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189 results for “DNA specimens”
Specimen photos of DNA sample MHNG Hydrozoa DNAX20
<p><strong>DNA sample number: Hydrozoa </strong><strong>DNAX20</strong></p> <p><strong>Phylum: Cnidaria</strong></p> <p><strong>Class: Hydrozoa</strong></p> <p><strong>Family: Hydridae</strong></p> <p><strong>Species: <em>Hydra viridissima</em> Pallas, 1766</strong></p> <p><strong>life stage: polyp</strong></p> <p><strong>identified by: P. Schuchert</strong></p> <p><strong>collection locality: Switzerland, Geneva, Monniaz, Les Bois de l'Etang</strong></p> <p><strong>GPS: 46.251434 06.3032</strong></p> <p><strong>collection date: 22.06.2013</strong></p> <p><strong>depth: 0</strong></p> <p><strong>number of individuals or colonies: 1</strong></p> <p><strong>subsequent preservation: 95 % ethanol</strong></p> <p><strong>figured specimen used for DNA extraction: yes</strong></p> <p><strong>part used for DNA extraction: whole animal</strong></p> <p><strong>voucher specimen deposited: no</strong></p> <p><strong>comments: male and female gonads present</strong></p>
Integrative biodiversity inventories: characterizing lichen-forming fungal diversity in Glen Canyon National Recreation Area using DNA barcoding and vouchered specimens
<p>The Colorado River and its tributaries on the Colorado Plateau are home to unique desert river ecosystems and changing environmental conditions. Within this region, the Glen Canyon National Recreation Area (GCNRA) is comprised of rugged, high desert terrain and is managed by the United States National Parks Service as both a recreational and conservation area. Despite the ecological and economic importance of GCNRA, significant components of the ecological communities therein remain poorly characterized, including lichens. Accurately characterizing lichen-forming fungal diversity is challenging due to poorly known taxonomic groups, underexplored regions/habitats, and varying interpretations of morphological differences, including the recognition of environmentally modified forms. To better understand lichen diversity in GCNRA, we used an integrative taxonomic approach, incorporating both traditional morphology-based identification and information from the standard fungal DNA barcoding marker, the ITS, to compile a thorough inventory of lichen-forming fungi in Fifty-Mile Canyon. Vouchered lichen specimens were collected in 2019, and from these the ITS marker was sequenced. Candidate species-level lineages were delimited from family-level multiple sequence alignments using the Assemble Species by Automatic Partitioning web server. Specimens comprising DNA-based candidate species were then evaluated using traditional taxonomically diagnostic characters to link these, where possible, to currently described species. For Fifty-Mile Canyon, we document 100 putative species in 15 families, each represented by vouchered specimens, ITS sequence data, and photographic documentation. For comparison, a survey of historic records from GCNRA revealed a total of 124 documented lichen-forming fungal species throughout the NRA and adjacent land. Approximately 50% of the species documented in Fifty-Mile Canyon had not previously been found in GCNRA, and similar proportions of species diversity have been documented in GCNRA but not observed in our survey. We report three species new to North America – <em>Calogaya ferrugineoides</em> (H. Magn.) Arup, Froden & Sochting, <em>Endocarpon deserticola</em> T. Zhang, X. L. Wei & J. C. Wei and <em>Xanthocarpia ferrari</em> (Bagl.) Frödén, Arup & Søchting – verified using ITS sequencing data. In addition, <em>Circinaria squamulosa</em> sp. nov. is formally described here, currently known only from sandstone slabs in Fifty-Mile Canyon. However, the taxonomic identity of many of the candidate species from Fifty-Mile Canyon remained ambiguous at the species level, and some collections likely represent undescribed species-level lineages. Our results revealed unexpected, high species-level diversity of lichen-forming fungi at local scales and that overall lichen diversity across the entire GCNRA is likely vastly undercounted. These data – including DNA barcodes for the vast majority of lichen-forming fungi occurring in this canyon – provide an important resource that can be integrated into subsequent lichen biodiversity research in the southwestern United States and other semi-arid climates.</p>
Specimen photos of DNA sample MHNG Hydrozoa DNA1281
<p><strong>Taxonomy</strong></p> <p>Phylum: Cnidaria</p> <p>Class: Hydrozoa</p> <p>Family: Pandeidae</p> <p>Species: <em>Pandea conica </em>(Quoy & Gaimard, 1827)</p> <p>life stage: medusa</p> <p>identified by: P. Schuchert</p> <p>size: height after preservation 11 mm</p> <p> </p> <p><strong>Sample data </strong></p> <p>sample collected by: Maciej Mańko</p> <p>collection locality: Mediterranean, France, Bay of Villefranche-sur-Mer</p> <p>GPS: 43.685 7.315667</p> <p>collection date: 14.04.2017</p> <p>depth: 0-30 m</p> <p>gear: Regent net (680 µm mesh size)</p> <p>number of individuals or colonies: 1</p> <p>subsequent preservation: 95 % ethanol</p> <p>voucher specimen deposited: MHNG-INVE-97958</p> <p>figured specimen used for DNA extraction: yes</p> <p>part used for DNA extraction: half of animal</p> <p>DNA extraction date: 06.06.2017</p>
Specimen photos of DNA sample MHNG Hydrozoa DNA1061
<p><strong>Taxonomy</strong></p> <p><strong>Phylum: Cnidaria</strong></p> <p><strong>Class: Hydrozoa</strong></p> <p><strong>Family: Pandeidae</strong></p> <p><strong>Species: <em> Leuckartiara octona </em>(Fleming, 1823)</strong></p> <p><strong>life stage: medusa</strong></p> <p><strong>identified by: P. Schuchert</strong></p> <p><strong>size: 8 mm</strong></p> <p><strong>Sample data </strong></p> <p><strong>collection locality: Sweden, Kristineberg</strong></p> <p><strong>GPS: </strong><strong>58.243849 11.432305</strong></p> <p><strong>collection date: 03.10.2014</strong></p> <p><strong>depth: 0 m</strong></p> <p><strong>gear: dipping jar</strong></p> <p><strong>number of individuals or colonies: 1</strong></p> <p><strong>subsequent preservation: 95 % ethanol</strong></p> <p><strong>figured specimen used for DNA extraction: yes</strong></p> <p><strong>part used for DNA extraction: tentacle</strong></p> <p><strong>voucher specimen deposited: MHNG-INVE-89890</strong></p>
Specimen photos of DNA sample MHNG Hydrozoa DNA354
<p><strong>Taxonomy</strong></p> <p>Phylum: Cnidaria</p> <p>Class: Hydrozoa</p> <p>Family: Pandeidae</p> <p>Species: <em>Leuckartiara octona</em> Fleming, 1823) </p> <p>life stage: medusa</p> <p>identified by: P. Schuchert</p> <p> </p> <p><strong>Sample data </strong></p> <p>collection locality: France, Bay of Villefranche-sur-Mer, Mediterranean</p> <p>GPS: 43.686 7.317</p> <p>collection date: 04.04.2005</p> <p>depth: 0 m</p> <p>gear: plankton net</p> <p>number of individuals or colonies: 1</p> <p>subsequent preservation: 95 % ethanol</p> <p>voucher specimen deposited: no</p> <p>figured specimen used for DNA extraction: yes</p> <p>part used for DNA extraction: whole animal</p> <p> </p>
Supplementary material 1 from: Tedersoo L, Liiv I, Kivistik PA, Anslan S, Kõljalg U, Bahram M (2016) Genomics and metagenomics technologies to recover ribosomal DNA and single-copy genes from old fruit-body and ectomycorrhiza specimens. MycoKeys 13: 1-20. https://doi.org/10.3897/mycokeys.13.8140
Full information and metadata about the genomic and metagenomic samples : Explanation note: Detailed information about metadata, DNA quality and genomic/metagenomic results of fruit-body and EcM root tip samples.
Specimen photos of DNA sample MHNG Hydrozoa DNA884
<p><strong>Sample data </strong></p> <p>sample collected by: P. Schuchert</p> <p>collection locality: USA, WA, San Juan Island, Friday Harbor</p> <p>GPS: 48.545141°-123.012059°</p> <p>collection date: 20 MAY 2011</p> <p>depth: 0.5 m</p> <p>gear: dip jar</p> <p>number of individuals or colonies: >3</p> <p>subsequent preservation: 95 % ethanol</p> <p>voucher specimen deposited: no</p> <p>figured specimen used for DNA extraction: ? yes</p> <p>part used for DNA extraction: whole medusa</p> <p> </p> <p> </p> <p><strong>Taxonomy</strong></p> <p> </p> <p>Phylum: Cnidaria</p> <p>Class: Hydrozoa</p> <p>Family: Pandeidae</p> <p>Species: <strong><em>Stomotoca atra</em></strong> L. Agassiz, 1862 </p> <p>life stage: medusa</p> <p>identified by: P. Schuchert</p> <p>size: 11 mm diameter</p>
Supplementary material 2 from: Adeoba MI, Kabongo R, Van der Bank H, Yessoufou K (2018) Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae). ZooKeys 746: 105-121. https://doi.org/10.3897/zookeys.746.13502
Table S2 : Explanation note: List of 315 Cyprinidae specimens analysed in this study. Full names, voucher information, and geographic origins are presented. Accession numbers for ACDB (African Centre for DNA Barcoding at the University of Johannesburg), GenBank, and BOLD are also included.
Supplementary material 3 from: Adeoba MI, Kabongo R, Van der Bank H, Yessoufou K (2018) Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae). ZooKeys 746: 105-121. https://doi.org/10.3897/zookeys.746.13502
Table S3 : Explanation note: Matrix of the morphological characters used for character mapping along a phylogeny. Details of the characters (1–6) and sources are provided at the bottom of the table..
Data from: Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol
We report initial results from an ongoing effort to build a library of DNA barcode sequences for Dutch spiders and investigate the utility of museum collections as a source of specimens for barcoding spiders. Source material for the library comes from a combination of specimens freshly collected in the field specifically for this project and museum specimens collected in the past. For the museum specimens, we focus on 31 species that have been frequently collected over the past several decades. A series of progressively older specimens representing these 31 species were selected for DNA barcoding. Based on the pattern of sequencing successes and failures, we find that smaller-bodied species expire before larger-bodied species as tissue sources for single-PCR standard DNA barcoding. Body size and age of oldest successful DNA barcode are significantly correlated after factoring out phylogenetic effects using independent contrasts analysis. We found some evidence that extracted DNA concentration is correlated with body size and inversely correlated with time since collection, but these relationships are neither strong nor consistent. DNA was extracted from all specimens using standard destructive techniques involving the removal and grinding of tissue. A subset of specimens was selected to evaluate nondestructive extraction. Nondestructive extractions significantly extended the DNA barcoding shelf life of museum specimens, especially small-bodied species, and yielded higher DNA concentrations compared to destructive extractions. All primary data are publically available through a Dryad archive and the Barcode of Life database.
FIGURE 2 in An example of problems associated with DNA barcoding in tardigrades: a novel method for obtaining voucher specimens
FIGURE 2. Granulated cuticle and pores in a fresh (A, DIC) and an orcein stained (B, PhC) specimen of M. terminalis (C2868); C: Granulated cuticle (arrow head) and pores by SEM in M. terminalis (C2868); D: Smooth cuticle with pores in a fresh specimen of M. macrocalix (C2868, DIC); E: Granulated cuticle (arrow head) in the holotype of M. terminalis (C624- S60, DIC). Bar =10 µm (A, B, D, E); 5 µm (C)
FIGURE 1. A in An example of problems associated with DNA barcoding in tardigrades: a novel method for obtaining voucher specimens
FIGURE 1. A: Fresh specimen of M. terminalis; buccal pharyngeal apparatus with dorsal buccal armature (C2868, DIC); B: Fresh specimen of M. macrocalix; buccal pharyngeal apparatus with dorsal buccal armature (C2868, DIC). C: Claws with indented lunules on a hind leg of M. terminalis (C2868, SEM); D: Claws with indented lunules (arrow heads) on the hind legs of a fresh specimen of M. terminalis (C2868, DIC). Bar =10 µm (A, B, D); 5 µm (C)
FIGURE 5 in An example of problems associated with DNA barcoding in tardigrades: a novel method for obtaining voucher specimens
FIGURE 5. Neighbor joining dendrogram computed on Kimura 2-parameter distances. Numbers in bold indicate bootstrap values. Specimens are indicated with either GenBank accession numbers or with acronyms as in Table 1 (in bold).
FIGURE 3. A in An example of problems associated with DNA barcoding in tardigrades: a novel method for obtaining voucher specimens
FIGURE 3. A: Egg shell of M. terminalis (hologenophore C2868-N02 US2, DIC); B: Egg shell of M. terminalis by SEM (C2868); C: Egg shell of a M. terminalis paratype (C624-S44, PhC); D: Egg shell of M. cf. terminalis (C2341, PhC). Bar =10 µm (A, C, D); 1 µm (B).
FIGURE 5 in Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus Orestias (Teleostei: Cyprinodontidae)
FIGURE 5. Molecular phylogeny of Orestias complexes including 'fresh' species and morphotype ("morpho") representatives, and type specimens. Maximum clade credibility tree for rhodopsin sequences. Values at branch nodes refer to highest posterior probability of occurrence for clades (> 0.95); within parenthesis are shown posterior values when removing type specimens from the analysis. Scale bar below tree indicates sequence divergence. Type specimens are highlighted with an asterisk. See Table 2 for specimen acronyms.
FIGURE 2 in Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus Orestias (Teleostei: Cyprinodontidae)
FIGURE 2. Gel electrophoresis displaying extracted DNA (a) and amplified PCR fragments (b) in two historical samples of O. mulleri (MNHN 1981-1428#4 and #13). In a, columns 1–2: extracted DNA for specimen #4 (aliquots a and b); columns 3–4: extracted DNA for specimen #13 (aliquot a and b); column 5: negative DNA extraction control; M: molecular weight marker (100 bp ladder). In b, PCR amplification products for control region and rhodopsin are left and right to the molecular weight marker, respectively. Columns 1–2: specimen #4 (aliquots a and b); columns 3–4: specimen #13 (aliquots a and b); column 5: negative PCR control; column 6: positive PCR control. M: molecular weight marker (100 bp ladder).
FIGURE 3 in Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus Orestias (Teleostei: Cyprinodontidae)
FIGURE 3. Example of type specimens treated by incubation in GuSCN bath. Left/right sides: specimens before/after DNA extraction procedure. Damage scale (see Material and Methods): A and B = 1, C = 2 and D = 3. Scale bar represents 2 cm.
FIGURES NJ27–NJ30. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ27, Scrobipalpa acuminatella; NJ28, Sophronia gelidella; NJ29, Anthophila fabriciana; NJ30, Phiaris bipunctana. in Shared but overlooked: 30 species of Holarctic Microlepidoptera revealed by DNA barcodes and morphology
FIGURES NJ27–NJ30. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ27, Scrobipalpa acuminatella; NJ28, Sophronia gelidella; NJ29, Anthophila fabriciana; NJ30, Phiaris bipunctana.
FIGURES NJ17–NJ19, NJ21. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ17, Agonopterix conterminella. NJ18, Depressaria depressana; NJ19, Coleophora atriplicis; NJ21, Coleophora granulatella. in Shared but overlooked: 30 species of Holarctic Microlepidoptera revealed by DNA barcodes and morphology
FIGURES NJ17–NJ19, NJ21. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ17, Agonopterix conterminella. NJ18, Depressaria depressana; NJ19, Coleophora atriplicis; NJ21, Coleophora granulatella.
FIGURES NJ20, NJ22–NJ26. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ20, Coleophora glitzella; NJ22, Coleophora texanella; NJ23, Coleophora vitisella; NJ24, Scythris sinensis; NJ25, Altenia perspersella; NJ26, Gnorimoschema jalavai. in Shared but overlooked: 30 species of Holarctic Microlepidoptera revealed by DNA barcodes and morphology
FIGURES NJ20, NJ22–NJ26. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ20, Coleophora glitzella; NJ22, Coleophora texanella; NJ23, Coleophora vitisella; NJ24, Scythris sinensis; NJ25, Altenia perspersella; NJ26, Gnorimoschema jalavai.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.