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Data for: Temperature-mediated male condition shapes female fitness and oviposition preference in a butterfly
<p class="CxSpFirst">Habitat choice by ovipositing females critically shapes fitness in species lacking parental care. We aimed at manipulating female oviposition choosiness using the Glanville fritillary butterfly (<i>Melitaea cinxia</i>) as study species. We tested whether female choosiness is influenced by individual condition and/or that of the mating partner, which was manipulated experimentally by subjecting adults to night temperatures warmer than usual. Against our prediction, female life expectancy was not altered by the treatment and impacted her fitness only mildly. Males exposed to warm nights, on the other hand, lived shorter and females who mated with warm-exposed males sired larger clutches with higher hatching success, in line with the terminal investment hypothesis. We also tested whether females base their oviposition choices primarily on habitat type (open/shaded) or plant condition (dry/well-watered) under a semi-natural experimental set-up. We show that females choose primarily open habitats and within those habitats well-watered host plants. While female choosiness for oviposition was not affected by their own thermal treatment, mating with warm-exposed males also strengthened the female oviposition preference towards the generally preferred host plant species in this study (<i>Plantago lanceolata</i>). The present work brings new awareness on the often-neglected role of male condition in shaping female fitness and choice.</p>
Yield function fitting MatFlow demonstration
This is a completed MatFlow workflow for fitting yield functions from full-field crystal plasticity simulations.
Data from: The effects of short term detraining and retraining on physical fitness in elite soccer players
Purpose: The aim of this study was to examine the effects of aerobic high-intensity training with reduced volume and training cessation on body composition and physical fitness after the end of season and the time required to recapture physical fitness with intensified retraining following two weeks of detraining in elite soccer players. Method: Twenty male semi-professional soccer players participated in this study. The soccer players were assigned to either a group that completed high-intensity aerobic training (HAT, n = 10) or to a detraining and retraining group (DHAT, n = 10) for a 5-week period immediately after the end of the season. The first 2 weeks of the period, members of the HAT group performed high-intensity aerobic exercise (80–90% of HRmax, 12 min × 3, three times per week), whereas members of the DHAT group abstained from any physical activity. During the subsequent 3 weeks, members of both the HAT and DHAT groups completed high-intensity aerobic exercise. Exercise performance testing and body composition analysis were performed before; after 2 weeks of detraining; and at 1, 2 and 3 weeks of retraining. Results: Intensified high-intensity training for 5 weeks maintained the performance in the Yo-Yo Intermittent Recovery level 2 test (Yo-Yo IR2) and repeated sprints at any time point (P > 0.05). However 2 weeks of detraining resulted in significant decreases in the performance on the Yo-Yo IR2 (P < 0.01) and repeated sprints test (P < 0.05). Performance on the Yo-Yo IR2 enhanced after 2 weeks of retraining and was maintained up to 3 weeks after retraining, with no significant differences between conditions (P > 0.05). In addition, repeated sprint performance markedly decreased after the detraining period (P < 0.05) and was continuously lower compared to the baseline at 2 weeks after retraining (P < 0.05). Furthermore, this value reached baseline level at the end of the experimental period (P > 0.05). There were no significant differences between conditions in body composition, performance of agility, or sprint ability throughout the 5-week experimental period (P > 0.05). Conclusions: The present data suggest that short-term detraining after the competitive season can markedly decrease performances in the Yo-Yo IR2 test and repeated sprints. To return to a previous level of ability on the Yo-Yo IR2 and/or sprint test with retraining through high-intensity aerobic training after a period of detraining, a similar or longer period of retraining is required. However, the high-intensity training with reduced amount of training after competitive season can prevent reductions in physical fitness.
Data from: Limited indirect fitness benefits of male group membership in a lekking species
In group living species, individuals may gain the indirect fitness benefits characterising kin selection when groups contain close relatives. However, tests of kin selection have primarily focused on cooperatively breeding and eusocial species, whereas its importance in other forms of group living remains to be fully understood. Lekking is a form of grouping where males display on small aggregated territories, which females then visit to mate. As females prefer larger aggregations, territorial males might gain indirect fitness benefits if their presence increases the fitness of close relatives. Previous studies have tested specific predictions of kin selection models by using measures such as group-level relatedness. However, a full understanding of the contribution of kin selection in the evolution of group living requires estimating individuals' indirect fitness benefits across multiple sites and years. Using behavioural and genetic data from the black grouse (Tetrao tetrix), we show that the indirect fitness benefits of group membership were limited because newcomers joined leks containing few close relatives who had limited mating success. Males' indirect fitness benefits were higher in yearlings during increasing population density but overall remained small and only marginally changed the variation in male fitness. Kin selection acting through increasing group size has a limited influence on male fitness and is therefore unlikely to contribute substantially to the evolution and maintenance of lekking in this black grouse population.
Data from: Quantifying heritable variation in fitness-related traits of wild, farmed and hybrid Atlantic salmon families in a wild river environment
Farmed fish are typically genetically different from wild conspecifics. Escapees from fish farms may contribute one-way gene flow from farm to wild gene pools, which can depress population productivity, dilute local adaptations and disrupt coadapted gene complexes. Here, we reanalyse data from two experiments (McGinnity et al., 1997, 2003) where performance of Atlantic salmon (Salmo salar) progeny originating from experimental crosses between farm and wild parents (in three different cohorts) were measured in a natural stream under common garden conditions. Previous published analyses focussed on group-level differences but did not account for pedigree structure, as we do here using modern mixed-effect models. Offspring with one or two farm parents exhibited poorer survival in their first and second year of life compared with those with two wild parents and these group-level inferences were robust to excluding outlier families. Variation in performance among farm, hybrid and wild families was generally similar in magnitude. Farm offspring were generally larger at all life stages examined than wild offspring, but the differences were moderate (5–20%) and similar in magnitude in the wild versus hatchery environments. Quantitative genetic analyses conducted using a Bayesian framework revealed moderate heritability in juvenile fork length and mass and positive genetic correlations (>0.85) between these morphological traits. Our study confirms (using more rigorous statistical techniques) previous studies showing that offspring of wild fish invariably have higher fitness and contributes fresh insights into family-level variation in performance of farm, wild and hybrid Atlantic salmon families in the wild. It also adds to a small, but growing, number of studies that estimate key evolutionary parameters in wild salmonid populations. Such information is vital in modelling the impacts of introgression by escaped farm salmon.
Data from: Adaptive walks and distribution of beneficial fitness effects
We study the adaptation dynamics of a maladapted asexual population on rugged fitness landscapes with many local fitness peaks. The distribution of beneficial fitness effects is assumed to belong to one of the three extreme value domains, viz. Weibull, Gumbel, and Fréchet. We work in the strong selection-weak mutation regime in which beneficial mutations fix sequentially, and the population performs an uphill walk on the fitness landscape until a local fitness peak is reached. A striking prediction of our analysis is that the fitness difference between successive steps follows a pattern of diminishing returns in the Weibull domain and accelerating returns in the Fréchet domain, as the initial fitness of the population is increased. These trends are found to be robust with respect to fitness correlations. We believe that this result can be exploited in experiments to determine the extreme value domain of the distribution of beneficial fitness effects. Our work here differs significantly from the previous ones that assume the selection coefficient to be small. On taking large effect mutations into account, we find that the length of the walk shows different qualitative trends from those derived using small selection coefficient approximation.
Data from: Male investments in high quality sperm improve fertilization success, but may have negative impact on offspring fitness in whitefish
Many ejaculate traits show remarkable variation in relation to male social status. Males in disfavoured (subordinate) mating positions often invest heavily on sperm motility but may have less available resources on traits (e.g., secondary sexual ornaments) that improve the probability of gaining matings. Although higher investments in sperm motility can increase the relative fertilization success of subordinate males, it is unclear whether status-dependent differences in sperm traits could have any consequences for offspring fitness. We tested this possibility in whitefish (Coregonus lavaretus L.) by experimentally fertilizing the eggs of 24 females with the sperm of either highly-ornamented (large breeding tubercles, dominant) or less-ornamented (small tubercles, subordinate) males (split-clutch breeding design). In comparison to highly-ornamented individuals, less-ornamented males had higher sperm motility, which fertilized the eggs more efficiently, but produced embryos with impaired hatching success. Also offspring size and body condition were lower among less-ornamented males. Furthermore, sperm motility was positively associated with the fertilization success and offspring size, but only in highly-ornamented males. Together our results indicate that male investments on highly motile (fertile) sperm is not necessarily advantageous during later offspring ontogeny and that male status-dependent differences in sperm phenotype may have important effects on offspring fitness in different life-history stages.
Data from: Mutator genomes decay, despite sustained fitness gains, in a long-term experiment with bacteria
Understanding the extreme variation among bacterial genomes remains an unsolved challenge in evolutionary biology, despite long-standing debate about the relative importance of natural selection, mutation, and random drift. A potentially important confounding factor is the variation in mutation rates between lineages and over evolutionary history, which has been documented in several species. Mutation accumulation experiments have shown that hypermutability can erode genomes over short timescales. These results, however, were obtained under conditions of extremely weak selection, casting doubt on their general relevance. Here, we circumvent this limitation by analyzing genomes from mutator populations that arose during a long-term experiment with Escherichia coli, in which populations have been adaptively evolving for >50,000 generations. We develop an analytical framework to quantify the relative contributions of mutation and selection in shaping genomic characteristics, and we validate it using genomes evolved under regimes of high mutation rates with weak selection (mutation accumulation experiments) and low mutation rates with strong selection (natural isolates). Our results show that, despite sustained adaptive evolution in the long-term experiment, the signature of selection is much weaker than that of mutational biases in mutator genomes. This finding suggests that relatively brief periods of hypermutability can play an outsized role in shaping extant bacterial genomes. Overall, these results highlight the importance of genomic draft, in which strong linkage limits the ability of selection to purge deleterious mutations. These insights are also relevant to other biological systems evolving under strong linkage and high mutation rates, including viruses and cancer cells.
Data from: Evolution and plasticity of thermal performance: An analysis of variation in thermal tolerance and fitness in 22 Drosophila species
The thermal biology of ectotherms is often used to infer species' responses to changes in temperature. It is often proposed that temperate species are more cold-tolerant, less heat-tolerant, more plastic, have broader thermal performance curves (TPCs), and lower optimal temperatures, when compared to tropical species; however, relatively little empirical work has investigated these expectations. Here we measure thermal tolerance limits and thermal performance of the fitness components viability, developmental speed, and fecundity at seven temperatures in 22 species of Drosophila reared at a common temperature. For 10 of these species, we also measured thermal tolerance and thermal performance following developmental acclimation to three additional temperatures. Using these data, we test several fundamental hypotheses about the evolution and plasticity of heat and cold resistance and thermal performance. We find that cold (and to a lesser degree heat) tolerance varied between the species in a predictable pattern. This confirms the marked effect of evolutionary adaptation and acclimation on thermal tolerance. However, contrary to expectation, find that the breadth of thermal performance in fitness traits were similar in temperate, widespread and tropical species and we also find that the plasticity of TPCs is constrained. These data support the idea that thermal tolerance limits have evolved in response to extreme environmental conditions that limits species persistence whereas the temperature range for optimal thermal performance is likely under selection by the temperatures that prevail during the more benign seasons. Further, it calls to question the utility of TPCs in inferring ecological adaptation. We conclude that the thermal performance of fitness traits in Drosophila species are temporally and spatially stable and that thermal tolerance varies considerably across latitudes.
Data from: Adaptation to resistant hosts increases fitness on susceptible hosts in the plant parasitic nematode Globodera pallida
Trade-offs between virulence (defined as the ability to infect a resistant host) and life-history traits are of particular interest in plant pathogens for durable management of plant resistances. Adaptation to plant resistances (i.e., virulence acquisition) is indeed expected to be associated with a fitness cost on susceptible hosts. Here, we investigated whether life-history traits involved in the fitness of the potato cyst nematode Globodera pallida are affected in a virulent lineage compared to an avirulent one. Both lineages were obtained from the same natural population through experimental evolution on resistant and susceptible hosts, respectively. Unexpectedly, we found that virulent lineages were more fit than avirulent lineages on susceptible hosts: they produced bigger cysts, containing more larvae and hatching faster. We thus discuss possible reasons explaining why virulence did not spread into natural G. pallida populations.
Data from: Heterozygosity–fitness correlations in a wild mammal population: accounting for parental and environmental effects
HFCs (heterozygosity–fitness correlations) measure the direct relationship between an individual's genetic diversity and fitness. The effects of parental heterozygosity and the environment on HFCs are currently under-researched. We investigated these in a high-density U.K. population of European badgers (Meles meles), using a multimodel capture–mark–recapture framework and 35 microsatellite loci. We detected interannual variation in first-year, but not adult, survival probability. Adult females had higher annual survival probabilities than adult males. Cubs with more heterozygous fathers had higher first-year survival, but only in wetter summers; there was no relationship with individual or maternal heterozygosity. Moist soil conditions enhance badger food supply (earthworms), improving survival. In dryer years, higher indiscriminate mortality rates appear to mask differential heterozygosity-related survival effects. This paternal interaction was significant in the most supported model; however, the model-averaged estimate had a relative importance of 0.50 and overlapped zero slightly. First-year survival probabilities were not correlated with the inbreeding coefficient (f); however, small sample sizes limited the power to detect inbreeding depression. Correlations between individual heterozygosity and inbreeding were weak, in line with published meta-analyses showing that HFCs tend to be weak. We found support for general rather than local heterozygosity effects on first-year survival probability, and g2 indicated that our markers had power to detect inbreeding. We emphasize the importance of assessing how environmental stressors can influence the magnitude and direction of HFCs and of considering how parental genetic diversity can affect fitness-related traits, which could play an important role in the evolution of mate choice.
ReGraviST Fitting Script and RawData
<p><em>This work has been further developed and published as a separate, more comprehensive paper. <br><strong>Available at: <a href="https://zenodo.org/records/15612467">DOI 10.5281/zenodo.15612467</a></strong></em></p>
Supplementary data for: "Progenitor properties of type II supernovae: fitting to hydrodynamical models using Markov chain Monte Carlo methods"
<p>This entry contains a grid of bolometric light curve and photospheric velocity models applied to stellar evolution progenitors. A full description of the models can be found in Martinez et al. 2020, A&A, 642, A143.</p>
A set of drinking horn fittings and a chain No.2
Metal elements of the equipment from the so-called ducal tomb: A set of drinking horn fittings and a chain No.2 ID no.: SZA7/ 00/709, SZA7 / 00/760, SZA7 / 00/707 Archaeological Museum in Kraków https://muzea.malopolska.pl/en/objects-list/1573 Digitalisation: RDW MIC, Virtual Małopolska project Source: Objaverse 1.0 / Sketchfab
Wmid-d5320a - Cruciform strap fitting
An incomplete copper alloy openwork cruciform mount or strap fitting, of probable Post Medieval dating (AD 1600 to AD 1800). The strap fitting is cruciform in shape, with four projecting arms. Each arm is the same and terminates in an rounded knop, with a circular sectioned copper alloy rivet placed through it. Beneath the terminal knop is an openwork triangular shape, with rounded sides, which continue into a central square openwork. It represents a two strand ropework design. The edges have been rounded. The reverse is flat and undecorated. For more information, please visit the online database record available at: https://finds.org.uk/database/artefacts/record/id/1072794 Source: Objaverse 1.0 / Sketchfab
Representations and associated fitness values of protein sequences
<p>We studied the ability to predict protein fitness from sequence using our method <a href="https://github.com/amillig/MERGE" target="_blank" rel="noopener">MERGE</a> and other methods (i.e., ECNet, eUniRep, EVmutation, One-Hot, and UniRep). The following files are included in this repository:</p> <ul> <li>The folder <em>ECNet</em> contains the braw, csv, and fasta files required to run <a href="https://github.com/luoyunan/ECNet" target="_blank" rel="noopener">ECNet</a>.</li> <li>The folders <em>eUniRep, </em><em>MERGE, One-Hot</em>, and <em>UniRep</em> contain csv files including the names and fitness values of protein variants as well as a numerical representation of their sequence. The folder <em>MERGE </em>also contains representations of the wild type sequences as npy files in the <em>wts</em> folder.</li> <li>The folder <em>Params</em> contains params files generated with <a href="https://github.com/debbiemarkslab/plmc" target="_blank" rel="noopener">PLMC</a>.</li> <li>The script <em>get_performances.py</em> enables to generate models using different methods (i.e., eUniRep, EVmutation, MERGE, One-Hot, Pure_ML, and UniRep) and to determine their performance for predicting the fitness of protein variants from sequence.</li> </ul> <p><strong>References</strong></p> <table> <tbody> <tr> <td><a href="https://doi.org/10.1038/s41467-021-25976-8" target="_blank" rel="noopener">ECNet</a></td> <td> <p>Luo, Y., Jiang, G., Yu, T. et al. ECNet is an evolutionary context-integrated deep learning framework for protein engineering. Nat Commun 12, 5743 (2021).</p> </td> </tr> <tr> <td><a href="https://doi.org/10.1038/s41592-021-01100-y" target="_blank" rel="noopener">eUniRep</a></td> <td>Biswas, S., Khimulya, G., Alley, E.C. et al. Low-N protein engineering with data-efficient deep learning. Nat Methods 18, 389–396 (2021)</td> </tr> <tr> <td><a href="https://doi.org/10.1038/nbt.3769" target="_blank" rel="noopener">EVmutation</a></td> <td>Hopf, T., Ingraham, J., Poelwijk, F. et al. Mutation effects predicted from sequence co-variation. Nat Biotechnol 35, 128–135 (2017).</td> </tr> <tr> <td><a href="https://doi.org/10.1038/s41592-019-0598-1" target="_blank" rel="noopener">UniRep</a></td> <td>Alley, E.C., Khimulya, G., Biswas, S. et al. Unified rational protein engineering with sequence-based deep representation learning. Nat Methods 16, 1315–1322 (2019).</td> </tr> </tbody> </table> <p> </p>
[PART 3] How to fit a round peg in a square hole: Pseudomonas aeruginosa acyl-CoA dehydrogenases and structure-guided inversion of their substrate specificity.
<p>Metadynamics data for the PaFADE1</p> <p>1320- PaFadE1 8PNS noCoA +FAD + G129M A295E - metadynamics, 10A3 OPLS4 T3P<br>1321- PaFadE1 8PNS noCoA +FAD WT - metadynamics, 10A3 OPLS4 T3P</p>
[PART 2] How to fit a round peg in a square hole: Pseudomonas aeruginosa acyl-CoA dehydrogenases and structure-guided inversion of their substrate specificity.
<p>Classical unbiased molecular dynamics dataset generated with Maestro 2023.4</p> <p>1320- PaFadE1 8PNS noCoA +FAD + G129M A295E, 10A3 OPLS4 T3P<br>1321- PaFadE1 8PNS noCoA +FAD WT, 10A3 OPLS4 T3P</p>
Fitness improvements after a six-week plyometric program in young basketball players
<p>This is the database of the article "Fitness improvements after a six-week plyometric program in young basketball players".</p>
Fitting parameters for "Concurrent Observation of High-frequency EMIC Waves and Low-harmonic Fast MS Waves within a Magnetic Dip in the Inner Magnetosphere"
<p>1. whamp_input_ionfit_*.mat</p> <p>The fitting parameters for the growth rate calculation of HFEMIC waves, which includes: </p> <div> <div>Bi-Maxwellian distribution parameters:</div> <div>PlasmaModel.B - magnetic field in nT</div> <div>PlasmaModel.Species.m - mass/mass_proton (0 means electron)</div> <div>PlasmaModel.Species.n - density in cm^-3</div> <div>PlasmaModel.Species.t - temperature in eV</div> <div>PlasmaModel.Species.a - anisotropy, Tperp/Tpara</div> <div> </div> </div> <p>2. shell_dist_*.mat</p> <p>The fitting parameters for the growth rate calculation of MS waves, which includes:</p> <div>Bi-Maxwellian distribution parameters:</div> <div>PlasmaModel.B - magnetic field in nT</div> <div>PlasmaModel.Species.m - mass/mass_proton (0 means electron)</div> <div>PlasmaModel.Species.n - density in cm^-3</div> <div>PlasmaModel.Species.t - temperature in eV</div> <div>PlasmaModel.Species.a - anisotropy, Tperp/Tpara</div> <div> </div> <div>Partial shell distribution parameters:</div> <div> <div>PlasmaModel.Shell.m - mass/mass_proton (0 means electron)</div> <div>PlasmaModel.Shell.ns - density in cm^-3</div> <div>PlasmaModel.Shell.sigma - the degree of pitch angle anisotropy</div> <div>PlasmaModel.Shell.Vs - the shell speed in m/s <div>PlasmaModel.Shell.theta_s - the thermal spread of the shell in m/s</div> </div> </div>
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.