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829 results for “Evolvability”
Evolving therapies, neurocognitive outcomes, and functional independence in adult survivors of childhood glioma
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Data for: How frictional slip evolves
<p>songlin.shi@mail.huji.ac.il</p>
Supplementary Materials of the Manuscript: "Evolving a Methodology for Assessing Pesticide Pressure on Water Bodies under Data Scarce Conditions in compliance with the European Green Deal – Case Study on Marmara Basin in Türkiye-ID:sustainability-2755948"
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Evolving Trends in Granulomatous Mastitis Research: A Bibliometric Analysis; Tables & Figures
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Probing fossil magnetic field effects in the core of evolved low-mass stars using mixed-mode frequencies
<p>The recent discovery of the moderate differential rotation between the core and the envelope of intermediate-mass (IM) main-sequence and evolved stars, and the population of IM red giants presenting a surprisingly low-amplitude of their mixed modes (i.e. modes that behave as acoustic modes in their external envelope and as gravity modes in their core) could both be the signature of a strong magnetic field trapped inside the radiative regions of IM stars. Indeed, stars more massive than 1.1 solar mass are known to develop a convective core during their main sequence. The field generated by the dynamo triggered by this convection could be the progenitor of a strong fossil magnetic field trapped inside the core of the star for the rest of its evolution. In this context, the mixed modes observed thanks to space-based asteroseismology can constitute an excellent probe of the deepest layers in IM evolved stars: such magnetic fields may impact their propagation inside the core of these stars, and these perturbations should be visible in asteroseismic data. To unravel which constraints can be obtained from these observations, we theoretically investigate the effects of a plausible mixed magnetic field with various amplitudes on the mixed-mode frequencies of red giants. Applying a perturbative method, we estimate the magnetic splitting of the frequencies of simulated mixed dipolar modes that depends on the magnetic field strength and its configuration. A complete asymptotic analysis is derived, showing the potential of asteroseismology to probe the magnetism at each depth as this is done for stellar rotation. The effects of the mass and the metallicity of the stars are also explored. Finally, we infer an upper limit for the strength of the field and the associated lower limit for the timescale of its action to redistribute angular momentum in stellar interiors.</p>
Molecular basis for the evolved instability of a human G-protein coupled receptor
<p>Membrane proteins are prone to misfolding and degradation. This is particularly true for mammalian forms of the gonadotropin-releasing hormone receptor (GnRHR). Although they function at the plasma membrane, mammalian GnRHRs accumulate within the secretory pathway. Their apparent instability is believed to have evolved through selection for attenuated GnRHR activity. Nevertheless, the molecular basis of this adaptation remains unclear. We show that adaptation coincides with a C-terminal truncation that compromises the translocon-mediated membrane integration of its seventh transmembrane domain (TM7). We also identify a series of polar residues in mammalian GnRHRs that compromise the membrane integration of TM2 and TM6. Reverting a lipid-exposed polar residue in TM6 to an ancestral hydrophobic residue restores expression with no impact on function. Evolutionary trends suggest variations in the polarity of this residue track with reproductive phenotypes. Our findings suggest that the marginal energetics of cotranslational folding can be exploited to tune membrane protein fitness.</p>
Earth and life evolve together- a comment on Yamahira et al.
<p><span><span><span>The provocative study by Yamahira et al. hypothesizes that one species, <i>Oryzias setnai</i>, endemic to coastal areas of west-flowing streams of the Western Ghats, is the sister species of all other ricefishes and that it diverged in the late Mesozoic. They conclude India is the center of origin of ricefishes, the ancestral lineage of which subsequently diversified and dispersed to occupy its current broad range throughout Asia and Southeast Asia. This scenario is presented as the only possible conclusion from the molecular phylogenetic analysis. We challenge their scenario and conclusions based on a reanalysis of their data.</span></span></span></p>
Combining metabolomics and experimental evolution reveals key mechanisms underlying longevity differences in laboratory evolved Drosophila melanogaster populations
<p>Experimental evolution with Drosophila melanogaster has been used extensively for decades to study aging and longevity. In recent years, the addition of DNA and RNA sequencing to this framework has allowed researchers to leverage the statistical power inherent to experimental evolution to study the genetic basis of longevity itself. Here, we incorporated metabolomic data into to this framework to generate even deeper insights into the physiological and genetic mechanisms underlying longevity differences in three groups of experimentally evolved D. melanogaster populations with different aging and longevity patterns. Our metabolomic analysis found that aging alters mitochondrial metabolism through increased consumption of NAD<sup>+</sup> and increased usage of the TCA cycle. Combining our genomic and metabolomic data produced a list of biologically relevant candidate genes. Among these candidates, we found significant enrichment for genes and pathways associated with neurological development and function, and carbohydrate metabolism. While we do not explicitly find enrichment for aging canonical genes, neurological dysregulation and carbohydrate metabolism are both known to be associated with accelerated aging and reduced longevity. Taken together, our results provide plausible genetic mechanisms for what might be driving longevity differences in this experimental system. More broadly, our findings demonstrate the value of combining multiple types of omic data with experimental evolution when attempting to dissect mechanisms underlying complex and highly polygenic traits such as aging.</p>
Color, activity period, and eye structure in four lineages of ants: Pale, nocturnal species have evolved larger eyes and larger facets than their dark, diurnal congeners
<p>The eyes of insects display an incredible diversity of adaptations to enhance vision across the gamut of light levels they experience. One commonly studied contrast is the difference in eye structure between nocturnal and diurnal species, with nocturnal species typically having features that enhance eye sensitivity such as larger eyes, larger eye facets, and larger ocelli. In this study, we compared eye structure between workers of closely related nocturnal and diurnal above-ground foraging ant species (Hymenoptera: Formicidae) in four genera (<em>Myrmecocystus, Aphaenogaster, Temnothorax, Veromessor</em>). In all four genera, nocturnal species tend to have little cuticular pigment (pale), while diurnal species are heavily pigmented (dark), hence we could use cuticle coloration as a surrogate for activity pattern. Across three genera (<em>Myrmecocystus, Aphaenogaster, Temnothorax</em>), pale species, as expected for nocturnally active animals, had larger eyes, larger facet diameters, and larger visual spans compared to their dark, more day-active congeners. This same pattern occurred for one pale species of <em>Veromessor</em>, but not the other. There were no consistent differences between nocturnal and diurnal species in interommatidial angles and eye parameters both within and among genera. Hence, the evolution of eye features that enhance sensitivity in low light levels do not appear to have consistent correlated effects on features related to visual acuity. A survey across several additional ant genera found numerous other pale species with enlarged eyes, suggesting these traits evolved multiple times within and across genera. We also compared the size of the anterior ocellus in workers of pale versus dark species of <em>Myrmecocystus</em>. In species with larger workers, the anterior ocellus was smaller in pale than in dark species, but this difference mostly disappeared for species with smaller workers. Presence of the anterior ocellus also was size-dependent in the two largest pale species.</p>
Figure 3 in The First Cases of Evolving Glyphosate Resistance in UK Poverty Brome (Bromus sterilis) Populations
Figure 3. Calculated glyphosate ED50 values for 11 field-collected B. sterilis populations from the United Kingdom. Error bars are standard error of ED50 parameter estimates.
Functionally Important Residues from Graph Analysis of Co-evolved Dynamical Couplings
<p>This dataset contains input files and trajectories for class A β-lactamase SHV-1.</p>
Membrane modeling results from Surface Evolver
<h3>Summary</h3> <p>Three sets of membrane shapes of genus 0 generated in Surface Evolver (Brakke, 1992) are published here. </p> <p>The first set "ZS" reproduces the shapes that were published in Ziherl & Svetina (2005) (bi-layer energy with fixed integrated mean curvature, volume and area). In addition we report on energy values and deliver the shapes as .obj-files. The .dmp files are dumps from the Evolver runs, derived from Frickenhaus (2024).</p> <p>With the same approach, the second set "ST" was created, focusing on axisymmetric stick-like shapes, such as the UnduStick that has been investigated in detail in Frickenhaus & Wölper (2024). </p> <p>The third set "SC" deals with a Helfrich-flow energy functional, where instead of setting a mean curvature constraint, spontaneous curvature $H_0$ enters the bending energy functional.</p> <p>In all three sets energy minimization was done as much as possible, using Newton iteration (hessian_seek) along the surface normals, and gradient decent iterations until energy remained constant. The triangulation was adapted (see command macro gogo in .dmp files) by allowing tangential moves for some steps, equiangulation, vertex averaging, as well as edge length adaptation. File names may indicate non-equilibrium (-ne) or a saddle point (-saddle).</p> <p>Constraint target values are changed in a step-wise manner, writing out the complete data and macros for restarts after every step in a Surface Evolver dump-file automatically. Macros govu and gocu are for volume and curvature change, respectively. dv and dc are the corresponding volume/ curvature change per govo/ gocu cycle. If the triangulation becomes degenerate narrow, it may lead to automatic popping off (budding), i.e. seperation into two bodies. However, quantities volume, curvature and energy are not split up accordingly. </p> <p>The data was created during a project week on Scientific Programming at the University of Bremen, Germany (Mathematics, Summer 2024).</p> <h3>License/ Citation</h3> <p>The data is licensed CC-BY-4.0.</p> <p>When using the code, please cite appropriatly:</p> <p>Frickenhaus, S., Parmar, J. M., Mardomkhah, R., & Asadian, P. (2024). Membrane modeling results from Surface Evolver [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.12805964" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.12805964</a></p> <h3>Contributions</h3> <p>RM and PA created the ZS data; JMP created the ST data, and SF created the SC data.</p> <h3>References</h3> <p>K.A. Brakke (1992) The Surface Evolver. Exp. Math. 1(2) <a href="https://dblp.org/db/journals/em/em1.html#Brakke92">https://dblp.org/db/journals/em/em1.html#Brakke92</a> 141-165</p> <p>P. Ziherl and S. Svetina (2005), Nonaxisymmetric phospholipid vesicles: Rackets, boomerangs, and starfish. EPL 70 690, <a href="https://doi.org/10.1209/epl/i2004-10527-4">doi: 10.1209/epl/i2004-10527-4</a></p> <p>S. Frickenhaus, (2024). Exploration of extreme vesicle shapes and their modular structure (1.0). Zenodo. <a href="https://doi.org/10.5281/zenodo.11199344" target="_blank" rel="noopener">doi: 10.5281/zenodo.11199344</a></p> <p>S. Frickenhaus, C. Wölper, (2024). MembraneR - a membrane modeling environment in R (Version 1). Zenodo. <a href="https://doi.org/10.5281/zenodo.12721406" target="_blank" rel="noopener">doi: 10.5281/zenodo.12721406</a></p>
Data and figures for "Evolving interdisciplinary contributions to global societal challenges: A 50-year overview"
<div>This package accompanies the <a href="https://doi.org/10.1016/j.wdp.2025.100728">paper</a> titled <em>"Evolving interdisciplinary contributions to global societal challenges: A 50-year overview",</em> available on arXiv. The datasets and figures included are derived from data obtained through the <a href="https://openalex.org">OpenAlex</a> API. For further details, please refer to the original <a href="https://doi.org/10.1016/j.wdp.2025.100728">paper</a>. <h2>Suppl_data_1.csv</h2> Domains are labelled by 𝛼 = 1, ..., 4, where 1: Life Sciences, 2: Social Sciences, 3: Physical Sciences, and 4: Health Sciences. <p> </p> <table> <tbody> <tr> <td><strong>pyear</strong></td> <td>Year of publication</td> </tr> <tr> <td><strong>nwork</strong></td> <td>Number of publications, indexed in OpenAlex</td> </tr> <tr> <td><strong>nwork𝛼</strong></td> <td>Number of publications in domain 𝛼, indexed in OpenAlex</td> </tr> <tr> <td><strong>nIDR</strong></td> <td> <p>Number of publications with ’multi-/inter-/trans-disciplinar*’ in Title or Abstract, indexed in OpenAlex</p> </td> </tr> <tr> <td><strong>nIDR𝛼</strong></td> <td>Number of publications in domain 𝛼 with ’multi-/inter-/trans-disciplinar*’ in Title or Abstract, indexed in OpenAlex</td> </tr> <tr> <td><strong>%nIDR </strong></td> <td>Ratio of nIDR to nwork (in %) </td> </tr> <tr> <td><strong>%nIDR𝛼 </strong></td> <td>Ratio of nIDR𝛼 to nwork𝛼 (in %)</td> </tr> </tbody> </table> <p> </p> <h2>Suppl_data_2.csv</h2> Disciplines (the level-0 concepts defined in OpenAlex) are labelled by k = 1, ..., 19, where 1: Political Science, 2: Philosophy, 3: Economics, 4: Business, 5: Psychology, 6: Mathematics, 7: Medicine, 8: Biology, 9: Computer Science, 10: Geology, 11: Chemistry, 12: Art, 13: Sociology, 14: Engineering, 15: Geography, 16: History, 17: Materials Science, 18: Physics, and 19: Environmental Science. <p> </p> </div> <div> <div> <table> <tbody> <tr> <td><strong>idwork</strong></td> <td>Work identifier starting with ‘W’, as defined in OpenAlex</td> </tr> <tr> <td><strong>pyear</strong></td> <td>Year of publication</td> </tr> <tr> <td><strong>citation</strong></td> <td>Number of citations, as of April 2024, indexed in OpenAlex</td> </tr> <tr> <td><strong>discip<em>k</em></strong></td> <td>Score of affinity to each of the level-0 concepts defined in OpenAlex (<em>k</em> = 1, ..., 19)</td> </tr> <tr> <td> <p><strong>SDG<em>m</em></strong></p> </td> <td> <p>Score of affinity to each of the United Nations’ Sustainable Development Goals (SDGs) (<em>m</em> = 1, ..., 17)</p> </td> </tr> </tbody> </table> </div> <div> <p> </p> </div> </div>
Data from: Experimentally evolved and phenotypically plastic responses to enforced monogamy in a hermaphroditic flatworm
Sexual selection is considered a potent evolutionary force in all sexually reproducing organisms, but direct tests in terms of experimental evolution of sexual traits are still lacking for simultaneously hermaphroditic animals. Here, we tested how evolution under enforced monogamy affected a suite of reproductive traits (including testis area, sex allocation, genital morphology, sperm morphology and mating behaviour) in the outcrossing hermaphroditic flatworm Macrostomum lignano, using an assay that also allowed the assessment of phenotypically plastic responses to group size. The experiment comprised 32 independent selection lines that evolved under either monogamy or polygamy for 20 generations. While we did not observe an evolutionary shift in sex allocation, we detected effects of the selection regime for two male morphological traits. Specifically, worms evolving under enforced monogamy had a distinct shape of the male copulatory organ and produced sperm with shorter appendages. Many traits that did not evolve under enforced monogamy showed phenotypic plasticity in response to group size. Notably, individuals that grew up in larger groups had a more male-biased sex allocation and produced slightly longer sperm than individuals raised in pairs. We conclude that, in this flatworm, enforced monogamy induced moderate evolutionary but substantial phenotypically plastic responses.
Data from: Obligately silent males sire more offspring than singers in a rapidly evolving cricket population
How sexual traits are gained and lost in the wild remains an important question in evolutionary biology. Pacific field crickets (Teleogryllus oceanicus) in Hawaii provide an unprecedented opportunity to investigate the factors facilitating evolutionary loss of a sexual signal in real time. Natural selection from an acoustically-orienting parasitoid fly drove rapid evolution of a novel, silent male morph. While silent (flatwing) males enjoy protection from the fly, they face difficulty attracting mates. We tested how offspring production varies in association with three male attributes affected by the spread of flatwing: wing morph (flatwing or normal-wing), age (flatwings should survive longer than singers), and exposure to calling song during rearing (wild populations with many flatwings lack ambient calling song). Per mating event, flatwings sired more offspring than singers, and older males were mounted more quickly by females when presented with standard courtship song. Despite prior work showing that male age and acoustic experience influences sperm characteristics associated with fertilization, age and song exposure had no influence on male offspring production per mating. This represents the first evidence that the silent male morph possesses a reproductive advantage that may help compensate for precopulatory barriers to mate attraction.
Data from: Additive genetic variance in polyandry enables its evolution, but polyandry is unlikely to evolve through sexy or good sperm processes
Polyandry is widespread despite its costs. The sexually selected sperm hypotheses ('sexy' and 'good' sperm) posit that sperm competition plays a role in the evolution of polyandry. Two poorly studied assumptions of these hypotheses are the presence of additive genetic variance in polyandry and sperm competitiveness. Using a quantitative genetic breeding design in a natural population of Drosophila melanogaster, we first established the potential for polyandry to respond to selection. We then investigated whether polyandry can evolve through sexually selected sperm processes. We measured lifetime polyandry and offensive sperm competitiveness (P2) while controlling for sampling variance due to male x male x female interactions. We also measured additive genetic variance in egg-to-adult viability and controlled for its effect on P2 estimates. Female lifetime polyandry showed significant and substantial additive genetic variance and evolvability. In contrast, we found little genetic variance or evolvability in P2 or egg-to-adult viability. Additive genetic variance in polyandry highlights its potential to respond to selection. However, the low levels of genetic variance in sperm competitiveness suggest the evolution of polyandry may not be driven by sexy sperm or good sperm processes.
Data from: Yeast adapts to a changing stressful environment by evolving cross-protection and anticipatory gene regulation.
Organisms can protect themselves against future environmental change. An example is cross-protection, where physiological adaptation against a present environmental stressor can protect an organism against a future stressor. Another is anticipation, where an organism uses information about its present environment to trigger gene expression and other physiological changes adaptive in future environments. "Predictive" abilities like this exist in organisms that have been exposed to periodic changes in environments. It is unknown how readily they can evolve. To answer this question, we carried out laboratory evolution experiments in the yeast Saccharomyces cerevisiae. Specifically, we exposed three replicate populations of yeast to environments that varied cyclically between two stressors, salt stress and oxidative stress, every 10 generations, for a total of 300 generations. We evolved six replicate control populations in only one of these stressors for the same amount of time. We analyzed fitness changes and genome-scale expression changes in all these evolved populations. Our populations evolved asymmetric cross protection, where oxidative stress protects against salt stress but not vice versa. Gene expression data also suggest the evolution of anticipation and basal gene expression changes that occur uniquely in cyclic environments. Our study shows that highly complex physiological states that are adaptive in future environments can evolve on very short evolutionary time scales.
Data from: Negative epistasis between beneficial mutations in an evolving bacterial population
Epistatic interactions between mutations play a prominent role in evolutionary theories. Many studies have found that epistasis is widespread, but they have rarely considered beneficial mutations. We analyzed the effects of epistasis on fitness for the first five mutations to fix in an experimental population of Escherichia coli. Epistasis depended on the effects of the combined mutations—the larger the expected benefit, the more negative the epistatic effect. Epistasis thus tended to produce diminishing returns with genotype fitness, although interactions involving one particular mutation had the opposite effect. These data support models in which negative epistasis contributes to declining rates of adaptation over time. Sign epistasis was rare in this genome-wide study, in contrast to its prevalence in an earlier study of mutations in a single gene.
Data from: Escherichia coli populations in unpredictably fluctuating environments evolve to face novel stresses through enhanced efflux activity
There is considerable understanding about how laboratory populations respond to predictable (constant or deteriorating environment) selection for single environmental variables such as temperature or pH. However, such insights may not apply when selection environments comprise multiple variables that fluctuate unpredictably, as is common in nature. To address this issue, we grew replicate laboratory populations of Escherichia coli in nutrient broth whose pH and concentrations of salt (NaCl) and hydrogen peroxide (H2O2) were randomly changed daily. After ~170 generations, the fitness of the selected populations had not increased in any of the three selection environments. However, these selected populations had significantly greater fitness in four novel environments which have no known fitness-correlation with tolerance to pH, NaCl or H2O2. Interestingly, contrary to expectations, hypermutators did not evolve. Instead, the selected populations evolved an increased ability for energy-dependent efflux activity that might enable them to throw out toxins, including antibiotics, from the cell at a faster rate. This provides an alternate mechanism for how evolvability can evolve in bacteria and potentially lead to broad-spectrum antibiotic resistance, even in the absence of prior antibiotic exposure. Given that environmental variability is increasing in nature, this might have serious consequences for public health.
Fluctuating environments promote evolvability by shaping adaptive variation accessible to populations (Data)
<p>Data used in "Fluctuating environments promote evolvability by shaping adaptive variation accessible to populations", along with the scripts and analysis files. These include the configuration files used for Avida and the Wright-Fisher simulations. </p>
ScienceDex guides
Understand access before you commit
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.