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Figure 3 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figure 3. BI tree for nuclear gene 28S. BI posterior probabilities and ML bootstrap values are shown above and below branches, if ≥0.9 or ≥70%, respectively. Asterisks indicate type specimens, with a single asterisk for paratypes and a double asterisk for holotypes.
Figure 5 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figure 5. Scatterplot of principal component analysis 1. Members of lineages are indicated by a ⅔ confidence interval ellipse.
Figures 38–48 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 38–48. Heterolepisma cooloola sp. nov. holotype ♀, unless indicated otherwise by specimen number(38) habitus (K.377754); (39) posterior comb of pronotum with scale; (40) head; (41) scape, pedicel and basal intervals of flagellum, from above; (42) idem, from below; (43) antenna, most distal surviving interval; (44) mandible; (45) idem, detail of molar and incisor regions; (46) maxilla, only larger setae of palp illustrated; (47) idem, lacinia and galea (QM 207012); (48) ultimate article of maxillary palp of ♂ (QM 207012). Scale bars = 0.1 mm unless otherwise indicated.
Figures 66–77 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 66–77. Heterolepisma cooloola sp. nov. holotype ♀, unless otherwise indicated by specimen number (66) urotergite IV; (67) urotergite V, right lateral comb; (68) idem, left sublateral comb; (69) idem, left submedial comb; (70) right side of urotergite VIII (K.261189); (71) infralateral comb of urotergite IX; (72) urotergite X; (73) urotergite X of paratype (QM 207012); (74) urosternite IV; (75) posterior comb of urosternite V; (76) urosternites VII, VIII, IX and ovipositor; (77) base of stylus VII. Scale bars = 0.1 mm.
Figure 2 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figure 2. BI trees for mitochondrial genes 16S and COI. BI posterior probabilities and ML bootstrap values are shown above and below branches, if ≥0.9 or ≥70%, respectively.Asterisks indicate type specimens, with a single asterisk for paratypes and a double asterisk for holotypes.
Figs 30–35 in Description of a new species of Loxosceles Heineken & Lowe (Araneae, Sicariidae) recluse spiders from Hidalgo, Mexico, under integrative taxonomy: morphological and DNA barcoding data (CO1 + ITS2)
Figs 30–35. Variation of the male palps, left palps, prolateral views. 30–33. Loxosceles tolantongo sp. nov. 30–32. Tourist Center Grutas de Tolantongo, Municipality of Cardonal, Hidalgo (type locality). 33. 500 m west of the entrance No. 5 to the Tourist Center Grutas de Tolantongo, Municipality of Cardonal, Hidalgo. 34–35. Loxosceles jaca Gertsch & Ennik, 1983. 2.5 km north of Jacala de Ledezma, Municipality of Jacala de Ledezma, Hidalgo. Scale bars = 0.5 mm.
Fig. 56 in Description of a new species of Loxosceles Heineken & Lowe (Araneae, Sicariidae) recluse spiders from Hidalgo, Mexico, under integrative taxonomy: morphological and DNA barcoding data (CO1 + ITS2)
Fig. 56. Maximum likelihood tree inferred from the concatenated matrix (CO1 + ITS2) of species of Loxosceles Heineken & Lowe, 1832 from Mexico. Colors of branches and bars indicate different species. Numbers above bars represent the delimitation methods: 1 = morphology (M); 2 = neighbor joining (NJ); 3 = ABGD with initial partitions (IP); 4–5 = ABGD with recursive partitions (RP); 6 = GMYC yule analysis; 7 = GMYC coalescent analysis; 8 bPTP with ML; 9 = bPTP with IB. Numbers below bars represent species recovered for each delimitation method. Red numbers correspond to Bayesian posterior probabilities, black numbers are bootstrap support values from the ML analysis.
Figs 20–25 in Description of a new species of Loxosceles Heineken & Lowe (Araneae, Sicariidae) recluse spiders from Hidalgo, Mexico, under integrative taxonomy: morphological and DNA barcoding data (CO1 + ITS2)
Figs 20–25. Loxosceles tolantongo sp. nov., ♂ holotype (CNAN-T01317). 20–22. Left palp, prolateral, dorsal and retrolateral views, respectively. 23–25. Detail of the bulb and embolus, retrolateral, dorsal and apical views, respectively. Scale bars: 20–22 = 0.5 mm; 23–25 = 0.2 mm.
Fig. 54 in Description of a new species of Loxosceles Heineken & Lowe (Araneae, Sicariidae) recluse spiders from Hidalgo, Mexico, under integrative taxonomy: morphological and DNA barcoding data (CO1 + ITS2)
Fig. 54. Maximum likelihood tree inferred from CO1 gene of species of Loxosceles Heineken & Lowe, 1832 from Mexico. Colors of branches and bars indicate different species. Numbers above bars represent the delimitation methods: 1 = morphology (M); 2 = neighbor joining (NJ); 3 = ABGD with initial partitions (IP); 4–6 = ABGD with recursive partitions (RP); 7 = GMYC yule analysis; 8 = GMYC coalescent analysis; 9 = bPTP with ML; 10 = bPTP with IB. Numbers below bars represent species recovered for each delimitation method. Red numbers on branches correspond to Bayesian posterior probabilities, black numbers are bootstrap support values from the ML analysis.
BAGS: an automated barcode, audit & grade system for DNA barcode reference libraries
<p>Biodiversity studies greatly benefit from molecular tools, such as DNA metabarcoding, which provides an effective identification tool in biomonitoring and conservation programmes. The accuracy of species-level assignment, and consequent taxonomic coverage, relies on comprehensive DNA barcode reference libraries. The role of these libraries is to support species identification, but accidental errors in the generation of the barcodes may compromise their accuracy. Here we present an R-based application, BAGS (Barcode, Audit & Grade System; https://github.com/tadeu95/BAGS), that performs automated auditing and annotation of cytochrome c oxidase subunit I (COI) sequences libraries, for a given taxonomic group of animals, available in the Barcode of Life Data System (BOLD). This is followed by implementing a qualitative ranking system that assigns one of five grades (A to E) to each species in the reference library, according to the attributes of the data and congruency of species names with sequences clustered in Barcode Index Numbers (BINs). Our goal is to allow researchers to obtain the most useful and reliable data, highlighting and segregating records according to their congruency. Different tests were performed to perceive its usefulness and limitations. BAGS fulfils a significant gap in the current landscape of DNA barcoding research tools by quickly screening reference libraries to gauge the congruence status of data and facilitate the triage of ambiguous data for posterior review. Thereby, BAGS has the potential to become a valuable addition in forthcoming DNA metabarcoding studies, in the long term contributing to globally improve the quality and reliability of the public reference libraries.</p>
Fig 5 in A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library
Fig 5. Neighbour-joining tree showing all available DNA barcodes for species in family Rhinolophidae reported from Peninsular Malaysia. The percentage of pseudoreplicate trees (±70%) in which the DNA barcodes clustered together in the bootstrap test (500 pseudoreplicates) are shown above the branches. Abbreviation as follows: PM = Peninsular Malaysia, VN = Vietnam, BN = Borneo (including Sabah & Sarawak of East Malaysia, Brunei and Kalimantan Indonesia), TH = Thailand, LA = Laos, SM = Sumatera Indonesia, JV = Java Indonesia, IND = India, CH = China, CM = Cambodia, MN = Myanmar. https://doi.org/10.1371/journal.pone.0179555.g005
Fig 4 in A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library
Fig 4. Neighbour-joining tree showing all available DNA barcodes for species in family Hipposideridae reported from Peninsular Malaysia. The percentage of pseudoreplicate trees (±70%) in which the DNA barcodes clustered together in the bootstrap test (500 pseudoreplicates) are shown above the branches. Abbreviation as follows: PM = Peninsular Malaysia, VN = Vietnam, BN = Borneo (including Sabah & Sarawak of East Malaysia, Brunei and Kalimantan Indonesia), TH = Thailand, LA = Laos, SM = Sumatera Indonesia, CH = China, CM = Cambodia. https://doi.org/10.1371/journal.pone.0179555.g004
Fig 2 in A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library
Fig 2. Neighbour-joining tree showing all available DNA barcodes for species in family Pteropodidae reported from Peninsular Malaysia. The percentage of pseudoreplicate trees (±70%) in which the DNA barcodes clustered together in the bootstrap test (500 pseudoreplicates) are shown above the branches. Abbreviation as follows: PM = Peninsular Malaysia, VN = Vietnam, JV = Java, Indonesia, BN = Borneo (including Sabah, Sarawak, Brunei and Kalimantan), TH = Thailand, LA = Laos. https://doi.org/10.1371/journal.pone.0179555.g002
Fig 3 in A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library
Fig 3. Neighbour-joining tree showing all available DNA barcodes for species in families Emballonuridae, Megadermatidae, Molossidae and Nycteridae reported from Peninsular Malaysia. The percentage of pseudoreplicate trees (±70%) in which the DNA barcodes clustered together in the bootstrap test (500 pseudoreplicates) are shown above the branches. Abbreviation as follows: PM = Peninsular Malaysia, VN = Vietnam, BN = Borneo (including Sabah & Sarawak of East Malaysia, Brunei and Kalimantan Indonesia), TH = Thailand, LA = Laos, SM = Sumatera Indonesia, CH = China. https://doi.org/10.1371/journal.pone.0179555.g003
SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes
<p>The accurate quantification of eukaryotic species abundances from bulk samples remains a key challenge for community ecology and environmental biomonitoring. We resolve this challenge by combining shotgun sequencing, mapping to reference DNA barcodes or to mitogenomes, and three correction factors: (a) a percent‐coverage threshold to filter out false positives, (b) an internal‐standard DNA spike‐in to correct for stochasticity during sequencing, and (c) technical replicates to correct for stochasticity across sequencing runs. The SPIKEPIPE pipeline achieves a strikingly high accuracy of intraspecific abundance estimates (in terms of DNA mass) from samples of known composition (mapping to barcodes R<sup>2</sup> = .93, mitogenomes R<sup>2</sup> = .95) and a high repeatability across environmental‐sample replicates (barcodes R<sup>2</sup> = .94, mitogenomes R<sup>2</sup> = .93). As proof of concept, we sequence arthropod samples from the High Arctic, systematically collected over 17 years, detecting changes in species richness, species‐specific abundances, and phenology. SPIKEPIPE provides cost‐efficient and reliable quantification of eukaryotic communities.</p>
FIGURE 11 in Description of a new Oriental stonefly species, Phanoperla constanspina (Plecoptera: Perlidae) from Mindanao, Philippines and association of life stages using DNA barcoding
FIGURE 11. Phanoperla constanspina sp. nov. male nymphal habitus illustrating two general body pigmentation types. (A) (Haplotype: N-J 25. m) Pale to lighter brown, sometimes with darker wingpad tips. (B) (Haplotype: N-G 49. m). Dark to darker brown, sometimes with dark to black wingpads.
FIGURE 8 in Description of a new Oriental stonefly species, Phanoperla constanspina (Plecoptera: Perlidae) from Mindanao, Philippines and association of life stages using DNA barcoding
FIGURE 8. Phanoperla constanspina sp. nov. egg. (A) Entire egg. (B) Chorionic details. (C) Collar end (D) Anterior end. Scale = 100 µm.
Supplementary material 1: Accumulation Curve Data from: DNA Barcoding of the parasitoid wasp subfamily Doryctinae (Hymenoptera: Braconidae) from Chamela, Mexico - Biodiversity Data Journal 3: e5109 (18 May 2015) https://doi.org/10.3897/BDJ.3.e5109
Table containing the Process ID of specimens sampled and Barcode Index Number (BIN) used for the species accumulation curve.
Figure 3. from: DNA Barcoding of the parasitoid wasp subfamily Doryctinae (Hymenoptera: Braconidae) from Chamela, Mexico - Biodiversity Data Journal 3: e5109 (18 May 2015) https://doi.org/10.3897/BDJ.3.e5109
Figure 3. - DNA barcoding species accumulation curve for the Doryctinae from the CBS (Suppl. material 1).
Figure 1. from: DNA Barcoding of the parasitoid wasp subfamily Doryctinae (Hymenoptera: Braconidae) from Chamela, Mexico - Biodiversity Data Journal 3: e5109 (18 May 2015) https://doi.org/10.3897/BDJ.3.e5109
Figure 1. - Study area. The Chamela Biological Station (IB-UNAM), located within the Chamela-Cuixmala Biosphere Reserve in the estate of Jalisco, Mexico.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.