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85 results for “Barcoding analysis”
BARCODE: high throughput screening and analysis of soft active materials
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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.
Data from: Comparison of diets for largemouth and smallmouth bass in Eastern Lake Ontario using DNA barcoding and stable isotope analysis
Largemouth (LMB: Micropterus salmoides) and Smallmouth Bass (SMB: Micropterus dolomieu) are important species in the recreational fisheries of the Laurentian Great Lakes. The invasion of the Round Goby (Neogobius melanostomus) into these lakes has changed several facets of black bass biology, but there is still much to learn about the relationship between these species. Previous dietary analyses have shown Round Goby to be important prey for bass, but have been limited by low visual identification rates of dissected stomach items. Within the present study, DNA barcoding and stable isotope analysis improve prey identification and provide a more quantitative dietary analysis of adult black bass in Lake Ontario, comparing the importance of Round Goby as prey between these two species. Eighty-four LMB (406mm fork length ±4mm SEM) and two hundred sixty-four SMB (422mm ±2mm) obtained as tournament mortalities had prey identified using DNA-based methods. Round Goby was the most prevalent prey species for both predators. The diet of LMB was three times more diverse than that of SMB, which almost entirely consists of Round Goby. Our results provide further support that recent increases in the size of Lake Ontario bass are a result of Round Goby consumption, and that the effects of this dietary shift on body condition are greater for SMB. Techniques developed in this study include: reverse-oriented dual priming oligonucleotides used as blocking primers for predator DNA, and an automated design approach of restriction fragment length polymorphism tests for identifying prey DNA barcodes.
FIGURE 10 in DNA barcode based phylogeographic analysis of the Aricia anteros (Freyer, 1838) species complex (Lepidoptera: Lycaenidae) with description of a new subspecies from SE Europe
FIGURE 10. Aricia anteros kalmius ssp. nov., butterflies of the second generation in nature. A, male, near Orlovskoe village, 1 August 2023. B, male, near Orlovskoe village, 1 August 2023. C, female, near Orlovskoe village, 1 August 2023. Photo: R. Botman.
FIGURE 9 in DNA barcode based phylogeographic analysis of the Aricia anteros (Freyer, 1838) species complex (Lepidoptera: Lycaenidae) with description of a new subspecies from SE Europe
FIGURE 9. Aricia anteros kalmius ssp. nov., butterflies of the first generation in nature. A, male, near Pyshchevyk village,11 May 2008. B, male, near Orlovskoe village, 15 May 2021. C, female on Sedum sp., near Pyshchevyk village, 01 June 2006. Photo: R. Botman.
FIGURE 8 in DNA barcode based phylogeographic analysis of the Aricia anteros (Freyer, 1838) species complex (Lepidoptera: Lycaenidae) with description of a new subspecies from SE Europe
FIGURE 8. The host plant of A. anteros kalmius ssp. nov. Beketov's storksbill (Erodium beketowii Schmalh). 5 May 2020. Photo: R. Botman.
FIGURE 6 in DNA barcode based phylogeographic analysis of the Aricia anteros (Freyer, 1838) species complex (Lepidoptera: Lycaenidae) with description of a new subspecies from SE Europe
FIGURE 6. Male genitalia of A. anteros kalmius ssp. nov. (specimen VL629 is shown). A Lateral view. B. Right valve, internal view and left valve, dorsal view. C. Uncus and branches of the gnathos, dorsal view.
FIGURE 5 in DNA barcode based phylogeographic analysis of the Aricia anteros (Freyer, 1838) species complex (Lepidoptera: Lycaenidae) with description of a new subspecies from SE Europe
FIGURE 5. Species of the subgenus Aricia (Ultraaricia). Males. A–B, A. anreros dombaiensis, Georgia, Tiliabuli Mt, 2150–2500 m, 41.53861°N, 43.62806°E, 29 June 2013, V.Lukhtanov leg. C–D, Lectotype of A. crassipuncta, [Turkey], Kasikoporan, 01 July 1883, [Chr]istoph leg. E–F, A. bassoni, Israel, Anti-Lebanon Mts Range, Hermon Mt, 33.285°N, 35.7619°E, 1400–1450m, 2 May 2016. G–H, A. vandarbani, Azerbaijan, Talysh Mts, Lerik, 1000 m, 38.78°N, 48.43°E, 27 July 2003, V. Lukhtanov leg. Scale = 2 cm.
FIGURE 4. Aricia anteros kalmius ssp. nov. A–B in DNA barcode based phylogeographic analysis of the Aricia anteros (Freyer, 1838) species complex (Lepidoptera: Lycaenidae) with description of a new subspecies from SE Europe
FIGURE 4. Aricia anteros kalmius ssp. nov. A–B, Holotype, VL626, ♂, Donetsk Region, Orlovskoe, 47.260°N, 37.743°E, 01 Aug 2023 R.V.Botman. C–D, VL628, Paratype, ♂, Donetsk Region, Orlovskoe, 47.260°N, 37.743°E, 01 Aug 2023 R.V.Botman. E–F, Paratype, ♀, Donetsk Region, Orlovskoe, 47.260°N, 37.743°E, 01 Aug 2023 R.V.Botman. G–H, ♂, Donetsk Region, Mariupol district, 117 km SSE from the centre of Donetsk, left bank of the Kalmius river, Pyshchevyk vill. 47.242°N, 37.794°E, 16 June 2010, R. Botman leg. I–J, ♀, Donetsk Region, Mariupol district, 117 km SSE from the centre of Donetsk, left bank of the Kalmius river, Pyshchevyk vill. 47.242°N, 37.794°E, 16 June 2010, R. Botman leg. Scale = 2 cm.
FIGURE 2 in DNA barcode based phylogeographic analysis of the Aricia anteros (Freyer, 1838) species complex (Lepidoptera: Lycaenidae) with description of a new subspecies from SE Europe
FIGURE 2. The TCS haplotype network of the samples of the A. anteros species complex. Circles are proportional to sample size for each haplotype. Smallest black dots represent unsampled but predicted haplotypes, and mutations are shown as dashes. The species and subspecies clusters are highlighted in different colors. The first three letters of a species or subspecies name are used to designate the haplogroups Ant, Bas, Cra, Dom, Kal, Var, and Van.
FIGURE 3. A in DNA barcode based phylogeographic analysis of the Aricia anteros (Freyer, 1838) species complex (Lepidoptera: Lycaenidae) with description of a new subspecies from SE Europe
FIGURE 3. A map that schematically shows the distribution of taxa included in the A. anteros species complex. The map is based on the work of Hesselbarth et al. (1995), ten Hagen & Schurian (2009) and original data.
FIGURE 1 in DNA barcode based phylogeographic analysis of the Aricia anteros (Freyer, 1838) species complex (Lepidoptera: Lycaenidae) with description of a new subspecies from SE Europe
FIGURE 1. The Bayesian tree of the Aricia anteros species complex based on analysis of the mitochondrial COI barcodes. Numbers at nodes indicate Bayesian posterior probabilities (BPP) (higher than 0.5). The number after the name of the haplotype means the number of identified specimens with this haplotype. The species and subspecies clusters are highlighted in different colors. V is Aricia vandarbani. 1, 2, 3 and 4 are the major clades (see the text).
FIGURE 11. Identification tree. Neighbor-Joining analysis involving 20 in Six new species of Afrotropical Allodia (Diptera: Mycetophilidae): DNA barcodes indicate recent diversification with a single origin
FIGURE 11. Identification tree. Neighbor-Joining analysis involving 20 CO1 sequences. Evolutionary distances were calculated using the p-distance model. Abbreviations: M = male, F = female. Sequences retrieved from BOLD (Ratasingham & Hebert 2007) are labelled with Process ID (see Appendix 1). See methods for details.
Figure 3 in Detailed integrative taxonomic analysis reveals large-scale species misidentification of barnacles based on DNA barcoding data
Figure 3. Neighbour-joining tree for the three investigated barcode index numbers. Ŋe coloured sequences in each clade indicate our newly generated sequences of specimens with unequivocal morphological identification.
Figure 2 in Detailed integrative taxonomic analysis reveals large-scale species misidentification of barnacles based on DNA barcoding data
Figure 2. Morphology of unidentified Balanus sp. individuals of clade A (BOLD:AAG0069) (A), Balanus balanus (B), Balanus crenatus
Figure 1 in Detailed integrative taxonomic analysis reveals large-scale species misidentification of barnacles based on DNA barcoding data
Figure 1. Bubble plot of the correspondence between species assignments and the barcode index number (BIN; genetic clade). Ŋe size of the bubbles corresponds to the number of sequences contained in each combination of BIN and species assignment. Vertical lines highlight BINs that contain more than one species assignment, and horizontal lines highlight species assignments that are present in more than one BIN. Grey bubbles indicate a one-to-one match between BIN and species assignment. Coloured bubbles represent the three BINs that were investigated further by integrative taxonomic analysis.
FIGURE 2. Barcode Gap analysis between Ophiocordyceps nutans and O in Ophiocordyceps neonutans sp. nov., a new neotropical species from O. nutans complex (Ophiocordycipitaceae, Ascomycota)
FIGURE 2. Barcode Gap analysis between Ophiocordyceps nutans and O. neonutans based on the intraspecific and interspecific distances based on ITS region. Each dot represents a pairwise comparison. All interspecific pairwise comparisons are plotted in the column "A" and all intraspecifc ones are plotted in the column "B" of the axis X. Genetic distances are plotted in the axis Y.
FIGURES 78–83 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 78–83. Immature stages of South African Gracillariidae. 78, Phodoryctis tephrosiella, mines on Tephrosia rhodesica (Fabaceae). Gauteng, Tshwane, A. Sharp leg. 79, Conopobathra carbunculata, mines on Peltophorum africanum (Fabaceae), Limpopo, York, A. & I. Sharp leg. 80, Phyllonorycter grewiella, mine on Grewia hexamita (Malvaceae), A. & I. Sharp leg. 81, P. pseudogrewiella sp. nov., mines on Grewia flavescens (Malvaceae), Limpopo, Hoedspruit, A. & I. Sharp leg. 82, P. pseudogrewiella sp. nov., larva, ibidem. 83, P. pseudogrewiella sp. nov., mines and pupae, ibidem.
FIGURES 67–72 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 67–72. Immature stages of South African Gracillariidae. 67, Conopomorphina aptata, mine on Schotia brachypetala (Fabaceae), Limpopo, Hoedspruit, A. & I. Sharp leg. 68, Acrocercops syzygiena, mine on Syzygium cordatum (Myrtaceae), Gauteng, Tshwane, A. & I. Sharp leg. 69, A. syzygiena, larva, ibidem. 70, A. combreticola, mine on Combretum zeyheri (Combretaceae) Gauteng, Tshwane, A. Sharp leg. 71, Cryptolectica capnodecta, larva on Syzygium cordatum (Myrtaceae), Limpopo, Hoedspruit, A. & I. Sharp leg. 72, C. terminalina, mine on Terminalia sericea (Combretaceae), A. & I. Sharp leg.
FIGURES 84−88 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 84−88. Immature stages of South African Gracillariidae species. 84, Cameraria melhaniella sp. nov., larva on Melhania acuminata (Malvaceae), Limpopo, Hoedspruit, A. & I. Sharp leg. 85, Metriochroa pergulariae, mine on Pergularia daemia (Apocynaceae), Limpopo, Hoedspruit, A. & I. Sharp leg. 86, Phyllocnistis allisonae, mine on Protea rubropilosa (Proteaceae), Limpopo, Lopez Vaamonde leg. 87, Phyllocnistis magalismontani sp. nov., mine on Englerophytum magalismontanum (Sapotaceae), Limpopo, Hoedspruit, leg. A. & I. Sharp. 88, Phyllocnistis faureae, mine on Faurea saligna (Proteaceae), Gauteng, Tshwane, leg. A. Sharp.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.