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3,139 results for “fitting”
Natural variation at a single gene generates sexual antagonism across fitness components in Drosophila
<p class="MsoNormal"><span>Mutations with conflicting fitness effects in males and females accumulate in sexual populations, reducing their adaptive capa</span><span>city</span><span>. Although quantitative genetic studies indicate that sexually antagonistic polymorphisms are common</span><span>, their molecular basis and population genetic properties remain poorly understood</span><span>. Here, we show in fruit flies how natural variation at a single gene generates sexual antagonism through phenotypic effects on cuticular hydrocarbon (CHC) traits that function as both mate signals and protectors against abiotic stress</span><span></span><span> across a latitudinal gradient. Tropical populations of <em>Drosophila serrata </em><span>have </span>polymorphic CHCs producing sexual antagonism through opposing but sex-limited effects on these two fitness-related functions. We dissected this polymorphism to a single fatty-acyl CoA reductase gene, <em>DsFAR2-B</em>, that is expressed in oenocyte cells where CHCs are synthesised. RNAi mediated disruption of the <em>DsFAR2-B</em> ortholog in <em>D. melanogaster</em> oenocytes affected CHCs in a similar way to that seen in <em>D. serrata</em>. Population genomic analysis revealed that balancing selection likely operates at the <em>DsFAR2-B </em>locus in the wild. Our study provides insights into the genetic basis of sexual antagonism in nature and connects sexually varying antagonistic selection on phenotypes with balancing selection on genotypes that maintains molecular variation. </span></p>
Resistance of Dickeya solani strain IPO 2222 to lytic bacteriophage ΦD5 results in fitness tradeoffs for the bacterium during infection – protein mass fingerprints dataset
<p>Protein mass fingerprints (D. solani Tn5 mutants) dataset supporting the manuscript entitled: <strong>Resistance of </strong><em><strong>Dickeya solani</strong></em><strong> strain IPO 2222 to lytic bacteriophage </strong><strong>Φ</strong><strong>D5 results in fitness tradeoffs for the bacterium during infection.</strong></p>
The impacts of host association and perturbation on symbiont fitness
<p><span>Symbiosis benefits hosts in numerous ways, but much less is known about how host-association affects symbionts. While symbiont fitness can be mediated by host, symbiont, and/or environmental factors, recent works indicate that symbiont performance can depend on whether the symbiont is needed by the host, suggesting that symbiosis is not always beneficial for symbionts. To determine the impact of symbiosis on symbionts across the Tree of Life, we conducted a meta-analysis across 83 unique host-symbiont pairings under a range of spatial and temporal contexts. Specifically, we asked how symbiont fitness is altered outside of symbiosis, when host-symbiont interaction is under suboptimal conditions, or as hosts age. We found that intracellular symbionts associated with protists tend to have greater fitness outside of symbiosis, with the opposite trend for animal hosts. This result suggests that animals may be better at maintaining symbionts. Symbiont fitness also generally increased as hosts grow older. Moreover, symbionts that can proliferate in- and outside host cells performed better than those found exclusively inside or outside cells, suggesting that flexibility in growing location may help symbionts thrive. We discuss these fitness patterns in light of host-driven factors, where hosts exert influence over symbionts to suit their needs.</span></p>
Role of Social Aggregation in the Fitness Cost of Pyrethroid-resistant German Cockroaches
<p>The data reported in the dataset refer to fitness cost of German cockroach and the effect of group size on biological attributes of field German cockroach </p>
Research on The Fit of Head-face Medical Protective Equipment
<p>The database is from the research on the fit of head-face medical protective equipment. The Comfort Score is from the user comfort test and the Head-face Dimensions is from the 3D scanning headforms measurement.</p>
Pre-fitted Bayesian models for "Gene panel selection for targeted spatial transcriptomics"
<p>simulation_parameters_DARTFISH_slim.rds: Bayesian model fitted on the Zhang dataset.</p> <p>simulation_parameters_MERFISH_slim.rds: Bayesian model fitted on the Moffit dataset.</p> <p>simulation_parameters_osmFISH_slim.rds: Bayesian model fitted on the Codeluppi dataset.</p> <p> </p>
Embeddings from FLIP: benchmark tasks in fitness landscape inference for proteins
<p>ESM-1b embeddings used in FLIP. </p>
Manduca sexta experience high parasitoid pressures in the field but minor fitness costs of consuming plant secondary compounds
<p>Plant-herbivore co-evolutionary interactions have led to a range of plant defenses that minimize insect damage and a suite of counter-adaptations that allow herbivores to feed on defended plants. Consuming plant secondary compounds results in herbivore growth and developmental costs but can have beneficial effects such as deterrence or harm of parasitoid enemies. Therefore, the role of secondary compounds on herbivore fitness must be considered in the context of the abundance and level of harm from natural enemies and the costs herbivores incur feeding on plant secondary compounds.</p> <ol> <li>In this study, I combined field measurements of <em>Cotesia congregata</em> wasp parasitism pressure with detailed measurements of the costs of plant secondary compounds across developmental stages in the herbivore host, <em>Manduca sexta</em>.</li> <li>I show that <em>C. congregata</em> parasitoids exert large negative selective pressures, killing 31-57% of <em>M. sexta</em> larvae in the field. <em>Manduca sexta </em>developed fastest during instars most at risk for parasitoid oviposition but growth was slowed by consumption of plant secondary compounds. The negative effects of consuming plant secondary compounds as larvae influenced adult size traits but there were no immune, survival, or fecundity costs.</li> <li>These results suggest that developmental costs experienced by <em>M. sexta</em> herbivores consuming defensive compounds are minor in comparison to the strong negative survival pressures from abundant parasitoid enemies.</li> </ol>
Evidence that genomic incompatibilities and other multilocus processes impact hybrid fitness in a rattlesnake hybrid zone
<p>Hybrid zones provide valuable opportunities to understand the genomic mechanisms that promote speciation by providing insight into factors involved in intermediate stages of speciation. Here we investigate introgression in a hybrid zone between two rattlesnake species (<em>Crotalus viridis</em> and <em>C. oreganus concolor</em>) that have undergone historical allopatric divergence and recent range expansion and secondary contact. We use Bayesian genomic cline models to characterize genomic patterns of introgression between these lineages and identify loci potentially subject to selection in hybrids. We find evidence for a large number of genomic regions with biased ancestry that deviate from the genomic background in hybrids (i.e., excess ancestry loci), which tend to be associated with genomic regions with higher recombination rates. We also identify suites of excess ancestry loci that show highly correlated allele frequencies (including conspecific and heterospecific combinations) across physically unlinked genomic regions in hybrids. Our findings provide evidence for multiple multilocus evolutionary processes impacting hybrid fitness in this system.</p>
Fitness costs and benefits in response to artificial artesunate selection in Plasmodium
<p>The file contains the raw data from the experiments.</p> <p>The tabs are as follows:</p> <p>"EX1_Bird data" contains all the data in Experiment 1 (Experiments are clearly labelled in the manuscript)</p> <p>"EX2_Mosquito parasitaemia" contains the quantification of oocysts n Experiment 2</p> <p>"EX2_Mosquito_lht" contains the quantification of mosquito life history traits in Experiment 2</p> <p>"EX3_Mosquito parasite dynamics" contains the quantification of oocysts and sporozoites over several days carried out in Experiment 3</p> <p>The column names are self-explanatory</p>
Data from: Direct and indirect effects of cougar predation on bighorn sheep fitness
<div> <p>We sought to evaluate the direct and indirect fitness effects of intense cougar (<em>Puma concolor</em>) predation using 48 years of data on marked bighorn sheep (<em>Ovis canadensis</em>) in Ram Mountain, Alberta, Canada. We compared years of intense cougar predation with years with no or occasional cougar predation. We first quantified the effects of predation on neonatal, weaning, and overwinter lamb survival, three metrics potentially affected by direct and indirect effects. We then investigated the possible indirect effects of intense cougar predation on lamb production, female summer mass gain, and lamb mass at weaning. Indirect effects included a 14.2% decline in lamb production. Female summer mass gain decreased by 15.6 % and lamb mass at weaning declined by 8.0% in years of intense cougar predation. Here are the six datasets, joined with a README.md file for the data description, in addition to the six corresponding R scripts for replicating the results.</p> </div>
Dataset: Reach characteristics and best-fit effective resistance
<p>This dataset includes reach characteristics and model output for best-fit effective resistance for 37 river reaches in the Colorado Rockies. </p>
Data from: Anthropogenic nesting substrates increase parental fitness in a Neotropical songbird, the Pale-breasted Thrush (Turdus leucomelas)
<p>The failure of breeding attempts is a major hindrance to bird reproduction, making nest site choice under strong selective pressure. Urbanization may offer lower risk of nest predation to certain bird species, but the impact of using anthropogenic structures as nesting sites on parental fitness is seldom studied. We studied the effect of anthropogenic substrates and brood parasitism by the Shiny Cowbird (<em>Molothrus bonariensis</em>) on the nest success of a Neotropical songbird, the Pale-breasted Thrush (<em>Turdus leucomelas</em>). We monitored 263 nesting attempts between 2017 and 2020 to estimate daily survival rate (DSR), which represents the probability of a given nest survive until the next day. DSR was modelled as a response variable in function of substrate type (plants as "natural" or human buildings as "artificial") and brood parasitism as fixed factors, using as covariates year, a linear and a quadratic seasonal trends. Additionally, we tested the effect of these same explanatory variables on the number of fledglings per nest using a generalized linear mixed-effects model. Most nests (78.7%) were placed in artificial substrates and apparent nest success (i.e. the percentage of nesting attempts that produced at least one thrush fledgling) was higher in artificial (50.2%) than in natural substrates (37.5%). DSR was higher for nests in artificial than in natural substrates regardless of cowbird parasitism, whereas the number of fledglings per nest was higher both in artificial substrates and for nests without cowbird parasitism. We highlight that nesting in buildings significantly increases parental fitness in Pale-breasted Thrushes, which may favor their settlement in cities and potentially drive the evolution of this breeding behavior in urban birds.</p>
Data for the PPSN 2024 article: "Entropy, Trajectories, and Explainability for Frequency Fitness Assignment"
<p>Dataset for the PPSN 2024 article: "Entropy, Trajectories, and Explainability for Frequency Fitness Assignment"</p>
FIGURE 2 in Species distribution ranges of Ilyocryptus Sars, 1862 (Cladocera: Ilyocryptidae) fit the transitional zone between Boreal and Tropical Provinces in the Far East
FIGURE 2. Ilyocryptus yooni Jeong et al., 2012, an adult parthenogenetic female from a large pond in Ho Chi Minh City, South Vietnam: A, general view. B, setae at posterior valve margin. C, postabdomen. D, Its preanal portion. E, Distal portion of postabdomen. F, Antenna I. Scale bars: 0.1 mm.
FIGURE 1 in Species distribution ranges of Ilyocryptus Sars, 1862 (Cladocera: Ilyocryptidae) fit the transitional zone between Boreal and Tropical Provinces in the Far East
FIGURE 1.Original records of Ilyocryptus present in southern and northern territories of the Pacific Region only (A), and penetrating the transitional zone between Boreal ("Palaeactic") and Oriental Provinces (B). Abbreviations: WE—species widely distributed in North Eurasia; ST—southern tropical species; EN—Far Eastern endemics.
FIGURE. 3. Ilyocryptus bharwaji Battish, 1981 in Species distribution ranges of Ilyocryptus Sars, 1862 (Cladocera: Ilyocryptidae) fit the transitional zone between Boreal and Tropical Provinces in the Far East
FIGURE. 3. Ilyocryptus bharwaji Battish, 1981, parthenogenetic female from Klong Rangsit, Bangkok, Thailand: A, general view. B, Head, anterior view. C, postabdomen. D–E, Antenna I. F, antenna II. G–H, its exopod and endopod. Scale bars: 0.1 mm.
Outputs from fitted models across the cross-validation scenarios for 'Space-time species distribution modeling with opportunistic presence-only data: a case study of passerines in a protected area'
<p>Three Zenodo repositories are linked to the preprint <em>Space-time Species Distribution Modeling for Opportunistic Presence-Only Data: A Case Study of Passerines in a Protected Area </em>(Lasgorceux et al., unpublished, <a href="https://hal.science/hal-04616332">https://hal.science/hal-04616332</a>):</p> <ul> <li>Data, scripts and, code (Lasgorceux et al., Zenodo, <a href="https://doi.org/10.5281/zenodo.12545052">https://doi.org/10.5281/zenodo.12545052</a>)</li> <li>Outputs from fitted models across the cross-validation scenarios (Lasgorceux et al., Zenodo, <a href="https://doi.org/10.5281/zenodo.12544212">https://doi.org/10.5281/zenodo.12544212</a>)</li> <li>Supplementary information at (Lasgorceux et al., Zenodo, <a href="https://doi.org/10.5281/zenodo.12541412">https://doi.org/10.5281/zenodo.12541412</a>)</li> </ul> <p>This repository contains the outputs from fitted models across the cross-validation scenarios.</p> <p>In the folder <em>Ouputs_cross_validation</em>, each species is represented by a .RData file, numbered from 1 to 77 (excluding 7, which corresponds to <em>Bombycilla garrulus</em>; see the preprint for details). This dataset is specifically used to generate Figure 1, which shows the AUC of various cross-validation scenarios. To reproduce this figure in R, place all the files in the <em>Results/Fitted_models</em> folder and run the <em>Models_Outputs.R</em> script located in the <em>Results</em> folder of Lasgorceux et al., Zenodo, <a href="https://doi.org/10.5281/zenodo.12545052">https://doi.org/10.5281/zenodo.12545052.</a></p> <p>Note: These data have been separated due to memory requirements (23.14GB).</p>
Pylake example: Data to fit the Twistable Worm-Like Chain Model
Open the record for dataset details and reuse information.
Meshes, volume fractions, and normal vectors for paraboloid fit verification
<p>These datasets are used to verify the results of the paper "A Paraboloid Fitting Technique for Calculating Curvature from Piecewise-Linear Interface Reconstructions on 3D Unstructured Meshes" by Z. Jibben, N. N. Carlson, and M. M. Francois.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.