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9,786 results for “selection”
Data for: Interactions between environmental factors drive selection on cyanogenesis in Trifolium repens
<p>Phenotypic and genetic clines frequently evolve due to varying selection along environmental gradients. However, the specific environmental factors that impose differential selection are often multivariate and difficult to tease apart. We addressed this complexity using a factorial manipulation of watering, soil nutrients, and (simulated) herbivory in controlled conditions to better understand the agents of selection driving the evolution of clines in a polymorphic chemical antiherbivore defence, hydrogen cyanide (HCN), of the plant white clover (Trifolium repens L.). We found the presence or absence of the two metabolic components required for HCN production (cyanogenic glucosides and linamarase) to be more prominent determinants of vegetative growth and sexual reproduction in T. repens than HCN itself. We also found that the ability to produce one or both of cyanogenic glucosides or linamarase resulted in a growth advantage under drought and simulated herbivory that outweighs the metabolic cost of their production. These results support the view that the metabolic components underlying HCN play important roles beyond defence by increasing plant tolerance to stress. The growth advantage under drought, however, was diminished in the absence of nutrient addition, consistent with multivariate interactions as drivers of selection. This study provides novel insight into how a cosmopolitan plant has adapted to environmental gradients, and more generally, highlights the importance of considering interactions between multiple environmental factors when studying the evolution of phenotypic and genetic clines.</p>
Grid-to-Grid daily simulated soil moisture 1964-2018, at selected UK Soil Moisture Databank sites.
<p>This dataset contains Grid-to-Grid (G2G) daily simulated soil moisture time-series at selected UK Soil Moisture Databank (UKSMD) sites. It was created to facilitate an evaluation of G2G simulated soil moisture against the UKSMD neutron probe soil moisture observations (Bell et al., 2022). </p> <p>G2G (Bell et al., 2009) is a national-scale gridded hydrological model, which has been widely applied to simulate river flows and more recently soil moisture. Here, the model was run at 1km resolution from 01/01/1964 - 16/12/2019 across Great Britain. Simulated soil moisture time-series are provided for the 1km grid-cells closest to selected UKSMD site locations. The G2G simulates vertically-integrated soil moisture in units of mm/m. For further explanation of G2G soil moisture, please see Kay et al., 2022 (https://iopscience.iop.org/article/10.1088/1748-9326/ac7a4e). </p> <p>The data is provided as two plain text files:</p> <p>1) g2g_soilmoist_1964_2018.txt contains the simulated soil moisture values. The first three columns specify the simulation date (day, month, year). Subsequent columns are soil moisture (mm/m) time-series at each site, with the UKSMD site ID given as column headers. </p> <p>2) site_locations.csv contains the locations of the UKSMD sites. In some cases there were multiple tubes with slightly different locations within a larger site, and here we are providing the location of the specific tube used. Columns specify: SITE_NAME (the site ID), TUBE_NAME (the tube number), EASTING and NORTHING (easting and northing in British National Grid). The site ID and tube names used in this document are consistent with the UKSMD documentation. </p> <p>References:</p> <p>Bell, V. A., Kay, A. L., Jones, R. G., Moore, R. J., & Reynard, N. S. (2009). Use of soil data in a grid-based hydrological model to estimate spatial variation in changing flood risk across the UK. Journal of Hydrology, 377(3-4), 335-350.</p> <p>Bell, V.A.; Davies, H.N.; Fry, M.; Zhang, T.; Murphy, H.; Hitt, O.; Hewitt, E.J.; Chapman, R.; Black, K.B. (2022). Collated neutron probe measurements and derived soil moisture data, UK, 1966-2013. NERC EDS Environmental Information Data Centre. https://doi.org/10.5285/450bb14b-c711-47af-8792-f9bd88482cd4</p> <p>Kay, A. L., Lane, R. A., & Bell, V. A. (2022). Grid-based simulation of soil moisture in the UK: future changes in extremes and wetting and drying dates. Environmental Research Letters, 17(7), 074029.</p>
The contribution of Neanderthal introgression and natural selection to neurodegenerative diseases
<p>Files used to create binary annotations for LDSC in the following repository: https://github.com/RHReynolds/als-neanderthal-analysis.</p> <p>See the following link for details: https://github.com/RHReynolds/als-neanderthal-analysis/tree/main/raw_data/01_annotations</p>
Permafrost Thaw and its Impact on Arctic Infrastructure: A Site Selection Bibliography
<p>Project Bibliography for DRP Task 1.2.1. Cited sources were used in the site selection process. </p>
INSPIRE-seq simultaneously selects nanobodies for immune epitopes in the complex tumor microenvironment
<p>scRNAseq of CD45 magnetic microbeads enriched cells were isolated form Py8119 bearing mice (three mice per pool/group) two hours after injection of either PBS, insertless phage display, CD45, DCs, or CD8 specific VHHs phage display libraries. </p>
Adaptation to distinct habitats is maintained by contrasting selection at different life stages in sunflower ecotypes
<p><span>Conspecific populations living in adjacent but contrasting microenvironments represent excellent systems for studying natural selection. These systems are valuable because gene flow is expected to force genetic homogeneity except at loci experiencing divergent selection. A history of reciprocal transplant and common garden studies in such systems, and a growing number of genomic studies, have contributed to understanding how selection operates in natural populations. While selection can vary across different fitness components and life stages, few studies have investigated how this ultimately affects allele frequencies and the maintenance of divergence between populations. Here, we study two sunflower ecotypes in distinct, adjacent habitats by combining demographic models with genome-wide sequence data to estimate fitness and allele frequency change at multiple life stages. This framework allows us to estimate that only local ecotypes are likely to experience positive population growth</span> <span>(λ>1) and that the maintenance of divergent adaptation appears to be mediated via habitat- and life-stage-specific selection. We identify genetic variation, significantly driven by loci in chromosomal inversions, associated with different life history strategies in neighbouring ecotypes that optimize different fitness components and may contribute to the maintenance of distinct ecotypes. </span></p>
Contrasting genome-wide signatures of selection in two closely related Epichloe plant pathogen species
<p>Deposited here composite plots for each species, each pairwise population combination and each of the seven chromosomes as shown and referred to in the manuscript.</p> <p>The filename contains [species abbrevation]_[chromosome number]_[population 1]_[population 2]. Chromosome-wide SNP data and sweeps identified for the population pair are shown. The top panel shows pairwise FST values, averaged across 5kb windows. Shaded rectangles represent the locations of AT-rich regions. The second panel shows the absolute values of the integrated haplotype score (iHS) calculated at each SNP locus for which the ancestral allele state was known. Scores for pop1 are shown at the top and scores for pop2 are negatively transformed and showed at the bottom. Horizontal dashed lines indicate the 99.9% percentile threshold which was used as a cutoff to identify outlier SNPs and inferred iHS sweeps are shown as shaded rectangles. The third panel shows the cross-population extended haplotype homozygosity (XP-EHH) scores calculated between the two populations. Dashed lines indicate 99.9% percentile threshold which was used as a cutoff to identify outlier SNPs and inferred divergent sweeps are shown as shaded rectangles. Positive and negative XP-EHH values refer to the direction of selection: positive values indicate selection in pop1 negative values indicate selection in pop2. In the bottom panel, composite likelihood ratio (CLR) scores are plotted for pop1 (black) and pop2 (blue), colored dashed lines indicate respective 99.9% threshold and colored rectangles highlight inferred CLR-sweeps.</p>
Spatially and temporally varying selection influence species boundaries in two sympatric Mimulus
<p><span>Spatially and temporally varying selection can maintain genetic variation within and between populations, but it is less known how these forces influence divergence between closely related species. We identify the interaction of temporal and spatial variation in selection and their role in either reinforcing or eroding divergence between two closely related <em>Mimulus</em> species. Using repeated reciprocal transplant experiments with advanced generation hybrids we compare the strength of selection on quantitative traits involved in adaptation and reproductive isolation in <em>Mimulus</em> <em>guttatus</em> and <em>Mimulus</em> <em>laciniatus</em> between two years with dramatically different water availability. We found strong divergent habitat-mediated selection on traits in the direction of species differences during a drought in 2013, suggesting that spatially varying selection maintains species divergence. However, a relaxation in divergent selection on most traits in an unusually wet year (2019), including flowering time which is involved in pre-zygotic isolation, suggests that temporal variation in selection may weaken species differences. Therefore, we find evidence that temporally and spatially varying selection may have opposing roles in mediating species boundaries. Given our changing climate, future growing seasons are expected to be more similar to the dry year, suggesting that in this system climate change may actually increase species divergence. </span></p>
Experimental evidence for short term directional selection of epigenetic trait variation
<p>This Arabidosis data folder includes 5 folders providing the data and code associated with the publication entitled "Experimental evidence for short term directional selection of epigenetic trait variation" by Pujol et al. in Peer Community Journal:</p> <p>"in Silico 1000 resampling" folder includes two folders; one for Population 1, and one for Population 2, each including 24 files. Each file presents the 1000 lists of plant IDs that were randomly sampled to build control groups (listrand), and the corresponding lists of plant IDs selected on the basis of trait values to build the corresponding high (Top) and low (Bot) selection lines, for the strong (20) and weak (60) selection intensities.</p> <p>“phenotypic and epiril data” includes two csv files; data_pop1 and data_pop2, respectively for population 1 and 2, and a readme txt file that presents the data included in the files.</p> <p>“scripts R epigenomic selection” includes two R script files: “PCA_arabidopsis”, which includes the R code used to conduct the PCA analysis on epiRIL data and “Arabette_analysis_loop_Epigenotypes_data”, which is used to insert that epigenotype data in the analysis.</p> <p>“scripts R epigenomic validation” includes nine R scripts used to conduct tests of molecular epigenomic data validation and comparison with existing data from the literature: “Script 1 Extract 126 markers from BSMAP ouput files and apply methylkit”, “Script 2 Boxplots of the BS signal distribution for the 126 markers and their correspondence to published HMM classification”, “Script 3 Correlation between EM-seq and BS seq_published_data for the 126 markers”, “Script 4 Correlation between the BS signals of EM-seq and WGBS data for the 126markers”, “Script 5 Hierarchical clustering of the epiRILs EM-seq and published epigenomic data”, “cluster and PCA analysis of Col wt vs 24 sequenced epiRILs”, which filenames are self-explanatory. “methylkit_epiRILs_vs_Col_wt_DMCs” was used to use methylkit in order to identify Differentially Methylated Cytosines between epiRILs and in comparison to Col-0. “methylkit_tiles_script” was used to build the tiles in Methylkit. “verif DMR CHG context” was used to verify differentially methylated regions in the CHG context.</p> <p>“scripts R phenotypic selection” includes four R scripts “Arabette_analysis”, “Arabette_analysis_loop_Phenotypes_data”, “Arabette_analysis_loop_pop1_final”, “Arabette_analysis_loop_pop2_final” that were used to estimate the parameters used for comparing selection treatments, in other words, to estimate means and confidence intervals (“loop” scripts) in population 1 (“pop1” script) and population 2 (“pop2” script)</p>
98 selected publications analysed in-depth in the context of a systematic literature review on Computational Thinking in compulsory education
<p>This is the list of the <strong>98 publications from between 2016 and 2021 </strong>analysed in-depth through a review matrix in the context of the <strong>"</strong><a href="https://publications.jrc.ec.europa.eu/repository/handle/JRC128347">Reviewing Computational Thinking in Compulsory Education: State of Play and</a> <a href="https://publications.jrc.ec.europa.eu/repository/handle/JRC128347"> Practices from the Field</a><strong>"</strong> <strong>research study.</strong> The <a href="https://computhink2study.eu/">study</a> was designed, funded, and followed by the European Commission’s Joint Research Centre (JRC) to investigate <strong>how Computational Thinking (CT) is currently positioned within compulsory school education in Europe’s various Member States, as well as outside the EU</strong>. The study was carried out from April to December 2021 by the Institute for Educational Technology of the Italian National Research Council (CNR-ITD), together with European Schoolnet (EUN) and Vilnius University (VU).</p> <p>Bocconi, S., Chioccariello, A., Kampylis, P., Dagienė, V., Wastiau, P., Engelhardt, K., Earp, J., Horvath, M.A., Jasutė, E., Malagoli, C., Masiulionytė-Dagienė, V., & Stupurienė, G. (2022). <em>Reviewing Computational Thinking in Compulsory Education</em>. Publications Office of the European Union. <a href="https://doi.org/10.2760/126955">https://doi.org/10.2760/126955</a></p> <p> </p>
FIG. 4 in Cypsela micro-macromorphological characteristics of selected taxa of Centaurea L. from Turkey and their systematic importance
FIG. 4. — The UPGMA dendrogram shows dissimilarity distance of the examined Centaurea L. taxa according to combined data of cypsela and pappus morphology.
FIG. 3 in Cypsela micro-macromorphological characteristics of selected taxa of Centaurea L. from Turkey and their systematic importance
FIG. 3. — SEM micrographs of cypselas of C. spicata Boiss. (A), C. solstitialis L. (B), C. behen L. (C), C. rigida Banks & Sol. (D), C. antitauri Hayek (E). A1, B1, C1, D1, E1, general morphology of cypselas by LM; A2, A3, B2, B3, C2, C3, D2, D3, E2, E3, cypsela surfaces by SEM. Scaler bars: A1-E1, 1 mm; A2-C2, E2, 100 µm; D2, 200 µm; A3-E3, 10 µm.
FIG. 2 in Cypsela micro-macromorphological characteristics of selected taxa of Centaurea L. from Turkey and their systematic importance
FIG. 2. — SEM micrographs of cypselas of C. cataonica Boiss. & Hausskn. in Boiss. (A), C. haradjiannii Wagenitz (B), C. haussknechtii Boiss. (C), C. regia Boiss. var. regia (D), C. sclerolepis Boiss. (E). A1, B1, C1, D1, E1, general morphology of cypselas by LM; A2, A3, B2, B3, C2, C3, D2, D3, E2, E3, cypsela surfaces by SEM. Scale bars: A1-E1, 1 mm; A2, C2, D2, 20 µm; B2, E2, 200 µm; A3-E3, 10 µm.
FIG. 1 in Cypsela micro-macromorphological characteristics of selected taxa of Centaurea L. from Turkey and their systematic importance
FIG. 1. — SEM micrographs of cypselas of C. goksivriensis M. Bona (A), C. calcitrapa subsp. calcitrapa L. (B), C. calcitrapa subsp. cilicica (Boiss. & Bal.) Wagenitz (C), C. glastifolia L. (D), C. amanicola Hub.-Mor. (E). A1, B1, C1, D1, E1, general morphology of cypselas by LM; A2, A3, B2, B3, C2, C3, D2, D3, E2, E3, cypsela surfaces by SEM. Scale bars: A1-E1, 1 mm; A2, 200 µm; B2-D2, 100 µm; E2, 20 µm; A3-E3, 10 µm.
Sustainable recovery of critical elements from seawater saltworks bitterns by integration of high selective sorbents and reactive precipitation and crystallisation: Developing the probe of concept with on-site produced chemicals and energy
<p>The availability of raw mineral resources containing elements included in the Critical Raw Materials (CRMs) list is a growing concern for the European Union. Sea mining has been identified as a promising secondary source. In particular, brines obtained in solar saltworks (bitterns) contain relevant amounts of valuable CRMs such as Mg(II), B(III), other alkaline/alkaline earth metals (Rb(I), Cs(I), Sr(II)) and transition/post-transition elements (Co(II), Ga(III), Ge(IV)). However, the low concentration of some of these elements (µg/L) requires an effort to develop recovery routes that are sustainable and economically feasible where the required chemicals and energy are produced on-site from the saltworks bitterns (i.e. HCl and NaOH). Even the conventional recovery processes such as ion exchange, sorption and precipitation, which have proved to be competitive for metals recovery, are challenged in the case of Trace Elements (TEs). This work studies the recovery of TEs included in the CRMs list from saltworks bitterns after ion exchange processes. First, batch crystallisation and reactive precipitation were tested for some target elements in single-component solutions: Sr(II), Co(II), Ga(III), Ge(IV) and B(III). Then, the experiments were carried out with multi-component synthetic solutions assuming different scenarios of bittern streams coming out a selective extraction stage using sorption and ion exchange processes. The targeted elements were recovered except for Ge(IV), where alternative routes need to be evaluated, as its precipitation involves the use of tannic acid or sulphide solutions that could not be produced from the bitterns. However, a further concentration step would be necessary to achieve element concentrations closer to the mineral phases saturation. Moreover, model simulations were performed using the PHREEQC program, which provided a good prediction of the experimental trends obtained in most cases.</p>
Detecting frequency-dependent selection through the effects of genotype similarity on fitness components
<p>Frequency-dependent selection (FDS) is an evolutionary regime that can maintain or reduce polymorphisms. Despite the increasing availability of polymorphism data, few effective methods are available for estimating the gradient of FDS from the observed fitness components. We modeled the effects of genotype similarity on individual fitness to develop a selection gradient analysis of FDS. This modeling enabled us to estimate FDS by regressing fitness components on the genotype similarity among individuals. We detected known negative FDS on the visible polymorphism in a wild <em>Arabidopsis</em> and damselfly by applying this analysis to single-locus data. Further, we simulated genome-wide polymorphisms and fitness components to modify the single-locus analysis as a genome-wide association study (GWAS). The simulation showed that negative or positive FDS could be distinguished through the estimated effects of genotype similarity on simulated fitness. Moreover, we conducted the GWAS of the reproductive branch number in <em>Arabidopsis thaliana</em> and found that negative FDS was enriched among the top-associated polymorphisms of FDS. These results showed the potential applicability of the proposed method for FDS on both visible polymorphism and genome-wide polymorphisms. Overall, our study provides an effective method for selection gradient analysis to understand the maintenance or loss of polymorphism.</p>
Data from: Selection on an extreme-yet-conserved larval life-history strategy in a tapeworm
<p>Evolutionary stasis characterizes many phenotypes, even ones that seem suboptimal. Among tapeworms, <em>Schistocephalus solidus</em> and its relatives have some of the shortest developmental times in their first intermediate hosts, yet their development still seems excessively long considering they can grow faster, larger, and safer in the next hosts in their complex life cycles. I conducted four generations of selection on the developmental rate of <em>S. solidus</em> in its copepod first host, pushing a conserved-but-counterintuitive phenotype towards the limit of known tapeworm life-history strategies. Faster parasite development evolved and enabled earlier infectivity to the stickleback next host, but low heritability for infectivity moderated fitness gains. Fitness losses were more pronounced for slow-developing parasite families, irrespective of selection line, because directional selection released linked genetic variation for reduced infectivity to copepods, developmental stability, and fecundity. This deleterious variation is normally suppressed, implying development is canalized and thus under stabilizing selection. Nevertheless, faster development was not costly; fast-developing genotypes did not decrease copepod survival, even under host starvation, nor did they underperform in the next hosts, suggesting parasite stages in successive hosts are genetically decoupled. I speculate that, on longer time scales, the ultimate cost of abbreviated development is reduced size-dependent infectivity.</p>
Figs 10–13 in Peripatopsidae (Onychophora) from New Zealand - observations on selected morphs of the 'Peripatoides novaezealandiae-complex' in culture: morphological and reproductive aspects
Figs 10–13. Sketches of posterior ventral body surface. 10. Juvenile from Boundary stream, 2 months, genital area and papillae of anal cone still undifferntiated (30 x). 11. Juvenile from Boundary Stream, 5 months, female (30 x). 12. Juvenile from Woodville Gorge, 2 months, genital area and papillae of anal cone still undifferentiated (30 x). 13. Juvenile from Paengora Mataroa, 2 months, male (30 x).
Figs 6–9. Selected hatchlings and juveniles. 6 in Peripatopsidae (Onychophora) from New Zealand - observations on selected morphs of the 'Peripatoides novaezealandiae-complex' in culture: morphological and reproductive aspects
Figs 6–9. Selected hatchlings and juveniles. 6. Boundary Stream: premature hatchling with slime gland (25 x). 7. Juvenile from Ngapaerera: stage A (7 x). 8. Juvenile from Boundary Stream: stage A (7 x). 9. Juvenile from Monckton: stage C (10 x).
Figs 3–5 in Peripatopsidae (Onychophora) from New Zealand - observations on selected morphs of the 'Peripatoides novaezealandiae-complex' in culture: morphological and reproductive aspects
Figs 3–5. Diagram, micrograph and photograph of selected morphs. 3. Schematic sketch of Mohi Bush male: fifth leg, ventral view (Scale bar = 163 m). 4. SEM micrograph of genital pore: Monckton male (Fig. rotated approx. 45˚). 5. Monckton: premature hatchling (25 x).
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