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345 results for “COI barcodes”
FIGURES 14–20 in COI mtDNA barcoding and morphology for species delimitation in the spider genus Ixchela Huber (Araneae: Pholcidae), with the description of two new species from Mexico
FIGURES 14–20. Ixchela zapatai sp. nov. Male: 14–15, Habitus, lateral and dorsal views, respectively. 16, Carapace and chelicerae, frontal view. 17, Chelicerae, frontal view. 18, Chelicerae, lateral view. 19–20, Left palp, prolateral and retrolateral views, respectively. FAC, frontal apophysis of chelicerae, PAB: prolateroventral apophysis of bulb, VPP, ventrobasal protuberance of procursus. Scale bars: 0.5 mm (Fig. 17, 18), 1 mm (Figs 16, 19, 20), 2 mm (Figs 14, 15).
FIGURES 25–30. 25–28 in COI mtDNA barcoding and morphology for species delimitation in the spider genus Ixchela Huber (Araneae: Pholcidae), with the description of two new species from Mexico
FIGURES 25–30. 25–28, Living specimens (females) of Ixchela zapatai sp. nov. from type locality. 29–30, Temperate pine-oak forest at 2399 m.a.s.l. at the type locality (red arrow indicates the microhabitat where the specimens of I. zapatai sp. nov were collected).
FIGURES 3–9 in COI mtDNA barcoding and morphology for species delimitation in the spider genus Ixchela Huber (Araneae: Pholcidae), with the description of two new species from Mexico
FIGURES 3–9. Ixchela panchovillai sp. nov. Male: 3–4, Habitus, lateral and dorsal views, respectively. 5, Carapace and chelicerae, frontal view. 6, Chelicerae, frontal view. 7, Chelicerae, lateral view. 8–9, Left palp, prolateral and retrolateral views, respectively. PAB: prolateroventral apophysis of bulb, SAC: sclerotized apophysis of chelicerae, VAF: ventrodistal apophysis of femur, VPP, ventrobasal protuberance of procursus. Scale bars: 0.5 mm (Figs 6, 7), 1 mm (Figs 5, 8, 9), 2 mm (Figs 3, 4).
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>
Data from: Identification of Swedish mosquitoes based on molecular barcoding of the COI gene and SNP analysis
Mosquito-borne infectious diseases are emerging in many regions of the world. Consequently, surveillance of mosquitoes and concomitant infectious agents is of great importance for prediction and prevention of mosquito-borne infectious diseases. Currently, morphological identification of mosquitoes is the traditional procedure. However, sequencing of specified genes or standard genomic regions, DNA barcoding, has recently been suggested as a global standard for identification and classification of many different species. Our aim was to develop a genetic method to identify mosquitoes and to study their relationship. Mosquitoes were captured at collection sites in northern Sweden and identified morphologically before the cytochrome c oxidase subunit I (COI) gene sequences of 14 of the most common mosquito species were determined. The sequences obtained were then used for phylogenetic placement, for validation and benchmarking of phenetic classifications, and finally to develop a hierarchical PCR-based typing scheme based on single nucleotide polymorphism sites (SNPs) to enable rapid genetic identification, circumventing the need for morphological characterization. The results showed that exact phylogenetic relationships between mosquito taxa were preserved at shorter evolutionary distances, but at deeper levels they could not be inferred with confidence by using COI gene sequence data alone. Fourteen of the most common mosquito species in Sweden were identified by the SNP/PCR-based typing scheme, demonstrating that genetic typing using SNPs of the COI gene is a useful method for identification of mosquitoes with potential for worldwide application.
Mitochondrial DNA tree for COI sequences (DNA barcode) of the goby genus Trimma.
<p>Mitochondrial DNA tree for COI sequences (DNA barcode) of the goby genus Trimma</p>
FIGURE 8 in Oziella sibirica (Acari: Eriophyoidea: Phytoptidae), a new eriophyoid mite species described using confocal microscopy, COI barcoding and 3 D surface reconstruction
FIGURE 8. CLSM image of the internal genitalia of Oziella sibirica sp. nov. A. Spermatheca; B. Pre-spermathecal swelling (distal segment of spermathecal tube); C. Proximal segment of spermathecal tube; D. Longitudinal bridge; E. Transverse apodeme; F. Laterodistal fold of transversal apodeme.
FIGURE 6 in Oziella sibirica (Acari: Eriophyoidea: Phytoptidae), a new eriophyoid mite species described using confocal microscopy, COI barcoding and 3 D surface reconstruction
FIGURE 6. Oziella sibirica sp. nov., nymph. A. Dorsal view of the mite; B. Ventral view; C. Prodorsal shield; D. Coxigenital area; E. Right leg I (arrow indicates a spine); F. Right leg II; G. Typical 4/3-rayed empodium; H. Typical 4/4-rayed empodium; I. Abnormal empodium. Scale bar: A & B = 140; C & D = 50; E & F = 45; G, H & I = 12.
FIGURE 1. 3D in Oziella sibirica (Acari: Eriophyoidea: Phytoptidae), a new eriophyoid mite species described using confocal microscopy, COI barcoding and 3 D surface reconstruction
FIGURE 1. 3D model of Oziella sibirica sp. nov. prodorsal shield (the same female as Fig. 2C). A. Gray scale prodorsal shield, B. Colourised prodorsal shield (notifications of lines follows that of Amrine et al. 1994 & Amrine et al. 2003; admedian lines colourised in red, additional line between admedian and submedian-2 line colourised in black). Scale bar A & B = 30 mkm. Note: setae ve and c1 are short on images A & B because only proximal parts of the setae of eriophyoid mites can be observed on CLSM images using blue laser, 405 nm (Chetverikov 2012b).
FIGURE 2 in Oziella sibirica (Acari: Eriophyoidea: Phytoptidae), a new eriophyoid mite species described using confocal microscopy, COI barcoding and 3 D surface reconstruction
FIGURE 2. Variation of the prodorsal shield design among four females of Oziella sibirica sp. nov. (black & white inverted CLSM images). Admedian lines colourised in red (A & D), additional lines in green (B) and red (C; the same female as in Fig. 2A & 2B). Scale bar = 30 mkm.
FIGURE 4 in Oziella sibirica (Acari: Eriophyoidea: Phytoptidae), a new eriophyoid mite species described using confocal microscopy, COI barcoding and 3 D surface reconstruction
FIGURE 4. Microphotographs under light phase contrast microscopy (A & B) and CLSM (C & D) of Oziella sibirica sp. nov. A. Coxigenital region; B. Female prodorsal shield (arrows indicate the eye-like structures); C. Position and view of internal genitalia inside female; D. Epiandrium on male venter. Scale bar A, B, C, D = 20 mkm.
FIGURE 9 in Oziella sibirica (Acari: Eriophyoidea: Phytoptidae), a new eriophyoid mite species described using confocal microscopy, COI barcoding and 3 D surface reconstruction
FIGURE 9. Morphometrics of the internal genitalia of Oziella sibirica sp. nov. Length (A–B) and width (C–D) of spermatheca; length (E–F) and width (G–H) of prespermathecal swelling (distal segment of spermathecal tube); length (I–J) of proximal segment of spermathecal tube; length (J–K) of longitudinal bridge; half-length (K–L) of genital apodeme; maximal distance between left and right parts of transversal apodeme (L–M).
FIGURE 3 in Oziella sibirica (Acari: Eriophyoidea: Phytoptidae), a new eriophyoid mite species described using confocal microscopy, COI barcoding and 3 D surface reconstruction
FIGURE 3. Oziella sibirica sp. nov., female. A. Ventral view of the mite, B. Coxigenital area, C. Female prodorsal shield; D. Female internal genitalia, E. Empodium; F. Epiandrium, G. Leg I (arrow indicates a spine), H. Leg II. Scale bar: A = 130; B & C = 45; D = 35; E = 15; F = 45; G & H = 35.
FIGURE 5 in Oziella sibirica (Acari: Eriophyoidea: Phytoptidae), a new eriophyoid mite species described using confocal microscopy, COI barcoding and 3 D surface reconstruction
FIGURE 5. Oziella sibirica sp. nov., larva. A. Ventral view; B. Prodorsal shield and anterior part of opisthosoma; C. Coxisternal area and anteroventral region of opisthosoma; D. Right leg I, dorsal view; E. Right leg II, dorsal view; F. Typical 4/3-rayed empodium. Scale bar: A = 100; B & C = 45; D & E = 35; F = 10.
FIGURE 1. Neighbour joining COI gene tree using uncorrected p in Description of two final stadium platystictid larvae from Borneo, including that of Drepanosticta? attala Lieftinck, identified using DNA barcoding (Odonata: Zygoptera: Platystictidae)
FIGURE 1. Neighbour joining COI gene tree using uncorrected p–distance for Drepanosticta attala and D. barbatula adults and larva plus related platystictid taxa with Sinosticta hainanense as outgroup. All voucher specimens except that of D. barbatula have a six digit collection number with an RMNH.INS. prefix; this prefix is omitted in the figure for clarity.
FIGURE 1. Neighbour-joining COI gene tree using uncorrected p in Description of the final stadium larvae of Onychargia atrocyana Selys, 1865 from Sarawak, identified using DNA barcoding (Odonata: Zygoptera: Platycnemididae), with an overview of larval characters in the Platycnemididae
FIGURE 1. Neighbour-joining COI gene tree using uncorrected p-distance for Onychargia atrocyana using Paracnemis alluaudi and Podolestes harrissoni as outgroups. All voucher specimens have a six-digit collection number with an RMNH.INS. prefix; this prefix is omitted in the figure for clarity.
Figure 1. Neighbour joining COI gene tree using uncorrected p in Description of larvae of two species of Coeliccia Selys, 1865 from Sarawak, identified using DNA barcoding (Odonata: Platycnemididae)
Figure 1. Neighbour joining COI gene tree using uncorrected p-distance for species of the Coeliccia borneensis-group, including both adults and larvae of C. campioni and C.flavostriata, and their sampling sites (except for Lestes dissimulans all from Sarawak, East Malaysia). Coeliccia didyma and Lestes dissimulans are used as outgroups.
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Allen Brain Atlas
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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.