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3,292 results for “DNA Barcode”
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: 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.
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.
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>
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.
F I G U R E 2 in Assessing the diversity of Australian tarantulas (Araneae: Theraphosidae) using DNA barcoding and iterative species delimitation
F I G U R E 2 Histogram of HKY pairwise distance with bars increasing by 0.25 pairwise distance.
Figure 2 in DNA barcoding for the identification of Limonia crane flies (Diptera: Limoniidae) from China, including a new species and a newly recorded species
Figure 2. Barcoding gap of Limonia COI sequences.
Figure 1 in DNA barcoding, visual-guide resource, new localities and host associations of genus Periglischrus Oudemans, 1902 (Acari: Mesostigmata, Spinturnicidae) from Minas Gerais, Brazil
Figure 1 Geographical distribution of sampling localities ofPeriglischrus spp.
Table 2. A in DNA barcoding of the genus Verbascum (Scrophulariaceae) in the Arabian Peninsula
<p><b>Table 2.</b> A comparison of the individual and combined datasets from parsimony analysis.</p><table><tbody><tr><th></th><th>ITS</th><th><i>matK</i></th><th><i>rbcL</i></th><th><i>trnL</i></th><th>Combined chloroplastic</th><th>Combined chloroplastic and ITS</th></tr></tbody><tbody><tr><th>No. of sequences</th><td>62</td><td>62</td><td>62</td><td>62</td><td>62</td><td>62</td></tr><tr><th>Alignment length (bp)</th><td>449</td><td>735</td><td>561</td><td>819</td><td>2115</td><td>2564</td></tr><tr><th>No. of variable characters (%)</th><td>239 (53.2)</td><td>16 (2.1)</td><td>7 (1.2)</td><td>16 (2.3)</td><td>39 (1.8)</td><td>375 (14.6)</td></tr><tr><th>No. of informative characters (%)</th><td>50 (11.1)</td><td>54 (7.3)</td><td>10 (1.7)</td><td>35 (4.2)</td><td>99 (4.6)</td><td>342 (13.3)</td></tr><tr><th>No. of most equally parsimonious trees</th><td>10,000</td><td>7</td><td>6</td><td>1455</td><td>390</td><td>10,000</td></tr><tr><th>Tree length</th><td>380</td><td>73</td><td>20</td><td>58</td><td>156</td><td>939</td></tr><tr><th>Consistency index</th><td>0.8763</td><td>0.9726</td><td>1.0000</td><td>0.9310</td><td>0.9295</td><td>0.8807</td></tr><tr><th>Retention index</th><td>0.8309</td><td>0.9835</td><td>1.0000</td><td>0.9728</td><td>0.9618</td><td>0.8724</td></tr><tr><th>Rescaled consistency index</th><td>0.7282</td><td>0.9565</td><td>1.0000</td><td>0.9057</td><td>0.8940</td><td>0.7684</td></tr></tbody></table>
Data from: Establishing community-wide DNA barcode references for conserving mangrove forests in China
<p><b>Background:</b> Mangrove ecosystems have been the focus of global attention for their crucial role in sheltering coastal communities and retarding global climate change by sequestering 'blue carbon'. China is relatively rich in mangrove diversity, with one-third of the ca. 70 true mangrove species and a number of mangrove associate species occurring naturally along the country's coasts. Mangrove ecosystems, however, are widely threatened by intensifying human disturbances and rising sea levels. The urgent need to protect mangrove ecosystems could be assisted by using barcoding technology, which provides rapid species identification. </p> <p><b>Results</b>: To investigate this potential, 898 plant specimens were collected from 33 of the major mangrove sites in China. Based on the morphologic diagnosis, the specimens were assigned to 72 species, including all 28 true mangrove species and all 12 mangrove associate species recorded in China. Three chloroplast DNA markers <i>rbcL</i>, <i>trnH-psbA</i>, <i>matK</i>, and one nuclear marker <i>ITS2</i> were chosen to investigate the utility of using barcoding to identify these species. According to the criteria of barcoding gaps in genetic distance, sequence similarity and phylogenetic monophyly, we propose that a single marker, <i>ITS2</i>, is sufficient to barcode the species of mangroves and their associates in China. Furthermore, <i>rbcL</i> or <i>trnH-psbA</i> can also be used to gather supplement confirming data. In using these barcodes, we revealed a very low level of genetic variation among geographic locations in the mangrove species, which is an alert to their vulnerability to climate and anthropogenic disturbances. </p> <p><strong>Conclusion:</strong> We suggest to use <em>ITS2</em> to barcode mangrove species and terrestrial coastal plants in South China. The DNA barcode sequences we obtained would be valuable in monitoring biodiversity and the restoration of ecosystems, which are essential for mangrove conservation.</p>
Dataset: DNA barcodes and microsatellites: how they complement for species identification in the complex genus Tamarix (Tamaricaceae)
<p class="CuerpoA">DNA barcoding allows the identification of an organism by comparing the sequence of selected DNA regions (barcodes) with a previously compiled database, and it can be useful for taxonomic identification of species in complex genera, such as <i>Tamarix</i>. Many species of this genus show convergent morphology, which leads to frequent errors in their identification. Highly variable genetic markers, such as microsatellites or short sequence repeats (SSR), could be used to differentiate species where DNA barcodes fail. Here, we tested the ability of both, five different marker regions (<i>rbcL</i>, <i>matK</i>, ITS, <i>trnH</i>-<i>psbA</i>, and <i>ycf1</i>), and 14 microsatellites, to properly identify <i>Tamarix</i> species, especially those from the Mediterranean Basin, and compared the pros and cons of the different analytical methods for species identification. DNA barcoding allows the genetic identification of certain species in <i>Tamarix</i>. The two-locus barcodes <i>matK</i>+ITS and ITS+<i>ycf1</i> were the best-performing combinations, allowing up to 69% and 70%, respectively, correct identification. However, DNA barcoding failed in phylogenetically close groups, such as many Mediterranean species. The use of SSR can aid the identification of species, and the combination of both types of data (DNA barcoding and SSR) improved the success. The combination of data was especially relevant in detecting the presence of hybridization processes, which are common in the genus. However, caution must be exercised when choosing the clustering methods for the SSR data, since different methods can lead to very different results.</p>
A new taxonomist-curated reference library of DNA barcodes for Neotropical electric fishes (Teleostei: Gymnotiformes)
<p>DNA barcoding is a useful tool for identifying species; however, successful barcode-based identification requires a reference library of barcode sequences from accurately identified specimens. Here we present a reference library of <em>co1</em> barcode sequences for the Neotropical electric knifefish order Gymnotiformes (Teleostei: Ostariophysi), a model taxon for studies of tropical diversification and biogeography, genomics, behaviour, and neurobiology. Our library contains barcodes for 167 of the ca. 270 valid species of gymnotiforms derived from geo-referenced museum voucher specimens, and includes sequences from 26 type specimens and 21 specimens from type localities, most of which we collected. To assess the state of gymnotiform barcodes in two main public barcode repositories, GenBank and BOLD, we compared the barcodes in these databases to our reference library. Our analysis shows that a considerable proportion of gymnotiform barcodes in GenBank and BOLD are mis- or unidentified. We encourage taxonomists to develop and publish barcode reference libraries composed of carefully curated barcode sequences.</p>
Data from: Evaluating species richness using proteomic fingerprinting and DNA-barcoding – a case study on meiobenthic copepods from the Clarion Clipperton Fracture Zone
<p><span>The Clarion Clipperton Fracture Zone (CCZ) is a vast deep-sea region harboring a highly diverse benthic fauna, which will be affected by potential future deep-sea mining of metal-rich polymetallic nodules. Despite the need for conservation plans and monitoring strategies in this context, the majority of taxonomic groups remains scientifically undescribed. However, molecular rapid assessment methods such as DNA-barcoding and Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) provide the potential to accelerate specimen identification and biodiversity assessment significantly in the deep-sea areas. In this study, we successfully applied both methods to investigate the diversity of meiobenthic copepods in the eastern CCZ, including the first application of MALDI-TOF MS for the identification of these deep-sea organisms. Comparing several different species delimitation tools for both datasets, we found that biodiversity values were very similar, with Pielou's Evenness varying between 0.97 and 0.99 in all datasets. Still, direct comparisons of species clusters revealed differences between all techniques and methods, which are likely caused by the high number of rare species being represented by only one specimen, despite our extensive dataset of more than 2000 specimens. Hence, we regard our study as a first approach toward setting up a reference library for mass spectrometry data of the CCZ in combination with DNA-barcodes. We conclude that proteome fingerprinting, as well as the more established DNA-barcoding, can be seen as a valuable tool for rapid biodiversity assessments in the future, even when no reference information is available.</span></p>
Data and Files for Zito, Rigon and Dunson (2022): "Inferring taxonomic affiliation from DNA barcoding aiding in discovery of new taxa"
<p>This folder contains the data and the R code to reproduce the figures and tables in the paper Zito, Rigon and Dunson (2022) - "Inferring Taxonomic placement from DNA barcoding aiding in discovery of new taxa", accepted as open access publication in Methods in Ecology and Evolution.</p> <p>The file "main_FinBOL.R" reproduces the tables in the main document and in the Supporting information available online for the analysis of the FinBOL data, while "main_Simulation_Section4_SI.R" reproduces the simulation in Section 4 of the Supporting information. </p> <p>All data are saved in the folder "data". For replicability purposes, we added version 2.13 of the RDP classifier to the repository, in the folder "RDP/java". This has been downloaded from https://sourceforge.net/projects/rdp-classifier/. </p> <p>For questions, contact the author at alessandro.zito@duke.edu<br> </p>
Figure 3 in Hydrodroma angelieri (Acari, Hydrachnidia: Hydrodromidae) a new water mite species from Corsica based on morphological and DNA barcode evidence
Figure 3 Neighbor-joining tree based on studiedHydrodroma COI sequences.
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Allen Brain Atlas
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