding on fitness may generate sexual conflict over parental effort in social animals.</p>
Data from: Inter-generational costs of oxidative stress: reduced fitness in daughters of mothers that experienced high levels of oxidative damage during reproduction
<p>Parental condition transfer effects occur when the parents' physiological state during reproduction affects offspring performance. Oxidative damage may mediate such effects, yet evidence that oxidative damage experienced by parents during reproduction negatively affects offspring fitness is scarce and limited to early life stages. We show in Japanese quail (<em>Coturnix japonica</em>) that maternal levels of oxidative damage, measured during reproduction, negatively predict the number of offspring produced by daughters. This maternal effect on the daughter's reproductive success was mediated by an effect on hatching success, rather than the number of eggs laid by daughters. We also observed a negative association between the father's oxidative damage levels and the number of eggs laid by daughters, but a positive association between the father's oxidative damage levels and the hatching success of these eggs. These opposing paternal effects cancelled each other out, resulting in no overall effect on the number of offspring produced by daughters. No significant association between a female's own level of oxidative damage during reproduction and her reproductive success was observed. Our results suggest that oxidative damage experienced by parents may be a better predictor of an individual's reproductive performance than oxidative damage experienced by the individual itself. Although the mechanisms underlying these parental condition transfer effects are currently unknown, changes in egg composition or (epi-)genetic alterations of gametes may play a role. These findings highlight the importance of an inter-generational perspective when quantifying costs of physiological stress.</p>
Extreme reproductive skew at the dawn of sociality is consistent with inclusive fitness theory but problematic for routes to eusociality
<p>To understand the earliest stages of social evolution we need to identify species that are undergoing the initial steps into sociality. <em>Amphylaeus morosus</em> is the only unambiguously known social species in the bee family Colletidae and represents an independent origin of sociality within the Apoidea. This allows us to investigate the selective factors promoting the transition from solitary to social nesting. Using genome-wide SNP genotyping, we infer robust pedigree relationships to identify maternity of brood and intracolony relatedness for colonies at the end of the reproductive season. We show that <em>A. morosus</em> forms both matrifilial and full-sibling colonies, both involving complete or almost complete monopolization over reproduction. In social colonies, the reproductive primary was also the primary forager with the secondary female remaining in the nest, presumably as a guard. Social nesting provided significant protection against parasitism and increased brood survivorship in general. We show that secondary females gain large indirect fitness benefits from defensive outcomes, enough to satisfy the conditions of inclusive fitness theory, despite an over-production of males in social colonies. These results suggest an avenue to sociality that involves high relatedness and, very surprisingly, extreme reproductive skew in its earliest stages and raises important questions about the evolutionary steps in pathways to eusociality.</p>
Data for Eirew et al Accurate determination of CRISPR-mediated gene fitness in transplantable tumours
<p>Derived counts files and experimental metadata for Eirew et al Accurate determination of CRISPR-mediated gene fitness in transplantable tumours.</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
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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.