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3,292 results for “DNA Barcode”
Data from: MetaBARFcoding: DNA-barcoding of regurgitated prey yields insights into Christmas Shearwater (Puffinus nativitatis) foraging ecology at Hōlanikū (Kure Atoll), Hawaiʻi
<p>Morphological identification of digested prey remains from a generalist predator can be challenging, especially when attempting to match degraded remains to taxonomic keys. DNA techniques, whereby prey is sequenced and matched to large public nucleotide sequence databases, are increasingly being used to augment morphological identification. We used "metaBARFcoding" (DNA metabarcoding) to target a region of the cytochrome <i><u>c</u></i> oxidase subunit I mitochondrial gene to identify prey in highly-digested regurgitations from Christmas Shearwaters <i>Puffinus nativitatis </i>at Hōlanikū (Kure Atoll). Metabarcoding was used to bulk-process 92 water samples from regurgitations collected from 2009-2017, providing an overview of the seabird's diet. We additionally Sanger sequenced 100 prey items from 50 randomly chosen regurgitations to verify that metabarcoding characterized key components of the diet. The metabarcoding technique identified 87 unique taxa from 29 families of fish and squid, spanning diverse taxa, including reef-associated, pelagic-oceanic, and mesopelagic species. Rare prey (frequency of occurrence <u><</u> 5% of samples) constituted 66% of the species richness, demonstrating the highly diverse diet of this generalist predator. Overall, 81% of the families detected in the contemporary diet were previously documented in Christmas Shearwater diets from the Northwestern Hawaiian Islands. Our results indicate that metabarcoding the cytochrome <i>c</i> oxidase subunit I (COI) region is useful in identifying a wide range of taxa from highly digested regurgitations, thus facilitating this approach to study seabird diets.</p>
FIGURE 2 in DNA barcodes for Cladocera and Copepoda from Mexico and Guatemala, highlights and new discoveries
FIGURE 2. Neighbour–joining tree of 440 COI sequences from 61 cladoceran species using K2P distances. The number of specimens sequenced, localities, and general distribution is in brackets. Abbreviations used: N = North; C = Center; S = South; CA = Canada; G = Guatemala; GE= Germany; MX = Mexico, ON = Ontario. Specimen details are available from BOLD (www.barcodinglife.org). * Sequences derive from cultured specimens; ** Sequences derive from cultured and wild specimens.
Assessing candidate DNA barcodes for Chinese and internationally traded timber species
<p>Accurate identification of species from timber is an essential step to help control illegal logging and forest loss. However, current approaches to timber identification based on morphological and anatomical characteristics have limited species resolution. DNA barcoding is a proven tool for plant species identification, but there is a need to build reliable reference data across broad taxonomic and spatial scales. Here, we construct a species barcoding library consisting of 1,550 taxonomically diverse timber species from 656 genera and 124 families, representing a comprehensive genetic reference data set for Chinese timber species and international commercial traded timber species, using four barcodes (<i>rbc</i>L, <i>mat</i>K, <i>trn</i>H–<i>psb</i>A, and ITS2). The ITS2 fragment was found to be the most efficient locus for Chinese timber species identification among the four barcodes tested, both at the species and genus level, despite its low recovery rate. Nevertheless, the barcode combination <i>mat</i>K+<i>trn</i>H–<i>psb</i>A+ITS2 was required as a complementary barcode to distinguish closely related species in complex datasets involving internationally traded timber species. Comparative analyses of family-level discrimination and species/genus ratios indicated that the inclusion of closely related species is an important factor affecting the resolution ability of barcodes for timber species verification. Our study indicates that although nuclear ITS2 is the most efficient single barcode for timber species authentication in China, complementary combinations like <i>mat</i>K+<i>trn</i>H–<i>psb</i>A+ITS2 are required to provide broader discrimination power. These newly-generated sequences enrich the existing publicly available databases, especially for tropical and subtropical evergreen timber trees and this current timber species barcode reference library can serve as an important genetic resource for forestry monitoring, illegal logging prosecution and biodiversity projects.</p>
Supplementary material 9 from: Mahima K, Umapathy S, Sudhakar JV, Sathishkumar R (2021) Systematic reinstatement of highly sacred Ficus krishnae based on differences in morphology and DNA barcoding from Ficus benghalensis (Moraceae). PhytoKeys 186: 121-138. https://doi.org/10.3897/phytokeys.186.74086
Figure S4. Maximum Clade Credibility (MCC) tree from Bayesian analysis using the ITS2 DNA barcode marker with posterior probabilities values in percentage that are shown at nodes
Supplementary material 10 from: Mahima K, Umapathy S, Sudhakar JV, Sathishkumar R (2021) Systematic reinstatement of highly sacred Ficus krishnae based on differences in morphology and DNA barcoding from Ficus benghalensis (Moraceae). PhytoKeys 186: 121-138. https://doi.org/10.3897/phytokeys.186.74086
Figure S5. Maximum Clade Credibility (MCC) tree from Bayesian analysis using the trnH-psbA DNA barcode marker with posterior probabilities values in percentage that are shown at nodes.
Supplementary material 8 from: Mahima K, Umapathy S, Sudhakar JV, Sathishkumar R (2021) Systematic reinstatement of highly sacred Ficus krishnae based on differences in morphology and DNA barcoding from Ficus benghalensis (Moraceae). PhytoKeys 186: 121-138. https://doi.org/10.3897/phytokeys.186.74086
Figure S3. Parsimony distribution of the morphological characters and their status on the MCC Bayesian tree
FIGURE 6 in New records of water mites (Acari, Hydrachnidia) from Iran with the description of one new species based on morphology and DNA barcodes
FIGURE 6. Neighbor-joining tree based on studied Monatractides COI sequences. The optimal tree with the sum of branch length = 0.33301736 is shown. The analysis involved 9 nucleotide sequences. There were a total of 669 positions in the final dataset.
FIGURE 5 in New records of water mites (Acari, Hydrachnidia) from Iran with the description of one new species based on morphology and DNA barcodes
FIGURE 5. Partial NJ trees calculated with COI sequences of Sperchon papillosus and S. compactilis with BIN assignment. The optimal tree with the sum of branch length = 0.06613391 is shown. The analysis involved 7 nucleotide sequences. There were a total of 669 positions in the final dataset.
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 79 in Taxonomy of Diamesa steinboecki group (Diptera: Chironomidae: Diamesinae) with description and DNA barcoding of new species. I. Subgroups steinboecki and longipes
FIGURE 79. Bayesian inference (BI) trees based on the cytochrome c oxidase I (COI) nucleotide sequence data of the genus Diamesa Meigen and outgroup Pseudokiefferiella parva (Edwards) Bayesian posterior probabilities (higher than 0.7) are given above tree nodes. Specimens obtained in this study are in bold.
FIGURES 68–74 in Taxonomy of Diamesa steinboecki group (Diptera: Chironomidae: Diamesinae) with description and DNA barcoding of new species. I. Subgroups steinboecki and longipes
FIGURES 68–74. Type localities of Diamesa dragani sp. nov. (68), D. kownackii sp. nov. (69–70), D. maisaraensis sp. nov. (71), D. marinskiyi sp. nov. (72), D. steinboecki Goetghebuer (73) and D. sakartvella Kownacki et Kownacka (74). 68, unnamed stream of Bolshoi On River basin, alt. 2063 m a. sea l., Sayan Mountains (photo by S.V. Dragan); 69, unnamed stream of Somnitelnaya River basin, Wrangel Island (photo by E.A. Makarchenko); 70, Somnitelnaya River, upper stream, alt. 205–210 m a. sea l., Wrangel Island (photo by O.A. Khruleva); 71, Maisara River near Maisara Pass, alt. 4168 m a. sea l., Pamir Mountains (photo by D.M. Palatov); 72, Zienzan River, Tien Shan Mountains, alt. 1923 m a. sea l., Xinjiang Uygur Autonomous Region, China (photo by D.M. Palatov); 73, Balm stream, Massif of Aiguilles–Rouges, French Alps (photo by Pierre Clévenot); 74, Skazdon River near the Tsey (Tseyskoe gorge), alt. 1943 m a. sea l., North Caucasus (photo by D.M. Palatov).
FIGURES 37–44 in Taxonomy of Diamesa steinboecki group (Diptera: Chironomidae: Diamesinae) with description and DNA barcoding of new species. I. Subgroups steinboecki and longipes
FIGURES 37–44. Males of Diamesa zagrosica sp. nov. (37, 41), D. sakartvella Kownacki et Kownacka (38, 42) and D. moubayedi sp. nov. (39–40, 43–44). 37, head; 38, 41, hypopygium in dorsal view; 40, hypopygium in dorsal view without tergite IX; 42, wing; 43, tergite IX; 44, anal point in lateral view.
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.