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22,710 results for “Plants for planting”
Data used in manuscript Carbon sequestration potential of street tree plantings in Helsinki
<p>Data and model runs used in manuscript "Carbon sequestration potential of street tree plantings in Helsinki". This data set includes model runs for the Surface Urban Energy and Water balance Scheme (SUEWS) and soil carbon model Yasso.</p> <p><br> The data files are:</p> <p><strong>Met_Gapfilling</strong></p> <ul> <li>ConvertMeteorologyInput.m (MATLAB) is the main file and functions gapfilling.m (with other measurements) and gapfillingfill.m (with interpolations) are used in the gap filling</li> <li>Includes files for meteorological measurement data <ul> <li>Airport: Data from Helsinki-Vantaa airport; airportdata.m, where data is cleaned</li> <li>Precipitation: Data from multiple locations; Pres_Gap.m for gap filling precipitation and function PrecipitationGap.m</li> <li>Roof: Data from rooftop</li> <li>SMEARIII: Monthly meteorological data from Kumpula (2003-2016)</li> </ul> </li> <li>SUEWS_met file for the final gap filled meteorological files for SUEWS </li> </ul> <p><strong>Fits</strong></p> <ul> <li>Includes FitCO2_parameter.m for fitting CO2 parameters for SUEWS</li> <li>Includes functions Pho6.m and Resp0.m that have the function forms</li> <li>Includes data files for measurement data <ul> <li>CO2Data: Canopy photosynthesis and canopy respiration estimated with SPP model (KumpulaX.out for Tilia site and Kumpula2X.out for Alnus site)</li> <li>Met_2016: Meteorology from Kumpula for June to August in 2016</li> <li>SWCdata: Soil water content from two streets and three soil types</li> </ul> </li> </ul> <p><strong>ModelRuns</strong></p> <ul> <li>SUEWS model runs separately for Alnus and Tilia sites <ul> <li>Includes input and output files and model codes</li> <li>Alnus site includes both the Baserun and Finalrun</li> </ul> </li> <li>Yasso model runs <ul> <li>Model run in file yasso.f90</li> <li>Output files: DecRate...txt includes three soil types and values for each month from 2002 to 2016</li> <li>Yasso_meteorology_month.m creates meteorological input files for Yasso (Clim_month_xx.txt) using meteorology from SUEWS</li> <li>Lifetimerun: 30 year simulations that includes estimations for leaves and pruned branches</li> </ul> </li> </ul> <p><strong>FigCodes</strong></p> <ul> <li>Includes MATLAB codes for figures and statistics</li> <li>Includes measurement data for CO2, sap flow and SWC</li> </ul> <p> </p>
Data from: Virus infection and host plant suitability affect feeding behaviors of cannabis aphid (Hemiptera: Aphididae), a newly described vector of potato virus Y
<p>Aphids are the most prolific vectors of plant viruses resulting in significant yield losses to crops worldwide. P<span>otato virus Y (PVY) </span>is transmitted in a non-persistent manner by 65 species of aphids. <span>With the increasing acreage of hemp </span>(<i>Cannabis sativa</i> L.) (Rosales: Cannabaceae) <span>in the U.S, we were interested to know if the cannabis aphid (<i>Phorodon cannabis</i> Passerini) </span><span>(Hemiptera: Aphididae) </span><span>is a potential vector of PVY.</span> Here, we conduct transmission assays and utilize the electrical penetration graph (EPG) technique to determine whether cannabis aphids can transmit PVY to hemp (host) and potato (non-host) (<i>Solanum tuberosum</i> L.) (Solanales: Solanaceace). We show for the first time that the cannabis aphid is an efficient vector of PVY to hemp (96%) and potato (91%) using cohorts of aphids. In contrast, individual aphids transmitted the virus more efficiently to hemp (63%) compared to potato (19%). During the initial 15 minutes of EPG recordings, aphids demonstrated lower number and time spent performing intracellular punctures on potato compared to hemp, which may in part explain low virus transmission to potato using individual aphids. During the entire 8-hour recording, viruliferous aphids spent less time ingesting phloem compared to non-viruliferous aphids on hemp. This reduced host suitability could potentially cause aphids to disperse to more suitable hosts thereby increasing virus transmission. Overall, our study shows that cannabis aphid is an efficient vector of PVY, and that virus infection and host plant suitability affect feeding behaviors of the cannabis aphid in ways which may increase virus transmission.</p>
Data for: Evaluation of a full-scale wastewater treatment plant with ozonation and different post-treatments using a broad range of in vitro and in vivo bioassays
<p>This repository contains research data linked to the following publication: Kienle, C., Werner, I., Fischer, S., Lüthi, C., Schifferli, A., Besselink, H., Langer, M., McArdell, C.S. and Vermeirssen, E.L.M. 2022. Evaluation of a full-scale wastewater treatment plant with ozonation and different post-treatments using a broad range of <em>in vitro</em> and <em>in vivo</em> bioassays. Water Research, 118084. https://doi.org/10.1016/j.watres.2022.118084</p> <p>Abstract: Micropollutants present in the effluent of wastewater treatment plants (WWTPs) after biological treatment are largely eliminated by effective advanced technologies such as ozonation. Discharge of contaminants into freshwater ecosystems can thus be minimized, while simultaneously protecting drinking water resources. However, ozonation can lead to reactive and potentially toxic transformation products. To remove these, the Swiss Federal Office for the Environment recommends additional "post-treatment" of ozonated WWTP effluent using sand filtration, but other treatments may be similarly effective. In this study, 48 h composite wastewater samples were collected before and after full-scale ozonation, and after post-treatments (full-scale sand filtration, pilot-scale fresh and pre-loaded granular activated carbon, and fixed and moving beds). Ecotoxicological tests were performed to quantify the changes in water quality following different treatment steps. These included standard <em>in vitro</em> bioassays for the detection of endocrine, genotoxic and mutagenic effects, as well as toxicity to green algae and bacteria, and flow-through <em>in vivo</em> bioassays using oligochaetes and early life stages of rainbow trout.</p> <p>Results show that ozonation reduced a number of ecotoxicological effects of biologically treated wastewater by 66 - 93 %: It improved growth and photosynthesis of green algae, decreased toxicity to luminescent bacteria, reduced concentrations of hormonally active contaminants and significantly changed expression of biomarker genes in rainbow trout liver. Bioassay results showed that ozonation did not produce problematic levels of reaction products overall. Small increases in toxicity observed in a few samples were reduced or eliminated by post-treatments. However, only relatively fresh granular activated carbon (analyzed at 13,000 - 20,000 bed volumes) significantly reduced effects additionally (by up to 66 %) compared to ozonation alone. Inhibition of algal photosynthesis, rainbow trout liver histopathology and biomarker gene expression proved to be sufficiently sensitive endpoints to detect the change in water quality achieved by post-treatment.</p>
Dataset of the paper "Machine learning for expert-level image-based identification of very similar species in the hyperdiverse plant bug family Miridae (Hemiptera: Heteroptera)"
<p>This dataset contains 3792 images of 26 plant bug (Insecta: Heteroptera: Miridae: Mirini) species used to test the performance of a CNN in species recognition. All jpg files are 1920 pixels on the long size and additionally available as an archive file to facilitate download of the entire dataset. </p> <p>Bar code labels (unique specimen identifiers or USIs) were attached to all examined specimens used for this study. Further information such as additional photographs of habitus and genitalic structures, georeferenced coordinates of each locality, specimens dissected, notes, collecting method can be obtained from the Heteroptera Species Pages (http://research.amnh.org/pbi/heteropteraspeciespage/) which assembles available data from a specimen database and are also provided as an Excel spreadsheet (file _Adelphocoris_CNN_label_data.xlsx).</p>
Viroplant Project - Microcosm studies on the effect of bacteriophages used as plant protection products on soil microbial communities
<p>This file contains the description, data and DNA analyses on the effect of bacteriophages with a potential to be used as plant protecction products on the structure and function of soil microbial communities. The objective was to evaluate two different microcsom incubation systems with phages and microbial cells from soil, or soil itself and to analyses in a time dependent manner how the phages affect the natural soil microbiomes. The microbial communities were quantified with qPCR and their diversity analyzed with PCR amplified 16S rRNA gene sequences. Bioinformatic analyses were used to evaluate microbial community responses</p>
Plant pathogens provide clues to the origin of bat white-nose syndrome Pseudogymnoascus destructans
<p>Phylogenomic analyses of P. destructans.</p> <p>This is a snapshot of the GitLab repository available at https://gitlab.gwdg.de/molsysevol/pseudogymnoascus-destructans-phylogeny/.</p>
Simple attributes predict the value of plants as hosts to fungal and arthropod communities
Fungal and arthropod consumers constitute the vast majority of global terrestrial biodiversity. Yet, the link from richness and composition of producer (plant) communities to the richness of consumer communities is poorly understood. Fungal and arthropod species richness could be a simple function of producer species richness at a site. Alternatively, it could be a complex function of chemical and structural properties of the producer species making up communities. We used databases on plant-fungus and plant-arthropod trophic links to derive the richness of consumer biota per associated plant species (coined link score). We assessed how well link scores could be predicted by simple attributes of plant species. Next, we used a multi-taxon inventory of 130 sites, representing all major habitat types in a country (Denmark), to investigate whether link scores summed over plant species in communities (coined link sum) could outperform simple plant species richness as predictor of fungal and arthropod richness at the sites. We found plant species' link scores for both fungi and arthropods to be positively related to plant size, regional occupancy, nativeness and ectomycorrhizal status. Link-based indices generally improved the prediction of richness of fungal and arthropod communities. For fungal communities, both observed link sum (from databases) and predicted link sum (from plant attributes) had high predictive power, while plant richness alone had none. For arthropod communities, predictive performance varied between functional groups. For both fungi and arthropods, richness predictions were further improved by considering abiotic habitat conditions. Our results underline the importance of plants as niche space for the megadiverse groups of arthropods and fungi. The plant-attribute approach holds promise for predicting local and regional consumer richness in areas of the world lacking detailed plant-consumer databases.
A case-study for improved reusability of plant phenotyping data with MIAPPE
<p>Accompanying datasets for manuscript, "A case-study for improved reusability of plant phenotyping data with MIAPPE".</p> <p>The ZIP archives in this repository contain the source files and the output files that this manuscript refers to.</p>
Fig. 2. – Species prediction for a grid cell. A in Geographical patterns of woody plants' functional traits in Burkina Faso
Fig. 2. – Species prediction for a grid cell. A. Average of maximal plant size; B. Percentage of spinescent species; C. Percentage of species containing latex; D. Percentage of species with compound leaves.
Fig. 1. – Study area. A in Geographical patterns of woody plants' functional traits in Burkina Faso
Fig. 1. – Study area. A. Species richness of the 129 woody plants, distribution records and position of Burkina Faso within Africa; B. Names of landscape elements and cities mentioned in the results.
State of biodiversity documentation in the Philippines: Metadata gaps, taxonomic biases, and spatial biases in the DNA barcode data of animal and plant taxa in the context of species occurrence data
<p>These files can be categorized into three groups: (1) raw datasets obtained from public databases (i.e., GBIF, BOLD, and GenBank), (2) manually edited files needed for parsing and analysis, and (3) supplementary files for spatial analysis. All are used in the examination of gaps and biases present in Philippine biodiversity data, which can direct research on the taxa and spatial regions that need more sampling.</p>
ARCHIMED-φ simulation files for the simulation of Design A from the article "When architectural plasticity fails to counter the light competition imposed by planting design: an in silico approach using a functional-structural model of oil palm"; in silico Plants journal
<p>Input files for the simulation of Design A in ARCHIMED-φ from the article "When architectural plasticity fails to counter the light competition imposed by planting design: an in silico approach using a functional-structural model of oil palm"; in silico Plants journal.</p> <p>See https://archimed-platform.github.io/archimed-phys-user-doc/ for more details on the model.</p> <p>Make a simulation by opening a terminal at the root of the folder and type: `java -jar .\archimed-phys.jar .\DesignA_MockUpA_seed1_MAP_72.yml`.</p>
Data from: Global plant-frugivore trait matching is shaped by climate and biogeographic history
<p>Species interactions are influenced by the trait structure of local multi-trophic communities. However, it remains unclear whether mutualistic interactions, in particular, can drive trait patterns at the global scale, where climatic constraints and biogeographic processes gain importance. Here we evaluate global relationships between traits of frugivorous birds and palms (<em>Arecaceae</em>), and how these relationships are affected, directly or indirectly, by assemblage richness, climate and biogeographic history. We leverage a new and expanded gape size dataset for nearly all avian frugivores, and find a positive relationship between gape size and fruit size, that is, trait matching, which is influenced indirectly by palm richness and climate. We also uncover a latitudinal gradient in trait matching strength, which increases towards the tropics and varies among zoogeographic realms. Taken together, our results suggest trophic interactions have consistent influences on trait structure, but that abiotic, biogeographic and richness effects also play important, though sometimes indirect, roles in shaping the functional biogeography of mutualisms.</p>
Data from: Metabarcoding of soil environmental DNA replicates plant community variation but not specificity
<blockquote> <p>While metabarcoding of plant DNA from their environment is an exciting method that can supplement inventorying of live plant species, the accuracy and specificity has yet to be fully assessed over complex continuous landscapes. In this work, we evaluate plant community profiles produced via metabarcoding of soil by comparing them to a morphological survey. We assessed plant communities by metabarcoding of soil DNA in 130 sites along ecological gradients (nutrients, succession, moisture) in Denmark using chloroplast <i>trn</i>L region (10-143 bp) primer set and compared the resulting communities to communities produced with a longer nuclear ITS2 region (~216 bp) and a morphological survey. We found that the community variation observed within the morphological survey was well represented by molecular surveys, with significant correlation with both community composition and richness using both primer sets. While the majority of the ITS2 sequences could be assigned to species (over 80%), we had less success with the <i>trn</i>L sequences (70%), which was only possible after restricting the reference database to local species. We conclude that the community profiles produced by metabarcoding can be highly effective in performing large-scale macroecological studies. However, the discovery rates and taxonomic assignments produced via metabarcoding remained inferior to morphological surveys, but manual curation of databases improves the <i>specificity</i> of assignments made by the <i>trn</i>L primers, and improves the <i>accuracy</i> of the assignments made with the ITS2 primers. Finally, we suggest that a greater percentage of named diversity would be recovered by increasing soil sampling with the use of additional universal primer sets.</p> </blockquote>
Rates of premature fruit drop for 201 plant species on Barro Colorado Island, Panama
<p>Pre-dispersal seed mortality caused by premature fruit drop is a potentially important source of plant mortality, but one which has rarely been studied in the context of tropical forest plants. Of particular interest is premature fruit drop triggered by enemies, which – if density-dependent – could contribute to species co-existence in tropical forest plant communities. </p> <p>We used a long-term (31 year) dataset on seed and fruit fall obtained through weekly collections from a network of seed traps in a lowland tropical forest (Barro Colorado Island, Panama) to estimate the proportion of seeds prematurely abscised for 201 woody plant species. To determine whether enemy attack might contribute to premature fruit drop we tested whether plant species abscise more of their fruit prematurely if they: (1) have attributes hypothesised to be associated with high levels of enemy attack, and (2) are known to be attacked by one enemy-group (insect seed predators). We also tested (3) whether mean rates of premature fruit drop for plant species are phylogenetically conserved.</p> <p>Overall rates of premature fruit drop were high in the plant community. Across all species, 39% of seeds were abscised before completing their development. Rates of premature seed abscission varied considerably among species and could not be explained by phylogeny. Premature seed abscission rates were higher in species which are known to host pre-dispersal insect seed predators and species with attributes that were hypothesised to make them more susceptible to attack by pre-dispersal enemies, namely species which (1) have larger seeds, (2) have a greater average height, (3) have temporally predictable fruiting patterns, and (4) are more abundant at the study site.</p> <p><em>Synthesis. </em>Premature fruit drop is likely to be a major source of seed mortality for many plant species on Barro Colorado Island. It is plausible that pre-dispersal seed enemies, such as insect seed predators, contribute to community-level patterns of premature fruit drop and have the potential to mediate species co-existence through stabilising negative density dependence. Our study suggests that the role of pre-dispersal enemies in structuring tropical plant communities should be considered alongside the more commonly studied post-dispersal seed and seedling enemies.</p>
Local communities' perceptions of wild edible plant and mushroom change: A systematic review
<p>These datasets are the basis of publication "Local communities’ perceptions of wild edible plant and mushroom change: A systematic review", DOI: https://doi.org/10.1016/j.gfs.2021.100601<br> File GFS_paperIDs.csv lists the articles that are included in the systematic review with their identification numbers.<br> File GFS_data_papers.csv contains data related to the articles reporting on changes of wild edible plants.<br> File GFS_data_plants.csv contains data related to the plant species that are affected by the changes.<br> File GFS_variable_desriptions.txt informs about the variables in files GFS_data_papers.csv and GFS_data_plants.csv.</p>
Replicated radiation of a plant clade along a cloud forest archipelago dataset
<p>Raw data complementary of https://github.com/eaton-lab/Orienotinus-phylogeny repository</p> <p>Assembly output of <em>Oreinotinus </em>species (<em>Viburnum</em>, Adoxaceae) using ipyrad pipeline and morphological matrix:</p> <p>List of files:</p> <ul> <li><code>full_dataset.loci</code> Custom format that shows each individual locus with variable sites indicated.</li> <li><code>full_dataset.phy </code>Concatenated RAD loci in Phylip format</li> <li><code>full_dataset.seqs.hdf5</code> Sequences formated as HDF5 file</li> <li><code>full_dataset.snps</code> Phylip files that includes only variable sites (SNPs)</li> <li><code>full_dataset.snps.hdf5</code> SNPs formated as HDF5 file</li> <li><code>full_dataset.snpsmap</code> Information about location (locus) of SNPs</li> <li><code>full_dataset_stats.txt</code> Statistics about the assembly</li> <li><code>leaf_traits_measurements.tsv</code> TSV file that contains leaf measurments used in the discriminant analyses.</li> <li><code>canopy_data.txt</code> Canopy cover data</li> <li><code>central_plateau_data.txt</code> Macroenvironmental data for the Chiapas central plateau</li> <li><code>full_distribution.txt</code> Specimen metadata and coordinates for all the points for Oreinotinus distribution</li> <li><code>leaf_wetness_temp.txt</code> Climate station data for leaf wetness, temperature</li> <li><code>leaf_traits_measurements.tsv</code> TSV file that contains leaf measurments used in the discriminant analyses.</li> <li><code>tree_accessions.txt</code> Species-level tree accessions with specimen metadata</li> </ul>
InpactorDB: A Plant classified lineage-level LTR retrotransposon reference library for free-alignment methods based on Machine Learning
<p>LTR retrotransposons are mobile elements that make up the major part of most plant genomes. Their identification and annotation via bioinformatics approaches represent a major challenge in the era of massive plant genome sequencing. In addition to their involvement in the variation in genome size, these elements are also associated in the function and structure of different chromosomal regions and in the alteration of the function of coding regions, among others. Several plant retrotransposon sequence databases of LTR retrotransposons are available with public access such as PGSB, RepetDB or restricted access such as Repbase. Although they are useful for approaches to identify LTR-RTs in new genomes by similarity, the elements of these databases are not classified down to the lineage/family level. with great depth. </p> <p>Here, we present InpactorDB a semi-curated dataset composed of 130,511 elements from 195 plant genomes (belonging to 108 plant species), classified down to the lineage level. This data set has been used to train two deep neural networks (one fully connected and one convolutional) for fast classification of elements. Used in lineage-level classification approaches, we obtain a score above 98% of F1-score, precision and recall. </p> <p>In order to classify elements of the ‘LTR_STRUC’ and ‘EDTA’ datasets, we used the methodology proposed by Inpactor, which uses homology-based strategy with known coding domains belonging to LTR-RTs. We utilized the RexDB domain library as reference. LTR-RTs were classified into superfamilies, Gypsy (RLG) or Copia (RLC) and sub-classified into lineages according to the similarities of five different amino acid reference domains (GAG, AP, RT, RNAseH, and INT domains). In addition, we applied filters to remove keep only intact elements:</p> <p>1) to remove predicted elements with domains from two different superfamilies (i.e. Gypsy and Copia),</p> <p>2) or elements with domains belonging to two or more different lineages,</p> <p>3) to remove elements with lengths different than those reported by Gypsy Database (GyDB) with a tolerance of 20%,</p> <p>4) to delete incomplete elements which has less than three identified domains, and</p> <p>5) to remove elements with insertions of TE class II (reported in Repbase). </p> <p>The final non-redundant version of InpactorDB consists of 67,305 LTR retrotransposons. Both redundant and non-redundant versions of InpactorDB are available in Fasta format in which sequences have identifiers with the following general Identification code:</p> <p>>Superfamily-Lineage-plant_family-specie-source-length-ID,</p> <p>Where Superfamily can is either RLC (for Copia) or RLG (for Gypsy), Lineage/family follows following the RexDB nomenclature, source (can be Repbase, RepetDB, PGSB, LTR_STRUC or EDTA datasets), length, and ID, is a unique number which identify each element inside the InpactorDB.</p>
Genetic structure in patchy populations of a candidate foundation plant: a case study of Leymus chinensis using genetic and clonal diversity
<p><strong>PREMISE</strong>: The distribution of genetic diversity on the landscape has critical ecological and evolutionary implications. This may be especially the case on a local scale for foundation plant species since they create and define ecological communities, contributing disproportionately to ecosystem function.</p> <p><strong>METHODS</strong>: We examined the distribution of genetic diversity and clones, which we defined first as unique multilocus genotypes (MLG), and then by grouping similar MLGs into multilocus lineages (MLL). We used 186 markers from inter-simple sequence repeats (ISSR) across 358 ramets from 13 patches of the foundation grass <em>Leymus chinensis</em>. We examined the relationship between genetic and clonal diversities, their variation with patch-size, and the effect of the number of markers used to evaluate genetic diversity and structure in this species.</p> <p><strong>RESULTS</strong>: Every ramet had a unique MLG. Almost all patches consisted of individuals belonging to a single MLL. We confirmed this with a clustering algorithm to group related genotypes. The predominance of a single lineage within each patch could be the result of the accumulation of somatic mutations, limited dispersal, some sexual reproduction with partners mainly restricted to the same patch, or a combination of all three.</p> <p><strong>CONCLUSIONS</strong>: We found strong genetic structure among patches of <em>L. chinensis</em>. Consistent with previous work on the species, the clustering of similar genotypes within patches suggests that clonal reproduction combined with somatic mutation, limited dispersal, and some degree of sexual reproduction among neighbors causes individuals within a patch to be more closely related than among patches.</p>
Data for manuscript: Ecological lags govern the pace and outcome of plant community responses to 21st century climate change
<p>These data were used in the analyses reported in Block et al. "Ecological lags govern the pace and outcome of plant community responses to 21st century climate change".</p>
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Allen Brain Atlas
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