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3,292 results for “DNA Barcode”
FIGURES 1–6 in Taxonomy of some Boreoheptagyiini Brundin (Diptera: Chironomidae Diamesinae) from the mountains of Central Asia and the Middle East, with description and DNA barcoding of new taxa
FIGURES 1–6. Palatovia lorestanica sp. nov., male. 1, lobe of pronotum (straightened); 2, anterior part of mesonotum in dorsal view; 3, median volsella and aedeagal lobe in ventral view; 4, hypopygium in dorsal view; 5–6, subapical part of gonostylus. MVo—median volsella; Al—aedeagal lobe. Scale bars: Figs. 1, 4—100 μm; Fig. 2—200 μm; Figs. 3, 5–6—50 μm.
FIGURES 22–27 in Taxonomy of some Boreoheptagyiini Brundin (Diptera: Chironomidae Diamesinae) from the mountains of Central Asia and the Middle East, with description and DNA barcoding of new taxa
FIGURES 22–27. Boreoheptagyia joeli sp. nov. (22–26) and B. phoenicia Moubayed (27), males. 22, thorax in lateral view; 23–24, hypopygium in dorsal view; 25, antenna; 26, middle part of hypopygium without tergite IX; 27, gonostylus.
FIGURE 46 in Taxonomy of some Boreoheptagyiini Brundin (Diptera: Chironomidae Diamesinae) from the mountains of Central Asia and the Middle East, with description and DNA barcoding of new taxa
FIGURE 46. Bayesian tree based on mitochondrion COI gene for available members of the tribe Boreoheptagiini. Pagastia orientalis (Tshernovskij) (tribe Diamesini) was used as outgroup to root the tree. Bayesian posterior probabilities (PP) are given above tree nodes and bootstrap support values found in the ML analysis are shown below nodes. Specimens obtained in this study are in bold.
Data from: Predominant east to west colonisations across major oceanic barriers: insights into the phylogeographic history of the hydroid superfamily Plumularioidea, suggested by a mitochondrial DNA barcoding marker
We provide preliminary insights into the global phylogeographic and evolutionary patterns across species of the hydrozoan superfamily Plumularioidea (Cnidaria: Hydrozoa). We analysed 1114 16S sequences of 198 putative species of Plumularioidea collected worldwide. We investigated genetic connections and divergence in relation to present-day and ancient biogeographic barriers, climate changes and oceanic circulation. Geographical distributions of most species are generally more constrained than previously assumed. Some species able to raft are dispersed widely. Human-mediated dispersal explains some wide geographical ranges. Trans-Atlantic genetic connections are presently unlikely for most of the tropical-temperate species, but were probably more frequent until the Miocene-Pliocene transition, before restriction of the Tethys Sea and the Central American Seaway. Trans-Atlantic colonisations were predominantly directed westwards through (sub)tropical waters. The Azores were colonized multiple times and through different routes, mainly from the east Atlantic, at least since the Pliocene. Extant geminate clades separated by the Isthmus of Panama have predominantly Atlantic origin. Various ancient colonisations mainly directed from the Indian Ocean to the Atlantic, occurred through the Tethys Sea and around South Africa in periods of lower intensity of the Benguela upwelling. Thermal tolerance, population sizes, dispersal strategies, oceanic currents, substrate preference and land barriers are important factors for dispersal and speciation of marine hydroids.
FIGURE 1 in Additional DNA barcodes confirm recent morphological species concepts and synonymies in Callomyia Meigen (Diptera: Platypezidae)
FIGURE 1. Neighbour-Joining tree of 30 Callomyia specimens and two outgroup specimens with COI sequences ≥550 bp, including sex, unique voucher number, sequence length, geographic locality and GenBank number. Bracketed species names are the current species concepts used in Cumming & Wheeler (2016) and include Nearctic synonyms and misidentifications (shown on branch terminals) that are found in Kessel & Buegler (1972).
Supplementary material 1 from: Martínez-Domínguez L, Nicolalde-Morejón F, Lorea-Hernández FG, Vergara-Silva F, Stevenson DWm (2020) A novelty in Ceratozamia (Zamiaceae, Cycadales) from the Sierra Madre del Sur, Mexico: biogeographic and morphological patterns, DNA barcoding and phenology. PhytoKeys 156: 1-25. https://doi.org/10.3897/phytokeys.156.53502
File S1. GenBank accession numbers of sequences used in the analyses for ITS and matK, respectively. Sequences were generated by this study are in bold.
Supplementary material 2 from: Nugent CM, Adamowicz SJ (2020) Alignment-free classification of COI DNA barcode data with the Python package Alfie. Metabarcoding and Metagenomics 4: e55815. https://doi.org/10.3897/mbmg.4.55815
File S2 – Python script for custom grid search of hyperparameters for optimization of the neural network
Supplementary material 3 from: Nugent CM, Adamowicz SJ (2020) Alignment-free classification of COI DNA barcode data with the Python package Alfie. Metabarcoding and Metagenomics 4: e55815. https://doi.org/10.3897/mbmg.4.55815
File S3 – The parameters utilized in the grid search for each of the five machine learning algorithms tested in the design of the Alfie package
Supplementary material 4 from: Nugent CM, Adamowicz SJ (2020) Alignment-free classification of COI DNA barcode data with the Python package Alfie. Metabarcoding and Metagenomics 4: e55815. https://doi.org/10.3897/mbmg.4.55815
File S4 – Jupyter notebook with tutorial demonstrating how to apply the Alfie classifier in the Python programming language, and how to train custom alignment-free classifiers using the Alfie training module
Evaluating the genetic variation of the COI gene of Insecta: Implications for DNA barcoding, metabarcoding and species delimitation studies
<p>The genetic variation of the COI gene has a great effect on the final results of the species delimitation studies. However, little research has comprehensively investigated the genetic divergence in COI among Insecta. The fast-growing COI data in BOLD provide an opportunity for comprehensively appraising the genetic variation in COI among Insecta. We calculated the K2P distance of 64,414 insect species downloaded from BOLD. The match ratios of the clustering analysis based on different thresholds were compared among 4,288 genera (35,068 species). Besides, we also compared the match ratios obtained from two species delimitation methods: the clustering analysis (distance-based method) and the bPTP analysis (tree-based method). Furthermore, the effectiveness of two different results of the bPTP analysis: bPTP_h and bPTP_ml was also tested. Approximately one-quarter of the species of Insecta showed high intraspecific genetic variation (> 3%), and a conservative estimate of this value is 12.05-22.58%. The application of empirical thresholds (e.g., 2% and 3%) in the clustering analysis may result in the overestimation of species diversity. In metabarcoding studies, a threshold of 3% can only be used to estimate the insect diversity roughly. As for the clustering analysis, the "threshOpt" or "localMinima" algorithms can provide a priori value for the researcher. Nevertheless, if the minimum interspecific genetic distance of congeneric species was greater than or equal to 2%, it is possible to avoid overestimating the species diversity based on the empirical thresholds. Besides, the match ratios of the bPTP_ml results were higher than those of the bPTP_h results. As for the bPTP analysis, the bPTP_ml results were recommended. If a proper threshold was selected, the clustering analysis may outperform the bPTP analysis.</p>
FIGURES 2A–C. P in Description of larva and female of Polypedilum (Probolum) bullum Zhang & Wang with DNA barcodes
FIGURES 2A–C. P. (Pro.) bullum Zhang & Wang, female. A, wing. B, hypopygium. C, dorsmesal lobe and ventrolateral lobe.
FIGURES 1A–H. P in Description of larva and female of Polypedilum (Probolum) bullum Zhang & Wang with DNA barcodes
FIGURES 1A–H. P. (Pro.) bullum Zhang & Wang, male. A, wing. B, terminal scale of front tibia. C, hypopygium. D–H, superior volsella.
FIGURES 21–27 in Review of the genus Shilovia Makarchenko (Diptera: Chironomidae: Diamesinae Boreoheptagyiini) from the mountains of Central Asia, with morphological description and DNA barcoding of known species
FIGURES 21–27. Shilovia rara Makarchenko (21, 24–25), S. xinhuawangi sp. nov. (22, 27) and S. yakovlevi sp. nov. (23, 26), males. 21–23, gonostylus; 24, inferior volsella and basal lobe of gonocoxite; 25–27, sternapodeme, phallapodeme and aedeagal lobe. Scale bars: 50 µm.
FIGURES 16–20 in Review of the genus Shilovia Makarchenko (Diptera: Chironomidae: Diamesinae Boreoheptagyiini) from the mountains of Central Asia, with morphological description and DNA barcoding of known species
FIGURES 16–20. Shilovia xinhuawangi sp. nov. (16) and S. yakovlevi sp. nov. (17–20), males. 16, legs; 17, basal part of wing; 18, dorsal part of mesonotum; 19, gonocoxite and gonostylus; 20, part of hypopygium in dorsal view. Designations are the same as in Figures 1–9.
FIGURES 28–31 in Review of the genus Shilovia Makarchenko (Diptera: Chironomidae: Diamesinae Boreoheptagyiini) from the mountains of Central Asia, with morphological description and DNA barcoding of known species
FIGURES 28–31. Type localities of Shilovia rara Makarchenko (28–29), S. xinhuawangi sp. nov. (30), and S. yakovlevi sp. nov. (31). 28, Varzob River near Kondara Gorge, Varzod District, Tajikistan (photo by M.V. Vinarski); 29, Itelgi River, Chatkal District, Kyrgyzstan, (photo by E.S. Chertoprud); 30, Daong River, Xinjiang Uygur Autonomous Region, China (photo by M.V. Vinarski); 31, Zhemenei River, East Kazakhstan Region, Kazakhstan (photo by M.V. Vinarski).
Supplementary material 1 from: Kodada J, Jäch MA, Freitag H, Čiamporová-Zaťovičová Z, Goffová K, Selnekovič D, Čiampor Jr F (2020) Ancyronyx lianlabangorum sp. nov., a new spider riffle beetle from Sarawak, and new distribution records for A. pulcherrimus Kodada, Jäch & Čiampor based on DNA barcodes (Coleoptera, Elmidae). ZooKeys 1003: 31-55. https://doi.org/10.3897/zookeys.1003.55541
Table S1. Pairwise genetic distances (Kimura 2-parameter distance) between nucleotide sequences of Ancyronyx and Graphelmis species based on the 648 bp barcoding fragment of COI.
Supplementary material 4 from: Kodada J, Jäch MA, Freitag H, Čiamporová-Zaťovičová Z, Goffová K, Selnekovič D, Čiampor Jr F (2020) Ancyronyx lianlabangorum sp. nov., a new spider riffle beetle from Sarawak, and new distribution records for A. pulcherrimus Kodada, Jäch & Čiampor based on DNA barcodes (Coleoptera, Elmidae). ZooKeys 1003: 31-55. https://doi.org/10.3897/zookeys.1003.55541
Table S3. Pairwise genetic distances (p-distance) between 29 amino acid sequences (216 positions) of Ancyronyx species and the genus Graphelmis (outgroup).
Supplementary material 2 from: Kodada J, Jäch MA, Freitag H, Čiamporová-Zaťovičová Z, Goffová K, Selnekovič D, Čiampor Jr F (2020) Ancyronyx lianlabangorum sp. nov., a new spider riffle beetle from Sarawak, and new distribution records for A. pulcherrimus Kodada, Jäch & Čiampor based on DNA barcodes (Coleoptera, Elmidae). ZooKeys 1003: 31-55. https://doi.org/10.3897/zookeys.1003.55541
Table S2. DNA barcoding patterns of the variable nucleotide positions in the 648 bp long COI sequence alignment of the Ancyronyx pulcherrimus clade.
Figs 1–6 in Alleviating the taxonomic impediment of DNA barcoding and setting a bad precedent: names for ten species of 'Astraptes fulgerator' (Lepidoptera: Hesperiidae: Eudaminae) with DNA-based diagnoses
Figs 1–6. Intraspecific variation in final instar larval Astraptes spp. 1–3. A. fruticibus 03-SRNP-14690, 05-SRNP-45170, 03-SRNP-30304; 4–6. A. inflatio 02-SRNP-32206, 05-SRNP-96, 02-SRNP-24519; images from Janzen & Hallwachs (2009), which the authors have indicated are in the public domain (Janzen et al., 2009).
FIGURE 9 in DNA barcodes, morphology and geographic distribution confirm a new butterfly species in the genus Rhamma (Lepidoptera: Lycaenidae)
FIGURE 9. Neighbor Joining identification tree. Rhamma eleonorae sp. nov sequences are denoted as: Rhamma sp 1 BMC16124 and 22302. Note the placement of Rhamma arria from Llanos de Cuiva. The distances were computed using the Kimura 2-parameter method (Kimura 1980) and are in the units of the number of base substitutions per site. The analysis involved 42 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 577 positions in the final dataset. Analyses were conducted in MEGA7 (Kumar et al. 2016).
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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.