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4,144 results for “ITS barcode”
Appendix 4 in Morphometry and DNA barcoding reveal cryptic diversity in the genus Enteromius (Cypriniformes: Cyprinidae) from the Congo basin, Africa
Appendix 4. PC loadings of the PCA in Fig. 5. Most important loadings indicated in bold.
Appendix 3 in Morphometry and DNA barcoding reveal cryptic diversity in the genus Enteromius (Cypriniformes: Cyprinidae) from the Congo basin, Africa
Appendix 3. PC loadings of the PCA in Fig. 4. Most important loadings indicated in bold.
Figure 37 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figure 37. Heterolepisma cooloola sp. nov. from leaf litter at Carlo Point.
Figure 1 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figure 1. Collection localities.
Figure 6 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figure 6. Heterolepisma coorongooba sp. nov. Glen Davis, NSW.
Data from: Using full-length metabarcoding and DNA barcoding to infer community assembly for speciose taxonomic groups: a case study
<p>How insect communities are assembled in nature remains largely unknown. In particular, whether habitat filtering or competition serves as the main mechanism in forming insect communities is rarely subject to an in-depth investigation. One bottleneck lies in the difficulty of species identification when dealing with a large number of diverse insects. However, High-Throughput Sequencing (HTS) technology coupled with classic DNA barcoding offers a great opportunity to infer community assembly for this speciose group. In this study, using 13,909 full-length barcodes obtained by Sanger sequencing or the SOAPBarcode metabarcoding method, we showed that competition was the main assembly mechanism for the moth communities studied in temperate forests of China. The two sequencing methods showed highly consistent results with regards to both diversity composition and community assembly mechanism. Significant phylogenetic signals and structure suggested that the focal moth communities were the result of the non-neutral assembly process, which was further confirmed by results of neutral assembly test that accounted for immigration and speciation rates. In conclusion, HTS coupled with a well-curated DNA barcode library can facilitate community assembly inferences, especially for speciose taxonomic groups.</p>
Dataset for: Molecular diversity of dragonflies in high altitude Andean lakes through DNA barcoding
<p>Genetic and morphological identification of dragonflies' larvae species in three high elevation Andean tropical lakes was done using DNA barcoding of the cytochrome oxidase 1 gene (COI). Phylogeny allowed inferring the evolutionary relationships of at least 5 species (from 74 samples) that belong to two different families within the Odonata order.</p>
Data from: Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae)
Premise of the Study The internal transcribed spacer (ITS) region is situated between 18S and 26S in a polycistronic rRNA precursor transcript. It had been proved to be the most commonly sequenced region across plant species to resolve phylogenetic relationships ranging from shallow to deep taxonomic levels. Despite several taxonomical revisions in Cassiinae, a stable phylogeny remains elusive at the molecular level, particularly concerning the delineation of species in the genera Cassia, Senna and Chamaecrista. This study addresses the comparative potential of ITS datasets (ITS1, ITS2 and concatenated) in resolving the underlying morphological disparity in the highly complex genera, to assess their discriminatory power as potential barcode candidates in Cassiinae. Methodology A combination of experimental data and an in-silico approach based on threshold genetic distances, sequence similarity based and hierarchical tree-based methods was performed to decipher the discriminating power of ITS datasets on 18 different species of Cassiinae complex. Lab-generated sequences were compared against those available in the GenBank using BLAST and were aligned through MUSCLE 3.8.31 and analysed in PAUP 4.0 and BEAST1.8 using parsimony ratchet, maximum likelihood and Bayesian inference (BI) methods of gene and species tree reconciliation with bootstrapping. DNA barcoding gap was realized based on the Kimura two-parameter distance model (K2P) in TaxonDNA and MEGA. Principal Findings Based on the K2P distance, significant divergences between the inter- and intra-specific genetic distances were observed, while the presence of a DNA barcoding gap was obvious. The ITS1 region efficiently identified 81.63% and 90% of species using TaxonDNA and BI methods, respectively. The PWG-distance method based on simple pairwise matching indicated the significance of ITS1 whereby highest number of variable (210) and informative sites (206) were obtained. The BI tree-based methods outperformed the similarity-based methods producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses. Conclusion The reticulated phylogenetic hypothesis using the ITS1 region mainly supported the relationship between the species of Cassiinae established by traditional morphological methods. The ITS1 region showed a higher discrimination power and desirable characteristics as compared to ITS2 and ITS1 + 2, thereby concluding to be the locus of choice. Considering the complexity of the group and the underlying biological ambiguities, the results presented here are encouraging for developing DNA barcoding as a useful tool for resolving taxonomical challenges in corroboration with morphological framework.
Data from: Life cycle matters: DNA barcoding reveals contrasting community structure between fern sporophytes and gametophytes
Ferns are the only major lineage of vascular plants that have nutritionally independent sporophyte (diploid) and gametophyte (haploid) life stages. However, the implications of this unique life cycle for fern community ecology have rarely been considered. To compare patterns of community structure between fern sporophytes and gametophytes, we conducted a survey of the ferns of the islands of Moorea and Tahiti (French Polynesia). We first constructed a DNA barcode library (plastid rbcL and trnH–psbA) for the two island floras including 145 fern species. We then used these DNA barcodes to identify more than 1300 field-collected gametophytes from 25 plots spanning an elevational gradient from 200 to 2000 m. We found that species richness of fern sporophytes conforms to the well-known unimodal (i.e., mid-elevation peak) pattern, reaching a maximum at ca. 1000 – 1200 m. Moreover, we found that fern sporophyte communities become increasingly phylogenetically clustered at high elevations. In contrast, species richness of fern gametophytes was consistent across sites, and gametophytes showed no correlation of phylogenetic community structure with elevation. Turnover of sporophyte and gametophyte communities was closely linked with elevation at shallow phylogenetic levels, but not at deeper nodes in the tree. Finally, we found several species for which gametophytes had broader ranges than sporophytes, including a vittarioid fern with abundant gametophytes but extremely rare sporophytes. Our study highlights the importance of including diverse life history stages in surveys of community structure, and has implications for the possible impacts of climate change on the distribution of fern diversity.
Longer is not always better: optimizing barcode length for large-scale species discovery and identification
New techniques for the species-level sorting of millions of specimens are needed in order to accelerate species discovery, determine how many species live on earth, and develop efficient biomonitoring techniques. These sorting methods should be reliable, scalable and cost-effective, as well as being largely insensitive to low-quality genomic DNA, given that this is usually all that can be obtained from museum specimens. Mini-barcodes seem to satisfy these criteria, but it is unclear how well they perform for species-level sorting when compared to full-length barcodes. This is here tested based on 20 empirical datasets covering ca. 30,000 specimens (5,500 species) and six clade-specific datasets from GenBank covering ca. 98,000 specimens (>20,000 species). All specimens in these datasets had full-length barcodes and had been sorted to species-level based on morphology. Mini-barcodes of different lengths and positions were obtained in silico from full-length barcodes using a sliding window approach (3 windows: 100-bp, 200-bp, 300-bp) and by excising nine mini-barcodes with established primers (length: 94 – 407-bp). We then tested whether barcode length and/or position reduces species-level congruence between morphospecies and molecular Operational Taxonomic Units (mOTUs) that were obtained using three different species delimitation techniques (PTP, ABGD, objective clustering). Surprisingly, we find no significant differences in performance for both species- or specimen-level identification between full-length and mini-barcodes as long as they are of moderate length (>200-bp). Only very short mini-barcodes (<200-bp) perform poorly, especially when they are located near the 5' end of the Folmer region. The mean congruence between morphospecies and mOTUs was ca. 75% for barcodes >200-bp and the congruent mOTUs contain ca. 75% of all specimens. Most conflict is caused by ca. 10% of the specimens that can be identified and should be targeted for re-examination in order to efficiently resolve conflict. Our study suggests that large-scale species discovery, identification, and metabarcoding can utilize mini-barcodes without any demonstrable loss of information compared to full-length barcodes.
Data from: DNA barcoding identifies cryptic animal tool materials
<p>Some animals fashion tools and other constructions out of plant materials to aid foraging, reproduction, self-maintenance, and protection. The choice of raw materials can affect the structure and mechanical properties of the resulting artefacts, with significant fitness consequences. Documenting animals' material preferences is challenging, however, as manufacture behaviour is often difficult to observe directly, and materials may be processed so heavily that they lack identifying features. Here, we use DNA barcoding techniques to identify, from just a few recovered tool specimens, the plant species New Caledonian crows (<em>Corvus moneduloides</em>) use for crafting elaborate hooked stick tools in one of our long-term study populations. The method succeeded where extensive fieldwork using conventional approaches had failed, including targeted observations, radio-tracking, bird-mounted video-cameras, and behavioural experiments with wild and temporarily captive subjects. We believe that DNA barcoding will prove useful for investigating many other tool and construction behaviours, helping to unlock significant research potential across a wide range of study systems.</p>
DNA barcoding of selected alpine beetles with focus on Curculionoidea (Coleoptera)
<p>Supplementary Figures 3 and 4 to the following article: DNA barcoding of selected alpine beetles with focus on Curculionoidea (Coeloptera). Revue Suisse de Zoologie, in press.</p>
FIGURE 1 in Use of DNA barcoding to distinguish the malaria vector An opheles neivai in Colombia
FIGURE 1. Collection municipalities map for Anopheles neivai in Colombia (CO) and Panama (PA).
Figure 21. from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
Figure 21. - Eupolybothrus cavernicolus Komerički & Stoev sp. n., paratype, 3D model, volume rendering, created with CTVox, virtual rotation and dissection. Movie available at: YouTube.
Figure 22. from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
Figure 22. - Movie of Eupolybothrus cavernicolus Komerički & Stoev sp. n., holotype, filmed ex-situ in a plastic container. Movie available at: YouTube.
Simulated barcoded Rep-seq datasets (IGH, barcode length: 15 nt)
<p>Simulated barcoded Rep-seq libraries with various amplification error rates for repertoire from doi.org/10.5281/zenodo.823351. Barcode errors, barcode collisions and chimeric reads are introduced into datasets. Barcodes are encoded in headers.</p>
NextClone and CloneDetective: An Integrated Nextflow Pipeline and R Package for Clonal Barcode Extraction and Quantification
<p>Raw FASTQ files for the DNA-seq data required to replicate the analyses presented at: https://phipsonlab.github.io/NextClone-analysis/.</p>
DNA barcoding is currently unreliable for species identification in Crayfish
<p>DNA barcoding is commonly used for species identification. Despite this, there has not been a comprehensive assessment of the utility of DNA barcoding in crayfishes (<em>Decapoda</em>: <em>Astacidea</em>). Here we examined the extent to which local barcoding gaps (used for species identification) and global barcoding gaps (used for species discovery) exist among crayfishes, and whether global gaps, if present, met a previously suggested 10 × threshold.</p> <p>Using publicly available mitochondrial COI sequence data from the National Center for Biotechnology Information's nucleotide database, we created two versions of the COI datasets used for downstream analyses: one focused on the number of unique haplotypes (N<sub>H</sub>) per species, and another that focused on total number of sequences (N<sub>S</sub>; i.e., including redundant haplotypes) per species. Ultimately, a total of 81 species were included, with 58 species and five genera from family <em>Cambaridae</em> and 23 species from three genera from family <em>Parastacidae</em>.</p> <p>We found that local barcoding gaps were present in only 30 species (20 members of <em>Cambaridae </em>and 10 <em>Parastacidae</em>). Global barcoding gaps were detected in only four genera (<em>Cambarus, Cherax, Euastacus, and Tenuibranchiurus</em>), and they were all well below the previously suggested 10× threshold. We propose that a ~5x threshold could act as a more appropriate working hypothesis for species discovery. While the N<sub>H</sub> and N<sub>S</sub> datasets yielded largely similar results, there were some discrepant inferences.</p> <p>Currently, the utility of DNA barcoding for species identification and discovery in crayfish is quite limited, and caution should be exercised when molecular approaches are used in place of taxonomic expertise.</p> <p>Assessment of the evidence for local and global barcoding gaps is important for understanding the reliability of molecular species identification and discovery, but outcomes are dependent on the current state of taxonomy. As this improves (e.g., via resolving species complexes, possibly elevating some subspecies to the species-level status, and redressing specimen misidentifications in natural history and other collections), so too will the utility of DNA barcoding.</p>
Wing geometric morphometrics and COI barcoding of Culex pipiens subgroup in the Republic of Korea
<p>Two members of the <em>Culex pipiens</em> subgroup, <em>Culex pallens</em> and <em>Culex pipiens</em> f. <em>molestus</em>, are known to occur in the Republic of Korea (ROK). These species exhibit morphologically similar features and are challenging to distinguish below the species level. Therefore, this study utilized wing geometric morphometrics (GM) on the right wing of the <em>Culex pipiens</em> subgroup, alongside sequencing of the cytochrome <em>c</em> oxidase subunit I (<em>COI</em>) region. Mosquitoes were collected from 11 locations between June and October to minimize regional and seasonal variations. Additionally, <em>Culex pipiens</em> f. <em>pipiens</em>, which is not native to the ROK, was included in the analysis. <em>Culex tritaeniorhynchus</em>, <em>Aedes albopictus</em>, and <em>Anopheles sinensis</em>, the primary vectors in the ROK, were used as outgroups for comparison. All three taxa within the <em>Culex pipiens</em> subgroup could be identified with an 82.4%–97.0% accuracy using GM. However, a comparison of the <em>COI</em> regions of the <em>Culex pipiens</em> subgroup revealed no clear differences between the taxa. These data can be used for accurate identification, contributing to effective mosquito control, in addition to providing a foundation for evolutionary and ecological studies on wing shape differences.</p>
F I G U R E 4 in Assessing the diversity of Australian tarantulas (Araneae: Theraphosidae) using DNA barcoding and iterative species delimitation
F I G U R E 4 Legend on next page.
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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.