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69 results for “directed evolution”
A 31-Year Bibliometric Review of Team Effectiveness Research: Evolution, Trends, and Future Directions (DATA).
<p>This dataset is derived from a comprehensive study of team effectiveness over three decades, utilizing bibliometric techniques to examine scholarly publications across multiple databases. The repository includes bibliometric data from 6,051 publications related to team effectiveness, featuring metadata such as authors, titles, publication years, citations, and keywords.</p> <h3>Repository Structure:</h3> <p>The data shared in this repository is organized as follows:</p> <ul> <li><strong>Bibliometrix database.xlsx:</strong> This excel file contains information on 6051 publications in the field of Team Effectiveness downloaded from the Scopus and Web of Science databases using specific search terms and inclusion criteria detailed in our associated paper (see our publication for more information on the methodology). The file contains the necessary headers for direct use in the Biblioshiny interface of the bibliometrix library for R.</li> <li><strong>List of stop words.txt:</strong> This file contains keywords, separated by commas, that we have decided to eliminate from our analyses due to their potential to introduce bias in the results.</li> <li><strong>List of synonyms.txt:</strong> This file contains groups of semantically synonymous keywords, separated by semicolons. Each line represents a group of synonyms, with the first keyword being the one that Bibliometrix will use to replace all other keywords in that line.</li> <li><strong>Appendix [A-H].pdf:</strong> List of appendices that complement the results of the study carried out.</li> </ul> <h3>Recommended Usage:</h3> <div> <div> <div> <div> <p>This dataset is ideal for researchers interested in conducting new analyses of research trends, co-authorship network analysis, and thematic evolution in the field of team effectiveness. For example, researchers can narrow the scope to focus exclusively on team effectiveness in educational contexts. Our publication provides all the necessary details to replicate or extend our methodology. For any queries related to the data, please contact <strong>Yeray Barrios-Fleitas</strong> at <em><a rel="noreferrer">y.d.c.barriosfleitas@utwente.nl</a></em>.</p> </div> </div> </div> </div> <div> </div> <h3>License and Citation:</h3> <p>The data are distributed under the CC BY license. Please cite any use of this dataset using the following format:<br>Barrios Fleitas, Y., Marcella A.M.G., Eysink, T.H., & Rensink , A. (2025). A 31-Year Bibliometric Review of Team Effectiveness Research: Evolution, Trends, and Future Directions. ZENODO, <a href="https://doi.org/10.5281/zenodo.12082529" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.12082529</a></p>
Data and custom codes from "Rapid evolution in salmon life-history induced by direct and indirect effects of fishing"
<p>Data and custom codes from Czorlich, Y., Aykanat, T., Erkinaro, J., Orell, P. & Primmer, C.R. (2021) <em>Rapid evolution in salmon life-history induced by direct and indirect effects of fishing. </em>Science.</p> <p><strong>Codes:</strong></p> <p>The R file "Fishing_effort_parallel.R" was used to estimate fishing effort/intensity (beta in equation 8) given the length distribution, the gear-specific catchability and harvest rate</p> <p>"Fishing_selection_estimate.R" was used to estimate fishery-induced selection at <em>vgll3.</em></p> <p><strong>Datasets:</strong></p> <p>Genetic_phenotypic_data.xlsx: Genetic and phenotypic data about salmon from the Teno mainstem population</p> <p>sonar_data.xlsx: Number of salmon per length class entering the river in 2018 and 2019. The length classes of salmon caught in those years by one of the fishing methods are also included</p> <p>annual_catch_data.xlsx: Total mass (kg) of salmon caught by each fishing method between 1975 to 2014.</p> <p>Environmental_data.xlsx: Data about Barents Sea temperature, biomass of key species, fishing data</p> <p>individual_weight_salmon_catches.xlsx: Individual weight of salmon caught with different fishing gears in the last decades</p> <p><strong>Data sources:</strong></p> <p>- Genetic data (Tenojoki population, random sampling): From Czorlich et al. 2018, https://datadryad.org/stash/dataset/doi:10.5061/dryad.7hm4708</p> <p>- Data about krill biomass (1980 – 2013) were taken from (<em>1</em>, <em>2</em>).</p> <p>- Capelin biomass estimated from acoustic survey and the landed capelin catches were derived from (<em>3</em>) for 1973 – 2013.</p> <p>- Herring biomass data were retrieved from (<em>4</em>) for the 1973-1998 period. Herring biomass was calculated from the number of 1-2 year old herring and the mean weight per age as reported in (<em>3</em>) for 1988 – 2013.</p> <p>- The annual biomass of cod (a predator of forage fish) was derived from VPA analyses ((<em>5</em>), table 3.24). Landed cod biomass was also taken from (<em>5</em>).</p> <p>- An index for mesozooplankton (a forage fish food source) corresponding to the sum of <em>Calanus</em> biomass indices from different parts of the Barents Sea was used (<em>6</em>).</p> <p>- The annual sea temperature in the Kola section of the Barents Sea measured in the upper 200 meters was from <a href="http://www.pinro.vniro.ru/">pinro.vniro.ru</a></p> <p>- The total number of nets used to catch salmon in the Finnmark coastal region was calculated for each year using data from (7)</p> <p>- Other data were generated for this study, please check the Material and Methods. </p> <p><em>References:</em></p> <p>1. E. Eriksen, P. Dalpadado, Long-term changes in Krill biomass and distribution in the Barents Sea: Are the changes mainly related to capelin stock size and temperature conditions? <em>Polar Biology</em>. <strong>34</strong>, 1399–1409 (2011).</p> <p>2. ICES, “Report of the Working Group on the Integrated Assessments of the Barents Sea. ICES CM 2017/SSGIEA:04. 186 pp.” (2017).</p> <p>3. ICES, “Report of the Arctic Fisheries Working Group (AFWG). ICES CM 2015/ACOM:05. 639 pp.” (2015).</p> <p>4. R. Toresen, O. J. Østvedt, Variation in abundance of Norwegian spring-spawning herring (Clupea harengus, Clupeidae) throughout the 20th century and the influence of climatic fluctuations. <em>Fish and Fisheries</em>. <strong>85</strong>, 385–391 (2000).</p> <p>5. ICES, “Report of the Arctic Fisheries Working Group (AFWG). ICES CM 2016/ACOM:06. 621 pp.” (2016).</p> <p>6. L. C. Stige et al., Spatiotemporal statistical analyses reveal predator-driven zooplankton fluctuations in the Barents Sea. <em>Progress in Oceanography</em>. <strong>120</strong>, 243–253 (2014).</p> <p>7. E. Niemelä, T. Kalske, E. Hassinen, “Numbers of fishing gears used in Kolarctic salmon project area, numbers of allowed sites for salmon fishing and numbers of salmon fishermen in Finnmark; development until the year 2013” (2013).</p>
An in silico guided directed evolution of protease: Spotlighting the beneficial positions
<p>Supplementary Information for "An in silico guided directed evolution of protease: Spotlighting the beneficial positions".</p>
The evolution of lexical semantics dynamics, directionality, and drift: S4
<p>Supplementary Material (S4) for the study "The evolution of lexical semantics dynamics, directionality, and drift", for Frontiers in Communication, Special Issue "<a href="https://www.frontiersin.org/research-topics/38650/the-evolution-of-meaning-challenges-in-quantitative-lexical-typology?fbclid=IwAR3AeXx_11P-8CZG0UavlOgqvbVo6MlMxX8AejtPiREAKmeLyy3LIB3Ux24">The Evolution of Meaning: Challenges in Quantitative Lexical Typology</a>", ed. Gerd Carling & Annemarie Verkerk</p>
Data and reproducible code for Honor et al: Direct and indirect fitness effects of competition limit evolution of allelopathy in an invading plant
<p><span>Upon introduction to new continents, invading species encounter novel communities of consumers, pathogens, and competitors. Both phenotypic plasticity and rapid evolution can facilitate adaptation across these heterogenous communities, facilitating further invasion. However, the rate and extent of adaptive evolution on contemporary timescales can be constrained by phenotypic plasticity and limits imposed by genetic co-variation for traits under selection.</span></p> <p><span>We measured phenotypic plasticity and quantified genetic co-variation for growth, competition, and fitness among </span>23 naturally inbred seed families <span>of <em>Alliaria petiolata</em> (garlic mustard) </span>collected across its invasive range in eastern North America. After growing a self-pollinated generation in a uniform common garden to reduce maternal effects, we reared second-generation plants in a <span>two-year greenhouse and field experiment with naïve soil from an uninvaded habitat. W</span>e measured selection gradients and lifetime fitness when reared alone, with an intraspecific competitor, and under interspecific competition with naïve <em>Acer saccharum </em>(sugar maple) saplings.</p> <p>Total glucosinolate production was strongly correlated with the production of chlorophyll a (Chl a) (<em>R<sup>2</sup></em> = 0.45) such that first principal component (PC1) accounted for 84% of variation in these two traits. Furthermore, PC1 exhibited high plasticity across growing environments (p < 0.001) with limited broad-sense heritability (<em>H<sup>2</sup> </em>= 2.91; p = 0.08). In contrast, investment in glucosinolate production relative to Chl a (PC2) was significantly heritable (<em>H</em><sup><em>2</em> </sup>=16.91, p < 0.001) with minimal plasticity across treatments. Causal analysis revealed that plastic variation for higher Chl a + glucosinolate production (PC1) had an indirect positive effect on A. petiolata fitness via a direct, negative effect on <em>A. saccharum</em> performance. In contrast, heritable variation for higher glucosinolate investment (PC2) had a direct, positive effect on <em>A. saccharum</em> performance and an indirect negative effect on A. petiolata fitness. </p> <p>Applying causal inference, we find that evolution of allelopathy in <em>A. petiolata</em> has been constrained by (i) a lack of genetic variation, (ii) selection against glucosinolate investment under interspecific competition, and (iii) phenotypic plasticity. These factors limit adaptive evolution but maintain fitness during population growth as plants switch from interspecific to intraspecific competition during invasion.</p>
Data from: The sequential direct and indirect effects of mountain uplift, climatic niche and floral trait evolution on diversification dynamics in an Andean plant clade
<p><span>Why and how organismal lineages radiate is commonly studied through either assessing abiotic factors (biogeography, geomorphological processes, climate) or biotic factors (traits, interactions). Despite increasing awareness that both abiotic and biotic processes may have important joint effects on diversification dynamics, few attempts have been made to quantify the relative importance and timing of these factors, and their potentially interlinked direct and indirect effects, on lineage diversification.</span></p> <p><span>We here combine assessments of historical biogeography, geomorphology, climatic niche, vegetative and floral trait evolution to test whether these factors jointly, or in isolation, explain diversification dynamics of a Neotropical plant clade (Merianieae, Melastomataceae). After estimating ancestral areas and disparification over time in climate and trait space, we employ Phylogenetic Path Analyses as a synthesis tool to test eleven hypotheses on the individual direct and indirect effects of these factors on diversification rates.</span></p> <p><span>We find strongest support for interlinked effects of colonization of the uplifting Andes during the mid-Miocene and rapid abiotic climatic niche evolution in explaining a burst in diversification rate in Merianieae. Within Andean habitats, later disparification in floral trait space allowed for the exploitation of wider pollination niches (i.e., shifts from bee to vertebrate pollinators), but did not affect diversification rates. Our approach of including both vegetative and floral trait evolution, rare in assessments of plant diversification in general, highlights important pre-adaptations to mountain colonization, specifically woody habit and larger flowers. Overall, and in concert with the idea that ecological opportunity is a key element of evolutionary radiations, our results suggest that a combination of rapid niche evolution and pre-adapted traits were critical for the exploitation of newly available niche space in the Andes in the mid-Miocene. Further, our results emphasize the importance of incorporating both abiotic and biotic factors into the same analytical framework if we aim to quantify the relative and interlinked effects of these processes on diversification.</span></p>
Data from: The sequential direct and indirect effects of mountain uplift, climatic niche and floral trait evolution on diversification dynamics in an Andean plant clade
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Data and reproducible code for Honor et al: Direct and indirect fitness effects of competition limit evolution of allelopathy in an invading plant
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The contributions of direct and indirect selection to the evolution of mating preferences
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Data from: Habitat deterioration promotes the evolution of direct development in metamorphosing species
<p>Although metamorphosis is widespread in the animal kingdom, several species have evolved life cycle modifications to avoid complete metamorphosis. Some species, e.g., many salamanders and newts, have deleted the adult stage via a process called paedomorphosis. Others, e.g., some frog species and marine invertebrates, no longer have a distinct larval stage and reach maturation via direct development. Here we study which ecological conditions can lead to the loss of metamorphosis via the evolution of direct development. To do so, we use size-structured consumer-resource models in conjunction with the adaptive-dynamics approach. In case the larval habitat deteriorates, individuals will produce larger offspring and in concert accelerate metamorphosis. While this leads to the evolutionary transition from metamorphosis to direct development when the adult habitat is highly favourable, the population will go extinct in case the adult habitat does not provide sufficient food in order to escape metamorphosis. With a phylogenetic approach we furthermore show that among amphibians the transition of metamorphosis to direct development is indeed, in line with model predictions, conditional on and preceded by the evolution of larger egg sizes.</p>
A dual selection system for directed evolution to identify allosteric transcription factor PobR variants responsive to different aromatic compounds
<p>This dataset includes all the raw data of our characterization experiments during the work titled “A dual selection system for directed evolution to identify allosteric transcription factor PobR variants responsive to different aromatic compounds”.</p>
FIG. 2 in Direct optimization, sensitivity analysis, and the evolution of the hymenopteran superfamilies
FIG. 2. (continued).
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>
Data from: Direct evidence of permeability evolution of Nanan granite after two cooling paths under different confining pressures: A comparative study
<p>Permeability decides the mass transfer behavior and plays a key role in the heat extraction of enhanced geothermal systems (EGSs), and the aim of the injection of cooling water is to enhance permeability within the geothermal reservoirs. Direct evidence of how cool water affecting permeability evolution is still limited. Therefore, we explored the permeability evolution of Nanan granite after air and water cooling under different confining pressures combined with optical microscopy and X-ray CT observation. We found that there are lots of microdefects observed in Nanan granite after two cooling paths, which dominantly drives the evolution of permeability from a microscopic scale. The permeabilities of granite under water-cooling condition are always larger than those under air-cooling condition, and water-cooling treatment further enhances the permeability of specimens. The permeabilities of granite specimens after two cooling paths decrease with confining stress. More microcracks and better connectivity among microcracks produce a larger permeability within the specimen after water cooling. The observed microcracks are regarded as the seepage channels and direct microscale evidence of permeability evolution of granite after two cooling paths. Our results may suggest that water injection is an efficient way for permeability enhancement due to thermal microcracks propagation in thermal simulation.</p>
Data from: Habitat deterioration promotes the evolution of direct development in metamorphosing species
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Data from: Direct evidence of permeability evolution of Nanan granite after two cooling paths under different confining pressures: A comparative study
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Data from: Cope's Rule in a modular organism: directional evolution without an overarching macroevolutionary trend
Cope's Rule describes increasing body size in evolutionary lineages through geological time. This pattern has been documented in unitary organisms but does it also apply to module size in colonial organisms? We address this using 1169 cheilostome bryozoans ranging through the entire 150 million years of their evolutionary history. The temporal pattern evident in cheilostomes as a whole shows no overall change in zooid (module) size. However, individual subclades show size increases: within a genus, younger species often have larger zooids than older species. Analyses of (paleo)latitudinal shifts show that this pattern cannot be explained by latitudinal effects (Bergmann's Rule) coupled with younger species occupying higher latitudes than older species (an 'out of the tropics' hypothesis). While it is plausible that size increase was linked to the advantages of large zooids in feeding, competition for trophic resources and living space, other proposed mechanisms for Cope's Rule in unitary organisms are either inapplicable to cheilostome zooid size or cannot be easily evaluated. Patterns and mechanisms in colonial organisms cannot and should not be extrapolated from the better-studied unitary organisms. And even if macroevolution simply comprises repeated rounds of microevolution, evolutionary processes occurring with lineages are not always detectable from macroevolutionary patterns.
Data from: Direct detection of male quality can facilitate the evolution of female choosiness and indicators of good genes: evolution across a continuum of indicator mechanisms
The evolution of mating displays as indicators of male quality has been the subject of extensive theoretical and empirical research for over four decades. Research has also addressed the evolution of female mate choice favoring such indicators. Yet, much debate still exists about whether displays can evolve through the indirect benefits of female mate choice. Here, we use a population genetic model to investigate how the extent to which females can directly detect male quality influences the evolution of female choosiness and male displays. We use a continuum framework that incorporates indicator mechanisms that are traditionally modelled separately. Counter to intuition, we find that intermediate levels of direct detection of male quality can facilitate, rather than impede, the evolution of female choosiness and male displays in broad regions of this continuum. We examine how this evolution is driven by selective forces on genetic quality and on the display, and find that direct detection of male quality results in stronger indirect selection favoring female choosiness. Our results imply that displays maybe more likely to evolve when female choosiness has already evolved to discriminate perceptible forms of male quality. They also highlight the importance of considering general female choosiness, as well as preference, in studies of "good genes".
Evaluation of Machine Learning-Assisted Directed Evolution Across Diverse Combinatorial Landscapes
<p>Refer to the <a href="https://github.com/fhalab/SSMuLA">SSMuLA Github repository</a> for the associated code</p> <p>See our <a href="https://doi.org/10.1101/2024.10.24.619774">paper</a> titled "Evaluation of Machine Learning-Assisted Directed Evolution Across Diverse Combinatorial Landscapes"</p> <p> </p>
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>
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