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11 results for “Crop evolution”
Supporting data and code for: Host plant and insecticides shape the evolution of genetic and clonal diversity in a major aphid crop pest
<p>This is the first release of the final data and code for the article accepted for publication in <em>Evolutionary Applications</em> journal. It contains the necessary scripts to produce most of the analyses and figures of the manuscript. All the necessary data can be found in the 'data' folder.</p>
Data from: Weed evolution: genetic differentiation among wild, weedy, and crop radish
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Data from: Effective specialist or jack of all trades? Experimental evolution of a crop pest in fluctuating and stable environments
<p>Understanding pest evolution in agricultural systems is crucial for developing effective and innovative pest control strategies. Types of cultivation, such as crop monocultures versus polycultures or crop rotation, may act as a selective pressure on pests' capability to exploit the host's resources. In this study, we examined the herbivorous mite <em>Aceria tosichella</em> (commonly known as wheat curl mite), a widespread wheat pest, to understand how fluctuating versus stable environments influence its niche breadth and ability to utilize different host plant species. We subjected a wheat-bred mite population to replicated experimental evolution in a single-host environment (either wheat or barley), or in an alternation between these two plant species every three mite generations. Next, we tested the fitness of these evolving populations on wheat, barley, and on two other plant species not encountered during experimental evolution, namely rye and smooth brome. Our results revealed that the niche breadth of <em>A. tosichella</em> evolved in response to the level of environmental variability. The fluctuating environment expanded the niche breadth by increasing the mite's ability to utilize different plant species, including novel ones. Such an environment may thus promote flexible host-use generalist phenotypes. However, the niche expansion resulted in some costs expressed as reduced performances on both wheat and barley as compared to specialists. Stable host environments led to specialized phenotypes. The population that evolved in a constant environment consisting of barley increased its fitness on barley without the cost of utilizing wheat. However, the population evolving on wheat did not significantly increase its fitness on wheat, but decreased its performance on barley. Altogether, our results indicated that, depending on the degree of environmental heterogeneity, agricultural systems create different conditions that influence pests' niche breadth evolution, which may in turn affect the ability of pests to persist in such systems.</p>
Dataset for "Population-level transposable element expression dynamics influence trait evolution in a fungal crop pathogen"
<p><strong>Supplementary Tables</strong></p> <p><strong>Supplementary Table S1: </strong>SRA accession list of RNAseq reads.</p> <p><strong>Supplementary Table S2:</strong> Genomic localization of TEs in gene elements and 10 kb windows upstream and downstream of the transcription start site (TSS) in the reference genome IPO323.</p> <p><strong>Supplementary Table S3:</strong> Genome-wide TE insertion polymorphism (TIPs) in the pathogen population. 0 represents TE absence and 1 represents TE presence.</p> <p><strong>Supplementary Table S4:</strong> Gene expression (log-transformed RPKM) values across the population.</p> <p><strong>Supplementary Table S5:</strong> Locus-specific transcript abundance at individual TE loci (FPKM) across individuals.</p> <p><strong>Supplementary Table S6:</strong> Percent of expressed copies within each TE family in the reference genome IPO323 and percent expressed TE copies in each TE family across the population.</p> <p><strong>Supplementary Table S7:</strong> Linkage disequilibrium of TIP in the genome and neighboring SNPs within the 600bp distance from the TE loci.</p> <p><strong>Supplementary Table S8:</strong> Genome-wide association mapping of the virulence-associated trait (PLACP: percent leaf area covered by pycnidia) and TE insertion polymorphisms in the genome.</p> <p><strong>Supplementary Table S9:</strong> TIPs in the genome significantly associated with metabolite peak intensity variation in the pathogen population (filtered by Bonferroni threshold).</p>
Supplementary Tables for "Population-level transposable element expression dynamics influence trait evolution in a fungal crop pathogen"
<p><strong>Supplementary Table S1:</strong> Genomic localization of TEs in gene elements and 10 kb windows upstream and downstream of the transcription start site (TSS) in the reference genome IPO323.</p><p><strong>Supplementary Table S2:</strong> Genome-wide TE insertion polymorphism (TIPs) in the pathogen population. 0 represents TE absence and 1 represents TE presence.</p><p><strong>Supplementary Table S3:</strong> Gene expression (log transformed RPKM) values across the population.</p><p><strong>Supplementary Table S4:</strong> Locus-specific transcript abundance at individual TE loci (FPKM) across individuals.</p><p><strong>Supplementary Table S5:</strong> Percent of expressed copies within each TE family in the reference genome IPO323 and percent expressed TE copies in each TE family across the population.</p><p><strong>Supplementary Table S6:</strong> Linkage disequilibrium of TIP in the genome and neighboring SNPs within the 600bp distance from the TE loci.</p><p><strong>Supplementary Table S7:</strong> Genome-wide association mapping of the virulence-associated trait (PLACP: percent leaf area covered by pycnidia) and TE insertion polymorphisms in the genome.</p><p><strong>Supplementary Table S8:</strong> metabolite peak variation in the pathogen population for individual isolates</p><p><strong>Supplementary Table S9:</strong> TIPs in the genome significantly associated with metabolite peak intensity variation in the pathogen population (filtered by Bonferroni threshold).</p><p><strong>Supplementary Table S10: </strong>SRA accession list of RNAseq reads.</p>
Data from: Diversifying mechanisms in the on-farm evolution of crop mixtures
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Data from: Effective specialist or jack of all trades? Experimental evolution of a crop pest in fluctuating and stable environments
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Price evolution of crop products in Spain and its influence in the general price indices
<p>Dataset containing the monthly prices of different crop products in Spain's wholesale markets, as well as aggregated prices and price indexes (general and agriculture-specific) with lower frequency (quarterly and yearly). Some of the relevant attributes are month and year, product name and price. The time range includes 2017-2019 period, however, not all the fields are populated.</p>
Data from: Analysis of phylogenetic relationships and genome size evolution of the Amaranthus genus using GBS indicates the ancestors of an ancient crop
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Data from: Type of fitness cost influences the rate of evolution of resistance to transgenic Bt crops
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Data from: Shifts and disruptions in resource-use trait syndromes during the evolution of herbaceous crops
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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.