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3,292 results for “DNA Barcode”
Figure 1 from: Jordaens K, Sonet G, Braet Y, de Meyer M, Backeljau T, Goovaerts F, Bourguignon L, Desmyter S (2013) DNA barcoding and the differentiation between North American and West European Phormia regina (Diptera, Calliphoridae, Chrysomyinae). ZooKeys 365: 149-174. https://doi.org/10.3897/zookeys.365.6202
Figure 1 - Lateral (top) and dorsal (bottom) view of the male copulatory organs of Phormia regina from W Europe (left) and N America (right) with a detail of the penis (middle).
Supplementary figure 3 from: Jordaens K, Sonet G, Braet Y, de Meyer M, Backeljau T, Goovaerts F, Bourguignon L, Desmyter S (2013) DNA barcoding and the differentiation between North American and West European Phormia regina (Diptera, Calliphoridae, Chrysomyinae). ZooKeys 365: 149-174. https://doi.org/10.3897/zookeys.365.6202
Supplementary figure 3 - Neighbour-Joining tree (p-distances) of a 633 bp fragment of the nuclear 28S gene. Bootstrap values ≥ 70% are shown at the nodes. N gives the number of specimens of that haplotype. EU = Phormia regina haplotypes from W Europe; NA = Phormia regina haplotypes from N America.
Figure 3 from: Stahls G, Laiho J (2013) DNA barcodes identify Central-Asian Colias butterflies (Lepidoptera, Pieridae). ZooKeys 365: 175-196. https://doi.org/10.3897/zookeys.365.5879
Figure 3 - Neighbour-Joining tree using the Tamura-Nei model with gamma distributed rates for the RpS2 sequences.
Figure 2 from: Mankga L, Kowiyou Y, Moteetee A, Daru B, van der Bank M (2013) Efficacy of the core DNA barcodes in identifying processed and poorly conserved plant materials commonly used in South African traditional medicine. ZooKeys 365: 215-233. https://doi.org/10.3897/zookeys.365.5730
Figure 2 - Evaluation of barcode gaps in matK, rbcLa and rbcLa + matK for commonly used medicinal plants of South Africa. A Boxplots indicate the genetic variation between interspecific distance and intraspecific distance; the boxplots clearly shows significant differences between inter- and intraspecific distances for all gene regions tested (P < 0.001; see text) B Lineplot of the barcode gap for the commonly used plants in South African medicine. For each gene region, the grey lines correspond to the furthest intraspecific distance (bottom of line value), and the closest interspecific distance (top of line value). The red lines show where this relationship is reversed, i.e. cases where there is no barcode gap.
Figure 3 from: Marescaux J, Van Doninck K (2013) Using DNA barcoding to differentiate invasive Dreissena species (Mollusca, Bivalvia). ZooKeys 365: 235-244. https://doi.org/10.3897/zookeys.365.5905
Figure 3 - RFLP analysis of the COI gene to distinguish Dreissena rostriformis bugensis (Q haplotype) and Dreissena polymorpha (Z haplotype) using the endonucleases (A) Nla IV (B) Hinf I (C) Nla III and (D) Scr FI. Lane 1, 1-kb ladder; lane 2, non-digested fragment of quagga mussel; lane 3, Q1 haplotype; lane 4, Q2 haplotype; lane 5, Z1 haplotype; lane 6, Z2 haplotype; lane 7, Z3 haplotype; lane 8, Z4 haplotype; lane 9, Z5 haplotype; lane 10, 100-bp ladder.
Figure 1 from: Marescaux J, Van Doninck K (2013) Using DNA barcoding to differentiate invasive Dreissena species (Mollusca, Bivalvia). ZooKeys 365: 235-244. https://doi.org/10.3897/zookeys.365.5905
Figure 1 - Barcoding analysis based on a fragment of 654 base pairs of the COI gene. a) NJ analysis of K2P-pairwise distances b) "barcoding gap" method based on the K2P-pairwise distance.
Figure 1 from: Mankga L, Kowiyou Y, Moteetee A, Daru B, van der Bank M (2013) Efficacy of the core DNA barcodes in identifying processed and poorly conserved plant materials commonly used in South African traditional medicine. ZooKeys 365: 215-233. https://doi.org/10.3897/zookeys.365.5730
Figure 1 - Examples ofmedicinal herbs bought at Faraday muthi market in Johannesburg A different medicinal herbs in bags B Seeds of Entada rheedii (tindili) C mixed herbs (fembo) D A twig of Adenia gummifera (mphinde umshaye) E Barks of Vachellia sp. (umkhanya-kute) F Bulb of Boophane disticha (umqotho) G mixed herbs H Myrothamnus flabellifolius (vuka) I Barks of Vachellia sp. (umkhanya-kute) J Sarcostemma viminale (ube nam) K Plant of Clivia sp. (mayime) L Stangeria eriopus (imfingo) M mixed herbs (isihlalakahle) N Tuber (umbonsi) O Helichrysum sp. (impepo) and P Twigs of Synadenium cupulare (umdletshane). Names in brackets are vernacular names in isiZulu.
Figure 2 from: Marescaux J, Van Doninck K (2013) Using DNA barcoding to differentiate invasive Dreissena species (Mollusca, Bivalvia). ZooKeys 365: 235-244. https://doi.org/10.3897/zookeys.365.5905
Figure 2 - Haplotype networks based on a fragment of 654 base pairs of the COI gene. Our seven haplotypes are labelled: Q1 and Q2 for haplotypes 1 and 2 (belonging to Dreissena rostriformis bugensis) / Z1 to Z5 for the 5 other haplotypes (belonging to Dreissena polymorpha).
Figure 3 from: Miller J, Beentjes K, van Helsdingen P, IJland S (2013) Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol. ZooKeys 365: 245-261. https://doi.org/10.3897/zookeys.365.5787
Figure 3 - DNA concentration (log10 transformed) for specimens in the time series study that yielded or failed to yield a successful DNA barcode sequence arranged by A body size B year collected. Successes (filled circles) and failures (while circles) partitioned into destructive (red) and nondestructive (blue) DNA extraction methods.
Figure 2 from: Sonet G, Nagy Z, Mortelmans J, Vandewynkel C, Grootaert P (2013) Using DNA barcodes for assessing diversity in the family Hybotidae (Diptera, Empidoidea). ZooKeys 365: 263-278. https://doi.org/10.3897/zookeys.365.6070
Figure 2 - Subtrees showing cases where ranges of intra- and interspecific distances do not seem consistent with the current taxonomy and would require more investigation. See details in text. Circles represent branch supports. Bootstrap values are according to circles' size, bootstrap values are shown in numbers when > 80%.
Figure 2 from: Miller J, Beentjes K, van Helsdingen P, IJland S (2013) Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol. ZooKeys 365: 245-261. https://doi.org/10.3897/zookeys.365.5787
Figure 2 - Sequencing success for the time series study of 31 spider species frequently collected in the Netherlands. Data for each species arranged horizontally along a time axis (year of collection). Small circles represent standard destructive extraction; outer circle represents nondestructive extraction. Red small circle and blue outer circle indicate successful sequencing, unfilled circles represent failed attempts; half-filled circle indicates mixed success among multiple specimens for that species and year. Solid horizontal lines extend from the present to the oldest successful DNA barcode based on destructive extraction for each species; where nondestructive extraction yielded successful DNA barcode from older specimens, this is indicated by a dashed line. Data are arranged according to a neighbour joining tree (A) or by species body size (B). Spider families and major lineages (Orbiculariae and 'RTA' clade) are indicated in A. AGE Agelenidae AMA Amaurobiidae ARA Araneidae CLU Clubionidae COR Corinnidae LIN Linyphiidae LYC Lycosidae PHI Philodromidae PIS Pisauridae SAL Salticidae THD Theridiidae THO Thomisidae ZOR Zoridae.
Figure 1 from: Miller J, Beentjes K, van Helsdingen P, IJland S (2013) Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol. ZooKeys 365: 245-261. https://doi.org/10.3897/zookeys.365.5787
Figure 1 - A Sequencing success profile for specimens included in this study. Data are species attempted, all specimens in the study including the time series, and fresh specimens collected in 2010 or later. Success expressed as a percentage appears on the blue (success) portion of each bar B Sequencing success rates for fresh (collected 2010 or later) and older specimens grouped by decade. Data given for all extractions regardless of method, and also partitioned into destructive and nondestructive extraction methods. Total number of specimens attempted and the subset of specimens attempted using nondestructive extraction given in parentheses. Note that the relatively high success rate for nondestructive extractions of specimens from the 1960s is based on two successes out of four attempts.
Figure 2 from: Sonet G, Jordaens K, Nagy Z, Breman F, de Meyer M, Backeljau T, Virgilio M (2013) Adhoc: an R package to calculate ad hoc distance thresholds for DNA barcoding identification. ZooKeys 365: 329-336. https://doi.org/10.3897/zookeys.365.6034
Figure 2 - Estimation of the ad hoc distance threshold. Example of output obtained using the function adhocTHR with default settings (30 arbitrary distance thresholds, linear fit and an estimated relative identification error (RE) of 5%). The following message was given by the function: "for a RE of 0.05 use a threshold of 0.0334".
Figure S1 from: Yessoufou K, Van Der Bank H, Herbert D, Greenfield R (2013) Revisiting species delimitation within the genus Oxystele using DNA barcoding approach. ZooKeys 365: 337-354. https://doi.org/10.3897/zookeys.365.5356
Figure S1 - The only parsimonious tree obtained from the maximum parsimony (MP) analysis. Topology of species groupings is similar to that of the Bayesian tree (see Figure 3). Node supports are reported on the branches; the first value is bootstrap support from MP analysis; the second value in bracket indicates the posterior probability obtained from Bayesian analysis; only moderate to high node support values are indicated; Jujubinus exasperatus is used as outgroup; A-E indicates different possible species-units in the dataset: A (Oxystele tabularis), B (Oxystele variegata), C (Oxystele impervia), D (Oxystele sinensis), E (Oxystele tigrina), as in Figure 3.
Figure S2 from: Yessoufou K, Van Der Bank H, Herbert D, Greenfield R (2013) Revisiting species delimitation within the genus Oxystele using DNA barcoding approach. ZooKeys 365: 337-354. https://doi.org/10.3897/zookeys.365.5356
Figure S2 - Bayesian tree assembled using MrBayes indicating the groupings of specimens and the posterior probability of the nodes.
Figure 4 from: Yessoufou K, Van Der Bank H, Herbert D, Greenfield R (2013) Revisiting species delimitation within the genus Oxystele using DNA barcoding approach. ZooKeys 365: 337-354. https://doi.org/10.3897/zookeys.365.5356
Figure 4 - Patterns of shell colour within the genus Oxystele. A–C Oxystele variegata from Namibia, 5 km north of Swakopmund, diameter 22.2 mm (NMSA E6038) D–F Oxystele impervia from the Western Cape, Groen Rivier, diameter 22.3 mm (NMSA E7353) G–I Oxystele sp. from theEastern Cape, Tsitsikamma National Park, diameter 16.5 mm (HVDBM058-10, NMSA W7371); the colour pattern of these specimens suggests Oxystele variegata, but these specimens group within the unit of Oxystele impervia J–L Oxystele sp. from the Northern Cape, Noup, diameter 18.0 mm (HVDBM185-10, NMSA W7608); the colour pattern suggests Oxystele impervia, but they group with Oxystele variegata (see Figure 4 and Appendix 2 for the phylogenetic groupings of these specimens and node supports; these groupings contradict their morphological identification).
Figure 3 from: Yessoufou K, Van Der Bank H, Herbert D, Greenfield R (2013) Revisiting species delimitation within the genus Oxystele using DNA barcoding approach. ZooKeys 365: 337-354. https://doi.org/10.3897/zookeys.365.5356
Figure 3 - Summary of both Bayesian and parsimonious trees. Values above branches indicate bootstrap supports; values under branches indicate posterior probability. All distinguished species are indicated at the tip of the tree. Branches without values indicate non-supported nodes; the small circle indicates a specimen of Oxystele impervia (HVDBM028-10) that was misidentified based on morphology; large circle indicates four specimens morphologically indistinguishable from Oxystele variegata (HVDBM070-10; DQ061092; HVDBM058-10; HVDBM059-10), but that are, based on both barcoding analysis of species delimitation (see Table 1) and phylogenetic tree analysis identified as Oxystele impervia (see also Appendices 1 and 2).
Figure 2 from: Yessoufou K, Van Der Bank H, Herbert D, Greenfield R (2013) Revisiting species delimitation within the genus Oxystele using DNA barcoding approach. ZooKeys 365: 337-354. https://doi.org/10.3897/zookeys.365.5356
Figure 2 - Determination of the threshold genetic distance for species identification. The density plot indicates transition between intra- and interspecific distances; the genetic distance corresponding to this transition (dip in the density graph, here approximately 0.05) indicates the suitable threshold to the dataset. This method does not require prior knowledge of species identity to get an indication of potential threshold values.
Figure 1 from: Sonet G, Nagy Z, Mortelmans J, Vandewynkel C, Grootaert P (2013) Using DNA barcodes for assessing diversity in the family Hybotidae (Diptera, Empidoidea). ZooKeys 365: 263-278. https://doi.org/10.3897/zookeys.365.6070
Figure 1 - Neighbour-Joining tree representing hybotid diversity of 339 selected samples. The tree was rooted with Empis tessellata (Empididae). Circles represent branch supports, bootstrap values are according to circles' size.
Figure 1 from: Yessoufou K, Van Der Bank H, Herbert D, Greenfield R (2013) Revisiting species delimitation within the genus Oxystele using DNA barcoding approach. ZooKeys 365: 337-354. https://doi.org/10.3897/zookeys.365.5356
Figure 1 - Evaluation of barcode gap in the dataset. A Boxplot of the interspecific (inter) and intraspecific genetic (intra) distances, indicating the existence of a barcode gap i.e. intraspecific distance is longer than intraspecific distance. The bottom and top of the boxes show the first and third quartiles respectively, the median is indicated by the horizontal line, the range of the data by the vertical dashed line and outliers (points outside 1.5 times the interquartile range) by Bold vertical lines B Lineplot of the barcode gap for the 56 Oxsystele specimens. For each specimen in the dataset, the grey lines indicate where the smallest interspecific distance (top of line value) is longer than the longest intraspecific distance (bottom of line value), therefore indicating existence of barcode gap; the red lines show where this pattern is reversed, and the closest non-conspecific is closer to the query than its nearest conspecific, i.e., the situation where there is no barcoding gap.
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
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DANDI Archive for NWB datasets
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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.