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Fig. 2 in Nest architecture development of grass-cutting ants
Fig. 2. Detail of the fungal chamber of Atta bisphaerica in different forms (A and B). Botucatu, SP, 2014.
Figure 2. The adult female with a in Different shades of snake: Peculiar coloration in an urban population of the Grass Snake, Natrix natrix (Linnaeus, 1758
Figure 2. The adult female with a peculiar blue coloration. From the top to bottom: blue coloration present at the margin of the last row of dorsal scales and ventral scales. The white underside of the throat is clearly visible; Dorsal view of the individual; The ventral color switches from white to black towards the tail and the blue color intensifies.
Figure 1. A in Different shades of snake: Peculiar coloration in an urban population of the Grass Snake, Natrix natrix (Linnaeus, 1758
Figure 1. A melanistic individual (top) and an individual from the subspecies N. n. persa (middle). A common occurring individual with black spots behind the head (bottom) captured at the locality.
Fig. 2 in Use of chemical inducers as a resistance trigger in Brachiaria grasses and sugarcane
Fig. 2. Mean (± SE) of dry matter in Brachiaria shoots in relation to cultivar (A), inducer (B), and the interaction between cultivar and inducer in Brachiaria roots (C), in sugarcane shoots in relation to the interaction between cultivar and inducer (D), and in sugarcane roots in relation to cultivar (E) and inducer (F). Bars with the same lowercase letter comparing cultivars and bars with uppercase letters comparing inducers do not differ by the Scott Knott test (P <0.05).
Fig. 1 in Use of chemical inducers as a resistance trigger in Brachiaria grasses and sugarcane
Fig. 1. Mean (± SE) of total phenolic compounds in Brachiaria shoots in relation to cultivar (A), inducer (B), and the interaction between cultivar and inducer in roots (C), in sugarcane shoots in relation to cultivar (D), and inducer (E), and in sugarcane roots in relation to cultivar (F) and inducer (G). Bars with the same lowercase letter comparing cultivars and bars with uppercase letters comparing inducers do not differ by the Scott Knott test (P <0.05).
Fig. 1 in A novel supermatrix approach improves resolution of phylogenetic relationships in a comprehensive sample of danthonioid grasses
Fig. 1. Geologic map of Florissant Fossil Beds National Monument in central Colorado, USA, modified from Evanoff et al. (2001: fig. 1). Areal extent of the Monument is outlined by thick gray line.
Fig. 2 in A novel supermatrix approach improves resolution of phylogenetic relationships in a comprehensive sample of danthonioid grasses
Fig. 2. Talpid mammal Oreotalpa florissantensis gen. et sp. nov., FLFO 5813 (holotype), right dentary with m1–m3 from UCM locality 92179, Florissant Formation, Florissant Fossil Beds National Monument, Colorado, USA; latest Eocene (Chadronian). SEM micrographs; in lingual (A), labial (B), and occlusal (C) views, and explanatory drawing of occlusal view (D). Anterior is to the right. Original drawing by Leigh Anne McConnaughey. For B, C, and D, anterior is to the right.
Selecting with colour in grass pea
<p>The images show a larger view of;</p> <p>a. <em>K-mer</em> analysis using a heatmap, used to identify the SNPs that are present in the gene candidates for <em>A</em> and investigate SNPs present in white flowered accessions but not present in the <em>A</em> reference gene (LS007).</p> <p>b. <em>A </em>gene heatmap showing some coloured accessions that had homozygous and heterozygous variations.</p> <p>c. <em>K-mer</em> analysis using a heatmap, used to identify the SNPs that are present in the gene candidates for <em>A2</em> and investigate SNPs present in white flowered accessions but not present in the <em>A2</em> reference gene</p> <p>d.<em> K-mer</em> analysis using a heatmap, used to identify the SNPs that are present in the gene candidates for <em>B </em>and investigate SNPs present in white flowered accessions but not present in the<em> B </em>reference<em> </em>gene.</p>
Grass Phylogeny Working Group III: data repository
<p><strong>Grass Phylogeny Working Group III: data repository</strong></p> <p>Phylogenetic analyses of the grass family (Poaceae) using nuclear and plastid data. The data set includes 1153 accessions corresponding to 1133 accepted species. Genomic data was obtained from different sources including target capture, shotgun, transcriptomes and annotated genomes. Nuclear markers (Angiosperm353 gene set) were assembled from short read data using HybPiper or a custom assembly pipeline optimized for low coverage shotgun data. Plastid genes were either retrieved from published plastome sequences or assembled here using getOrganelle. This data set also includes the results of a gene tree-species tree reconciliation analysis using GeneRax.</p> <p> </p> <p>Contact persons:</p> <p>Matheus E. Bianconi (matheus-enrique.bianconi@univ-tlse3.fr), Jan Hackel (jan.hackel@uni-marburg.de), Maria S. Vorontsova (m.vorontsova@kew.org)</p> <p> </p> <p>Content description</p> <p><strong>1. Metadata</strong></p> <ul> <li><code>gpwgIII_samples_metadata_taxonomy.tsv</code></li> </ul> <p>Tab-separated file with details for all 1,702 accessions used in this study. Columns: analysis_ID - ID in nuclear analyses; analysis_ID_plastome - ID in plastome analyses; acc_species - accepted species name; acc_species_author - taxonomic species authority; acc_genus - accepted genus name; acc_genus_author - taxomomic genus authority; publication - associated prior publication; data type - type of sequence data; isolate - laboratory isolate ID; voucher_ID - herbarium voucher ID; germplasm_ID - germplasm collection ID; repo_accession - accession number in public repository; plastome_accession - accession number of assembled plastome sequence; removed_nuclear - reason for removal from nuclear tree, if applicable; removed_plastome - reason for removal from plastome tree, if applicable; soreng2022_genus - genus name in Soreng et al. 2022, https://doi.org/10.1111/jse.12847; subtribe, tribe, subfamily, major.clade - classification according to Soreng et al. 2022.</p> <p><strong>2. Nuclear data</strong></p> <p><em>- Dataset1 ("main")</em><br>Number of samples: 1153<br>Number of genes: 331<br>Alignment trimming threshold: gt = 0.1 (removed sites > 90% missing data)<br>Genes per sample: > 166</p> <p><em>- Dataset2 ("strict trimming")</em><br>Number of samples: 1153<br>Number of genes: 315<br>Alignment trimming threshold: gt = 0.5 (removed sites > 50% missing data)<br>Genes per sample: > 158</p> <p><em>- Dataset3 (dataset 1 without shotgun samples)</em><br>Number of samples: 841<br>Number of genes: 331<br>Alignment trimming threshold: gt = 0.1 (removed sites > 90% missing data)<br>Genes per sample: > 166</p> <p><strong>2.1. Raw sequences</strong></p> <p>Raw Ang353 sequence assemblies for all samples (pre-trimming and filtering)</p> <ul> <li><code>raw_Ang353_sequences.zip</code></li> </ul> <p><strong>2.2 Nuclear gene alignments</strong></p> <p>Trimmed alignments from datasets 1, 2 and 3.</p> <ul> <li><code>alignments_dataset1_main_final.zip</code></li> <li><code>alignments_dataset2_strict_trimming_final.zip</code></li> <li><code>alignments_dataset3_no_shotgun_final.zip</code></li> </ul> <p><strong>2.3. Nuclear gene trees</strong><br>Gene trees inferred using RAxML (GTRCAT, 100 bootstraps) for the alignments from datasets 1, 2 and 3.</p> <ul> <li><code>gene_trees_dataset1_main_final.zip</code></li> <li><code>gene_trees_dataset2_strict_trimming_final.zip</code></li> <li><code>gene_trees_dataset3_no_shotgun_final.zip</code></li> </ul> <p><strong>2.4. Multigene species trees</strong><br>Multigene species trees obtained using Astral-Pro3 from gene trees for datasets 1, 2 and 3. </p> <ul> <li><code>astralpro_trees.zip</code>, which includes: <ul> <li>trees_Ang353_grasses_dataset1_main_gtrcat.astralpro</li> <li>trees_Ang353_grasses_dataset2_strict_trimming_gtrcat.astralpro</li> <li>trees_Ang353_grasses_dataset3_no_shotgun_gtrcat.astralpro</li> </ul> </li> </ul> <p><strong>3. Gene tree–species tree reconciliation</strong></p> <ul> <li><code>generax.zip</code></li> </ul> <p>Compressed zip archive with input files and results, including log files, of the GeneRax reconciliation analysis. One subfolder for each of the four analyses run: "all_tribes", "Andropogoneae", "Bambusoideae", "Triticeae".</p> <ul> <li><code>transfers_reconciliation_analyses.zip</code>, which includes: <ul> <li>transfers_all_all_tribes.tsv: Tab-separated file with all transfers inferred with the tribe-level Poaceae reconciliation analysis. Each line represents one transfer inferred.</li> <li>transfers_all_Andropogoneae.tsv: Tab-separated file with all transfers inferred with the Andropogoneae reconciliation analysis. Each line represents one transfer inferred.</li> <li>transfers_all_Bambusoideae.tsv: Tab-separated file with all transfers inferred with the Bambusoideae reconciliation analysis. Each line represents one transfer inferred.</li> <li>transfers_all_Triticeae.tsv: Tab-separated file with all transfers inferred with the Triticeae reconciliation analysis. Each line represents one transfer inferred.</li> <li>transfers_counts_all_tribes.tsv: Tab-separated file with aggregated transfer counts, in both directions for each reticulate connection, from the tribe-level Poaceae reconciliation analysis.</li> <li>transfers_counts_Andropogoneae.tsv: Tab-separated file with aggregated transfer counts, in both directions for each reticulate connection, from the Andropogoneae reconciliation analysis.</li> <li>transfers_counts_Bambusoideae.tsv: Tab-separated file with aggregated transfer counts, in both directions for each reticulate connection, from the Bambusoideae reconciliation analysis.</li> <li>transfers_counts_Triticeae.tsv: Tab-separated file with aggregated transfer counts, in both directions for each reticulate connection, from the Triticeae reconciliation analysis.</li> </ul> </li> </ul> <p><strong>4. Plastome data</strong></p> <p>Alignment and phylogenetic tree from plastome data.</p> <ul> <li><code>plastome_files.zip</code>, which includes <ul> <li>reduced_plastome_concat_CDS_trnLtrnF_trimmed.fna-out.fas: FASTA file with the final, concatenated DNA alignment of 71 plastome regions for 910 accessions, after data filtering.</li> <li>partitions.txt: Text file with positions of the 71 plastome regions in the concatenated alignment.</li> <li>plastome_concat_CDS_trnLtrnF_trimmed_TBE.raxml.support: Plastome tree with Transfer Bootstrap Expectation values as node labels.</li> <li>RAxML_bipartitions.plastome_concat_CDS_trnLtrnF_trimmed: Maximum likelihood plastome tree inferred with RAxML, with Felsenstein bootstrap values as node labels.</li> <li>RAxML_bootstrap.plastome_concat_CDS_trnLtrnF_trimmed: 100 rapid bootstrap pseudoreplicate plastome trees inferred with RAxML.</li> <li>RAxML_info.plastome_concat_CDS_trnLtrnF_trimmed: RAxML analysis log file.</li> <li>nuc_plastome_matching_tips.tab: Tab-separated file with accessions matched in nuclear-plastome comparison.</li> </ul> </li> </ul> <p><strong>5. Poaceae-specific reference Ang353 dataset</strong><br>Reference sequence dataset used for the assembly of Ang353 sequences in this study.</p> <ul> <li><code>target_Ang353_sequences_grasses.zip</code></li> </ul> <p><strong>6. Shotgun assembly script</strong></p> <p>Custom script used for the assembly of Ang353 sequences from shotgun data</p> <ul> <li><code>shotgun_assembler_script.zip</code>, which includes: <ul> <li>shotgun_assembler_Ang353_sequences.sh: script for assembly of short reads from shotgun data</li> <li>template_manifest_file.tsv: TAB-separated file to specify sample names and location of short read files (required by the assembly script)</li> <li>list_Ang353_genes_orthofinder.txt: list of Ang353 gene identifiers (required by the assembly script)</li> </ul> </li> </ul> <p><strong>7. Quartet metrics script</strong></p> <p>R script to calculate the Quartet Concordance (QC) and Quartet Differential (QD) metrics from the gene tree frequencies/proportions for each quartet at a branch, following Pease et al. 2018 (American Journal of Botany, <span><a href="https://doi.org/10.1002/ajb2.1016" target="_blank" rel="nofollow noopener noreferrer">https://doi.org/10.1002/ajb2.1016</a></span>).</p> <ul> <li><code>quartet_metrics.R</code></li> </ul>
Linked collectors and determiners for: Do Nymphs Of The Treehopper Stictolobus Minutus (Funkhouser) (Hemiptera: Membracidae) Specialize On Grasses?.
Natural history specimen data linked to collectors and determiners held within, "Do Nymphs Of The Treehopper Stictolobus Minutus (Funkhouser) (Hemiptera: Membracidae) Specialize On Grasses?". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/c8756f54-d5c7-41b7-b912-d860d34854cf">https://bionomia.net/dataset/c8756f54-d5c7-41b7-b912-d860d34854cf</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/c8756f54-d5c7-41b7-b912-d860d34854cf">https://gbif.org/dataset/c8756f54-d5c7-41b7-b912-d860d34854cf</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Checklist of Serengeti Ecosystem Grasses.
Natural history specimen data linked to collectors and determiners held within, "Checklist of Serengeti Ecosystem Grasses". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/e396bc9e-99f8-4187-85c5-ef2b4e500392">https://bionomia.net/dataset/e396bc9e-99f8-4187-85c5-ef2b4e500392</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/e396bc9e-99f8-4187-85c5-ef2b4e500392">https://gbif.org/dataset/e396bc9e-99f8-4187-85c5-ef2b4e500392</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: On the identity and distribution of the Old World grass feeding leafhopper species Soractellus nigrominutus Evans (Hemiptera: Cicadellidae: Deltocephalinae: Paralimnini).
Natural history specimen data linked to collectors and determiners held within, "On the identity and distribution of the Old World grass feeding leafhopper species Soractellus nigrominutus Evans (Hemiptera: Cicadellidae: Deltocephalinae: Paralimnini)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/da9a5786-f24b-4ca9-a29f-38f0dc3d16ac">https://bionomia.net/dataset/da9a5786-f24b-4ca9-a29f-38f0dc3d16ac</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/da9a5786-f24b-4ca9-a29f-38f0dc3d16ac">https://gbif.org/dataset/da9a5786-f24b-4ca9-a29f-38f0dc3d16ac</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Grasses of the Forest Herbarium Ibadan (FHI) Nigeria.
Natural history specimen data linked to collectors and determiners held within, "Grasses of the Forest Herbarium Ibadan (FHI) Nigeria". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/beefc0e5-520f-446c-8d7a-2e1c35394144">https://bionomia.net/dataset/beefc0e5-520f-446c-8d7a-2e1c35394144</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/beefc0e5-520f-446c-8d7a-2e1c35394144">https://gbif.org/dataset/beefc0e5-520f-446c-8d7a-2e1c35394144</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: All herbarium specimens of grasses from Madagascar and the surrounding islands: family Poaceae, sector AFM.
Natural history specimen data linked to collectors and determiners held within, "All herbarium specimens of grasses from Madagascar and the surrounding islands: family Poaceae, sector AFM". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/ac8e5183-e233-4168-96a5-67541049aa67">https://bionomia.net/dataset/ac8e5183-e233-4168-96a5-67541049aa67</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/ac8e5183-e233-4168-96a5-67541049aa67">https://gbif.org/dataset/ac8e5183-e233-4168-96a5-67541049aa67</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: All herbarium specimens of grasses held at TAN herbarium.
Natural history specimen data linked to collectors and determiners held within, "All herbarium specimens of grasses held at TAN herbarium". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/9d68dae3-0851-4277-a7d5-ab997758a10d">https://bionomia.net/dataset/9d68dae3-0851-4277-a7d5-ab997758a10d</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/9d68dae3-0851-4277-a7d5-ab997758a10d">https://gbif.org/dataset/9d68dae3-0851-4277-a7d5-ab997758a10d</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Research database of Madagascar grasses compiled by Maria Vorontsova.
Natural history specimen data linked to collectors and determiners held within, "Research database of Madagascar grasses compiled by Maria Vorontsova". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/15d76f87-6d16-4948-b4d5-f7d50a168aa6">https://bionomia.net/dataset/15d76f87-6d16-4948-b4d5-f7d50a168aa6</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/15d76f87-6d16-4948-b4d5-f7d50a168aa6">https://gbif.org/dataset/15d76f87-6d16-4948-b4d5-f7d50a168aa6</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Revision of some Malagasy forage grasses and their relatives within Brachiaria, Echinochloa, Moorochloa, and Urochloa.
Natural history specimen data linked to collectors and determiners held within, "Revision of some Malagasy forage grasses and their relatives within Brachiaria, Echinochloa, Moorochloa, and Urochloa". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/c4f6aff5-779a-4664-b1ea-c01e26931a7f">https://bionomia.net/dataset/c4f6aff5-779a-4664-b1ea-c01e26931a7f</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/c4f6aff5-779a-4664-b1ea-c01e26931a7f">https://gbif.org/dataset/c4f6aff5-779a-4664-b1ea-c01e26931a7f</a>. Formatted as a Frictionless Data package.
Raw Data: Breeding alfalfa (Medicago sativa L.) in mixture with grasses
<p>Meta information and full raw data that was used for publication "Breeding alfalfa (<em>Medicago sativa</em> L.) in mixture with grasses"</p> <p>Experiment conducted at Agroscope, Reckenholzstrasse 191, 8046 Zürich, Switzerland</p> <p>Author: Christoph Grieder</p> <p> </p>
Data from: Genetic and functional variation across regional and local scales is associated with climate in a foundational prairie grass
<ul> <li>Global change forecasts in ecosystems require knowledge of within species diversity, particularly of dominant species within communities. We assessed site-level diversity and capacity for adaptation of the dominant species of the shortgrass steppe biome of the Central US, Bouteloua gracilis.</li> <li>We quantified genetic diversity from 17 sites across regional scales, north-south from New Mexico to South Dakota, and local scales in Northern Colorado. We also quantified phenotype and plasticity within and among sites and determined the extent to which phenotypic diversity in B. gracilis was related to climate.</li> <li>Genome sequencing indicated pronounced population structure at the regional scale, and local differences indicated gene flow and/or dispersal may also be limited. Within a common environment, we found evidence for genetic divergence in biomass-related phenotypes, plasticity, and phenotypic variance, indicating functional divergence and different adaptive potential. Phenotypes differentiated according to climate, chiefly median Palmer Hydrological Drought Index and other aridity metrics.</li> <li>Our results indicate conclusive differences in genetic variation, phenotype, and plasticity in this species and suggest a mechanism explaining variation in shortgrass steppe community responses to global change. This analysis of B. gracilis intraspecific diversity across spatial scales will improve conservation and management of the shortgrass steppe ecosystem moving forward.</li> </ul>
Figure 1. Odonaspis ruthae Kotinsky. A in First record of the Bermuda grass scale Odonaspis ruthae Kotinsky, 1915 (Hemiptera: Coccomorpha: Diaspididae) in Colombia
Figure 1. Odonaspis ruthae Kotinsky. A. Adult female (larger oval shape scale cover) and male (elongate test, e.g., specimen on left side of photo) and female (smaller round tests) second-instar nymphs after removing the leaf sheaths of its host. B. Close-up of adult female tests in life. C. Adult female as seen on slide. D. Details of the pygidium (dorsal side). E. Details of the pygidium (ventral side).
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.