Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
79
datasets available to search
ShareScore release 0.9.0
Dataset results
79 results for “evolution strategies”
Data and code for theoretical analyses for the evolution of biogenic volatile organic compounds (BVOCs) emission strategy
<p>These are Python code for analysis and JSON data obtained by simulation with the lattice model.</p> <p>To visualize figures better, we have slightly modified the content of "LatticeModelVisualization.ipynb".</p>
Data supplementing the article "Diatom DNA metabarcoding for biomonitoring : strategies to avoid major taxonomical and bioinformatical biases limiting molecular indices capacities" K. Tapolczai, F. Keck, A. Bouchez, F. Rimet, M. Kahlert and V. Vasselon submitted to "Frontiers in Ecology and Evolution" journal
<p>These data supplement the article "Diatom DNA metabarcoding for biomonitoring : strategies to avoid major taxonomical and bioinformatical biases limiting molecular indices capacities" K. Tapolczai, F. Keck, A. Bouchez, F. Rimet, M. Kahlert and V. Vasselon submitted to "Frontiers in Ecology and Evolution" journal.</p> <p>The directory contains the following files:</p> <p><strong>464_samples_fastq_files_(mothur).rar </strong>- contains the 464 fastq files proceed together during the Mothur bioinformatics treatments to produce the OTUs and ISUs tables. As the contig and the demultiplexing steps were performed by the sequencing platform, there is 1 fastq file per sample. From this 464 samples OTU/ISU tables, only information regarding 76 samples were used in this study and are listed in the "<strong>76_samples_list_(mothur).xlsx" </strong>file<strong>.</strong></p> <p><strong>76_samples_list_(mothur).xlsx </strong>- contains the information regarding the 76 samples used to create the OTUs and ISUs tables presented in the paper.</p> <p><strong>76_samples_R1_R2_fastq_files(DADA2).rar - </strong>contains the raw demultiplexed fastq files (R1.fastq and R2.fastq) for each of the 76 samples used in this study to produce the ESVs table using the DADA2 bioinformatics pipeline.</p>
Ecology drives the evolution of diverse social strategies in Pseudomonas aeruginosa
<p><span>Bacteria often cooperate by secreting molecules that can be shared as public goods between cells. Because the production of public goods is subject to cheating by mutants that exploit the good without contributing to it, there has been great interest in elucidating the evolutionary forces that maintain cooperation. However, little is known on how bacterial cooperation evolves under conditions where cheating is unlikely of importance. Here we use experimental evolution to follow changes in the production of a model public good, the iron-scavenging siderophore pyoverdine, of the bacterium <i>Pseudomonas aeruginosa</i>. After 1200 generations of evolution in nine different environments, we observed that cheaters only reached high frequency in liquid medium with low iron availability. Conversely, when adding iron to reduce the cost of producing pyoverdine, we observed selection for pyoverdine hyper-producers. Similarly, hyper-producers also spread in populations evolved in highly viscous media, where relatedness between interacting individuals is increased. Whole-genome sequencing of evolved clones revealed that hyper-production is associated with mutations involving genes encoding quorum-sensing communication systems, while cheater clones had mutations in the iron-starvation sigma factor or in pyoverdine biosynthesis genes. Our findings demonstrate that bacterial social traits can evolve rapidly in divergent directions, with particularly strong selection for increased levels of cooperation occurring in environments where individual dispersal is reduced, as predicted by social evolution theory. Moreover, we establish a regulatory link between pyoverdine production and quorum-sensing, showing that increased cooperation with respect to one trait (pyoverdine) can be associated with the loss (quorum-sensing) of another social trait.Bacteria often cooperate by secreting molecules that can be shared as public goods between cells. Because the production of public goods is subject to cheating by mutants that exploit the good without contributing to it, there has been great interest in elucidating the evolutionary forces that maintain cooperation. However, little is known on how bacterial cooperation evolves under conditions where cheating is unlikely of importance. Here we use experimental evolution to follow changes in the production of a model public good, the iron-scavenging siderophore pyoverdine, of the bacterium <i>Pseudomonas aeruginosa</i>. After 1200 generations of evolution in nine different environments, we observed that cheaters only reached high frequency in liquid medium with low iron availability. Conversely, when adding iron to reduce the cost of producing pyoverdine, we observed selection for pyoverdine hyper-producers. Similarly, hyper-producers also spread in populations evolved in highly viscous media, where relatedness between interacting individuals is increased. Whole-genome sequencing of evolved clones revealed that hyper-production is associated with mutations involving genes encoding quorum-sensing communication systems, while cheater clones had mutations in the iron-starvation sigma factor or in pyoverdine biosynthesis genes. Our findings demonstrate that bacterial social traits can evolve rapidly in divergent directions, with particularly strong selection for increased levels of cooperation occurring in environments where individual dispersal is reduced, as predicted by social evolution theory. Moreover, we establish a regulatory link between pyoverdine production and quorum-sensing, showing that increased cooperation with respect to one trait (pyoverdine) can be associated with the loss (quorum-sensing) of another social trait.</span></p>
Ecology drives the evolution of diverse social strategies in Pseudomonas aeruginosa
Open the record for dataset details and reuse information.
An age-dependent ovulatory strategy explains the evolution of dizygotic twinning in humans
Open the record for dataset details and reuse information.
Evolution of population-specific migration routes in the great reed warbler <em>Acrocephalus arundinaceus</em>: Evidence of a novel spring migration strategy
Open the record for dataset details and reuse information.
Evolution of a novel female reproductive strategy in Drosophila melanogaster populations subjected to long term protein restriction
Open the record for dataset details and reuse information.
Model output data for "Negative density-dependent dispersal emerges from the joint evolution of density- and body condition-dependent dispersal strategies"
<p>Empirical studies have documented both positive and negative density-dependent dispersal, yet most theoretical models predict positive density dependence as a mechanism to avoid competition. Several hypotheses have been proposed to explain the occurrence of negative density-dependent dispersal, but few of these have been formally modeled. Here, we developed an individual based model of the evolution of density-dependent dispersal. This model is novel in that it considers the effects of density on dispersal directly, and indirectly through effects on individual condition. Body condition is determined mechanistically, by having juveniles compete for resources in their natal patch. We found that the evolved dispersal strategy was a steep, increasing function of both density and condition. Interestingly, although populations evolved a positive density-dependent dispersal strategy, the simulated metapopulations exhibited negative density-dependent dispersal. This occurred because of the negative relationship between density and body condition: high density sites produced low condition individuals that lacked the resources required for dispersal. Our model therefore generates the novel hypothesis that observed negative density-dependent dispersal can occur when high density limits the ability of organisms to disperse. We suggest that future studies consider how phenotype is linked to the environment when investigating the evolution of dispersal.</p>
Data from: Outcomes of co-infection by two potyviruses: implications for the evolution of manipulative strategies
Recent studies have documented effects of plant-viruses on host plants that appear to enhance transmission by insect vectors. But, almost no empirical work has explored the implications of such apparent manipulation for interactions among co-infecting pathogens. We examined single and mixed infections of two potyviruses, Watermelon mosaic virus (WMV) and Zucchini yellow mosaic virus (ZYMV), that frequently co-occur in cucurbitaceae populations and share the same aphid vectors. We found that ZYMV isolates replicated at similar rates in single and mixed infections, while WMV strains accumulated to signficantly lower levels in the presence of ZYMV. Furthermore, ZYMV induced changes in leaf colour and volatile emissions that enhanced aphid (Aphis gossypii) recruitment to infected plants. In contrast, WMV did not elicit strong effects on plant-aphid interactions. Nevertheless, WMV was still readily transmitted from mixed infections, despite fairing poorly in in-plant competition. These findings suggest that pathogen effects on host-vector interactions may well influence competition among co-infecting pathogens. For example, if non-manipulative pathogens benefit from the increased vector traffic elicited by manipulative competitors, their costs of competition may be mitigated to some extent. Conversely, the benefits of manipulation may be limited by free-rider effects in systems where there is strong competition among pathogens for host resources and/or access to vectors.
Data from: How parasite interaction strategies alter virulence evolution in multi-parasite communities
The majority of organisms host multiple parasite species, each of which can interact with hosts and competitors through a diverse range of direct and indirect mechanisms. These within-host interactions can directly alter the mortality rate of coinfected hosts and alter the evolution of virulence (parasite induced host mortality). Yet we still know little about how within-host interactions affect the evolution of parasite virulence in multi-parasite communities. Here, we modeled the virulence evolution of two coinfecting parasites in a host population in which parasites interacted through cross immunity, immune suppression, immunopathology, or spite. We show (1) that these within-host interactions have different effects on virulence evolution when all parasites interact with each other in the same way vs. when coinfecting parasites have unique interaction strategies, (2) that all of these interactions cause the evolution of lower virulence in some hosts, and higher virulence in other hosts, depending on the hosts infection status, and (3) that for cross immunity and spite, whether parasites increased or decreased the evolutionarily stable virulence in coinfected hosts depended on interaction strength. These results improve our understanding of virulence evolution in complex parasite communities, and show that virulence evolution must be understood at the community scale.
Data from: The evolution of alternative adaptive strategies for effective communication in noisy environments
Animals communicating socially are expected to produce signals that are conspicuous within the habitats in which they live. The particular way in which a species adapts to its environment will depend on its ancestral condition and evolutionary history. At this point, it is unclear how properties of the environment and historical factors interact to shape communication. Tropical Anolis lizards advertise territorial ownership using visual displays in habitats where visual motion or 'noise' from windblown vegetation poses an acute problem for the detection of display movements. We studied eight Anolis species that live in similar noise environments, but belong to separate island radiations with divergent evolutionary histories. We found that species on Puerto Rico displayed at times when their signals were more likely to be detected by neighboring males and females (during periods of low noise). In contrast, species on Jamaica displayed irrespective of the level of environmental motion, apparently because these species have a display that is effective in a range of viewing conditions. Our findings appear to reflect a case of species originating from different evolutionary starting points evolving different signal strategies for effective communication in noisy environments.
Phage-host co-evolution has led to distinct generalized transduction strategies
Open the record for dataset details and reuse information.
A Dual Anchoring Strategy for the Directed Evolution of Improved Artificial Transfer Hydrogenases Based on Carbonic Anhydrase
<p>Data underlying the figures in the publication “A Dual Anchoring Strategy for the Directed Evolution of Improved Artificial Transfer Hydrogenases Based on Carbonic Anhydrase”, published in <em>ACS Cent. Sci. </em><em><strong>2021</strong></em><em>, 7, 11, 1874–1884.</em></p> <p><a href="https://pubs.acs.org/doi/full/10.1021/acscentsci.1c00825">https://pubs.acs.org/doi/full/10.1021/acscentsci.1c00825</a></p> <p>Table of contents:</p> <p><strong>1. Triplicates_20210118-YC-NCCR.xlsx</strong>: Experimental data for <em>Figures 3e</em>.</p> <p><strong>2. HRMS_Data.pdf</strong>: HRMS data for <em>Table 3</em>.</p> <p><strong>3. Table4_Raw.xlsx</strong>: Raw data for <em>Table 4</em>.</p> <p><strong>4. Table1_Table2_Raw.xlsx</strong>: HRMS data for <em>Table 1</em> and <em>Table 2</em>.</p> <p><strong>5. Preparative.xlsx</strong>: Raw data for <em>Table 2, </em>entries 10 and 11.</p>
Evolution of winter moulting strategies in European and North American migratory passerines
<p>Moult is critical for birds as it replaces damaged feathers and worn plumage, enhancing flight performance, thermoregulation, and communication. In passerines, moult generally occurs on the breeding grounds during the post-breeding period once a year. However, some species of migrant passerines that breed in the Nearctic and western Palearctic regions have evolved different moulting strategies that involve moulting on the overwintering grounds. Some species forego moult on the breeding grounds and instead complete their prebasic moult on the overwintering grounds. Other species moult some or all feathers a second time (prealternate moult) during the overwintering period. Using phylogenetic analyses, we explored the po<span>tential drivers of the evolution of winter moults in Nearctic and western Palearctic breeding passerines. Our results indicate an association between longer photoperiods and the presence of prebasic and prealternate moults on the overwintering grounds for both Nearctic and western Palearctic species. We also found a relationship between prealternate moult and </span><span><span>generalist and water</span></span><span> habitats for western Palearctic species. Finally, the complete prealternate moult in western Palearctic passerines was linked to longer days on the overwintering grounds and longer migration distance. Longer days may favour the evolution of winter prebasic moult by increasing </span><span><span>the time window when birds can absorb essential nutrients</span></span><span> for moult. Alternatively, for birds undertaking a prealternate moult at the end of the overwintering period, longer days may increase exposure to feather-degrading ultra-violet radiation, necessitating the replacement of feathers. Our study underlines the importance of the overwintering grounds in the critical process of moult for many passerines that breed in th</span>e Nearctic and western Palearctic regions.</p>
A translation-independent directed evolution strategy to engineer aminoacyl-tRNA synthetases_NGS data analysis
<p>These data files are associated with the NGS analysis done in the publication :"A translation-independent directed evolution strategy to engineer aminoacyl-tRNA synthetases". This compressed file contains the raw file as well as the processed files to arrive at the conclusions published. The python scripts used for processing the data are available on github (link provided in the manuscript).</p>
Associated data for "Optimisation strategies for directed evolution without sequencing"
<p>Associated publication available at https://www.biorxiv.org/content/10.1101/2024.03.18.585521v1. Code for visualisation available at https://github.com/nesou2/direvo_sim (PLOS_figures/PLOS_figures.ipynb).</p>
Precipitation predictability drives evolution of drought strategies in the common poppy, Papaver rhoeas
<ol> <li>Current climate change leads to an increase in the frequency and intensity of droughts and to decreased precipitation predictability. The few studies investigating plant evolutionary responses to contrasting predictability regimes showed that intrinsic precipitation predictability shapes plant phenotypic variation, drives evolution of phenotypic plasticity, and can vary in strength and direction of selection. This suggests that the selection pressure induced by decreased precipitation predictability may lead to plants coping better with severe drought events. </li> <li>To investigate whether past precipitation predictability influences plant responses to different drought conditions, we performed a common-garden experiment applying control, short-term and long-term drought treatments on seedlings of <em>Papaver rhoeas</em> (Papaveraceae) whose progenitors experienced less versus more precipitation predictability treatments for three consecutive generations. In addition, to assess whether competition modulates plant responses, half of the plants were grown together with the widespread herbaceous plant <em>Galium album </em>(Rubiaceae).</li> <li>In the presence of long drought episodes, plants whose progenitors experienced less predictable precipitation survived longer than those whose progenitors experienced more predictable precipitation. Furthermore, plants whose progenitors experienced less predictable precipitation had lower biomass, which is likely to reduce water loss via transpiration, and, across all drought treatments, they showed lower root investment. However, no trait differences were detected under competition, indicating that interspecific competition may limit the expression of evolutionary responses to changes induced by precipitation predictability.</li> <li>Altogether our results indicate that lower precipitation predictability mainly promotes the evolution of drought-escape and drought-avoidance strategies. Overall, our experiment highlights that precipitation predictability is an important evolutionary driver of plant functional responses, potentially shifting evolutionary trajectories of plants under increasing intensity of drought events. </li> </ol>
Evolution of Management Strategies of Heart Failure Patients With Implantable Defibrillators
ClinicalTrials.gov study NCT00873899. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Data from: The evolution of alternative adaptive strategies for effective communication in noisy environments
Open the record for dataset details and reuse information.
Evolution of winter moulting strategies in European and North American migratory passerines
Open the record for dataset details and reuse information.
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.