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1,998 results for “Herbarium specimen”
Text-fig. 11. Lectotype specimen Orobanche rubens WALLROTH. in Wallroth´S Collection Of Vascular Plants In The Herbarium Of The National Museum, Prague
Text-fig. 11. Lectotype specimen Orobanche rubens WALLROTH.
Text-fig. 8. Lectotype specimen of Malva neglecta WALLROTH. in Wallroth´S Collection Of Vascular Plants In The Herbarium Of The National Museum, Prague
Text-fig. 8. Lectotype specimen of Malva neglecta WALLROTH.
Text-fig. 4. Lectotype specimen of Camelina sylvestris WALLROTH. in Wallroth´S Collection Of Vascular Plants In The Herbarium Of The National Museum, Prague
Text-fig. 4. Lectotype specimen of Camelina sylvestris WALLROTH.
Herbarium specimens reveal a cryptic invasion of polyploid Centaurea stoebe in Europe - ITS1 dataset
<h3>Description of the data and file structure</h3> <p>We genotyped the ITS1 locus of 178 herbarium specimens using protocol described in Suchan et al. (2018; https://doi.org/10.1111/1755-0998.12948) and processed using custom script. The specimens were chosen after morphological determination of their cytotypes (morphological determination accuracy: 97.8%). We choose this subsample (3.5% of the total number of specimens) to represent comparable distributional ranges and collection dates across both cytotypes, including specimens from both the native and expanded ranges of tetraploid <em>C. stoebe</em>. Genotyping of the ITS1 locus unambiguously identifies the cytotype, as all tetraploid samples exhibit a unique ribotype B, which has never been found in diploid samples (Mráz et al., 2012; https://doi.org/10.1016/j.ympev.2011.11.006).</p> <h4>Files and variables</h4> <p><strong>File: Centaurea_stoebe_ITS1_script.sh</strong></p> <p>Description: This file contains the script used for processing raw sequence data to obtain a table with the numbers of reads in each sample mapping to the obtained ITS1 variants. The software used was: PEAR v0.9.6, cutadapt v.3.2, vsearch v2.28.1</p> <p><strong>File: Centaurea_stoebe_sample_list.xlsx</strong></p> <p>Description: This file contains a list of analyzed herbarium specimens.</p> <p>Variables</p> <ul> <li>ID - sample ID</li> <li>Lab working no. - Identifier of the samples in the ITS1 analyses, specifically in the Centaurea_stoebe_ITS1_sequence_numbers.xlsx file</li> <li>Morphology-based estimation - ploidy of the sample estimated with morphology (2 - diploid, 4 - tetraploid)</li> <li>ITS seq based estimation - ploidy of the sample estimated using ITS1 sequencing (2 - diploid, 4 - tetraploid)</li> <li>Congruence(1)/mismatch(0) - congruence (1) or mismatch (0) between morphological and genetic policy estimation</li> <li>Country of origin</li> <li>Herbarium</li> <li>Herbarium coll. number</li> <li>Collector</li> <li>Collection year</li> <li>Locality</li> <li>Latitude</li> <li>Longitude</li> </ul> <p><strong>File: Centaurea_stoebe_ITS1_sequences.fasta</strong></p> <p>Description: This file contains sequences of the obtained ITS1 variants.</p> <p><strong>File: Centaurea_stoebe_ITS1_sequence_numbers.xlsx</strong></p> <p>Description: This file contains a table with the numbers of reads in each sample mapping to the obtained ITS1 variants.</p> <p>Variables</p> <ul> <li>OTU - ITS1 variant number</li> <li>size - number of sequences from the total data clustered to the variant</li> <li>next columns contain numbers of reads mapped to each ITS1 variant for each sample</li> </ul> <h3>Code/software</h3> <p>The code to process sequence data is included in Centaurea_stoebe_ITS1_script.sh file. The software used was: PEAR v0.9.6, cutadapt v.3.2, vsearch v2.28.</p>
Fourier transform infrared spectroscopy as a non-destructive method for analysing herbarium specimens
<p>Dried plant specimens stored in herbaria are an untapped treasure chest of information on environmental conditions, plant evolution and change over many hundreds of years. Due to their delicate nature and irreplaceability, there is limited access for analysis to these sensitive samples, particularly where chemical data is obtained using destructive techniques. Fourier transform infrared spectroscopy (FTIR) is a chemical analysis technique that can be applied non-destructively to understand chemical bonding information and therefore functional groups within the sample. This provides the potential for understanding geographic, spatial and species-specific variation in plant biochemistry. Here we demonstrate the use of mid-FTIR microspectroscopy for the analysis of <em>Drosera</em> <em>rotundifolia</em> herbaria specimens, which were collected 100 years apart from different locations. Principal component and hierarchical clustering analysis enabled successful differentiation between three main regions on the plant (lamina, tentacle stalk and tentacle head), and between the different specimens. Lipids and protein spectral regions were particularly sensitive differentiators of plant tissues. Differences between the different sets of specimens were smaller. This study demonstrates that relevant information can be extracted from herbarium specimens using FTIR, with little impact on the specimens. FTIR therefore provides the potential as a powerful tool to unlock historic information within herbaria.</p>
Data from: Pollen on stigmas of herbarium specimens: a window into the impacts of a century of environmental disturbance on pollen transfer
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Data from: Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance
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Data from: Specimen-based analysis of morphology and the environment in ecologically dominant grasses: the power of the herbarium
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Data from: Carbon isotope trends across a century of herbarium specimens suggest CO2 fertilization of C4 grasses
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Data from: Herbarium specimens reveal increasing herbivory over the past century
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Fourier transform infrared spectroscopy as a non-destructive method for analysing herbarium specimens
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Data from: Tracking population genetic signatures of local extinction with herbarium specimens
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Data from: Nitrogen content of herbarium specimens from arable fields and mesic meadows reflect the intensifying agricultural management during the 20th century
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Archive of JPG image files of Herbarium specimens from Columbia used in the BRAVO project.
<p>Archive of JPG image files of Herbarium specimens used in the BRAVO project.</p> <p>The individual images of herbarium specimens will also be included in the Zenodo project (in time)</p> <p>The project will pull these files into the workbench <a href="http://bravo.rbge.info/">http://bravo.rbge.info/</a></p> <p>The metadata for these images is included in the Zenodo project.</p>
Fine-grained automated visual analysis of herbarium specimens for phenological data extraction: an annotated dataset of reproductive organs in Strepanthus herbarium specimens
<p>This dataset contains annotations of 31 herbarium specimens of <em>Streptanhus tortuosus Kellogg</em> for which we have we carefully and manually drew and annotated the contours of four reproductive organs: “bud”, “flower”, “immature fruit” and “mature fruit”.</p> <p>The dataset can be used to assess the ability of automated methods to count and detect precisely the shapes of these reproductive organs, with a view to conducting phenological studies.</p> <p>The annotations are formatted in accordance with the COCO data format, a usual format for object detection tasks in the field of Computer Vision. The annotations are divided into two files:</p> <ul> <li>train_21_full_masks.json contains the mask coordinates and labels of 21 herbarium sheets that can be used for training models</li> <li>test_10_full_masks.json contains the mask coordinates and labels of 10 other herbarium that can be used as a groundtruth file for evaluating the predictions, typically with the COCO evaluation scripts (<a href="https://github.com/cocodataset/cocoapi">https://github.com/cocodataset/cocoapi</a>)</li> </ul> <p>Please refer to the following publication for a first assessment of this dataset with a Mask-RCNN approach:</p> <p><em>H. Goëau, A. Mora-Fallas, J. Champ, N. Love, S. Mazer, E. Mata-Montero, A. Joly, P. Bonnet. </em>2020. New fine-grained method for automated visual analysis of herbarium specimens: a case study for phenological data extraction. <em>Applications in Plant Sciences </em></p> <p> </p> <p> </p> <p> </p> <p> </p>
Data from: Next-generation sampling: pairing genomics with herbarium specimens provides species-level signal in Solidago (Asteraceae)
Premise of the study: The ability to conduct species delimitation and phylogeny reconstruction with genomic data sets obtained exclusively from herbarium specimens would rapidly enhance our knowledge of large, taxonomically contentious plant genera. In this study, the utility of genotyping by sequencing is assessed in the notoriously difficult genus Solidago (Asteraceae) by attempting to obtain an informative single-nucleotide polymorphism data set from a set of specimens collected between 1970 and 2010. Methods: Reduced representation libraries were prepared and Illumina-sequenced from 95 Solidago herbarium specimen DNAs, and resulting reads were processed with the nonreference Universal Network-Enabled Analysis Kit (UNEAK) pipeline. Multidimensional clustering was used to assess the correspondence between genetic groups and morphologically defined species. Results: Library construction and sequencing were successful in 93 of 95 samples. The UNEAK pipeline identified 8470 single-nucleotide polymorphisms, and a filtered data set was analyzed for each of three Solidago subsections. Although results varied, clustering identified genomic groups that often corresponded to currently recognized species or groups of closely related species. Discussion: These results suggest that genotyping by sequencing is broadly applicable to DNAs obtained from herbarium specimens. The data obtained and their biological signal suggest that pairing genomics with large-scale herbarium sampling is a promising strategy in species-rich plant groups.
FIGURE. Map representing all 419 in The type specimens in Eugen von Halácsy´s Herbarium Graecum
FIGURE. Map representing all 419 identified collecting localities of type specimens deposited in Halácsy´s Herbarium Graecum depicted as red dots.
Supplementary material 1 from: Gueidan C, Li L (2022) A long-read amplicon approach to scaling up the metabarcoding of lichen herbarium specimens. MycoKeys 86: 195-212. https://doi.org/10.3897/mycokeys.86.77431
Table S1. List of specimens used for this study, including their voucher information, plate location, indexing, amplicon concentration and sequencing results, both as an output from SMRT tools (CCSs) and as an output from DADA2 (sequence variants). Table S2. List of the 64 barcode sequences used to index the samples. Used barcode pairs are listed in Table S1
FIG.2 in Three new species of Solanum from Kenya: using herbarium specimens to document environmental change.
FIG.2. Solanum polhillii Voronts. sp. nov. A. Habit in sheltered habitat. B. Underside of leaf showing stellate trichomes. C. Stellate trichome. D. Habit in exposed habitat. E. Bud. F. Flower. G. Immature fruit. H. Mature fruit. I. Seed. Drawn from herbarium specimens. A, B, C, E, Ffrom Verdcourt 3838. Ddrawn from Greenway 9086. Gand Hfrom Verdcourt et al. 2672. Ifrom Greenway 10671. Scale bar: A, D = 2.5 cm; B, I = 2.5 mm; C = 0.5 mm; E, G, H = 1 cm; F = 2 cm. Drawn by Lucy T. Smith.
FIG. 5 in Three new species of Solanum from Kenya: using herbarium specimens to document environmental change.
FIG. 5. Three new species and their habitats in Kenya. A – D. Solanum polhillii Voronts. sp. nov. on Mount Suswa. E – H. Solanum phoxocarpum Voronts. sp. nov. in the Aberdare National Park. I – L. Solanum malindiense sp. nov. at the Mayungu beach. Photographs A – Hby Maarten Christenhusz. Photographs I – L by Maria Vorontsova.
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