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4,144 results for “ITS barcode”
Figure 6 from: Smit J, Reijnen B, Stokvis F (2013) Half of the European fruit fly species barcoded (Diptera, Tephritidae); a feasibility test for molecular identification. ZooKeys 365: 279-305. https://doi.org/10.3897/zookeys.365.5819
Figure 6 - Best Close Match (BCM) identification of the stripped dataset, e.g. excluding singletons and Urophora (n = 414). Proportions of true positives (TP), false positives (FP), false negatives (FN) and true negatives (TN) are given for 30 arbitrary distance thresholds ranging from 0.15 to 0.00. For each threshold the percentages of precision, accuracy and discarded queries were calculated.
Figure 5 from: Smit J, Reijnen B, Stokvis F (2013) Half of the European fruit fly species barcoded (Diptera, Tephritidae); a feasibility test for molecular identification. ZooKeys 365: 279-305. https://doi.org/10.3897/zookeys.365.5819
Figure 5 - Best Close Match (BCM) identification of the entire dataset (n = 555). Proportions of true positives (TP), false positives (FP), false negatives (FN) and true negatives (TN) are given for 30 arbitrary distance thresholds ranging from 0.15 to 0.00. For each threshold the percentages of precision, accuracy and discarded queries were calculated.
Figure 4 from: Smit J, Reijnen B, Stokvis F (2013) Half of the European fruit fly species barcoded (Diptera, Tephritidae); a feasibility test for molecular identification. ZooKeys 365: 279-305. https://doi.org/10.3897/zookeys.365.5819
Figure 4 - Identification rates of all five criteria: Neighbour-Joining (NJT) sensu Hebert et al. (2003), revised criteria (NJT_M) according to Meier et al. (2006), and Best Match (BM), Best Close Match (BCM) and All Species Barcodes (ASB) also described by Meier et al. (2006) for four different datasets, including singletons and with (n = 555) or without (n = 452) Urophora, and the same excluding singletons (n = 514) and (n = 414) respectively.
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 3 from: Smit J, Reijnen B, Stokvis F (2013) Half of the European fruit fly species barcoded (Diptera, Tephritidae); a feasibility test for molecular identification. ZooKeys 365: 279-305. https://doi.org/10.3897/zookeys.365.5819
Figure 3 - Box plots depicting the variation in mean distances using K2P-distance modeling of sequence divergence for intraspecific, interspecific difference among the species and genera, as well as the ingroup genera with the outgroup genus.
Figure 7 from: Smit J, Reijnen B, Stokvis F (2013) Half of the European fruit fly species barcoded (Diptera, Tephritidae); a feasibility test for molecular identification. ZooKeys 365: 279-305. https://doi.org/10.3897/zookeys.365.5819
Figure 7 - Relative ID errors at 30 arbitrary threshold values for a. the entire dataset (n = 555), b. the stripped dataset, e.g. excluding singletons and Urophora (n = 414) and c. the stripped dataset excluding the problematic Terellia groups. Linear regression was used to infer the ad hoc threshold for the 95th percentile of the correctly identified queries and the relative ID error does not exceed 5%. In (a) and (b) this value is below 0.00, only in (c) this value is positive: 0.051 (R-square 0.91).
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: Smit J, Reijnen B, Stokvis F (2013) Half of the European fruit fly species barcoded (Diptera, Tephritidae); a feasibility test for molecular identification. ZooKeys 365: 279-305. https://doi.org/10.3897/zookeys.365.5819
Figure 2 - The Neighbour-Joining tree of the entire dataset based on COI barcodes. Terminal branches have been collapsed in order to save space, the total number of specimens is given in brackets and the area surface of the triangle represents the amount of variation. When a terminal branch contains two species, both names are provided as well as their respective number of specimens. If a branch contains more than two species only the number of species as well as the number of specimens are given. Bootstrap values above 50 (1000 replicates) are given at the nodes.
Figure 10 from: Smit J, Reijnen B, Stokvis F (2013) Half of the European fruit fly species barcoded (Diptera, Tephritidae); a feasibility test for molecular identification. ZooKeys 365: 279-305. https://doi.org/10.3897/zookeys.365.5819
Figure 10 - The Neighbour-Joining tree of the genus Urophora inferred from COI barcodes. Bootstrap values above 50 (1000 replicates) are given at the nodes.
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: Sonet G, Jordaens K, Braet Y, Bourguignon L, Dupont E, Backeljau T, de Meyer M, Desmyter S (2013) Utility of GenBank and the Barcode of Life Data Systems (BOLD) for the identification of forensically important Diptera from Belgium and France. ZooKeys 365: 307-328. https://doi.org/10.3897/zookeys.365.6027
Figure 1 - Best matches obtained for each species using five different search procedures:Barcode fragment (642–658 bp) submitted to GenBank (1) and the public records of BOLD (2); barcode fragment submitted to the species level records of BOLD, including early-released sequences (3); barcode fragment and keyword "barcode" submitted to GenBank (4) and longer COI fragment (1412–1534 bp) submitted to GenBank (5). Numbers of haplotypes used as queries are between parentheses. Longer COI fragments were obtained for all species except for Protophormia terraenovae.
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.
Figure 5 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 5 - DNA barcode sequencing success for fresh specimens (collected 2010 or later). A Specimen body size not significantly different for successful vs. failed DNA barcode sequencing attempts (one-way ANOVA, F (1, 216) = 1.45, p = 0.230). Boxes are 25–75% quartiles bisected by the median, whisker lines drawn to the largest/smallest data point less than 1.5 times the box height, outliers less than 3 times the box height shown as circles, more than 3 shown as stars. B Most of the fresh specimens included in this study belonged to one of two clades: Orbiculariae (ORB) or the 'RTA' clade (RTA); only a handful of specimens represented older phylogenetic branches, such as haplogyne (HAP) spiders; no mygalomorph spiders were included; success expressed as a percentage appears on or above each bar. Success rate for Orbiculariae vs. 'RTA' clade specimens not significantly different (χ2 = 2.18, d.f. = 2, N = 220, p = 0.337).
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