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4,144 results for “ITS barcode”
FIGURE 4 in New records of water mites (Acari, Hydrachnidia) from Iran with the description of one new species based on morphology and DNA barcodes
FIGURE 4. Neighbor-joining tree based on studied Sperchon COI sequences. The optimal tree with the sum of branch length = 1.14769493 is shown. The analysis involved 35 nucleotide sequences. There were a total of 670 positions in the final dataset.
FIGURE 3 in New records of water mites (Acari, Hydrachnidia) from Iran with the description of one new species based on morphology and DNA barcodes
FIGURE 3. Neighbor-joining tree based on studied Hydrodroma COI sequences. The optimal tree with the sum of branch length = 0.54910533 is shown. The analysis involved 11 nucleotide sequences. There were a total of 669 positions in the final dataset.
FIGURE 7 in New records of water mites (Acari, Hydrachnidia) from Iran with the description of one new species based on morphology and DNA barcodes
FIGURE 7. Neighbor-joining tree based on studied Torrenticola COI sequences. The optimal tree with the sum of branch length = 1.18947924 is shown. The analysis involved 36 nucleotide sequences. There were a total of 669 positions in the final dataset.
FIGURE 1 in New records of water mites (Acari, Hydrachnidia) from Iran with the description of one new species based on morphology and DNA barcodes
FIGURE 1. Hydrodroma golestanica sp. nov. (A, C holotype ♂, B, ♀ paratype): A-B = genital field; C = integument papillae; D = photograph of dorsal integument in tangential view. Scale bars = 100 μm.
FIGURE 2 in New records of water mites (Acari, Hydrachnidia) from Iran with the description of one new species based on morphology and DNA barcodes
FIGURE 2. Hydrodroma golestanica sp. nov., holotype ♂: A = palp, lateral view; B = palp, medial view (P-1 missing); C = gnathosoma; D = chelicera; E = IV-L-5 and -6, posterior view. Scale bars = 100 μm..
Supplementary material 1 from: Linh NN, Hang PLB, Hue HTT, Ha NH, Hanh HH, Ton ND, Hien LTT (2022) Species discrimination of novel chloroplast DNA barcodes and their application for identification of Panax (Aralioideae, Araliaceae). PhytoKeys 188: 1-18. https://doi.org/10.3897/phytokeys.188.75937
NCBI accession numbers of DNA barcoding sequences, and complete chloroplast genomes used in this study.
DNA barcoding reveals generalization and host overlap in hummingbird flower mites: implications for the Mating Rendezvous Hypothesis
Hummingbird flower mites are assumed to monopolize single host plant species due to sexual selection for unique mating rendezvous sites. We tested the main assumption of the Mating rendezvous hypothesis -extreme host specialization- by reconstructing interactions among tropical hummingbird flower mites and their host plants using DNA barcoding and taxonomic identifications. We collected 10,654 mites from 489 flowers. We extracted DNA from 1928 mite specimens and amplified the cytochrome c oxidase I (CO1) DNA barcode. We analyzed the network structure to assess the degree of generalization or specialization of mites to their host plants. We recorded 18 species of hummingbird flower mites from three genera (Proctolaelaps, Rhinoseius and Tropicoseius) interacting with 14 species of plants. We found that generalist mites are common, and congeneric mite species often share host plants. Our results challenge the assumption of strict specialization that supports this system as an example of mating rendezvous evolution.
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>
Supplementary material 1 from: Krčmar S, Kučinić M, Pezzi M, Bruvo Mađarić B (2022) DNA barcoding of the horsefly fauna (Diptera, Tabanidae) of Croatia with notes on the morphology and taxonomy of selected species from Chrysopsinae and Tabaninae. ZooKeys 1087: 141-161. https://doi.org/10.3897/zookeys.1087.78707
Morphological characteristics of females of some horseflies from subfamily Tabaninae and Chrysopsinae
FIGURE 11 in New Thai giant pill-millipede species, with new genetic barcoding data (Diplopoda Sphaerotheriida, Zephroniidae)
FIGURE 11. Zephronia chrysomallos Bhansali & Wesener sp. nov., holotype ♂ (NHMD MYR8826), drawings, A. Left posterior telopod, anterior view. B. Left posterior telopod, posterior view. Abbreviations: ct = crenulated teeth; imf = immovable finger; ss = sclerotized spot. Scale bars = 1 mm.
FIGURE 12 in New Thai giant pill-millipede species, with new genetic barcoding data (Diplopoda Sphaerotheriida, Zephroniidae)
FIGURE 12. Zephronia erawani Bhansali & Wesener sp. nov., holotype ♂ (NHMD K56-9), volume rendering based on microcomputed tomography. A. Habitus, lateral view. B. Habitus, ventro-lateral view. C. Habitus, ventral view. D. Habitus, anterior view. E. Body-ring architecture, cross section trough midbody-ring. Abbreviations: Ant = Antennae; As = anal shield; Cl = clypeus; Col = collum; Cp = central pad; Cx = coxa; Fe = femur; Gc = gnathochilarium; Go = gonopore; Ip = inner palpi; Lc = locking carina; o = ommatidia; Pl = pleurite; Pl1= pleurite 1; Pl2= pleurite 2; Po = postfemur; Pre = prefemur; Pt = paratergite; Stp = stigmatic plate; St = stipites; Ta = tarsus; Te = tergite; Tg = thoracic shield groove; Ti = tibia; Ts = thoracic shield. Not to scale.
FIGURE 8 in New Thai giant pill-millipede species, with new genetic barcoding data (Diplopoda Sphaerotheriida, Zephroniidae)
FIGURE 8. Zephronia chrysomallos Bhansali & Wesener sp. nov., holotype ♂ (ZFMK MYR8826), scanning electron micrographs. A. Left antennae, lateral view. B. Left sixth antennomere with antennal disc. C. Left antenna, disc. D. Gnathochilarium, apical view. E. Left lateral palpi. F. Left central pad, two types of sensory cones on central pad, detail. Abbreviations: ac = apical cone; ad = antennal disc; Cp = central pad; Hyp = hypopharynx; Ip = inner palpi; LL = lamellae lingulales; Sc = sensory cone; St = stipites.
FIGURE 7 in New Thai giant pill-millipede species, with new genetic barcoding data (Diplopoda Sphaerotheriida, Zephroniidae)
FIGURE 7. Zephronia chrysomallos Bhansali & Wesener sp. nov., paratype ♂ (ZFMK MYR11366), volume rendering based on micro-computed tomography. A. Habitus, lateral view. B. Habitus, ventro-lateral view. C. Habitus, ventral view. D. Habitus, anterior view. E. Body-ring architecture, cross section trough midbody-ring. Abbreviations: Ant = Antennae; As = anal shield; Cl = clypeus; Col = collum; Cx = coxa; Fe = femur; Gc = gnathochilarium; Go = gonopore; Ip = inner palpi; Lc = locking carina; O = ommatidia; Pl = pleurite; Pl1= pleurite 1; Pl2= pleurite 2; Pre = prefemur; Pt = paratergite; St = stigmatic plate; Ta = tarsus; Te = tergite; Tg = thoracic shield groove; Ti = tibia; Tr = tracheal apodeme; Ts = thoracic shield. Not to scale.
FIGURE 5 in New Thai giant pill-millipede species, with new genetic barcoding data (Diplopoda Sphaerotheriida, Zephroniidae)
FIGURE 5. Sphaerobelum meridionalis Bhansali & Wesener sp. nov., holotype ♂ (MHNG 4B-2), drawings, A. Left posterior telopod, anterior view. B. Left posterior telopod, posterior view. Abbreviations: ct = crenulated teeth; imf = immovable finger; ms = membranous spot; ss = sclerotized spot. Scale bars = 1 mm.
FIGURE 4 in New Thai giant pill-millipede species, with new genetic barcoding data (Diplopoda Sphaerotheriida, Zephroniidae)
FIGURE 4. Sphaerobelum meridionalis Bhansali & Wesener sp. nov., holotype ♂ (MHNG 4B-2), drawings, A. First left coxa with stigmatic plate, posterior view, arrow points to mesal coxal process. B. Left leg 9, posterior view, arrow points to mesal process on prefemur. C. Second left coxa with gonopore, posterior view. D. Left anterior telopod, lateral view. E. Right anterior telopod, meso-posterior view. F. Right anterior telopod, anterior view. G. Right anterior telopod, posterior view. Abbreviations: as = apical spine; cl = claw; Cx = coxa; Fe = femur; Go = gonopore; Po = postfemur; Pre = prefemur; Sp-p = second podomere process; St = stigmatic plate; Syn = syncoxite = tarsus; Ti = tibia; vs = ventral spines. Scale bars = 1 mm.
FIGURE 2 in New Thai giant pill-millipede species, with new genetic barcoding data (Diplopoda Sphaerotheriida, Zephroniidae)
FIGURE 2. Map of Thailand with known distribution of Sphaerobelum spp. and Zephronia spp. Star represents new species. Diamonds represent new localities. Fluorescent Green = S. meridionalis Bhansali & Wesener sp. nov.; Pink = S. aesculus; Brown = S. truncatum; Chrome yellow = Z. chrysomallos Bhansali & Wesener sp. nov.; White = Z. erawani Bhansali & Wesener sp. nov.; Black = Z. viridisoma; Red = Z. panhai; Dark green = Z. golovatchi; Purple = Z. siamensis; Orange = Z. enghoffi; Yellow = Z. lannaensis; Blue = Z. phrain. B. Habitus photograph of Z. chrysomallos Bhansali & Wesener sp. nov., holotype ♀ (ZFMK MYR8826).
FIGURE 1 in New Thai giant pill-millipede species, with new genetic barcoding data (Diplopoda Sphaerotheriida, Zephroniidae)
FIGURE 1. Maximum likelihood tree based on the COI sequence after 1000 bootstrap replicates analyzed with the General Time Reversible Model. Numbers on branches indicate bootstrap support. Codon positions included were 1st+2nd+3rd. All positions with less than 5% site coverage were eliminated. The tree is drawn to scale, with branch length indicating genetic distance. Orange and green box represent new species of Zephronia and Sphaerobelum, respectively.
FIGURE 3 in New Thai giant pill-millipede species, with new genetic barcoding data (Diplopoda Sphaerotheriida, Zephroniidae)
FIGURE 3. Sphaerobelum meridionalis Bhansali & Wesener sp. nov., holotype ♂ (MHNG 4B-2), scanning electron micrographs. A. Left antenna, lateral view. B. Right antenna, disc. C. Detail of apical cone. Abbreviations: ac = apical cone; Ad = antennal disc.
FIGURE 6 in New Thai giant pill-millipede species, with new genetic barcoding data (Diplopoda Sphaerotheriida, Zephroniidae)
FIGURE 6. Endoterga of midbody tergites, scanning electron micrographs. A. Sphaerobelum meridionalis Bhansali & Wesener sp. nov., holotype ♂ (MHNG 4B-2). B. Zephronia chrysomallos Bhansali & Wesener sp. nov., holotype ♂ (ZFMK MYR8826). Abbreviations: Ci = cuticular impression; Ia = inner area; Ma = middle area; Oa = outer area.
FIGURE 14 in New Thai giant pill-millipede species, with new genetic barcoding data (Diplopoda Sphaerotheriida, Zephroniidae)
FIGURE 14. Zephronia erawani Bhansali & Wesener sp. nov., holotype ♂ (NHMD K56-9), drawings, A. Left posterior telopod, anterior view. B. Left posterior telopod, posterior view. Abbreviations: ct = crenulated teeth; imf = immovable finger; ss = sclerotized spot. Scale bars = 1 mm.
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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)
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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.