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24 results for “artificial evolution”
Community diversity determines the evolution of synthetic bacterial communities under artificial selection
<p>These data and script are related to the article entitled "Community diversity determines the evolution of synthetic bacterial communities under artificial selection". This study reports the results of an experiment that involved bacterial communities differing for their richness level (1, 2, 4, 8, 16 species) and subjected to artificial selection or not. The property under selection was the optical density (OD). All the data needed to reproduce the figures and tables presented in the manuscript are provided.</p>
Enhanced Sequence-Activity Mapping and Evolution of Artificial Metalloenzymes by Active Learning
<p>This entry contains data, pretrained models and supplementary files for our enzyme engineering study:</p> <p><strong>Title:</strong> Enhanced Sequence-Activity Mapping and Evolution of Artificial Metalloenzymes by Active Learning<br><strong>Journal:</strong> ACS Central Science</p> <p>If you use any of the data or code in the <a href="https://github.com/lasgroup/ml-protein-design-sav-gold">repository</a>, please cite the paper.</p> <p>The contents of this entry are:</p> <ol> <li>Sequence embeddings needed for reproducing the code are found in data.zip. Unzip the contents of the folder to <code>/data</code> in the code structure. </li> <li>NGS sequencing analysis and raw data in <code>NGS analysis.zip</code></li> <li>10% subset of structures generated with the Rosetta software in <code>structures.zip</code></li> <li>Pretrained and saved models for plotting, clustering and further prediction are saved in <code>models.zip</code></li> <li>Raw assay data including our designed libraries by active learning are found in <code>assay_and_ML_data.zip</code></li> </ol>
Additional materials used in the paper "Towards Continuous Scientific Data Analysis and Hypothesis Evolution" on the Proceedings of the Thirty-First AAAI Conference on Artificial Intelligence (AAAI-17)
<p>This bundle contains a web page describing the materials used in the evaluation of the paper, along with references to the software and datasets, provenance metadata and workflows used. All the scripts and descriptions are included as well.</p>
CamoEvo: an open access toolbox for artificial camouflage evolution experiments
<p>Camouflage research has long shaped our understanding of evolution by natural selection, and elucidating the mechanisms by which camouflage operates remains a key question in visual ecology. However, the vast diversity of colour patterns found in animals and their backgrounds, combined with the scope for complex interactions with receiver vision presents a fundamental challenge for investigating optimal camouflage strategies. Genetic algorithms have provided a potential method for accounting for these interactions, but with limited accessibility. Here, we present CamoEvo, an open-access toolbox for investigating camouflage pattern optimisation by using tailored genetic algorithms, animal and egg maculation theory and artificial predation experiments. This system allows for camouflage evolution within the span of just 10-30 generations (~1-2 min per generation), producing patterns that are both significantly harder to detect and that are optimised to their background. CamoEvo was built in ImageJ to allow for integration with an array of existing open access camouflage analysis tools. We provide guides for editing and adjusting the predation experiment and genetic algorithm as well as an example experiment. The speed and flexibility of this toolbox makes it adaptable for a wide range of computer based phenotype optimisation experiments.</p>
Directed Evolution of a Surface-Displayed Artificial Allylic Deallylase Relying on a GFP Reporter Protein
<p>Data underlying the figures in the publication “Directed Evolution of a Surface-Displayed Artificial Allylic Deallylase Relying on a GFP Reporter Protein”, published in <em>ACS Catal</em>. <strong>2021</strong>, 11, 17, 10705–10712.</p> <p>https://pubs.acs.org/doi/10.1021/acscatal.1c02405</p> <p>Table of contents:</p> <p><strong>1. Dataset</strong>; Excel file with the experimental data for <em>figures 2a, 2b, 3b</em> and <em>5</em>, plus protocol for in vivo catalysis, sequencing data and the selection for rescreening.</p>
CamoEvo: an open access toolbox for artificial camouflage evolution experiments
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Data from: Evolution of cellular architecture and function of the hippocampus: Insights from the artificial selection experiment
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Data from: Hybridization, natural selection and evolution of reproductive isolation: a 25-years survey of an artificial sympatric area between two mosquito sibling species of the Aedes mariae complex
Natural selection can act against maladaptive hybridization between co-occurring divergent populations leading to evolution of reproductive isolation among them. A critical unanswered question about this process that provides a basis for the theory of speciation by reinforcement, is whether natural selection can cause hybridization rates to evolve to zero. Here we investigated this issue in two sibling mosquitoes species, Aedes mariae and Ae. zammitii, that show post-mating reproductive isolation (F1 males sterile) and partial pre-mating isolation (different height of mating swarms) that could be reinforced by natural selection against hybridization. In 1986, we created an artificial sympatric area between the two species and sampled about 20,000 individuals over the following 25 years. Between 1986 to 2011, the composition of mating swarms and the hybridization rate between the two species were investigated across time in the sympatric area. Our results showed that Ae. mariae and Ae. zammitii have not completed reproductive isolation since their first contact in the artificial sympatric area. We have discussed the relative role of factors such as time of contact, gene flow, strength of natural selection, and biological mechanisms causing prezygotic isolation to explain the observed results.
Data from: Potential rapid evolution of foot morphology in Italian plethodontid salamanders (Hydromantes strinatii) following the colonization of an artificial cave
How organisms respond to environmental change is a long-standing question in evolutionary biology. Species invading novel habitats provide an opportunity to examine contemporary evolution in action, and decipher the pace of evolutionary change over short time scales. Here we characterized phenotypic evolution in the Italian plethodontid salamander, Hydromantes strinatii following the recent colonization of an artificial cave by a forest floor population. When compared with a nearby and genetically related population in the natural forest floor and a nearby cave population, the artificial cave population displayed significant differences in overall foot shape, with more inter-digital webbing relative to the other populations. Further, this population evolved significantly larger feet, which corresponded more closely to those found in other cave populations than to forest floor populations to which the cave population is closely related. Finally, we quantified the rate of evolution for both foot shape and foot area, and found that both traits displayed large and significant evolutionary rates, at levels corresponding to other classic cases of rapid evolution in vertebrates. Together these findings reveal that the response to novel environmental pressures can be large and rapid, and that the anatomical shifts observed in the artificial cave population of H. strinatii may represent a case of rapid evolution in response to novel environmental pressures.
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>
Data from: Intense selective hunting leads to artificial evolution in horn size
The potential for selective harvests to induce rapid evolutionary change is an important question for conservation and evolutionary biology, with numerous biological, social and economic implications. We analyze 39 years of phenotypic data on horn size in bighorn sheep (Ovis canadensis) subject to intense trophy hunting for 23 years, after which harvests nearly ceased. Our analyses revealed a significant decline in genetic value for horn length of rams, consistent with an evolutionary response to artificial selection on this trait. The probability that the observed change in male horn length was due solely to drift is 9.9%. Female horn length and male horn base, traits genetically correlated to the trait under selection, showed weak declining trends. There was no temporal trend in genetic value for female horn base circumference, a trait not directly targeted by selective hunting and not genetically correlated with male horn length. The decline in genetic value for male horn length stopped, but was not reversed, when hunting pressure was drastically reduced. Our analysis provides support for the contention that selective hunting led to a reduction in horn length through evolutionary change. It also confirms that after artificial selection stops, recovery through natural selection is slow.
Artificial Intelligence Analysis of Initial Scan Evolution of Traumatic Brain Injured Patient to Predict Neurological Outcome
ClinicalTrials.gov study NCT04058379. IPD Sharing: NO. Countries: 1. Publications: 1.
Data from: Hybridization, natural selection and evolution of reproductive isolation: a 25-years survey of an artificial sympatric area between two mosquito sibling species of the Aedes mariae complex
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Data from: Intense selective hunting leads to artificial evolution in horn size
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Data from: Potential rapid evolution of foot morphology in Italian plethodontid salamanders (Hydromantes strinatii) following the colonization of an artificial cave
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Data from: Controlling for p-value inflation in allele frequency change in experimental evolution and artificial selection experiments
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Data from: Morph-specific artificial selection reveals a constraint on the evolution of polyphenisms
Theory predicts that the evolution of polyphenic variation is facilitated where morphs are genetically uncoupled and free to evolve towards their phenotypic optima. However, the assumption that developmentally plastic morphs can evolve independently has not been tested directly. Using morph-specific artificial selection, we investigated correlated evolution between the sexes and male morphs of the bulb mite Rhizoglyphus echinopus. Large 'fighter' males have a thick and sharply terminating pair of legs used to kill rival males, while small 'scrambler' males have unmodified legs, and search for unguarded females, avoiding fights. We selected on the relative leg width of only the fighter male morph, tracked the evolutionary responses in fighters and the correlated evolutionary responses in scramblers and females that were untouched by direct selection. Fighters diverged in relative leg thickness after six generations; assaying scramblers and females at the ninth generation we observed correlated responses in relative leg width in both. Our results represent strong evidence for the evolution of intraspecific phenotypic diversity despite correlated evolution between morphs and sexes, challenging the idea that male morphs are genetically uncoupled and free to independen- tly respond to selection. We, therefore, question the perceived necessity for genetic independence in traits with extreme phenotypic plasticity.
Data from: Evolution of sociability by artificial selection
<p>There has been extensive research on the ecology and evolution of social life in animals that live in groups. Less attention, however, has been devoted to apparently solitary species even though recent research indicates that they also possess complex social behaviors. To address this knowledge gap, we artificially selected on sociability, defined as the tendency to engage in non-aggressive activities with others, in fruit flies. Our goal was to quantify the factors that determine the level of sociability and the traits correlated with this feature. After 25 generations of selection, the high sociability lineages showed sociability scores about 50% higher than did the low sociability lineages. Experiments using the evolved lineages indicated that there were no differences in mating success between flies from the low and high lineages. Both males and females from the low lineages, however, were more aggressive than males and females from the high lineages. Finally, the evolved lineages maintained their sociability scores after ten generations of relaxed selection, suggesting no costs to maintaining low and high sociability, at least under our settings. Sociability is a complex trait, which we currently assess through genomic work on the evolved lineages.</p>
Data from: Stabilizing selection on sperm number revealed by artificial selection and experimental evolution
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Data from: Morph-specific artificial selection reveals a constraint on the evolution of polyphenisms
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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.