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The conflict between hosts and non-hosts changes the severity of diseases in degraded grassland plant communities

<p>load: disease severity of plant community</p> <p>richnes: species richness</p> <p>Nonhost: Non-hosts richness</p> <p>coverage: relative coverage</p> <p>RHost: relative hosts richness</p> <p>PD: Faith's phylogenetic distance</p> <p>beta: beta diversity of plant community</p> <p>SLA: CWM SLA</p> <p>LN: CWM leaf N content</p> <p>LP:CWM leaf P content</p> <p>NP: CWM leaf N:P</p> <p>group: degree of grassland degradation</p> <p>Shannon: Shannon index of plant community</p> <p>Simpson: Simpsion index of plant community</p> <p>Pielou: Pielou index of plant community</p> <p>marglef: Marglef index of plant community</p>

opencc-by-4.0May 2025View details →

Processed data supporting the manuscript "Cutting the sap: first molecular phylogeny of twig-girdler longhorn beetles (Coleoptera: Cerambycidae: Lamiinae: Onciderini) suggests shifts in host plant attack behaviors contributed to morphological evolution"

<div><strong>Processed data supporting the manuscript: </strong>Cutting the sap: first molecular phylogeny of twig-girdler longhorn beetles (Coleoptera: Cerambycidae: Lamiinae: Onciderini) suggests shifts in host plant attack behaviors contributed to morphological evolution</div> <div> </div> <div><strong>By:</strong> Diego de S. Souza 1, 2, Rowan L. K. French 3, José O. Silva Júnior 4, Eugenio H. Nearns 5, Luciane Marinoni 4, Ian P. Swift 6, Kelly B. Miller 7, Felix A. H. Sperling 2 & Marcela L. Monné 1</div> <div> </div> <div>1 Department of Entomology, National Museum, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.</div> <div>2 Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.</div> <div>3 Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.</div> <div>4 Department of Zoology, Federal University of Paraná, Curitiba, Paraná, Brazil.</div> <div>5 National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.</div> <div>6 California State Collection of Arthropods, Sacramento, California, USA.</div> <div>7 Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA.</div> <div> </div> <div>Corresponding author: Diego de S. Souza, dsouza@fieldmuseum.org. Current affiliation: Field Museum of Natural History, Chicago, Illinois, USA.</div> <div> </div> <div> </div> <div><strong>List of Contents: </strong></div> <div> </div> <div><strong>Onciderini_concat_matrix.phy</strong></div> <div>Concatenated matrix (cox1, Wg and CPS) used for the phylogenetic analyses of Onciderini (Coleoptera: Cerambycidae: Lamiinae: Onciderini). </div> <div> </div> <div><strong>PartitionFinder_AICc_best_scheme.txt</strong></div> <div>Results from PartitionFinder v2.1.1, containing the best partitioning scheme for the concatenated matrix of Onciderini, identified using the corrected Akaike Information Criterion (AICc), with model definitions for use in the phylogenetic analyses.</div> <div> </div> <div><strong>RAxML_Onciderini_concat_matrix (zip file)</strong></div> <div>- Onciderini_concat_matrix.phy: concatenated matrix (cox1, Wg and CPS) used in the RAxML phylogenetic analyses of Onciderini (Coleoptera: Cerambycidae: Lamiinae: Onciderini).</div> <div>- Partitions_AICc_RAxML.txt: partitioning scheme used in the RAxML analysis as predefined by PartitionFinder v2.1.1 using the corrected Akaike Information Criterion (AICc).</div> <div>- RAxML_bestTree.Onciderini_concat_matrix_ML: best-scoring maximum likelihood tree inferred by RAxML for the concatenated matrix of Onciderini.</div> <div>- RAxML_bipartitions.Onciderini_concat_matrix_final: bipartitions (clades) of the maximum likelihood tree inferred by RAxML with support values estimated from 1,000 pseudoreplicates.</div> <div>- RAxML_bipartitionsBranchLabels.Onciderini_concat_matrix_final: final maximum likelihood tree inferred by RAxML for the concatenated matrix of Onciderini, with labeled branches showing bootstrap support values.</div> <div>- RAxML_bootstrap.Onciderini_concat_matrix_bootstrap: bootstrap trees generated from a non-parametric bootstrap analysis in RAxML based on 1,000 pseudoreplicates.</div> <div>- RAxML_info.Onciderini_concat_matrix_bootstrap: log file containing details of the bootstrap analysis, including the settings and parameters used in the non-parametric bootstrap runs in RAxML.</div> <div>- RAxML_info.Onciderini_concat_matrix_final: log file summarizing the RAxML analysis, including settings and convergence statistics for the final maximum likelihood tree.</div> <div>- RAxML_info.Onciderini_concat_matrix_ML: log file containing details of the maximum likelihood tree search, including the parameters and models applied during the maximum likelihood analysis conducted by RAxML.</div> <div>- RAxML_log.Onciderini_concat_matrix_ML: log file of the maximum likelihood tree search for the concatenated matrix of Onciderini.</div> <div>- RAxML_parsimonyTree.Onciderini_concat_matrix_ML: parsimony starting tree used by RAxML during the maximum likelihood analysis for the concatenated matrix of Onciderini.</div> <div>- RAxML_result.Onciderini_concat_matrix_ML: maximum likelihood tree inferred by RAxML from the concatenated matrix of Onciderini, summarizing the tree topology and likelihood score for the best tree obtained.</div> <div> </div> <div><strong>BI_AICc_Onciderini_concat_matrix (zip file)</strong></div> <div>- BI_AICc_Onciderini_concat_matrix.nex: nexus file containing the concatenated matrix of Onciderini used for Bayesian Inference (BI), including the best-fit model scheme identified by PartitionFinder and MCMC parameters for running the analysis in MrBayes.</div> <div>- BI_AICc_Onciderini_concat_matrix.nex_r1_r2_combined_consensus.tree: consensus tree from two combined independent Bayesian Inference (BI) runs based on the concatenated matrix of Onciderini, after discarding the first 25% of initial generations as burn-in.</div> <div>- BI_AICc_Onciderini_concat_matrix.nex.run1.p: log file containing parameter values and likelihood scores from the first run of the Bayesian Inference (BI) based on the concatenated matrix of Onciderini.</div> <div>- BI_AICc_Onciderini_concat_matrix.nex.run2.p: log file containing parameter values and likelihood scores from the second run of the Bayesian Inference (BI) based on the concatenated matrix of Onciderini.</div> <div> </div> <div><strong>BEAST2_Onciderini_BD_lognormal (zip file)</strong></div> <div>- BEAUTi_Onciderini_BD_lognormal.xml: XML file generated by BEAUTi for running BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a lognormal distribution.</div> <div>- BEAST2_Onciderini_BD_lognormal_run[1-8].log: log files from eight independent runs of BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a lognormal distribution.</div> <div>- TreeAnnotator_Onciderini_BD_lognormal_run1-run8_consensus.out: TreeAnnotator output file combining the results of eight BEAST2 runs based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a lognormal distribution.</div> <div>- TreeAnnotator_Onciderini_BD_lognormal_run1-run8_consensus.tre: consensus tree from eight combined BEAST2 runs, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a lognormal distribution, after discarding the first 10% of initial generations as burn-in.</div> <div> </div> <div><strong>BEAST2_Onciderini_BD_exponential (zip file)</strong></div> <div>- BEAUTi_Onciderini_BD_exponential.xml: XML file generated by BEAUTi for running BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and an exponential distribution.</div> <div>- BEAST2_Onciderini_BD_exponential_[1-8].log: log files from eight independent runs of BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and an exponential distribution.</div> <div>- TreeAnnotator_Onciderini_BD_exponential_run1-run8_consensus.out: TreeAnnotator output file combining the results of eight BEAST2 runs based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and an exponential distribution.</div> <div>- TreeAnnotator_Onciderini_BD_exponential_run1-run8_consensus.tre: consensus tree from eight combined BEAST2 runs, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and an exponential distribution, after discarding the first 10% of initial generations as burn-in.</div> <div> </div> <div><strong>BEAST2_Onciderini_BD_uniform (zip file)</strong></div> <div>- BEAUTi_Onciderini_BD_uniform.xml: XML file generated by BEAUTi for running BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a uniform distribution.</div> <div>- BEAST2_Onciderini_BD_uniform_[1-8].log: log files from eight independent runs of BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a uniform distribution.</div> <div>- TreeAnnotator_Onciderini_BD_uniform_run1-run8_consensus.out: TreeAnnotator output file combining the results of eight BEAST2 runs based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a uniform distribution.</div> <div>- TreeAnnotator_Onciderini_BD_uniform_run1-run8_consensus.tre: consensus tree from eight combined BEAST2 runs, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a uniform distribution, after discarding the first 10% of initial generations as burn-in.</div> <div> </div> <div><strong>Comparative_analyses (zip file)</strong></div> <div><strong>RawData (folder):</strong> raw morphometric and girdling data, plus tree that was later pruned for downstream comparative analyses; these data were used as input for the OncidHeadDimorphism-DatasetPREP-FINAL.R data cleaning script. </div> <div>- Onciderini_BD_lognormal_run1-run8_consensus.nwk: newick version of TreeAnnotator_Onciderini_BD_lognormal_run1-run8_consensus.tre (outputted as a newick file by importing the .tre file into FigTree and exporting in newick format).</div> <div>- Measurements_Onciderini_Raw_Final.csv: individual-level raw morphometric data for Onciderini.</div> <div>- Behav_Matrix_2_states_trimmed_2022-12-15.csv: species-level data on girdling status for Onciderini species, with all Lochmaeocles species classified as girdlers (2 behavioral states across Onciderini species). </div> <div>- Matrix_3_states_trimmed_final.csv: species-level data on girdling status for Onciderini species, with all Lochmaeocles species classified as facultative girdlers (3 behavioral states across Onciderini species). </div> <div>- Matrix_2_states_trimmed_1LochGirdler_Final.csv: species-level data on girdling status for Onciderini species, with only one Lochmaeocles species (L. tessellatus) classified as a girdler (2 behavioral states across Onciderini species). </div> <div> </div> <div><strong>ProcessedData (folder): </strong>filtered data and pruned trees outputted by the OncidHeadDimorphism-DatasetPREP-FINAL.R script</div> <div>- oncid_f_36spp_clean.csv: dataset of species means and log-ratios for morphometric traits in females, plus girdling data; only includes species that have girdling data and are in the phylogenetic tree</div> <div>- oncid_m_42spp_clean.csv: dataset of species means and log-ratios for morphometric traits in males, plus girdling data; only includes species that have girdling data and are in the phylogenetic tree</div> <div>- oncid_sd_35spp_clean.csv: dataset of species means for sexual dimorphism in morphometric traits, plus girdling data; only includes species that have girdling data and are in the phylogenetic tree</div> <div>- oncid_girdlingbehav_allingroupspp_clean.csv: full dataset of girdling behavior for 56 Onciderini species that are in the phylogenetic tree; includes separate columns for the three alternative girdling classification schemes</div> <div>- oncid_tree_behavfull_56spp.nwk: pruned phylogenetic tree for the full girdling dataset (56 species)</div> <div>- oncid_tree_f_36spp.nwk: pruned phylogenetic tree for the female morphometric dataset (36 species)</div> <div>- oncid_tree_m_42spp.nwk: pruned phylogenetic tree for the male morphometric dataset (42 species)</div> <div>- oncid_tree_mf_43spp.nwk: pruned phylogenetic tree for all species with morphometric data for males or females; used for the stochastic character map next to the heatmap plot (Fig 4)</div> <div>- oncid_tree_sd_35spp.nwk: pruned phylogenetic tree for the sexual dimorphism dataset (35 species)</div> <div> </div> <div><strong>FittedModels (folder): </strong>fitted models (mvgls, model comparison analyses, OUM models, simmaps) outputted by the OncidHeadDimorphism-Analysis-FINAL.R script </div> <div>- MacroModelFits_logRtraits_f_36spp-2024-10-12.Rdata: summary of model comparison results for Brownian Motion (BM), single-peak Ornstein-Uhlenbeck (OU), multipeak OU (OUM), and multi-rate Brownian motion (BMM) models (univariate and multivariate) fitted to female morphometric data across 100 stochastic character maps of girdling behavior</div> <div>- MacroModelFits_logRtraits_m_42spp-2024-10-12.Rdata: summary of model comparison results for Brownian Motion (BM), single-peak Ornstein-Uhlenbeck (OU), multipeak OU (OUM), and multi-rate Brownian motion (BMM) models (univariate and multivariate) fitted to male morphometric data across 100 stochastic character maps of girdling behavior</div> <div>- MacroModelFits-SDDI-35spp_2024-10-11.Rdata: summary of model comparison results for Brownian Motion (BM), single-peak Ornstein-Uhlenbeck (OU), multipeak OU (OUM), and multi-rate Brownian motion (BMM) models (univariate and multivariate) fitted to sexual dimorphism data across 100 stochastic character maps of girdling behavior</div> <div>- mvgls-results-headsize-mf-2024-10-12.Rdata: fitted mvgls regression models for male and female traits (analyzed separately)</div> <div>- mvgls-results-sddi-2024-10-12.Rdata: fitted mvgls regression models for sexual dimorphism</div> <div>- OUM_headtraits_f_36spp-2024-10-12.Rdata: fitted OUM models and summary statistics for female head traits</div> <div>- OUM_headtraits_m_42spp-2024-10-12.Rdata: fitted OUM models and summary statistics for male head traits</div> <div>- OUM-SDDI-35spp-2024-10-12.Rdata: fitted OUM models and summary statistics for sexual dimorphism in head traits</div> <div>- simmaps_ard_full_2state.RDS: stochastic character maps of girdling behaviour for all 56 species with girdling data, with two behavioral states (girdling or non-girdling) - all Lochmaeocles species are classified as girdlers</div> <div>- simmaps_ard_full_3state.RDS: stochastic character maps of girdling behaviour for all 56 species with girdling data, with three behavioral states (girdling, non-girdling, or facultative girdling)</div> <div>- simmaps_ard_full_1Loch.RDS: stochastic character maps of girdling behaviour for all 56 species with girdling data, with two behavioral states (girdling or non-girdling) - only one Lochmaeocles species (L. tessellatus) is classified as a girdler</div> <div>- simmaps_ard_m.RDS: stochastic character map for the 42 species used in the analyses of male morphometric traits</div> <div>- simmaps_ard_f.RDS: stochastic character map for the 36 species used in the analyses of female morphometric traits</div> <div>- simmaps_ard.RDS: stochastic character map for the 35 species used in the sexual dimorphism analyses; 2 behavioral states.</div> <div> </div> <div><strong>Rscripts (folder): </strong>R scripts used to process data and run phylogenetic comparative analyses of head size and girdling behavior.</div> <div>- OncidHeadDimorphism-DatasetPREP-FINAL.R: R script used to filter data and prune trees from the RawData folder for downstream phylogenetic comparative analyses; outputs of this script are in the ProcessedData folder.</div> <div>- OncidHeadDimorphism-Analysis-FINAL.R: R script used to analyze data in the ProcessedData folder to answer questions about the origin and evolution of girdling behavior and the relationship between girdling and head size or head size sexual dimorphism; fitted models outputted by this script are in the FittedModels folder</div> <div>- OncidHeadDimorphism-Plots-FINAL.R: R script used to generate plots for the manuscript<br><br></div>

Data from: Assessing the effect of tissue and fire-response traits on plant growth rates post-disturbance in Eastern Australia

<p>Here is the necessary code and data to reproduce results published in 'Assessing the effect of tissue and fire-response traits on plant growth rates post-disturbance in Eastern Australia'.</p>

opencc-by-4.0Jun 2024View details →

Additional files for Horvath et al., 2024. Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning.

<p>Additional data for Horvath et al., 2024 (source code freeze, models, data, supplementary figures, tables and files(.</p>

Dataset: Effects of dietary exposure to plant toxins on bioaccumulation, survival, and growth of black soldier fly (Hermetia illucens) larvae and lesser mealworm (Alphitobius diaperinus) [larval performance]

Open the record for dataset details and reuse information.

Dataset: Effects of dietary exposure to plant toxins on bioaccumulation, survival, and growth of black soldier fly (Hermetia illucens) larvae and lesser mealworm (Alphitobius diaperinus) [concentrations]

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opencc-by-4.0Jun 2023View details →

Table 2 in New records of phytoseiid mites (Acari: Phytoseiidae) on solanaceous plants in the Syrian coastal region

<p><b>Table 2</b> Phytoseiid and associated phytophagous mites from each solanaceous species of each sampling site visited between 2018 and 2020 in Latakia and Tartus governorates in the Syrian coastal region.</p><table><tbody><tr><th>Site</th><th>Geographic coordinates /a.a.s.l.</th><th>Collection date</th><th>Plant species <b>(Type of locality)</b></th><th>Predatory mite species</th><th>Number of specimens</th><th><b>Associated phytophagous mites</b></th></tr><tr><th><b>Latakia</b></th></tr></tbody><tbody><tr><th>Zaghreen</th><td>35°43' 54.6"N, 35°52' 59.2"E</td><td>2-XI-2018</td><td><i>Solanum melongena Amblyseius swirskii</i></td><td>5&female;&female;, 2&male;&male;</td><td><i>Tetranychus urticae</i></td></tr><tr><td>/ 47 m</td><td></td><td>(Open-field)</td><td></td><td></td><td><i>Brevipalpus obovatus</i></td></tr><tr><th>Wadi Qandil</th><td>35°42'48.5"N 35°52' 08.7"E</td><td>4-XI-2018</td><td>S. melongena</td><td><i>A. swirskii</i></td><td>2&female;&female;, 1&male;, 2i*</td><td><i>T. urticae</i></td></tr><tr><td>/ 23 m</td><td></td><td>(Open-field)</td><td></td><td></td><td></td></tr><tr><th>Burj Islam</th><td>35°40'41.5"N, 35°47'46.0"E</td><td>4-XI-2018</td><td><i>S. melongena</i></td><td><i>Typhlodromus</i> (<i>Anthoseius</i>) <i>rickeri</i></td><td>2&female;&female;, 4i</td><td><i>T. urticae</i></td></tr><tr><td>/ 26 m</td><td></td><td>(Open-field)</td><td></td><td></td><td></td></tr><tr><th>Al-Qutailibiyah</th><td>35°18'43.1"N, 35°59'41.1"E</td><td>1-III-2019</td><td>S. lycopersicum</td><td><i>Phytoseiulus persimilis</i></td><td>1&female;</td><td><i>T. urticae</i></td></tr><tr><td>/ 74 m</td><td></td><td>(Greenhouse)</td><td></td><td></td><td></td></tr><tr><th>Al-Aaqbiyeh</th><td>35°16'27.8"N, 35°58'03.4"E</td><td>8-IX-2019</td><td>S. melongena</td><td><i>Neoseiulus barkeri</i></td><td>2&female;&female;</td><td><i>T. urticae</i></td></tr><tr><td>/ 20 m</td><td></td><td>(Open-field)</td><td></td><td></td><td></td></tr><tr><th>Al-Aaqbiyeh</th><td>35°16'43.7"N, 35°58' 20.7"E</td><td>8-IX-2019</td><td>S. melongena</td><td><i>P. persimilis</i></td><td>1&female;</td><td><i>T. urticae</i></td></tr><tr><td>/ 28 m</td><td></td><td>(Greenhouse)</td><td></td><td></td><td></td></tr><tr><th>Al-Borjan</th><td>35°18' 10.5"N, 35°57'46.0"E</td><td>8-IX-2019</td><td>S. melongena</td><td><i>P. persimilis</i></td><td>2&female;&female;</td><td><i>T. urticae</i></td></tr><tr><td>/ 32 m</td><td></td><td>(Open-field)</td><td></td><td></td><td></td></tr><tr><th>Al-Borjan</th><td>35°17'46.4"N, 35°58'45.0"E</td><td>8-IX-2019</td><td>S. melongena</td><td><i>Phytoseius finitimus</i></td><td>1&female;, 1&male;, 2i</td><td><i>T. urticae</i></td></tr><tr><td>/ 56 m</td><td></td><td>(Open-field)</td><td></td><td></td><td><i>Polyphagotarsonemus latus</i></td></tr><tr><th>Al-Mrouj</th><td>35°33'52.2"N, 35°45' 37.2"E</td><td>13-IX-2019</td><td>S. nigrum</td><td><i>P. persimilis</i></td><td>2&female;&female;, 3&male;&male;</td><td><i>T. urticae</i></td></tr><tr><td>/ 10 m</td><td></td><td>(Uncultivated)</td><td><i>Iphiseius degenerans</i></td><td>3&female;&female;, 1&male;</td><td></td></tr><tr><td></td><td></td><td></td><td><i>Typhlodromus</i> (<i>Typhlodromus</i>) <i>athiasae</i></td><td>2&female;&female;</td><td></td></tr><tr><th>AL-Maghrit</th><td>35°36'13.1"N, 35°49' 19.9"E</td><td>15-XI-2019</td><td>S. nigrum</td><td><i>I. degenerans</i></td><td>3&female;&female;</td><td><i>T. urticae</i></td></tr><tr><td>/ 60 m</td><td></td><td>(Uncultivated)</td><td><i>T</i>. (<i>A</i>.) <i>rickeri</i></td><td>2&female;&female;, 1&male;</td><td></td></tr><tr><th>Bereen</th><td>35°36' 00.8"N, 36°05'35.7"E</td><td>18-IX-2019</td><td>S. lycopersicum</td><td><i>Typhlodromus (Anthoseius) recki</i></td><td>2&female;&female;</td><td><i>T. urticae</i></td></tr><tr><td>/ 624 m</td><td></td><td>(Open-field)</td><td></td><td></td><td></td></tr><tr><th>Al-Dakleyiah</th><td>35°37'04.0"N, 36°04'28.7"E</td><td>18-IX-2019</td><td>S. melongena</td><td><i>P. persimilis</i></td><td>24&female;&female;, 10&male;&male;, 13i</td><td><i>T. urticae</i></td></tr><tr><td>/ 530 m</td><td></td><td>(Open-field)</td><td><i>T</i>. (<i>T</i>.) <i>athiasae</i></td><td>2&female;&female;, 1&male;, 1i</td><td></td></tr><tr><th>Er Ruwaysah</th><td>35°50'32.0"N, 35°52'42.3"E</td><td>19-XI-2019</td><td><i>S. melongena</i></td><td><i>T</i>. (<i>T</i>.) <i>athiasae</i></td><td>2&female;&female;</td><td><i>T. urticae</i></td></tr><tr><td>/ 33 m</td><td></td><td>(Open-field)</td><td></td><td></td><td></td></tr><tr><th>Al-Isawiyah</th><td>35°47'24.8"N, 35°51'02.5"E</td><td>19-XI-2019</td><td><i>S. melongena</i></td><td><i>T</i>.(<i>A</i>.) <i>recki</i></td><td>4&female;&female;</td><td><i>B. obovatus</i></td></tr><tr><td>/ 116 m</td><td></td><td>(Open-field)</td><td><i>P. finitimus</i></td><td>9&female;&female;, 1i</td><td></td></tr><tr><td></td><td></td><td></td><td><i>Euseius scutalis</i></td><td>10&female;&female;, 1i</td><td></td></tr><tr><th>Wadi Qandil</th><td>35°42'49.7"N, 35°51'28.7"E</td><td>26-XI-2019</td><td>S. melongena</td><td><i>A. swirskii</i></td><td>3&female;&female;</td><td><i>T. urticae</i></td></tr><tr><td>/ 20 m</td><td></td><td>(Open-field)</td><td><i>T</i>. (<i>T</i>.) <i>athiasae</i></td><td>1&female;</td><td></td></tr><tr><th>Slago</th><td>35°26' 13.7"N, 36°01'14.7"E</td><td>2-IX-2020</td><td><i>S. lycopersicum</i></td><td><i>T</i>. (<i>T</i>.) <i>athiasae</i></td><td>2&female;&female;</td><td><i>T. urticae</i></td></tr><tr><td>/ 154 m</td><td></td><td>(Open-field)</td><td><i>P. persimilis</i></td><td>3&female;&female;</td><td></td></tr><tr><td></td><td></td><td></td><td><i>Amblyseius andersoni</i></td><td>1&female;</td><td></td></tr><tr><th>Slago</th><td>35°26'18.0"N, 36°01'17.4"E</td><td>2-IX-2020</td><td>S. lycopersicum</td><td><i>P. persimilis</i></td><td>4&female;&female;</td><td><i>T. urticae</i></td></tr><tr><td>/ 162 m</td><td></td><td>(Open-field)</td><td><i>T</i>.(<i>A</i>.) <i>recki</i></td><td>1&female;</td><td></td></tr><tr><th>Rouiset Qasmin</th><td>35°37' 31.5"N, 35°53'55.4"E</td><td>29-X-2020</td><td>S. melongena</td><td><i>E. scutalis</i></td><td>4&female;&female;</td><td><i>T. urticae</i></td></tr><tr><td>/ 209 m</td><td></td><td>(Open-field)</td><td><i>P. finitimus</i></td><td>4&female;&female;</td><td></td></tr><tr><th>Zaghreen</th><td>35°43' 08.5"N, 35°53' 28.7"E</td><td>31-X-2020</td><td>S. melongena</td><td><i>P. persimilis</i></td><td>1&female;</td><td><i>T. urticae</i></td></tr><tr><td>/ 39 m</td><td></td><td>(Open-field)</td><td></td><td></td><td><i>B. obovatus</i></td></tr><tr><th>Zaghreen</th><td>35°43'05.0"N, 35°53' 24.5"E</td><td>31-X-2020</td><td>S. melongena</td><td><i>P. finitimus</i></td><td>1&female;</td><td><i>T. urticae</i></td></tr><tr><td>/ 40 m</td><td></td><td>(Open-field)</td><td></td><td></td><td><i>B. obovatus</i></td></tr><tr><td></td><td></td><td></td><td></td><td></td><td><i>Brevipalpus californicus</i></td></tr><tr><th>Asurskia</th><td>35°42'26.8"N, 35°54' 19.5"E</td><td>31-X-2020</td><td>S. melongena</td><td><i>A. swirskii</i></td><td>1&female;</td><td><i>T. urticae</i></td></tr><tr><td>/ 34 m</td><td></td><td>(Open-field)</td><td></td><td></td><td></td></tr><tr><th>Asurskia</th><td>35°42'26.5"N, 35°53' 27.5"E</td><td>31-X-2020</td><td>S. melongena</td><td><i>P. finitimus</i></td><td>10&female;&female;, 4&male;&male;</td><td><i>T. urticae</i></td></tr><tr><td>/ 32 m</td><td></td><td>(Open-field)</td><td><i>A. swirskii</i></td><td>3&female;&female;</td><td><i>B. obovatus</i></td></tr><tr><th><b>Tartus</b></th></tr><tr><th>Ibtellah</th><td>35°13'19.9"N, 35°59'17.9"E</td><td>27-IV-2019</td><td>S. melongena</td><td><i>P. persimilis</i></td><td>2&female;&female;, 2&male;&male;, 2i</td><td><i>T. urticae</i></td></tr><tr><td>/ 141 m</td><td></td><td>(Greenhouse)</td><td></td><td></td><td></td></tr><tr><th>Kharab Marqueh</th><td>35°02'49.3"N, 35°53'48.7"E</td><td>11-V-2019</td><td>S. lycopersicum</td><td><i>P. persimilis</i></td><td>6&female;&female;, 2&male;&male;, 5i</td><td><i>T. urticae</i></td></tr><tr><td>/ 20 m</td><td></td><td>(Greenhouse)</td><td></td><td></td><td></td></tr><tr><th>Al-Rawda</th><td>35°03'54.1"N, 35°53' 29.7"E</td><td>11-V-2019</td><td>S. melongena</td><td><i>P. persimilis</i></td><td>2&female;&female;</td><td><i>T. urticae</i></td></tr><tr><td>/ 13 m</td><td></td><td>(Greenhouse)</td><td><i>Neoseiulus californicus</i></td><td>4&female;&female;</td><td></td></tr><tr><th>Al-Khrab</th><td>35°02'49.3"N, 35°53'48.7"E</td><td>11-V-2019</td><td>S. nigrum</td><td><i>E. scutalis</i></td><td>8&female;&female;</td><td>none</td></tr><tr><td>/ 20 m</td><td></td><td>(Uncultivated)</td><td></td><td></td><td></td></tr><tr><th>Yahmoor</th><td>34°48'06.6"N, 35°58'11.5"E</td><td>31-V-2019</td><td>S. melongena</td><td><i>P. persimilis</i></td><td>62&female;&female;, 4&male;&male;, 2i</td><td><i>T. urticae</i></td></tr><tr><td>/ 57 m</td><td></td><td>(Greenhouse)</td><td><i>N. barkeri</i></td><td>1&female;</td><td></td></tr><tr><th>Talsnon</th><td>34°40' 22.8"N, 36°06' 11.4"E</td><td>13-VI-2019</td><td>S. melongena</td><td><i>P. persimilis</i></td><td>1&female;</td><td><i>T. urticae</i></td></tr><tr><td>/ 44 m</td><td></td><td>(Greenhouse)</td><td></td><td></td><td></td></tr><tr><th>Talsnon</th><td>34°40' 39.5"N, 36°06'00.4"E</td><td>13-VI-2019</td><td>S. melongena</td><td><i>P. persimilis</i></td><td>2&female;&female;</td><td><i>T. urticae</i></td></tr><tr><td>/ 44 m</td><td></td><td>(Greenhouse)</td><td></td><td></td><td></td></tr><tr><th>Maten Al-Sahel</th><td>35°01' 18.4"N, 35°54'34.8"E</td><td>15-VI-2019</td><td>S. lycopersicum</td><td><i>P. persimilis</i></td><td>3&female;&female;</td><td><i>T. urticae</i></td></tr><tr><td>/ 25 m</td><td></td><td>(Greenhouse)</td><td></td><td></td><td></td></tr><tr><th>Busayrah Al-Jadidah</th><td>34°59'35.3"N, 35°53' 24.5"E</td><td>15-VI-2019</td><td>S. lycopersicum</td><td><i>P. persimilis</i></td><td>1&female;, 4i</td><td><i>T. urticae</i></td></tr><tr><td>/ 10 m</td><td></td><td>(Greenhouse)</td><td></td><td></td><td></td></tr><tr><th>Zahed</th><td>34°41' 34.0"N, 36°00'05.2"E</td><td>1-VII-2019</td><td>S. melongena</td><td><i>P. persimilis</i></td><td>11&female;&female;, 11&male;&male;, 14i</td><td><i>T. urticae</i></td></tr><tr><td>/ 20 m</td><td></td><td>(Greenhouse)</td><td></td><td></td><td></td></tr><tr><th>Al-Qlue</th><td>35°15' 39.8"N, 35°56' 17.8"E</td><td>31-VII-2019</td><td>S. melongena</td><td><i>N. californicus</i></td><td>48&female;&female;, 24&male;&male;, 7i</td><td>1 none</td></tr><tr><td>/ 12 m</td><td></td><td>(Open-field)</td><td><i>E. scutalis</i></td><td>1&female;</td><td></td></tr><tr><th>Salib</th><td>35°06' 20.6"N, 36°06'29.3"E</td><td>20-X-2019</td><td>S. melongena</td><td><i>P. persimilis</i></td><td>4&female;&female;</td><td><i>T. urticae</i></td></tr><tr><td>/ 703 m</td><td></td><td>(Open-field)</td><td><i>P. finitimus</i></td><td>28&female;&female;, 4&male;, 1i</td><td></td></tr><tr><td></td><td></td><td></td><td><i>T</i>. (<i>T</i>.) <i>athiasae</i></td><td>1&female;</td><td></td></tr><tr><th>Nab’e El-Dulbah</th><td>34°55' 10.8"N, 36°08'48.5"E</td><td>24-IX-2020</td><td>S. melongena</td><td><i>P. persimilis</i></td><td>1&female;</td><td><i>T. urticae</i></td></tr><tr><td>/ 380 m</td><td></td><td>(Open-field)</td><td></td><td></td><td><i>Tenuipalpus punicae</i></td></tr><tr><th>Bait Yousef</th><td>34°55' 45.0"N, 36°12'51.2"E</td><td>24-IX-2020</td><td>S. lycopersicum</td><td><i>P. persimilis</i></td><td>3&female;&female;</td><td><i>T. urticae</i></td></tr><tr><td>/ 840 m</td><td></td><td>(Open-field)</td><td><i>P. finitimus</i></td><td>2&female;&female;</td><td></td></tr><tr><th>Bait Yousef</th><td>34°55'47.7"N 36°12'50.2"E</td><td>24-IX-2020</td><td>S. melongena</td><td><i>P. persimilis</i></td><td>10&female;&female;</td><td><i>T. urticae</i></td></tr><tr><td>/ 847 m</td><td></td><td>(Open-field)</td><td></td><td></td><td></td></tr><tr><th>Bait Yousef</th><td>34°55'37.7"N, 36°12'57.6"E</td><td>24-IX-2020</td><td>S. lycopersicum</td><td><i>P. persimilis</i></td><td>5&female;&female;</td><td><i>T. urticae</i></td></tr><tr><td>/ 888 m</td><td></td><td>(Open-field)</td><td></td><td></td><td></td></tr><tr><th>Al-Shaykh Badr</th><td>34°59'23.7"N, 36°03' 38.4"E</td><td>9-XI-2020</td><td>S. melongena</td><td><i>Euseius stipulatus</i></td><td>8&female;&female;, 1&male;</td><td><i>T. urticae</i></td></tr><tr><td>/ 508 m</td><td></td><td>(Open-field)</td><td></td><td></td><td><i>B. obovatus</i></td></tr><tr><th>Al-Wardieh</th><td>35°01'08.7"N, 36°02'49.3"E</td><td>9-XI-2020</td><td>S. melongena</td><td><i>P. finitimus</i></td><td>4&female;&female;, 1&male;</td><td><i>T. urticae</i></td></tr><tr><td>/ 479 m</td><td></td><td>(Open-field)</td><td><i>T</i>. (<i>A</i>.) <i>recki</i></td><td>1&female;</td><td><i>B. obovatus</i></td></tr></tbody></table><p>*: immatures; 1 associated with phytophagous thrips species.: a</p><p>*: immatures;: associated with a phytophagous thrips species.</p>

opencc-by-4.0Apr 2024View details →

Data and R code used in Hennecke et al. "Plant species richness and the root economics space drive soil fungal communities"

<p>To investigate how plant diversity and root traits relate to soil fungal communities, in 2021 we collected trait data from plots in the Jena Experiment (https://the-jena-experiment.de; funded by the DFG FOR 5000) and characterized fungal communities by sequencing, respiration and lipid fatty acid quantification. </p>

Plant-Bee Pollen Interaction Networks Based on Epanthidium tigrinum Nests in Fortaleza, Brazil (2019-2020)

<p>This dataset contains detailed ecological data on the interactions between the solitary bee species <em>Epanthidium tigrinum</em> and various flowering plants in an urban area of Fortaleza, Ceará, Brazil. The data were collected from May 2019 to November 2020, focusing on pollen analysis from nests of <em>E. tigrinum</em> using black cardboard trap nests.</p> <p><strong>Data Includes:</strong></p> <ul> <li><strong>LOCALITY</strong>: Geographic location of the study.</li> <li><strong>BEE_SPECIE</strong>: The species of bee studied, exclusively <em>Epanthidium tigrinum</em>.</li> <li><strong>FLOWER_SPECIES</strong>: Identified plant species based on pollen grains found in the nests.</li> <li><strong>INTERACTION_FREQUENCY</strong>: The frequency of interactions between <em>E. tigrinum</em> and flowering plants, quantified through pollen presence across analyzed slides.</li> <li><strong>NESTING_PERIOD</strong>: Classification of the nesting periods into <strong>High Nesting Period</strong> (June to September) and <strong>Low Nesting Period</strong> (remaining months).</li> <li><strong>YEAR</strong>: The years of data collection (2019 and 2020).</li> </ul> <p><strong>Potential Uses:</strong> This dataset is valuable for researchers studying plant-pollinator interactions, urban ecology, and the role of solitary bees in ecosystem services. It can be utilized in ecological modeling, conservation planning, and understanding the dynamics of pollinator communities in urban settings. Additionally, it may aid in the assessment of the impact of urbanization on pollinator behavior and plant diversity.</p>

Planting time data based on automated data collection

<p>In this dataset, the planting time information is based on data collected by the Risutec Asta documentation system. The data consisted of nine planting sites in western Finland (the coordinates of the study area are 60°41'52"N–61°59'38"N and 21°36'24"E–23°48'49"E). Mechanized planting was carried out by one machine entrepreneur using a crawler excavator fitted with a Risutec PM-160 planting device during the planting seasons of 2019 and 2020. A total of 72,711 seedlings were planted at the study sites (40.6 ha). </p> <p> </p> <p>The collected Asta data were used to define the time consumption and productivity of the excavator-based planting machine, considering the production time consumed at the planting worksites (hours), the loading time of the seedling cassette (minutes), the planting time per seedling (seconds), and the operating hour productivity (seedlings G<sub>15</sub>-hour<sup>–1</sup>, including short [<15 min] delays). The timestamps of each mechanically planted seedlings were presented in chronological order, including the start and end times of planting work.</p> <p> </p> <p>The calculated planting time per seedling (s seedling<sup>–1</sup>) is presented for each planting observation (seedling). The planting time per seedling was calculated by subtracting the timestamp of the previously planted seedling from the timestamp of the planted seedling. In practice, all productivity and time consumption calculations in the study are based on the calculated planting times per seedling. Further details regarding the calculations and employed methodologies can be found in the article (Kemppainen et al. 2024).</p> <p> </p> <p>Description of all variables in the dataset:</p> <p> </p> <p>Site = Number of study site (1–9) </p> <p>Seedling = Order number of planted seedling</p> <p>Date = Date of planting observation (format: DD.MM.YYYY)</p> <p>Timestamp = Time of planting observation (format: HH.MM.SS)</p> <p>Planting time (s) = Calculated planting time per seedling (seconds)</p> <p> </p> <p>Note: In the study by Kemppainen et al. (2024), all planting times of less than 4 s were excluded from the final dataset. Following the correction of the data, a total of 71 903 seedlings included in the final dataset. In addition, the planting time of the first seedling planted at the worksite was defined as 9 s because there was no previous timestamp for the first seedling to allow an exact calculation of the planting time.</p> <p> </p> <p>References</p> <p>Kemppainen K., Kärhä K., Laitila J., Sairanen A., Kankaanhuhta V., Viiri H., Peltola H. (2024). Evaluation of the productivity and costs of excavator-based mechanized tree planting in Finland based on automated data collection. <a href="https://www.silvafennica.fi/">Silva Fennica</a> vol. <a href="https://www.silvafennica.fi/volume/58/1">58</a> no. <a href="https://www.silvafennica.fi/issue/3292">5</a> article id <a href="https://www.silvafennica.fi/article/24047">24047</a>. <a href="https://doi.org/10.14214/sf.24047">https://doi.org/10.14214/sf.24047</a></p>

Medicinal Plant Utilisation and Environmental and Management Drivers Influencing Forest Medicinal Plants in the Czech Republic

<p>This data on medicinal plant utilization and the influence of environmental drivers on medicinal plant availability is part of a broader survey on forest ecosystem services and health conducted in the Czech Republic under the project "Excellent research as a support for the adaptation of forestry and timber industry to global change and the 4th industrial revolution"<em> (EVA 4.0) (</em>CZ.02.1.01/0.0/0.0/16_019/0000803).</p>

opencc-by-4.0Feb 2021View details →

Fig. 3 in Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa

Fig. 3. Continues. For caption, see next part.

Comparative genomics of Helotiales (Leotiomycetes) and in silico analysis of temperature adaptations of plant-associated genes

<p><span>Table S1: Genome assembly size and quality for every species in this study; </span></p> <p><span>Table S2: Genome annotation counts for P450, virulence factors, effectors, and CAZy genes and their temperature adaptation.</span></p>

opencc-by-4.0Nov 2024View details →

TABLE 1 in High-quality herbarium-label transcription by citizen scientists improves taxonomic and spatial representation of the tropical plant family Annonaceae

<p>TABLE 1. — Species per dataset and continent.</p><table><tbody><tr><th><b>Region</b></th><th><b>GBIF</b></th><th><b>Herbonautes</b></th><th><b>Herbonautes and not</b> <b>found in GBIF</b></th></tr></tbody><tbody><tr><th>Americas</th><td>700</td><td>248</td><td>7</td></tr><tr><th>Africa</th><td>268</td><td>189</td><td>17</td></tr><tr><th>Madagascar</th><td>79</td><td>79</td><td>10</td></tr><tr><th>Asia and Oceania</th><td>621</td><td>492</td><td>125</td></tr></tbody></table>

opencc-by-4.0Nov 2024View details →

Computed tomography (CT) was used to study the interaction of NMs with the plant cell tissue in vivo using Zeiss Xradia 510 system on Arabidopsis thaliana leaf. T

<p>This work was supported by the National Research Facility for Lab X-ray CT (NXCT) at the µ-VIS X-ray Imaging Centre, University of Southampton, through EPSRC grant EP/T02593X.</p>

opencc-by-4.0Nov 2024View details →

Insights into Heterocycle Biosynthesis in the Cytotoxic Polyketide Alkaloid Janustatin A from a Plant-Associated Bacterium

<p>Data underlying the manuscript 'Insights into Heterocycle Biosynthesis in the Cytotoxic Polyketide Alkaloid Janustatin A from a Plant-Associated Bacterium' by Leopold-Messer, Chawengrum and Piel.</p> <p>The repository contains:</p> <p>Sequencing data - Genbanks files of construct designs and ab1 files from Sanger sequencing. Contains both plasmids used to construct mutants, as well as sequencing data from final mutants.</p> <p>NMR data - MestReNova files of compounds 2-4.</p> <p>HPLC-MS data - Raw data collected on Thermo-Fisher instruments for the purified compounds (1-4) and the extract of all mutants. </p> <p>EICs - extracted ion chromatograms used to analyse the metabolic differences between mutants. These data are based on the raw files.</p> <p>Bioactivity data - cytotoxicity data of compounds 1-4. </p>

opencc-zeroDec 2017View details →

Data from: Plant community responses to long-term fertilization: changes in functional group abundance drive changes in species richness

Declines in species richness due to fertilization are typically rapid and associated with increases in aboveground production. However, in a long-term experiment examining the impacts of fertilization in an early successional community, we found it took 14 years for plant species richness to significantly decline in fertilized plots, despite fertilization causing a rapid increase in aboveground production. To determine what accounted for this lag in the species richness response, we examined several potential mechanisms. We found evidence suggesting the abundance of one functional group—tall species with long-distance (runner) clonality—drove changes in species richness, and we found little support for other mechanisms. Tall runner species initially increased in abundance due to fertilization, then declined dramatically and were not abundant again until later in the experiment, when species richness and the combined biomass of all other functional groups (non-tall runner) declined. Over 86 % of the species found throughout the course of our study are non-tall runner, and there is a strong negative relationship between non-tall runner and tall runner biomass. We therefore suggest that declines in species richness in the fertilized treatment are due to high tall runner abundance that decreases the abundance and richness of non-tall runner species. By identifying the functional group that drives declines in richness due to fertilization, our results help to elucidate how fertilization decreases plant richness and also suggest that declines in richness due to fertilization can be lessened by controlling the abundance of species with a tall runner growth form.

opencc-zeroMar 2020View details →

Data from: Global warming will affect the maximum potential abundance of boreal plant species

<p>Forecasting the impact of future global warming on biodiversity requires understanding how temperature limits the distribution of species. Here we rely on Liebig's Law of Minimum to estimate the effect of temperature on the maximum potential abundance that a species can attain at a certain location. We develop 95%-quantile regressions to model the influence of effective temperature sum on the maximum potential abundance of 25 common understory plant species of Finland, along 868 nationwide plots sampled in 1985. Fifteen of these species showed a significant response to temperature sum that was consistent in temperature-only models and in all-predictors models, which also included cumulative precipitation, soil texture, soil fertility, tree species and stand maturity as predictors. For species with significant and consistent responses to temperature, we forecasted potential shifts in abundance for the period 2041–2070 under the IPCC A1B emission scenario using temperature-only models. We predict major potential changes in abundance and average northward distribution shifts of 6–8 km yr−1. Our results emphasize inter-specific differences in the impact of global warming on the understory layer of boreal forests. Species in all functional groups from dwarf shrubs, herbs and grasses to bryophytes and lichens showed significant responses to temperature, while temperature did not limit the abundance of 10 species. We discuss the interest of modelling the 'maximum potential abundance' to deal with the uncertainty in the predictions of realized abundances associated to the effect of environmental factors not accounted for and to dispersal limitations of species, among others. We believe this concept has a promising and unexplored potential to forecast the impact of specific drivers of global change under future scenarios.</p>

opencc-zeroDec 2019View details →

An explicit test of Pleistocene survival in peripheral versus nunatak refugia in two high mountain plant species

<p>Pleistocene climate fluctuations had profound influence on the biogeographic history of many biota. As large areas in higher latitudes and high mountain ranges were covered by glaciers, biota were forced either to peripheral refugia (and possibly beyond to lowland refugia) or to interior refugia (nunataks), but nunatak survival remains controversial as it solely relies on correlative genetic evidence. Here, we test the nunatak hypothesis using two high alpine plant species of contrasting pollination modes (insect-pollinated Pedicularis aspleniifolia and wind-pollinated Carex fuliginosa) in the European Alps, a geographic model system to study Pleistocene biogeography. Employing the iDDC (integrative distributional, demographic and coalescent) approach, which couples species distribution modelling, spatial and temporal demographic simulation and Approximate Bayesian Computation, we explicitly test three hypotheses of glacial survival: (1) peripheral survival only, (2) nunatak survival only, and (3) nunatak plus peripheral survival. In P. aspleniifolia the nunatak plus peripheral survival hypothesis was supported by Bayes Factors (BF > 100), whereas in C. fuliginosa the peripheral survival only hypothesis, though best supported, could not be unambiguously distinguished from the nunatak plus peripheral survival hypothesis (BF = 5.58). These results are consistent with current habitat preferences (P. aspleniifolia extends to higher elevations) and the potential for genetic swamping, i.e., replacement of local genotypes via hybridization with immigrating genotypes (expected to be higher in the wind-pollinated C. fuliginosa). Although the persistence of plants on nunataks during glacial periods has been debated and studied over decades, this is one of the first studies to explicitly test the hypothesis instead of solely using correlative evidence.</p>