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189 results for “DNA specimens”
Data from: DNA barcodes from century-old type specimens using next generation sequencing
Type specimens have high scientific importance because they provide the only certain connection between the application of a Linnean name and a physical specimen. Many other individuals may have been identified as a particular species, but their linkage to the taxon concept is inferential. Because type specimens are often more than a century old and have experienced conditions unfavorable for DNA preservation, success in sequence recovery has been uncertain. The present study addresses this challenge by employing next generation sequencing (NGS) to recover sequences for the barcode region of the cytochrome c oxidase 1 gene from small amounts of template DNA. DNA quality was first screened in more than 1800 century-old type specimens of Lepidoptera by attempting to recover 164bp and 94bp reads via Sanger sequencing. This analysis permitted the assignment of each specimen to one of three DNA quality categories – high (164bp sequence), medium (94bp sequence), or low (no sequence). Ten specimens from each category were subsequently analyzed via a PCR-based NGS protocol requiring very little template DNA. It recovered sequence information from all specimens with average read lengths ranging from 458bp to 610bp for the three DNA categories. By sequencing ten specimens in each NGS run, costs were similar to Sanger analysis. Future increases in the number of specimens processed in each run promise substantial reductions in cost, making it possible to anticipate a future where barcode sequences are available from most type specimens.
Data from: DNA extraction method affects the detection of a fungal pathogen in formalin-fixed specimens using qPCR
Museum collections provide indispensable repositories for obtaining information about the historical presence of disease in wildlife populations. The pathogenic amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has played a significant role in global amphibian declines, and examining preserved specimens for Bd can improve our understanding of its emergence and spread. Quantitative PCR (qPCR) enables Bd detection with minimal disturbance to amphibian skin and is significantly more sensitive to detecting Bd than histology; therefore, developing effective qPCR methodologies for detecting Bd DNA in formalin-fixed specimens can provide an efficient and effective approach to examining historical Bd emergence and prevalence. Techniques for detecting Bd in museum specimens have not been evaluated for their effectiveness in control specimens that mimic the conditions of animals most likely to be encountered in museums, including those with low pathogen loads. We used American bullfrogs (Lithobates catesbeianus) of known infection status to evaluate the success of qPCR to detect Bd in formalin-fixed specimens after three years of ethanol storage. Our objectives were to compare the most commonly used DNA extraction method for Bd (PrepMan, PM) to Macherey-Nagel DNA FFPE (MN), test optimizations for Bd detection with PM, and provide recommendations for maximizing Bd detection. We found that successful detection is relatively high (80–90%) when Bd loads before formalin fixation are high, regardless of the extraction method used; however, at lower infection levels, detection probabilities were significantly reduced. The MN DNA extraction method increased Bd detection by as much as 50% at moderate infection levels. Our results indicate that, for animals characterized by lower pathogen loads (i.e., those most commonly encountered in museum collections), current methods may underestimate the proportion of Bd-infected amphibians. Those extracting DNA from archived museum specimens should ensure that the techniques they are using are known to provide high-quality throughput DNA for later analysis.
Data from: More than skin and bones: comparing extraction methods and alternative sources of DNA from avian museum specimens
Next-generation sequencing has greatly expanded the utility and value of museum collections by revealing specimens as genomic resources. As the field of museum genomics grows, so does the need for extraction methods that maximize DNA yields. For avian museum specimens, the established method of extracting DNA from toe pads works well for most specimens. However, for some specimens, especially those of birds that are very small or very large, toe pads can be a poor source of DNA. In this study, we apply two DNA extraction methods (phenol-chloroform and silica column) to three different sources of DNA (toe pad, skin punch, and bone) from ten historical avian museum specimens. We show that a modified phenol-chloroform protocol yielded significantly more DNA than a silica column protocol (e.g., Qiagen DNeasy Blood & Tissue Kit) across all tissue types. However, extractions using the silica column protocol contained longer fragments on average than those using the phenol-chloroform protocol, likely a result of loss of small fragments through the silica column. While toe pads yielded more DNA than skin punches and bone fragments, skin punches proved to be a reliable alternative source of DNA and might be especially appealing when toe pad extractions are impractical. Overall, we found that historical bird museum specimens contain substantial amounts of DNA for genomic studies under most extraction scenarios, but that a phenol-chloroform protocol consistently provides the high quantities of DNA required for most current genomic protocols.
Data from: Preservation-induced morphological change in salamanders and failed DNA extraction from a decades-old museum specimen: implications for Plethodon ainsworthi
<p>Natural history collections are important data repositories, but different chemical treatments of specimens can influence morphological measurements and DNA extraction, complicating taxonomic and conservation decisions dependent upon these data. One such example is the Bay Springs Salamander (<i>Plethodon ainsworthi</i>), the only United States amphibian categorized as Extinct by the IUCN.<i> </i>Recent research has proposed that <i>P. ainsworthi </i>is an invalid taxon, arguing that the 55-year-old type specimens' morphological distinctiveness from syntopic <i>P. mississippi</i> is a preservation artifact. To address this controversy, we tested for morphological changes across five experimental treatments in proxy <i>P. shermani</i> specimens, and we re-examined the datasets used to support the invalidity of <i>P. ainsworthi</i>. We also tested recently developed DNA extraction techniques on the putatively formalin-fixed <i>P. ainsworthi</i> holotype. We used Bayesian models to demonstrate that preservation method can differentially bias morphological measurements, with most methods causing lower estimates of mass and modestly higher estimates of snout-vent-length:head width ratio. These results are broadly consistent with previous studies of other vertebrates, but inconsistent with the hypothesis that <i>P. ainsworthi </i>type specimens are actually poorly preserved <i>P. mississippi</i>. Attempts to extract DNA from the <i>P. ainsworthi</i> holotype unfortunately proved unsuccessful, preventing conclusive resolution of its status and emphasizing the limitations of promising new methods. Nonetheless, we tentatively recommend continued recognition of <i>P. ainsworthi</i> as a valid but possibly extinct taxon. More generally, we invite all authors who study preserved specimens to recognize and report how certain chemical treatments might impact their results.</p>
Specimen photos of DNA sample MHNG Hydrozoa DNA1118
<p>Specimen photos of DNA sample MHNG Hydrozoa DNA1118</p> <p>Species Syrsia striata, medusa collected in Norway</p>
FIGURE 12 in Revision of the Australian Oenochroma vinaria Guenée, 1858 species-complex (Lepidoptera: Geometridae, Oenochrominae): DNA barcoding reveals cryptic diversity and assesses status of type specimen without dissection
FIGURE 12. Egg of Oenochroma barcodificata. sp. nov. freshly laid egg, scale bar 1 mm. (photo CY)
Specimen photos of DNA sample MHNG Hydrozoa DNA734
<p><strong>Sample data </strong></p> <p><strong>collection locality: United Kingdom, England, Cullercoats,</strong></p> <p><strong>GPS: </strong><strong>55.035 -1.4286 </strong></p> <p><strong>collection date: 00.03.2008</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: polyp</strong></p> <p><strong>voucher specimen deposited: MHNG-INVE-63261</strong></p> <p><strong>comments: field number GB09.05; polyps on <em>Hyas arenaeus, </em>medusae liberated with two tentacles, apical process present; hydroid in culture long-stemmed, buds on pedicels and stolons; 16S sequence identical to AM411422</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: polyp</strong></p> <p><strong>identified by: P. Schuchert</strong></p>
Specimen photos of DNA sample MHNG Hydrozoa DNA721
<p><strong>collection locality: United Kingdom, England, Cullercoats,</strong></p> <p><strong>GPS: </strong><strong>55.035 -1.4286 </strong></p> <p><strong>collection date: 26.03.2008</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: polyp</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: polyp</strong></p> <p><strong>identified by: P. Schuchert</strong></p>
Figure 6 from: Camacho AI, Dorda BA, Chillón BS, Rey I (2017) The collection of Bathynellacea specimens of MNCN (CSIC) Madrid: microscope slices and DNA extract. ZooKeys 678: 31-63. https://doi.org/10.3897/zookeys.678.11543
Figure 6 - Habitus of Parabathynellidae family: Paraiberobathynella cf. fagei (Delamare Deboutteville & Angelier, 1950) from Higuera cave, Murcia (Spain). Lateral view.
Figure 7 from: Camacho AI, Dorda BA, Chillón BS, Rey I (2017) The collection of Bathynellacea specimens of MNCN (CSIC) Madrid: microscope slices and DNA extract. ZooKeys 678: 31-63. https://doi.org/10.3897/zookeys.678.11543
Figure 7 - Permanent slides (special metal slides) of holotypes of the MNCN collections. Mounting medium: glycerine gelatin stained with methylene blue.
Figure 5 from: Camacho AI, Dorda BA, Chillón BS, Rey I (2017) The collection of Bathynellacea specimens of MNCN (CSIC) Madrid: microscope slices and DNA extract. ZooKeys 678: 31-63. https://doi.org/10.3897/zookeys.678.11543
Figure 5 - Number of species by families and continents present in the MNCN collections versus world.
Figure 9 from: Camacho AI, Dorda BA, Chillón BS, Rey I (2017) The collection of Bathynellacea specimens of MNCN (CSIC) Madrid: microscope slices and DNA extract. ZooKeys 678: 31-63. https://doi.org/10.3897/zookeys.678.11543
Figure 9 - Number of species (total and DNA extract) of Bathynellacea by families in the MNCN collections.
Figure 4 from: Camacho AI, Dorda BA, Chillón BS, Rey I (2017) The collection of Bathynellacea specimens of MNCN (CSIC) Madrid: microscope slices and DNA extract. ZooKeys 678: 31-63. https://doi.org/10.3897/zookeys.678.11543
Figure 4 - Number of genera of Bathynellacea by continents present in the MNCN collections versus world.
Figure 14 from: Camacho AI, Dorda BA, Chillón BS, Rey I (2017) The collection of Bathynellacea specimens of MNCN (CSIC) Madrid: microscope slices and DNA extract. ZooKeys 678: 31-63. https://doi.org/10.3897/zookeys.678.11543
Figure 14 - Number of records of Bathynellacea from Spain by Autonomous Communities in the MNCN collections.
Figure 8 from: Camacho AI, Dorda BA, Chillón BS, Rey I (2017) The collection of Bathynellacea specimens of MNCN (CSIC) Madrid: microscope slices and DNA extract. ZooKeys 678: 31-63. https://doi.org/10.3897/zookeys.678.11543
Figure 8 - Number of genera of Bathynellacea by families and continents in the MNCN collections versus world.
Figure 11 from: Camacho AI, Dorda BA, Chillón BS, Rey I (2017) The collection of Bathynellacea specimens of MNCN (CSIC) Madrid: microscope slices and DNA extract. ZooKeys 678: 31-63. https://doi.org/10.3897/zookeys.678.11543
Figure 11 - Number of holotypes (DNA extract) of Bathynellacea by continents and families in the MNCN collections.
Supplementary material 1 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 S1 : Explanation note: Taxonomy of African Cyprinidae and geographic origins.
Figure 5 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
Figure 5 - Parsimonious phylogenetic tree showing some plotted morphological characters, such as anal soft rays, barbels, dorsal soft rays, length, lip types, and ploidy status of 86 African Cyprinidae species.
Figure 4 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
Figure 4 - Neighbour-joining tree analysis using Rosenberg's (2007) test. Nodes in red are strongly supported nodes, indicating species monophyly.
Figure 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
Figure 2 - Evaluation of barcode gap in the dataset. Line plot of the barcode gap for the 315 Cyprinidae individuals. The black lines indicate where the smallest interspecific distance is longer than the longest intraspecific distance (bottom of line value), thus showing the existence of a barcode gap. The red lines show where this pattern is reversed.
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