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4,144 results for “ITS barcode”
Figure 5 in DNA barcoding and coalescent-based delimitation of endosymbiotic clevelandellid ciliates (Ciliophora: Clevelandellida): a shift to molecular taxonomy in the inventory of ciliate diversity in panesthiine cockroaches
Figure 5. Putative secondary structure models of the highly divergent helix 23e1 in the V4 region of the 18S rRNA molecule of 17 species of the order Clevelandellida isolated from the digestive tract of cockroaches. Arrowheads denote the molecular diagnostic characters.
FIGURE 1 in DNA barcoding reveals new records of invasive terrestrial flatworms (Platyhelminthes, Tricladida, Geoplanidae) in the Macaronesian region
FIGURE 1. Maximum-likelihood tree of invasive terrestrial flatworms, based on COI sequences. Bootstrap values are presented only for main clades. Countries are indicated after GenBank accession number. Red: specimens sequenced in this study. A. Caenoplana coerulea tree. B. Endeavouria septemlineata tree. C. Obama nungara tree.
FIGURE 13 in DNA barcoding of Sclerogibbidae and confirmation of the opposite sexes of Sclerogibba berlandi Benoit (Hymenoptera: Sclerogibbidae)
FIGURE 13. NJ tree based on 623bp COI sequences. The numbers in the tree indicate bootstrap values from 1,000 replicates. JN = unidentified species from Belize, probably belonging to Probethylus. KY = unidentified species from Pakistan M = male. F = female.
FIGURES 1–4. Sclerogibba berlandi Benoit. 1–2 in DNA barcoding of Sclerogibbidae and confirmation of the opposite sexes of Sclerogibba berlandi Benoit (Hymenoptera: Sclerogibbidae)
FIGURES 1–4. Sclerogibba berlandi Benoit. 1–2, ♀ (A1) in dorsal (1) and lateral (2) view. 3–4, ♂ (A2) in dorsal (3) and lateral (4) view. Specimens from Abu Dhabi, Houbara Protected Area. Scale bar: 1.6 mm for 1; 1.7 mm for 2; 2.6 mm for 3; 1.3 mm for 4.
FIGURES 9–12. 9–10 in DNA barcoding of Sclerogibbidae and confirmation of the opposite sexes of Sclerogibba berlandi Benoit (Hymenoptera: Sclerogibbidae)
FIGURES 9–12. 9–10, Sclerogibba crassifemorata Riggio & De Stefani-Perez: ♂ (A5) from Abu Dhabi, Houbara Protected Area, in dorsal (9) and lateral (10) view. 11–12, Caenosclerogibba longiceps (Richards), ♀ (A9) from Japan, Kyushu Island, Kagoshima Pref., Shiroyama, in dorsal (11) and lateral (12) view. Scale bar: 0.9 mm for 9; 1.1 mm for 10; 0.6 mm for 11 and 12.
FIGURES 5–8. 5–6 in DNA barcoding of Sclerogibbidae and confirmation of the opposite sexes of Sclerogibba berlandi Benoit (Hymenoptera: Sclerogibbidae)
FIGURES 5–8. 5–6, Sclerogibba talpiformis Benoit: ♂ (A6) from Abu Dhabi, Houbara Protected Area, in dorsal (5) and lateral (6) view. 7–8, Sclerogibba rossi Olmi: ♀ (A8) from Japan, Okinawa-jima Isl., Mihama, in dorsal (7) and lateral (8) view. Scale bar: 1.9 mm for 5; 1.6 mm for 6; 0.9 mm for 7 and 8.
Barcoded Bulk QTL mapping reveals highly polygenic and epistatic architecture of complex traits in yeast
<p>Mapping the genetic basis of complex traits is critical to uncovering the biological mechanisms that underlie disease and other phenotypes. Genome-wide association studies (GWAS) in humans and quantitative trait locus (QTL) mapping in model organisms can now explain much of the observed heritability in many traits, allowing us to predict phenotype from genotype. However, constraints on power due to statistical confounders in large GWAS and smaller sample sizes in QTL studies still limit our ability to resolve numerous small-effect variants, map them to causal genes, identify pleiotropic effects across multiple traits, and infer non-additive interactions between loci (epistasis). Here, we introduce barcoded bulk quantitative trait locus (BB-QTL) mapping, which allows us to construct, genotype, and phenotype 100,000 offspring of a budding yeast cross, two orders of magnitude larger than the previous state of the art. We use this panel to map the genetic basis of eighteen complex traits, finding that the genetic architecture of these traits involves hundreds of small-effect loci densely spaced throughout the genome, many with widespread pleiotropic effects across multiple traits. Epistasis plays a central role, with thousands of interactions that provide insight into genetic networks. By dramatically increasing sample size, BB-QTL mapping demonstrates the potential of natural variants in high-powered QTL studies to reveal the highly polygenic, pleiotropic, and epistatic architecture of complex traits.</p>
DNA barcode analyses improve accuracy in fungal species distribution models
<p class="western"><span>Species distribution models based on environmental predictors are useful to explain a species geographic range. For many groups of organisms, including fungi, the increase of occurrence data sets has generalized their use. However, fungal species are not always easy to distinguish, and taxonomy of many groups is not completely settled. This study explores the effect of taxonomic uncertainty in databases used for modeling fungal distributions. We analyze distribution models for three morphospecies from the corticioid genus <i>Xylodon</i> (Hymenochaetales, Basidiomycota), comparing models based on species names on vouchers specimens with models derived from species identified by DNA barcode. Differences in the contribution of predictors driving the distribution of each modeled taxon and the extent of their ranges were studied. Records under <i>X</i><i>ylodon</i><i> paradoxus</i>, <i>X</i>.<i> flaviporus</i> and <i>X</i>. <i>raduloides</i> were obtained from fungarium collections and GenBank repository. Two grouping criteria were used: (1) specimens were grouped by their collection or sequence voucher names and (2) specimens were grouped following molecular identification using ITS sequences through barcoding gap species recognition (BGSR). Climatic, geographic and biotic variables were used to predict the potential distribution of each taxon through MaxEnt algorithm. From the three morphospecies selected according to voucher names, up to 19 species candidates were detected using BGSR. Climatic variables were the most important predictors in distribution models made from names on voucher specimens, but their importance decreased when BGSR was applied. In general, the extent of species distributions was more restricted for taxa under BGSR. Our results show that taxonomic uncertainty has a strong effect in <i>Xylodon</i> species distribution models. Misleading results can be obtained when cryptic species or identification errors mask the actual diversity of the presence records. Preserved specimens in natural history collections offer the possibility to assess if the species name on labels matches the current species recognition criteria.</span></p>
FIGURE 6 in Comparisons of two cryptic Ampedus species (Coleoptera: Elateridae) by using classical systematics, ecological niche modeling, and DNA barcoding
FIGURE 6. MaxEnt model outputs for Ampedus samedovi. Minimum Training Presence threshold is applied to outputs.
FIGURE 5 in Comparisons of two cryptic Ampedus species (Coleoptera: Elateridae) by using classical systematics, ecological niche modeling, and DNA barcoding
FIGURE 5. MaxEnt model outputs for Ampedus platiai. Minimum Training Presence threshold is applied to outputs.
FIGURE 2 in Comparisons of two cryptic Ampedus species (Coleoptera: Elateridae) by using classical systematics, ecological niche modeling, and DNA barcoding
FIGURE 2. Distributions and collecting localities of Ampedus platiai and Ampedus samedovi. Red: Distribution of only A. platiai in the provinces, Blue: Distribution of only A. samedovi in the provinces, Yellow: Distribution of A. platiai and A. samedovi in the provinces (The map is designed in ArcGis 10.2).
FIGURE 1 in Comparisons of two cryptic Ampedus species (Coleoptera: Elateridae) by using classical systematics, ecological niche modeling, and DNA barcoding
FIGURE 1. Habitus and aedeagi photos of examined species. A–B. Ampedus platiai, C–D. A. samedovi, E–F. A. pomonae (Aedeagi of A. platiai and A. samedovi are redrawn from Kabalak 2010 and aedeagus of A. pomonae is redrawn from Platia 1994.). BML: Basal struts of median lobe, BP: Basal piece, ML: Median Lobe, PDT: Paramere distal tooth, PR: Paramere.
FIGURE 12 in Morphological description of a new species of Capnia (Plecoptera: Capniidae) with DNA barcoding of genus members from the Russian Far East
FIGURE 12. Bayesian inference (BI) tree based on the cytochrome c oxidase I (COI) nucleotide sequence data of the genus Capnia and outgroup Zwicknia rupprechti Bayesian posterior probabilities (≥0.7) are given above tree nodes and bootstrap support values found in the ML analysis (≥70 %) are shown below nodes. Specimens obtained in this study are in Bold.
FIGURES 4–7 in Morphological description of a new species of Capnia (Plecoptera: Capniidae) with DNA barcoding of genus members from the Russian Far East
FIGURES 4–7. Female of Capnia yavorskayae sp. nov. Paratype. 4. Mesothoracic sclerite, ventral: Bs—basisternum; Fs— furcasternum; Fsa—furcasternal arm; Fsp—furcasternal pit; Kes—katepisternum; Pfs—postfurcasternum; Prs—presternum; PPfs—prothoracic postfurcasternum; Sc—spinasternum; Tn—trochantin. 5–6. Abdominal tip, variation of the subgenital plate. 7. Vaginal complex (cleared) with genital opening, membranous genital cavity, inner tooth-shaped black sclerite.
FIGURES 1–3 in Morphological description of a new species of Capnia (Plecoptera: Capniidae) with DNA barcoding of genus members from the Russian Far East
FIGURES 1–3. Female of Capnia yavorskayae sp. nov. Paratype. 1. Habitus, dorsal. 2. Right forewing. 3. Right hindwing.
FIGURE. Known distribution of Petalidium mannheimerae (black dots; ●) based on specimens in Herbs PRE, PRU, and WIND. Also depicted are the distribution ranges of P. parvifolium (A. blue), P. linifolium (B. green), and P. lucens (C. orange). A black star (★) marks the locality (2220AA) of the lectotype of P. parvifolium (Fleck 548 in Herb. Z+ZT, barcode Z-000000924). A black triangle (▲) indicates the locality (2518DA) of the lectotype of P. parvifolium var. angustifolium (Fleck 520 in Herb. Z+ZR, barcode Z-000033079), considered a synonym of P. linifolium. A black square (■) depicts the locality (2219CB) of the lectotype of P. wilmaniae (Wilman Herb. KMG 1647 in Herb. BOL, barcode BOL138557, #BOL 15287), here considered a synonym of P. parvifolium. in Petalidium mannheimerae (Acanthaceae), a new species from Namibia and South Africa, with notes on the taxonomic identity of P. parvifolium
FIGURE. Known distribution of Petalidium mannheimerae (black dots; ●) based on specimens in Herbs PRE, PRU, and WIND. Also depicted are the distribution ranges of P. parvifolium (A. blue), P. linifolium (B. green), and P. lucens (C. orange). A black star (★) marks the locality (2220AA) of the lectotype of P. parvifolium (Fleck 548 in Herb. Z+ZT, barcode Z-000000924). A black triangle (▲) indicates the locality (2518DA) of the lectotype of P. parvifolium var. angustifolium (Fleck 520 in Herb. Z+ZR, barcode Z-000033079), considered a synonym of P. linifolium. A black square (■) depicts the locality (2219CB) of the lectotype of P. wilmaniae (Wilman Herb. KMG 1647 in Herb. BOL, barcode BOL138557, #BOL 15287), here considered a synonym of P. parvifolium.
FIGURE 19 in Morphology, molecular phylogenetics, and DNA barcoding revealed a new unusual species of the aphid genus Pleotrichophorus from the USA (Insecta, Hemiptera Aphididae)
FIGURE 19. Maximum-likelihood bootstrap consensus tree of Macrosiphini taxa. Pleotrichophorus samples new to this study are highlighted by the peach-colored box. Capitophorus species are highlighted by the blue box. The misidentified specimen of Pleotrichophorus glandulosus specimen reported by Choi et al. (2018) was recovered in a clade along with members of the genus Capitophorus. Support values from left to right are ML ultrafast bootstrap (>95; blue dot), standard non-parametric ML bootstrap (>75; red dot), and MP ultrafast bootstrap (>95; green dot). Nodes without labeled support values indicate that the support value was not significant for that analysis or was not recovered by that analysis.
FIGURE 18. K2P in Morphology, molecular phylogenetics, and DNA barcoding revealed a new unusual species of the aphid genus Pleotrichophorus from the USA (Insecta, Hemiptera Aphididae)
FIGURE 18. K2P neighbor-joining tree of Capitophorus and Pleotrichophorus COI barcodes with auto-collapsed clades with 0.005> average branch length. Collapsed terminal clusters are indicated by red, green, blue, or orange circles. Bootstrap values higher than 80% are indicated on branches with gray circles. Capitophorus species are indicated by blue branches. Pleotrichophorus glandulosus sensu Choi et al. 2018 and Capitophorus sp. from South Korea, China, and California are indicated in orange. Pleotrichophorus species are indicated by red branches. Pleotrichophorus blackmani sp. n., is indicated in green. COI barcodes identified as Pleotrichophorus glandulosus, P. pseudoglandulosus, and P. sp. from France, Russian Far East, and Eastern Canada are indicated in purple.
FIGURE 15 in Morphology, molecular phylogenetics, and DNA barcoding revealed a new unusual species of the aphid genus Pleotrichophorus from the USA (Insecta, Hemiptera Aphididae)
FIGURE 15. SEM of Pleotrichophorus glandulosus (Kaltenbach, 1846): head and body surface: (a) head and pronotum; (b) head trichoid sensilla; (c) trichoid sensilla of abdomen; (d) structure of the sensillum; (e) ultrastructure of the trichoid sensillum socket; (f, g) ultrastructure of the apices of trichoid sensilla; (h) abdominal cuticle surface; (i) ultrastructure of the cuticle surface.
FIGURE 17 in Morphology, molecular phylogenetics, and DNA barcoding revealed a new unusual species of the aphid genus Pleotrichophorus from the USA (Insecta, Hemiptera Aphididae)
FIGURE 17. SEM of Pleotrichophorus glandulosus (Kaltenbach, 1846): apterous viviparous female. mouthparts and legs sensilla: (a, b) URS with trichoid sensilla of two lengths (arrows) and very short type III basiconic sensilla (asterisk); (c) seven pairs of type III basiconic sensilla on the very apical end of URS; (d, e) trichoid sensilla on III FEMUR; (f) trichoid sensilla on the proximal part of III TIBIA; (g) trichoid sensilla on the distal part of III TIBIA; (h) HT I with three ventral setae setae and basal part of HT II with campaniform on the dorsal side (arrow); (i) distal end of HT II with long empodial setae (arrow).
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.