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66 results for “COI DNA barcode”
FIGURE 6 in Revision and phylogeny of the subaptera-group of Phyllodromica (Blattoptera: Blattellidae: Ectobiinae), including a parthenogenetic species and the evaluation of COI sequences for species identification (DNA barcoding)
FIGURE 6. Phyllodromica iberica morph #2, male. A Thoracal nota. B–F Abdominal tergites 5–9. (B) Tergite 5; (C) tergite 6 with a narrow transversal torus (white arrow heads) bearing bristles (white spots) in extraordinary density; (D) tergite 7, white arrow heads point to the shallow pouches appearing as crescent–shaped black shadows; (E) tergite 8; (F) tergite 9 on glass rod. G Terminalia with tergite 10 (sa), cerci and paraprocts. H Hook of left phallomere with the posterior end on the top. I Subgenital plate with remaining genital sclerites (without hook). Abbreviations: ap anterior process, bf bristle field cm central mound, cp conelike process, m mound, ml median lobe, mp medio-anterior process of right paraproct, r ridge between bristle fields, rp right paraproct, sa supraanal plate, se sinusoidal edge, sp shallow pit, tt transversal trough. Same scale for (B, C, G) and (D, E, H). Identification: Sp 267c/M2.
FIGURE 5 in Revision and phylogeny of the subaptera-group of Phyllodromica (Blattoptera: Blattellidae: Ectobiinae), including a parthenogenetic species and the evaluation of COI sequences for species identification (DNA barcoding)
FIGURE 5. Phyllodromica iberica morph #1, A–E, male. (A) Tergite 7 and (B) tergite 8 of a male specimen differing from the holotype in its colouration; (C) membrane glands of the left lateral region on the anterior border of tergite 6; (D) right paraproct; (E) distal end of tibia of the right mid leg (bearing 5 distal spines) in posterior view. F–I, female. (F, H) Different colour pattern of pronotum; (G, I) tergite 5. Abbreviations: mg membrane glands, mp medio-anterior process of right paraproct, rp right paraproct, sp spinelike process of right paraproct, tar tarsus, tib tibia. Same scale for (C, D) and (F–I). Identification: (A, B) Sp 330/3, (C, D) Sp 292b/M3 (holotype), (E) Sp 510/M1, (F, G) Sp 292b/W1, (H, I) Sp 292b/W2.
FIGURE 4 in Revision and phylogeny of the subaptera-group of Phyllodromica (Blattoptera: Blattellidae: Ectobiinae), including a parthenogenetic species and the evaluation of COI sequences for species identification (DNA barcoding)
FIGURE 4. Phyllodromica iberica morph #1, male, SEM pictures of tergal glandular structures. A–C, G Tergite 7. (A) Latero-frontal view from slightly above, anterior wall of trough slightly hollowed out anteriorly (white arrows); (B) lateral view of the glandular region from slightly above; (C) glandular region in dorsal view; (G) bristles of bristle field. D– F, H, I Tergite 8. (D) Dorsal view of the whole tergite, median emargination in the distribution of the bristles (white arrow heads); (E) latero-frontal view from slightly above; (F) dorsal view of the conelike process; (H) porous surface of the central mound; (I) soft villi on the surface of the conelike process. Abbreviations: bf bristle field, cm central mound, cp conelike process, m mound, r ridge, se sinusoidal edge, sp shallow pit, tt transversal trough. Identification: (A–C, E– I) Sp 270a/M4, (D) Sp 85/11.
FIGURE 3 in Revision and phylogeny of the subaptera-group of Phyllodromica (Blattoptera: Blattellidae: Ectobiinae), including a parthenogenetic species and the evaluation of COI sequences for species identification (DNA barcoding)
FIGURE 3. Phyllodromica iberica morph #1, male (holotype). A Thoracal nota. B–F Abdominal tergites 5–9. (B) Tergite 5 and (C) tergite 6 with membranous glands in the lateral region of the anterior margin of tergites (black arrows); (D) tergite 7, white arrow heads point to the shallow pouches appearing as crescent–shaped black shadows; (E) tergite 8; (F) tergite 9 on glass rod. G Terminalia with tergite 10 (sa), cerci and paraprocts. H Hook of left phallomere with the posterior end on the top. I Subgenital plate with remaining genital sclerites (without hook). Abbreviations: ap anterior process, bf bristle field, c cercus, cm central mound, cp conelike process, ll lateral lobe, m mound, mes mesonotum, met metanotum, ml median lobe, mp medio-anterior process, pml posterior median lobe, pro pronotum, r ridge between bristle fields, rp right paraproct, sa supraanal plate, se sinusoidal edge, sp shallow pits, tm tegmen, tr transversal ridge, tt transversal trough. Same scale for (B, C, G) and (D, E, H). Identification: Sp 292b/M3 (holotype).
FIGURE 2 in Revision and phylogeny of the subaptera-group of Phyllodromica (Blattoptera: Blattellidae: Ectobiinae), including a parthenogenetic species and the evaluation of COI sequences for species identification (DNA barcoding)
FIGURE 2. Phyllodromica subaptera (female). A Thoracal nota. B Abdominal tergite 5. C Subgenital plate with two apodemal processes (a). D Dorsal complex of genitalia with additional sclerite (as): ventral view, posterior end on top. E Additional sclerite in higher enlargement (equivalent to "black frame" in D). F Ventral complex of genitalia: laterosternal shelf with intersternal folds between the arms. Abbreviations: as additional sclerite, a apodemal process, bd dorsal sclerite of basivalvula, bv ventral sclerite of basivalvula, c cercus, i intersternal fold, is intercalary sclerite, l laterosternal shelf, ls laterosternite IX, pl posterior lobe of valvifer II, pp paraproct, pt paratergites, T9 tergite 9, T10 tergite 10, v valves. Same scale for (B, C) and (D, F). Identification: Sp 203c/W4.
FIGURE 1. A–C P in Revision and phylogeny of the subaptera-group of Phyllodromica (Blattoptera: Blattellidae: Ectobiinae), including a parthenogenetic species and the evaluation of COI sequences for species identification (DNA barcoding)
FIGURE 1. A–C P. iberica morph #1, habitus. (A) Male in dorsal view; (B) female in dorsal and (C) ventral view. D Oothek of P. quadracantha (lateral view). Abbreviations: a antenna, c cercus, fl coxa of foreleg, h head, hl coxa of hindleg, mes mesonotum, met metanotum, ml coxa of midleg, pm palpus maxillaris, pro pronotum, sub subgenital plate, T2–T10 tergites 2–10, tm tegmen. Same scale in A and B. Localities: (A–C) Sp 449a, (D) Sp 500.
Figure 1. Bayesian COI gene tree for 51 in Integrative taxonomy of the primitively segmented spider genus Ganthela (Araneae: Mesothelae: Liphistiidae): DNA barcoding gap agrees with morphology
Figure 1. Bayesian COI gene tree for 51 terminals of Ganthela, with the results of five different species delimitation approaches, in addition to morphology (see legend). Numbers above branches show posterior probability and bootstrap supports, and values below branches show mean intraspecific (black) and interspecific genetic distances (red), calculated as Kimura two-parameter (K2P)/p-distance. Species names and locality group terminals (for specimen codes, see Table 1) according to consensus results of species delimitation approaches.
Data from: Rapid and accurate taxonomic classification of insect (Class Insecta) cytochrome c oxidase subunit 1 (COI) DNA barcode sequences using a naïve Bayesian classifier
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Evaluating the genetic variation of the COI gene of Insecta: Implications for DNA barcoding, metabarcoding and species delimitation studies
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Supplementary material 1 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 S1 – Training, test, and validation data sets used in model training and analysis
Data from: Species diversity can be overestimated by a fixed empirical threshold: insights from DNA barcoding of the genus Cletus (Hemiptera: Coreidae) and the meta-analysis of COI data from previous phylogeographical studies
The use of genetic distances to identify species within the framework of DNA barcoding has to some extent improved the development of biodiversity studies. However, using a fixed empirical threshold to delimit species may lead to overestimating species diversity. In this study, we use a new data set of COI sequences for 366 specimens within the genus of Cletus as well as conduct an analysis on the same genetic data for collected morphologically defined species from previous phylogeographical studies, to test whether high intraspecific genetic divergences are common with the premises of comprehensive sampling. The results indicate C. graminis Hsiao & Cheng 1964, is the same species with C. punctiger (Dallas, 1852) and should be synonymized and that the distributional record of C. pugnator (Fabricius, 1787) in China is correct. High intraspecific genetic differentiations (0%–4.35%) were found in C. punctiger. Furthermore, as to the mined data, the maximum intraspecific K2P distances of 186 species (48.44% of 384) exceed 3%, and 101 species (26.30%) can be divided into two or more clusters with a threshold of 3% in cluster analysis. If genetic distance is used to delimit species boundaries, the minimum interspecific K2P distance of the congeneric species should be considered rather than only using the fixed empirical value; otherwise, the species richness may be overestimated in some cases.
Data from: COI is better than 16S rRNA for DNA barcoding Asiatic salamanders (Amphibia: Caudata: Hynobiidae)
The 5' region of the mitochondrial DNA (mtDNA) gene cytochrome c oxidase I (COI) is the standard marker for DNA barcoding. However, because COI tends to be highly variable in amphibians, sequencing is often challenging. Consequently, another mtDNA gene, 16S rRNA gene, is often advocated for amphibian barcoding. Herein, we directly compare the usefulness of COI and 16S in discriminating species of hynobiid salamanders using 130 individuals. Species identification and classification of these animals, which are endemic to Asia, is often based on morphology only. Analysis of Kimura 2-parameter genetic distances (K2P) documents the mean intraspecific variation for COI and 16S rRNA genes to be 1.4% and 0.3%, respectively. Whereas COI can always identify species, sometimes 16S cannot. Intra- and interspecific genetic divergences occasionally overlap in both markers thus reducing the value of a barcoding gap to identify genera. Regardless, COI is the better DNA barcoding marker for hynobiids. In addition to the comparison of two potential markers, high levels of intraspecific divergence in COI (>5%) suggest that both Onychodactylus fischeri and Salamandrella keyserlingii might be composites of cryptic species.
Figure 3 from: Raupach MJ, Rulik B, Spelda J (2022) Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea). ZooKeys 1082: 103-125. https://doi.org/10.3897/zookeys.1082.69851
Figure 3 Subtree of the Neighbor-joining topology based on Kimura 2-parameter distances of all analyzed specimens of Platyarthrus hoffmannseggii Brandt, 1833 and nearest neighbor. Branches with specimen ID-number from BOLD and sample localities. Numbers next to internal nodes are non-parametric bootstrap values (in %) with values higher than 80. BIN values are based on the barcode analysis from 05-06-2020. The isopod drawing by Christian Schmidt was obtained from Raupach (2005).
Supplementary material 2 from: Raupach MJ, Rulik B, Spelda J (2022) Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea). ZooKeys 1082: 103-125. https://doi.org/10.3897/zookeys.1082.69851
Neighbor-joining topology
Supplementary material 1 from: Raupach MJ, Rulik B, Spelda J (2022) Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea). ZooKeys 1082: 103-125. https://doi.org/10.3897/zookeys.1082.69851
Barcode analysis using the BOLD workbench
Figure 1 from: Raupach MJ, Rulik B, Spelda J (2022) Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea). ZooKeys 1082: 103-125. https://doi.org/10.3897/zookeys.1082.69851
Figure 1 Various woodlouse species of Germany AOniscus asellus Linnaeus, 1758 BArmadillidium nasatum Budde-Lund, 1885 CTrachelipus ratzeburgii (Brandt, 1833) DMesonicus alpicola (Heller, 1858) EPhiloscia muscorum (Scopoli, 1763) FHaplophthalmus mariae Strouhal, 1953 GArmadillidium opacum (C. Koch, 1841) HPlatyarthrus hoffmannseggii Brandt, 1833. Scale bar: 1 mm. Photograph credits: A–G Jörg Spelda H Armin Rose.
Supplementary material 3 from: Raupach MJ, Rulik B, Spelda J (2022) Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea). ZooKeys 1082: 103-125. https://doi.org/10.3897/zookeys.1082.69851
Neighbor-joining topology of the BOLD workbench including BIN analysis
Figure 2 from: Raupach MJ, Rulik B, Spelda J (2022) Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea). ZooKeys 1082: 103-125. https://doi.org/10.3897/zookeys.1082.69851
Figure 2 Neighbor-joining (NJ) topology of the analyzed isopod species based on Kimura 2-parameter distances. Triangles show the relative number of individual's sampled (height) and sequence divergence (width). Red triangles highlight terrestrial species with intraspecific maximum pairwise distances > 2.2%, whereas dark blue triangles indicate freshwater species with such distances. Numbers next to nodes represent non-parametric bootstrap values > 90% (1,000 replicates). Asterisks indicate species not recorded in Germany.
Fig. 2 in Application Of Dna Barcoding In Taxonomy And Phylogeny: An Individual Case Of Coi Partial Gene Sequencing From Seven Animal Species
Fig. 2. Phylogenetic position of E. roumanicus, Bayesian inference phylogenetic tree. Sequences obtained by us are written in bold.
FIGURE 12 in DNA barcodes: Evaluating the potential of COI to diffentiate closely related species of Elachista (Lepidoptera: Gelechioidea: Elachistidae) from Australia
FIGURE 12. Larval mines of the taxa of the Elachista zigzagger complex. A: A1; B: A2; C: B2.
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