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189 results for “DNA specimens”
FIG. 2 in DNA analysis of the lectotype specimen of Ulva nematoidea Bory (Ulvaceae, Chlorophyta) determines its synonymy with Ulva lactuca L.
FIG. 2. — RAxML phylogram based on rbcL gene sequences showing the evolutionary relationship of Ulva nematoidea Bory (GenBank accession number: OL542489) to representative Ulvaceae. Bootstrap support values based on 1000 replicates/Bayesian posterior probabilities are cited at the nodes. × indicates no locality given. -- or blank nodes indicate less than 70 % bootstrap support or less than 0.70 posterior probability. * denotes the sequence was generated from type material. The legend below represents the scale for nucleotide substitutions.
Morphological and DNA sequence data generated by Sanger sequencing and target capture methods for moss plants in the genus Fissidens from herbarium specimens
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Specimen photos of DNA sample MHNG-Hydrozoa-DNA126
<p>Specimen photos of DNA sample MHNG-Hydrozoa-DNA126</p> <p>species medusa of<strong><em> Staurodiscus gotoi </em></strong><strong>(Uchida, 1927) </strong></p>
Specimen photos of DNA sample MHNG-Hydrozoa-DNA1165
<p>Sample data</p> <p>collection locality: Norway, Korsfjord</p> <p>GPS: 60.1846°N 5.196°E</p> <p>collection date: 14.06.2016</p> <p>depth: 0-600 m</p> <p>gear:plankton net, vertical tow</p> <p>number of individuals or colonies: 1</p> <p>preservation: 95 % ethanol</p> <p>figured specimen used for DNA extraction: yes</p> <p>part used for DNA extraction: whole</p> <p>DNA extraction: 10.5281/zenodo.57067</p> <p>voucher specimen deposited: no</p> <p> </p> <p>Sample data</p> <p>Taxonomy</p> <p>Phylum: Cnidaria</p> <p>Class: Hydrozoa</p> <p>Family: Mitrocomidae</p> <p>Species: <em>Cosmetira pilosella</em> (Forbes, 1848)</p> <p>life stage: medusa</p> <p>identified by: P. Schuchert</p> <p>size: 8-10 mm diameter</p>
Specimen photos of DNA sample MHNG Hydrozoa DNAX13
<p><strong>DNA sample number: Hydrozoa </strong><strong>DNAX13</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 vulgaris </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, Lac de Neuchâtel, Gletterens</strong></p> <p><strong>GPS: 46.905161 06.9294</strong></p> <p><strong>collection date: 17.07.2013</strong></p> <p><strong>depth: 0</strong></p> <p><strong>gear: hand</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: infertile, substrate <em>Myriophyllum</em> sp.</strong></p> <p> </p>
Specimen photos of DNA sample MHNG Hydrozoa DNA1159
<p><strong>Sample data</strong></p> <p>sample collected by: P. Schuchert & A. Hosia</p> <p>collection locality: Raunefjord, Norway</p> <p>WGS84: 60.2575, 05.1393</p> <p>collection date: 14-06-2016</p> <p>depth: 0 – 200m</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: entire</p> <p>DNA extraction date: 04-07-2016</p> <p> </p> <p><strong>Taxonomy</strong></p> <p>Phylum: Cnidaria</p> <p>Class: Hydrozoa</p> <p>Family: Margelopsidae</p> <p>Species: <em>Margelopsis hartlaubii </em>Browne, 1903</p> <p>life stage: medusa</p> <p>identified by: P. Schuchert</p> <p> </p>
A specimen-level dataset of functional traits and DNA barcodes for Chinese bees
<p>The full potential for using DNA barcodes for profiling functional trait diversity has yet to be determined in plants and animals, thus we outline a general framework for quantifying functional trait diversity of insect community DNA and propose and assess the accuracy of three methods for achieving this. </p> <p>We built a novel dataset of traits and DNA barcodes for wild bees in China. An informatics framework was developed for phylogeny-based integration of these data and prediction of traits for any subject barcodes, and compared to two Blast-based methods of trait assignment. </p> <p>Under the specimen-level dataset, rate and accuracy of trait assigned dropped with an increase in distance between the query and its nearest reference member, though phylogenetic assignment was found to perform best under several criteria. For a wider range of compiled traits, conservative life-history traits showing the highest rates of assignment, for example sociality was predicted with confidence at 53%, parasitism at 44%, and nest location at 33%. </p> <p>Bayesian phylogenetic assignment of traits showed particular advantage over distance-based methods in the much lower rate that it would return incorrect state predictions when the query lacked relatives in the reference data. Automated, taxon-independent trait assignment might be applied at scale to either barcodes or metabarcodes in any invertebrates. With the further generation of integrated barcode and trait data, the assignment accuracy of the method is likely to increase. </p>
Specimen photos of DNA sample MHNG Hydrozoa DNA915
<p><strong>collection locality: Norway, Raunefjord</strong></p> <p><strong>GPS: </strong><strong>60.275 5.200</strong></p> <p><strong>collection date: 22.05.2012</strong></p> <p><strong>depth: 10 m</strong></p> <p><strong>gear: plankton net</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 medusa</strong></p> <p><strong>DNA extraction: </strong></p> <p><strong>voucher specimen deposited: no</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>
FIGURE 2 in DNA extracted from museum specimens of the 19 century provides a taxonomic resolution on the identity of the characid fish Psalidodon jequitinhonhae (Ostariophysi: Characiformes)
FIGURE 2 | Lectotype of Tetragonopterus rutilus jequitinhonhae, NMW 57760:2, 67.52 mm SL.
FIGURE 2 in Voucher Specimens For Dna Sequences Of Phytoseiid Mites (Acari: Mesostigmata)
FIGURE 2: DNA bands of the expected sizes were amplified for the mitochondrial Cytb fragment from A – Neoseiulus idaeus, from B – from Typhlodromus (Typhlodromus) exhilaratus. A – Lane M shows the molecular weight marker, C indicates the water control, C+ indicates the positive control, lanes 1-6 show the PCR products of a single N. idaeus specimen preliminarily treated with lactic acid. Image B: Lane M shows the molecular weight marker, Lanes 1-5 show the PCR products of a single T. (T.) exhilaratus specimen conserved in 100 % alcohol.
FIGURE 1 in Voucher Specimens For Dna Sequences Of Phytoseiid Mites (Acari: Mesostigmata)
FIGURE 1: Slide-mounted females of Typhlodromus (Typhlodromus) exhilaratus and Neoseiulus idaeus after genomic DNA extraction using a Qiagen DNeasy kit. A – dorsal shield of T. (T.) exhilaratus; B – ventral shields of T. (T.) exhilaratus; C – dorsal shield of Neoseiulus idaeus; D – ventral shields of Neoseiulus idaeus.
Data and code for: Trapped DNA fragments in marine sponge specimens unveil north Atlantic deep-sea fish diversity
<p>Sponges pump water to filter feed and for diffusive oxygen uptake. In doing so, trace DNA fragments from a multitude of organisms living around them are trapped in their tissues. Here we show that the environmental DNA retrieved from archived marine sponge specimens can reconstruct the fish communities at the place of sampling and discriminate North Atlantic assemblages according to biogeographic region (from Western Greenland to Svalbard), depth habitat (80–1600 m), and even the level of protection in place. Given the cost associated with ocean biodiversity surveys, we argue that targeted and opportunistic sponge samples – as well as the specimens already stored in museums and other research collections – represent an invaluable trove of biodiversity information that can significantly extend the reach of ocean monitoring.</p>
Data from: Characterizing DNA preservation in degraded specimens of Amara alpina (Carabidae: Coleoptera)
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Data and code for: Trapped DNA fragments in marine sponge specimens unveil north Atlantic deep-sea fish diversity
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A specimen-level dataset of functional traits and DNA barcodes for Chinese bees
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Specimen photos of DNA sample MHNG Hydrozoa DNA1633
<p><strong>DNA sample number: Hydrozoa </strong><strong>DNA1633, photos of specimens</strong></p> <p><strong>Sample data </strong></p> <p>sample collected by: Lucas Leclère</p> <p>collection locality: Bay of Villefranche-sur-Mer, France</p> <p>WGS84: -</p> <p>collection date: 15-MAR-2017</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: bell margin</p> <p>DNA extraction date: 30.10.2020</p> <p> </p> <p> </p> <p><strong>Taxonomy</strong></p> <p>Phylum: Cnidaria</p> <p>Class: Hydrozoa</p> <p>Family: Aequoriidae</p> <p>Species: <em>Aequorea</em> spec.</p> <p>life stage: medusa</p> <p>identified by: P. Schuchert</p> <p>size: 4-5 cm diameter, immature</p>
Specimen photos of DNA sample MHNG Hydrozoa DNA1634
<p><strong>DNA sample number: Hydrozoa </strong><strong>DNA1634, photos of specimens</strong></p> <p><strong>Sample data </strong></p> <p>sample collected by: Lucas Leclère</p> <p>collection locality: Bay of Villefranche-sur-Mer, France</p> <p>WGS84: -</p> <p>collection date: 15-MAR-2017</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: bell margin</p> <p>DNA extraction date: 30.10.2020</p> <p> </p> <p> </p> <p><strong>Taxonomy</strong></p> <p>Phylum: Cnidaria</p> <p>Class: Hydrozoa</p> <p>Family: Aequoriidae</p> <p>Species: <em>Aequorea</em> spec.</p> <p>life stage: medusa</p> <p>identified by: P. Schuchert</p> <p>size: 4-5 cm diameter, immature</p>
Data from: Disentangling the Pelomedusa complex using type specimens and historical DNA (Testudines: Pelomedusidae)
Recent research has shown that the helmeted terrapin (Pelomedusa subrufa), a species that occurs throughout sub-Saharan Africa, in Madagascar and the southwestern Arabian Peninsula, consists of several deeply divergent genetic lineages. Here we examine all nominal taxa currently synonymized with Pelomedusa subrufa (Bonnaterre, 1789) and provide mitochondrial DNA sequences of type specimens or topotypic material for most taxa. Lectotypes are designated for Testudo galeata Schoepff, 1792, Pentonyx capensis Duméril & Bibron, 1835, Pelomedusa nigra Gray, 1863, Pelomedusa galeata var. disjuncta Vaillant & Grandidier, 1910, and Pelomedusa galeata damarensis Hewitt, 1935. For Pelomedusa gasconi Rochebrune, 1884, a taxon without preserved type material, a neotype is designated. Type material of Pentonix americana Cornalia, 1849, a nominal species without credible type locality, is lost and its identity remains questionable. Also the holotype of Pelomedusa galeata orangensis Hewitt, 1935 is lost, but its allocation to the only genetic lineage occurring in South Africa is unambiguous. Phylogenetic analyses of type sequences or topotypic material reveal that the remaining nominal taxa represent three of the nine previously identified lineages of Pelomedusa. Among these three lineages is the South African one. Type specimens of Pentonyx gehafie Rüppell, 1835 correspond to an additional distinct lineage. The present study provides a sound basis for a subsequent integrative taxonomic revision of the Pelomedusa complex.
Data from: Collecting in collections: a PCR strategy and primer set for DNA barcoding of decades-old dried museum specimens
Natural history museums are vastly underutilized as a source of material for DNA analysis because of perceptions about the limitations of DNA degradation in older specimens. Despite very few exceptions, most DNA barcoding projects, which aim to obtain sequence data from all species, generally use specimens collected specifically for that purpose, instead of the wealth of identified material in museums, constrained by the lack of suitable PCR methods. Any techniques that extend the utility of museum specimens for DNA analysis therefore are highly valuable. This study first tested the effects of specimen age and PCR amplicon size on PCR success rates in pinned insect specimens, then developed a PCR primer set and amplification strategy allowing greatly increased utilization of older museum specimens for DNA barcoding. PCR success rates compare favourably with the few published studies utilizing similar aged specimens, and this new strategy has the advantage of being easily automated for high-throughput laboratory workflows. The strategy uses hemi-nested, degenerate, M13-tailed PCR primers to amplify two overlapping amplicons, using two PCRs per amplicon (i.e. four PCRs per DNA sample). Initial PCR products are reamplified using an internal primer and a M13 primer. Together the two PCR amplicons yield 559 bp of the COI gene from Coleoptera, Lepidoptera, Diptera, Hemiptera, Odonata and presumably also other insects. BARCODE standard-compliant data were recovered from 67% (56 of 84) of specimens up to 25 years old, and 51% (102 of 197) of specimens up to 55 years old. Given the time, cost and specialist expertise required for fieldwork and identification, 'collecting in collections' is a viable alternative allowing researchers to capitalize on the knowledge captured by curation work in decades past.
Data from: Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform
Genetic information is a valuable component of biosystematics, especially specimen identification through the use of species-specific DNA barcodes. Although many genomics applications have shifted to High-Throughput Sequencing (HTS) or Next-Generation Sequencing (NGS) technologies, sample identification (e.g., via DNA barcoding) is still most often done with Sanger sequencing. Here, we present a scalable double dual-indexing approach using an Illumina Miseq platform to sequence DNA barcode markers. We achieved 97.3% success by using half of an Illumina Miseq flowcell to obtain 658 base pairs of the cytochrome c oxidase I DNA barcode in 1,010 specimens from eleven orders of arthropods. Our approach recovers a greater proportion of DNA barcode sequences from individuals than does conventional Sanger sequencing, while at the same time reducing both per specimen costs and labor time by nearly 80%. In addition, the use of HTS allows the recovery of multiple sequences per specimen, for deeper analysis of genetic variation in target gene regions.
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Allen Brain Atlas
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OpenNeuro
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