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128 results for “model fit”
Complex models of sequence evolution improve fit, but not gene tree discordance, for tetrapod mitogenomes
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Chronogram or phylogram for ancestral state estimation? Model-fit statistics indicate the branch lengths underlying a binary character’s evolution: R scripts and simulated trees
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Long-term effects of antibiotic treatments on honeybee colony fitness – a modelling approach
<p><b>1.</b> Gut microbiome disequilibrium is increasingly <span>implicated </span>in host fitness reductions, including for the economically important and disease-challenged western honey bee, <i>Apis mellifera</i>. In lab experiments the antibiotic tetracycline, which is used to prevent American Foulbrood Disease in countries including the US, elevates honey bee mortality by disturbing the microbiome. It is unclear however, how elevated individual mortality affects colony level fitness.</p> <p><b>2.</b> We used an agent-based model (BEEHAVE) and empirical data to assess colony level effects of antibiotic-induced worker bee mortality, by measuring colony size. We investigated the relationship between the duration that the antibiotic-induced mortality probability is imposed for and colony size.</p> <p><b>3.</b> We found that when simulating antibiotic-induced mortality of worker bees from just 60 days per year, up to a permanent effect, the colony is reduced such that tetracycline treatment would not meet the European Food Safety Authority's (EFSA) honey bee protection goals. When antibiotic mortality was imposed for the hypothetical minimal exposure time, which assumes that antibiotics only impact the bee's fitness during the recommended treatment period of fifteen days in both spring and autumn, the colony fitness reduction was only marginally under the EFSA's threshold.</p> <p><b>4.</b> Synthesis and Applications: Modelling colony level impacts of antibiotic treatment shows that individual antibiotic-induced honey bee worker mortality can lead to colony mortality. To assess the full impact, the persistence of antibiotic-induced mortality in honey bees must be determined experimentally, <i>in vivo</i>. We caution that as the domestication of new insect species increases, maintaining healthy gut microbiomes is of paramount importance to insect health and commercial productivity. The recommendation from this work is to limit prophylactic use of antibiotics and to not exceed recommended treatment strategies for domesticated insects. This is especially important for highly social insects as excess antibiotic use will likely decrease colony growth and an increase in colony mortality.</p>
The evolutionary advantage of fitness-dependent recombination in diploids: a deterministic mutation–selection–balance model
<p>Recombination's omnipresence in nature is one of the most intriguing problems in evolutionary biology. The question of why recombination exhibits certain general features is no less interesting than that of why it exists at all. One such feature is recombination's fitness dependence (FD). The so far developed population-genetics models have focused on the evolution of FD recombination mainly in haploids, although the empirical evidence for this phenomenon comes mostly from diploids. Using numerical analysis of modifier models for infinite panmictic populations, we show here that FD recombination can be evolutionarily advantageous in diploids subjected to purifying selection. We ascribe this advantage to the differential rate of disruption of lower- vs higher-fitness genotypes, which can be manifested in selected systems with at least three loci. We also show that if the modifier is linked to such selected system, it can additionally benefit from modifying this linkage in a fitness-dependent manner. The revealed evolutionary advantage of FD recombination appeared robust to crossover interference within the selected system, either positive or negative. Remarkably, FD recombination was often favored in situations where any constant non-zero recombination was evolutionarily disfavored, implying a relaxation of the rather strict constraints on major parameters (e.g., selection intensity and epistasis) required for the evolutionary advantage of non-zero recombination formulated by classical models.</p>
Long-term research and hierarchical models reveal consistent fitness costs of being the last egg in a clutch
1. Maintenance of phenotypic heterogeneity in the face of strong selection is an important component of evolutionary ecology, as are the consequences of such heterogeneity. Organisms may experience diminishing returns of increased reproductive allocation as clutch or litter size increases, affecting current and residual reproductive success. Given existing uncertainty regarding trade-offs between the quantity and quality of offspring, we sought to examine the potential for diminishing returns on increased reproductive allocation in a long-lived species of goose, with a particular emphasis on the effect of position in the laying sequence on offspring quality. 2. To better understand the effects of maternal allocation on offspring survival and growth, we estimated the effects of egg size, timing of breeding, inter- and intra-annual variation, and position in the laying sequence on gosling survival and growth rates of black brent (Branta bernicla nigricans) breeding in western Alaska from 1987–2007. 3. We found that gosling growth rates and survival decreased with position in the laying sequence, regardless of clutch size. Mean egg volume of the clutch a gosling originated from had a positive effect on gosling survival (β = 0.095, 95% CRI: 0.024, 0.165), and gosling growth rates (β = 0.626, 95% CRI: 0.469, 0.738). Gosling survival (β = -0.146, 95% CRI: -0.214, -0.079) and growth rates (β = -1.286, 95% CRI: -1.435, -1.132) were negatively related to hatching date. 4. These findings indicate substantial heterogeneity in offspring quality associated with their position in the laying sequence. They also potentially suggest a trade-off mechanism for females whose total reproductive investment is governed by pre-breeding state. 20-Mar-2020
Spatz neutron reflectometer commissioning data and corresponding models to fits
<p>This is the data to the hot commissioning of the Spatz neutron reflectometer at the OPAL Research Reactor, ANSTO. The data also contains the Jupyter notebook to reduce the data to give complete reflectivity profile and contains the models used to fit the data within refnx using the GUI option. </p>
Northern shoveler data for "Sensitivity of binomial N-mixture models to overdispersion: the importance of assessing model fit"
<p>Repeated count data for Northern shoveler analyzed in Knape et al. Sensitivity of binomial N-mixture models to overdispersion: the importance of assessing model fit", Methods in Ecology and Evolution.</p> <p>count.csv contains Northern shoveler counts repeated 10 times at 50 sites in a 50 x 10 matrix. Each row corresponds to a specific site and columns correspond to visits.</p> <p>date.csv is a 50 x 10 matrix containing the julian date of each count, using the same ordering of visits (columns) and sites (rows) as in count.csv.</p> <p>site.csv contains covariates for each of the 50 sites. Sites (rows) are ordered in the same way as in count.csv and date.csv. The first column represents the area of water (ha) covered by the wetlands where the counts were conducted, the second columns is the percentage of the wetland area covered by reeds, and the third column is the latitude of the wetland in RT90 coordinates.</p> <p> </p> <p> </p>
Best fit Orphan stream model in the presence of the LMC
<p>We give the best fit stream model and orbit for Orphan in the presence of the LMC from the work of Erkal et al. 2019 (<a href="https://ui.adsabs.harvard.edu/abs/2019MNRAS.487.2685E">https://ui.adsabs.harvard.edu/abs/2019MNRAS.487.2685E</a>). As described in section 4 of that work, this best fit was achieved in a prolate Milky Way halo which responds to the LMC. See the table in the appendix of that work (A1) for the parameters used in the fit.</p> <p>The file containing the orbit (orphan_orbit.txt) gives the position of the Orphan progenitor, LMC, and Milky Way for the past 5 Gyr. The coordinates are Galactocentric in a right-handed system (i..e the Sun is at (-8.1,0,0) kpc and predominantly moving in the positive y direction). </p> <p>The file containing the stream (orphan_stream.txt) gives the position of the Orphan stream particles in Galactocentric coordinates as well as observables (ra,dec,distance,vr,pmra,pmdec) assuming the Sun is at (-8.1,0,0) kpc and moving with a velocity of (11.1,245,7.3) km/s. The stream is generated using the Lagrange point stripping technique as described in the paper. </p> <p>Please cite Erkal et al. 2019 if you make use of this simulation.</p>
Model Fit Figures for: The 100 pc White Dwarf Sample in the SDSS Footprint II. A New Look at the Spectral Evolution of White Dwarfs
<p>Figures for the model atmosphere fits to the spectroscopically confirmed white dwarfs in the 100 pc sample and the SDSS footprint (<span>arXiv:2412.04611). </span></p>
JWST spectra and best-fit SED models of massive quiescent galaxies from the Blue Jay survey.
<ul> <li>The JWST/NIRSpec spectra are stored as FITS tables which include wavelength (in angstrom, in rest-frame), calibrated flux, uncertainty, and best-fit model (in 1e-19 erg/s/cm^2/AA).</li> </ul>
Supplementary Data: Global fits of vector-mediated s-channel simplified models for scalar and fermionic dark matter with GAMBIT
<p>This record contains the YAML files, data files, and some of the plotting scripts for: "Global fits of vector-mediated s-channel simplified models for scalar and fermionic dark matter with GAMBIT". The paper can be found at https://arxiv.org/abs/2209.13266.</p> <p>Samples have been created using GAMBIT and figures can be reproduced with pippi.</p>
Estimation of best-fitting force, moment tensor, and depth for the 2022 Hunga-Tonga submarine volcanic eruption: Misfit plots in model parameter space
<p>Supporting documents for the correction of the publication <em>Multi‐Event Explosive Seismic Source for the 2022 Mw 6.3 Hunga Tonga Submarine Volcanic Eruption, </em>published in The Seismic Record (<a href="https://doi.org/10.1785/0320220027">https://doi.org/10.1785/0320220027</a>).</p>
Is my model fit for purpose? Validating a population model for predicting freshwater fish responses to flow management
<p>Models based on ecological processes ("process-explicit models") are often used to predict ecosystem responses to environmental changes or management scenarios. However, models are imperfect and need to be validated, ideally by testing their assumptions and outputs against independent empirical data sets. Examples of validation of process-explicit models are rare. Recently, stochastic population models have been developed to predict the likely responses (over 10-120 years) of a riverine fish (golden perch, Macquaria ambigua) to flow management in the Murray-Darling Basin (MDB) in eastern Australia, one of the world's most regulated river basins. Declines of golden perch (and other species) are a direct consequence of altered hydrology, and managers require information to predict how fish will respond to possible future hydrological conditions to guide the substantial investments in flow management. Here, we use two independent field data sets to validate our population model. We compared model predictions to observed trends to ask: (1) how do predicted population sizes and growth rates compare to observed data? (2) does the correlation between predicted and observed population sizes and growth rates vary among populations? (3) does the correlation between predicted and observed population sizes and growth rates vary across observed hydrological conditions? and (4) how do modelled and observed fish movement rates compare? We found reasonable correlations between fish population sizes and growth rates as predicted by the model and observed in independent data sets for several populations (Aim 1) but the strength of these correlations varied among populations (Aim 2) and hydrological conditions (Aim 3). Predicted and observed fish movement rates were strongly correlated (Aim 4). Population models are frequently used in conservation decision-making but are rarely validated. We demonstrate that: (1) validation can identify model strengths and weaknesses; (2) observed data sets often have inherent limitations that can preclude robust validations; (3) validation is likely be more common if appropriate observed data sets are available; and (4) validation should consider the purpose of modelling. Wider consideration of these messages would contribute to more critical examinations of models so they can be most appropriately used in conservation decision-making.</p>
Is my model fit for purpose? Validating a population model for predicting freshwater fish responses to flow management
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Camera-trap data for fitting the random encounter model to estimate densities of coyotes and black-tailed jackrabbits in the Mojave Desert
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Long-term research and hierarchical models reveal consistent fitness costs of being the last egg in a clutch
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Long-term effects of antibiotic treatments on honeybee colony fitness – a modelling approach
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Data for fitting spatial capture-recapture (SCR) models to estimate spatially explicit demographics of Mojave desert tortoises on a demography plot in California, USA
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The evolutionary advantage of fitness-dependent recombination in diploids: a deterministic mutation–selection–balance model
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Data from: Herbivory can increase plant fitness via reduced interspecific competition – evidence from models and mesocosms
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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.