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Fig. 2 in DNA barcoding and genetic variability of earthworms (Clitellata: Oligochaeta) with new records from Mizoram, India
Fig. 2 Results from ABGD analysis showing stable count of 24 OTUs
FIGURE 3 in Taxonomic delimitation of endemic Ficus amplocarpa and Ficus dalhousiae Complexes (Moraceae) by DNA barcoding
FIGURE 3. Ficus samples collection sites in Southern India.
Table 1 in DNA barcoding and morphology reveal exceptional species diversity of Scoparia (Lepidoptera: Crambidae) from the Hailuogou Glacier area, China
<p><b>Table 1.</b> Percentage of divergence in the cytochrome <i>c</i> oxidase subunit I (<i>COI</i>) gene sequences of the Scoparia species with out-groups</p><table><tbody><tr><th></th><th></th><th>1</th><th>2</th><th>3</th><th>4</th><th>5</th><th>6</th><th>7</th><th>8</th><th>9</th><th>10</th><th>11</th></tr></tbody><tbody><tr><th>1</th><td><i>Eudonia hexamera</i></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>2</th><td><i>Eudonia puellaris</i></td><td>6.7</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>3</th><td><b><i>Scoparia simplicissima</i> sp. nov.</b></td><td>7.9–8.2</td><td>7.9–8.1</td><td><b>0–0.3</b></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>4</th><td><b><i>Scoparia tribulosa</i> sp. nov.</b></td><td>8.7–9.3</td><td>10.5–11.0</td><td>6.2–6.9</td><td><b>0–0.5</b></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>5</th><td><b><i>Scoparia longispina</i> sp. nov.</b></td><td>8.4–8.7</td><td>8.9–9.2</td><td>5.1–6.2</td><td>6.4–7.3</td><td><b>0–1.5</b></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>6</th><td><b><i>Scoparia gibbosa</i> sp. nov.</b></td><td>8.0–9.3</td><td>8.7–10.0</td><td>6.2–7.4</td><td>7.3–8.8</td><td>5.6–7.5</td><td><b>0–1.7</b></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>7</th><td><i>Scoparia metaleucalis</i></td><td>9.7–10.8</td><td>10.8–11.7</td><td>8.2–9.6</td><td>10.8–12.4</td><td>9.1–9.9</td><td>10.1–11.8</td><td><b>0–1.5</b></td><td></td><td></td><td></td><td></td></tr><tr><th>8</th><td><i>Scoparia jiuzhaiensis</i></td><td>9.2–9.7</td><td>9.1–9.6</td><td>8.4–8.9</td><td>9.4–10.5</td><td>10.5–10.8</td><td>9.1–10.2</td><td>13.0–14.0</td><td><b>0–0.8</b></td><td></td><td></td><td></td></tr><tr><th>9</th><td><i>Scoparia brevituba</i></td><td>9.9–10.1</td><td>9.9–10.1</td><td>9.8–10.0</td><td>10.3–11.0</td><td>11.0–11.9</td><td>9.8–11.2</td><td>12.1–13.3</td><td>7.2–7.9</td><td><b>0–0.2</b></td><td></td><td></td></tr><tr><th>10</th><td><b><i>Scoparia globosa</i> sp. nov.</b></td><td>7.9–8.5</td><td>7.7–8.2</td><td>7.7–8.7</td><td>9.9–11.2</td><td>9.3–9.9</td><td>7.4–8.6</td><td>10.5–11.5</td><td>7.5–8.2</td><td>9.6–10.3</td><td><b>0–0.6</b></td><td></td></tr><tr><th>11</th><td><b><i>Scoparia annulata</i> sp. nov.</b></td><td>8.0–9.2</td><td>8.7–9.8</td><td>7.5–8.9</td><td>9.6–11.2</td><td>8.7–10.1</td><td>7.5–10.1</td><td>11.0–12.4</td><td>6.9–8.2</td><td>8.4–9.8</td><td>6.4–7.9</td><td>0–1.7</td></tr></tbody></table><p>All genetic distances (%) were corrected with the Kimura two-parameter (K2P) substitution model using MEGA 5; extreme values of intraspecific and interspecific distances are given (the numbers in bold are the intraspecific distances).</p>
Linked collectors and determiners for: Monophyly, review, six new species and DNA barcode of micropterous Afromontane Afropictinus (Heteroptera: Aradidae).
Natural history specimen data linked to collectors and determiners held within, "Monophyly, review, six new species and DNA barcode of micropterous Afromontane Afropictinus (Heteroptera: Aradidae)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/eeff9760-db0d-4b4d-ac0f-2ec2b7c729cd">https://bionomia.net/dataset/eeff9760-db0d-4b4d-ac0f-2ec2b7c729cd</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/eeff9760-db0d-4b4d-ac0f-2ec2b7c729cd">https://gbif.org/dataset/eeff9760-db0d-4b4d-ac0f-2ec2b7c729cd</a>. Formatted as a Frictionless Data package.
Data from: Promise and challenge of DNA barcoding in Venus slipper (Paphiopedilum)
Orchidaceae are one of the largest families of flowering plants, with over 27,000 species described and all orchids are listed in CITES. Moreover, the seedlings of orchid species from the same genus are similar. The objective of DNA barcoding is rapid, accurate, and automated species identification, which may be used to identify illegally traded endangered species from vegetative specimens of Paphiopedilum (Venus slipper), a flagship group for plant conservation with high ornamental and commercial values. Here, we selected eight chloroplast barcodes and nrITS to evaluate their suitability in Venus slippers. The results indicate that all tested barcodes had no barcoding gap and the core plant barcodes showed low resolution for the identification of Venus slippers (18.86%). Of the single-locus barcodes, nrITS is the most efficient for the species identification of the genus (52.27%), whereas matK + atpF-atpH is the most efficient multi-locus combination (28.97%). Therefore, we recommend the combination of matK + atpF-atpH + ITS as a barcode for Venus slippers. Furthermore, there is an upper limit of resolution of the candidate barcodes, and only half of the taxa with multiple samples were identified successfully. The low efficiency of these candidate barcodes in Venus slippers may be caused by relatively recent speciation, the upper limit of the barcodes, and/or the sampling density. Although the discriminatory power is relatively low, DNA barcoding may be a promising tool to identify species involved in illegal trade, which has broad applications and is valuable for orchid conservation.
Data from: Accelerating plant DNA barcode reference library construction using herbarium specimens: improved experimental techniques
A well-covered reference library is crucial for successful identification of species by DNA barcoding. The biggest difficulty in building such a reference library is the lack of materials of organisms. Herbarium collections are potentially an enormous resource of materials. In this study, we demonstrate that it is likely to build such reference libraries using the reconstructed (self-primed PCR amplified) DNA from the herbarium specimens. We used 179 rosaceous specimens to test the effects of DNA reconstruction, 420 randomly sampled specimens to estimate the usable percentage and another 223 specimens of true cherries (Cerasus, Rosaceae) to test the coverage of usable specimens to the species. The barcode rbcLb (the central four-sevenths of rbcL gene) and matK was each amplified in two halves and sequenced on Roche GS 454 FLX+. DNA from the herbarium specimens was typically shorter than 300 bp. DNA reconstruction enabled amplification fragments of 400–500 bp without bringing or inducing any sequence errors. About one-third of specimens in the national herbarium of China (PE) were proven usable after DNA reconstruction. The specimens in PE cover all Chinese true cherry species and 91.5% of vascular species listed in Flora of China. It is very possible to build well-covered reference libraries for DNA barcoding of vascular species in China. As exemplified in this study, DNA reconstruction and DNA-labelled next-generation sequencing can accelerate the construction of local reference libraries. By putting the local reference libraries together, a global library for DNA barcoding becomes closer to reality.
FIGURE 12 in DNA barcodes: Evaluating the potential of COI to diffentiate closely related species of Elachista (Lepidoptera: Gelechioidea: Elachistidae) from Australia
FIGURE 12. Larval mines of the taxa of the Elachista zigzagger complex. A: A1; B: A2; C: B2.
FIGURE 9 in DNA barcodes: Evaluating the potential of COI to diffentiate closely related species of Elachista (Lepidoptera: Gelechioidea: Elachistidae) from Australia
FIGURE 9. Female genitalia of the taxa of the Elachista zigzagger complex. A: B1; B: B2; C: B3.
FIGURE 3. Rhododendron baihuaense. A, Habitat. B, Leaves. C, Flowers. D in A new species of Rhododendron (Ericaceae) from the Gaoligong Mountains, Yunnan, China, supported by morphological and DNA barcoding data
FIGURE 3. Rhododendron baihuaense. A, Habitat. B, Leaves. C, Flowers. D, Fruits.
FIGURE 1 in Pinellia hunanensis (Araceae), a new species supported by morphometric analysis and DNA barcoding
FIGURE 1. Sketch map of East Asia, indicating distribution of Pinellia.
Figure 2 from: Oliveira D, Chaves C, Pinto J, Paupério J, Fonseca N, Beja P, Ferreira S (2021) DNA Barcoding of Portuguese Lacewings (Neuroptera) and Snakeflies (Raphidioptera) (Insecta, Neuropterida). ZooKeys 1054: 67-84. https://doi.org/10.3897/zookeys.1054.64608
Figure 2 Neighbour-joining tree of all obtained DNA sequences for Portuguese Neuroptera and Raphidioptera. Neighbour-joining tree constructed in PAUP* 4.0a167. Non-highlighted terminal branches represent the two outgroup sequences.
Figure 3 from: Oliveira D, Chaves C, Pinto J, Paupério J, Fonseca N, Beja P, Ferreira S (2021) DNA Barcoding of Portuguese Lacewings (Neuroptera) and Snakeflies (Raphidioptera) (Insecta, Neuropterida). ZooKeys 1054: 67-84. https://doi.org/10.3897/zookeys.1054.64608
Figure 3 Neighbour-joining tree of Chrysopidae DNA barcode sequences. Neighbour-joining tree constructed in PAUP* 4.0a167 and contrasted with the results from the ABGD analysis and BIN attribution. Bootstrap values under 90% omitted.
Figure 1 from: Oliveira D, Chaves C, Pinto J, Paupério J, Fonseca N, Beja P, Ferreira S (2021) DNA Barcoding of Portuguese Lacewings (Neuroptera) and Snakeflies (Raphidioptera) (Insecta, Neuropterida). ZooKeys 1054: 67-84. https://doi.org/10.3897/zookeys.1054.64608
Figure 1 Map of continental Portugal with sampling locations A sampling locations of the 8 captured specimens of Raphidioptera (N = 8) B sampling locations of the 235 captured specimens of Neuroptera (N = 67).
Supplementary material 2 from: Oliveira D, Chaves C, Pinto J, Paupério J, Fonseca N, Beja P, Ferreira S (2021) DNA Barcoding of Portuguese Lacewings (Neuroptera) and Snakeflies (Raphidioptera) (Insecta, Neuropterida). ZooKeys 1054: 67-84. https://doi.org/10.3897/zookeys.1054.64608
Genetic distances
Supplementary material 1 from: Oliveira D, Chaves C, Pinto J, Paupério J, Fonseca N, Beja P, Ferreira S (2021) DNA Barcoding of Portuguese Lacewings (Neuroptera) and Snakeflies (Raphidioptera) (Insecta, Neuropterida). ZooKeys 1054: 67-84. https://doi.org/10.3897/zookeys.1054.64608
Summary table of all used sequences and specimens, with country of origin
Figure 4 from: Oliveira D, Chaves C, Pinto J, Paupério J, Fonseca N, Beja P, Ferreira S (2021) DNA Barcoding of Portuguese Lacewings (Neuroptera) and Snakeflies (Raphidioptera) (Insecta, Neuropterida). ZooKeys 1054: 67-84. https://doi.org/10.3897/zookeys.1054.64608
Figure 4 Neighbour-joining tree of Hemerobiidae DNA barcode sequences. Neighbour-joining tree constructed in PAUP* 4.0a167 and contrasted with the results from the ABGD analysis and BIN attribution. Bootstrap values under 90% omitted. Subtrees were collapsed for the monophyletic morphologically identified species. Triangle size for each species is proportional to the intraspecific distance.
Figure 7. A in Two new species of Hudsonimyia Roback, 1979 (Diptera: Chironomidae: Tanypodinae) from Neotropical Region unveiled by morphology and DNA barcoding
Figure 7. A Kimura two-parameter neighbour-joining tree of sampled Hudsonimyia species.
FIGURE 4 in Redescription of Sphenanthias whiteheadi Talwar (Perciformes: Cepolidae) with DNA barcodes from the southern coasts of India
FIGURE 4. Male, Sphenanthias whiteheadi: X ray.
FIGURE 3 in Redescription of Sphenanthias whiteheadi Talwar (Perciformes: Cepolidae) with DNA barcodes from the southern coasts of India
FIGURE 3. Female, Sphenanthias whiteheadi.
FIGURE 2 in Redescription of Sphenanthias whiteheadi Talwar (Perciformes: Cepolidae) with DNA barcodes from the southern coasts of India
FIGURE 2. Male, Sphenanthias whiteheadi.
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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.