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48 results for “barcode references”
A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples
<p>[This repository contains the source data for the manuscript "A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples" by deWaard et al., 2019. BioRxiv]</p>
BAGS: an automated barcode, audit & grade system for DNA barcode reference libraries
<p>Biodiversity studies greatly benefit from molecular tools, such as DNA metabarcoding, which provides an effective identification tool in biomonitoring and conservation programmes. The accuracy of species-level assignment, and consequent taxonomic coverage, relies on comprehensive DNA barcode reference libraries. The role of these libraries is to support species identification, but accidental errors in the generation of the barcodes may compromise their accuracy. Here we present an R-based application, BAGS (Barcode, Audit & Grade System; https://github.com/tadeu95/BAGS), that performs automated auditing and annotation of cytochrome c oxidase subunit I (COI) sequences libraries, for a given taxonomic group of animals, available in the Barcode of Life Data System (BOLD). This is followed by implementing a qualitative ranking system that assigns one of five grades (A to E) to each species in the reference library, according to the attributes of the data and congruency of species names with sequences clustered in Barcode Index Numbers (BINs). Our goal is to allow researchers to obtain the most useful and reliable data, highlighting and segregating records according to their congruency. Different tests were performed to perceive its usefulness and limitations. BAGS fulfils a significant gap in the current landscape of DNA barcoding research tools by quickly screening reference libraries to gauge the congruence status of data and facilitate the triage of ambiguous data for posterior review. Thereby, BAGS has the potential to become a valuable addition in forthcoming DNA metabarcoding studies, in the long term contributing to globally improve the quality and reliability of the public reference libraries.</p>
Fig 5 in A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library
Fig 5. Neighbour-joining tree showing all available DNA barcodes for species in family Rhinolophidae reported from Peninsular Malaysia. The percentage of pseudoreplicate trees (±70%) in which the DNA barcodes clustered together in the bootstrap test (500 pseudoreplicates) are shown above the branches. Abbreviation as follows: PM = Peninsular Malaysia, VN = Vietnam, BN = Borneo (including Sabah & Sarawak of East Malaysia, Brunei and Kalimantan Indonesia), TH = Thailand, LA = Laos, SM = Sumatera Indonesia, JV = Java Indonesia, IND = India, CH = China, CM = Cambodia, MN = Myanmar. https://doi.org/10.1371/journal.pone.0179555.g005
Fig 4 in A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library
Fig 4. Neighbour-joining tree showing all available DNA barcodes for species in family Hipposideridae reported from Peninsular Malaysia. The percentage of pseudoreplicate trees (±70%) in which the DNA barcodes clustered together in the bootstrap test (500 pseudoreplicates) are shown above the branches. Abbreviation as follows: PM = Peninsular Malaysia, VN = Vietnam, BN = Borneo (including Sabah & Sarawak of East Malaysia, Brunei and Kalimantan Indonesia), TH = Thailand, LA = Laos, SM = Sumatera Indonesia, CH = China, CM = Cambodia. https://doi.org/10.1371/journal.pone.0179555.g004
Fig 2 in A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library
Fig 2. Neighbour-joining tree showing all available DNA barcodes for species in family Pteropodidae reported from Peninsular Malaysia. The percentage of pseudoreplicate trees (±70%) in which the DNA barcodes clustered together in the bootstrap test (500 pseudoreplicates) are shown above the branches. Abbreviation as follows: PM = Peninsular Malaysia, VN = Vietnam, JV = Java, Indonesia, BN = Borneo (including Sabah, Sarawak, Brunei and Kalimantan), TH = Thailand, LA = Laos. https://doi.org/10.1371/journal.pone.0179555.g002
Fig 3 in A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library
Fig 3. Neighbour-joining tree showing all available DNA barcodes for species in families Emballonuridae, Megadermatidae, Molossidae and Nycteridae reported from Peninsular Malaysia. The percentage of pseudoreplicate trees (±70%) in which the DNA barcodes clustered together in the bootstrap test (500 pseudoreplicates) are shown above the branches. Abbreviation as follows: PM = Peninsular Malaysia, VN = Vietnam, BN = Borneo (including Sabah & Sarawak of East Malaysia, Brunei and Kalimantan Indonesia), TH = Thailand, LA = Laos, SM = Sumatera Indonesia, CH = China. https://doi.org/10.1371/journal.pone.0179555.g003
Figure 3 in Butterfly-parasitoid-hostplant interactions in Western Palaearctic Hesperiidae: a DNA barcoding reference library
Figure 3. Mounted specimens illustrating the species of Microgastrinae recovered in this study. A, Cotesia glabrata Telenga ex Carcharodus alceae, Italy. Adult plus cocoons. Gregarious parasitoid; brood sizes vary considerably, host usually well grown or prepupal when killed. The other Cotesia species (near glabrata) look similar and behave in the same way. B, Dolichogenidea sp. near sicaria Marshall, ex Carcharodus alceae, Spain. Adult plus cocoon. Solitary parasitoid, killing the host while still quite young. C, Microgaster australis Thomson, ex Muschampia stauderi, Greece. Adult plus cocoon. Solitary parasitoid, usually killing the host as a prepupa. D, Microgaster nobilis Reinhard, ex Carcharodus alceae, Spain. Adult plus cocoon. Solitary parasitoid, usually killing the host as a prepupa. All specimens are in the collection of the National Museums of Scotland.
Figure 4 in Butterfly-parasitoid-hostplant interactions in Western Palaearctic Hesperiidae: a DNA barcoding reference library
Figure 4. Interaction matrices showing the recorded interactions of Hesperiidae and their hostplants (A), Hesperiidae and their parasitoids (B) and parasitoids and hostplants of Hesperiidae (C). White squares indicate recorded interactions between the taxa in the corresponding row and column, while blue squares indicate lack of interaction.
Figure 2 in Butterfly-parasitoid-hostplant interactions in Western Palaearctic Hesperiidae: a DNA barcoding reference library
Figure 2. Circular cladogram showing ecological interactions among European and North African Hesperiidae, their hostplants, and their microgastrine parasitoids, recovered through DNA barcoding for Hesperiidae and/or parasitoids. Hesperiid, parasitoid and plant cladograms are coloured in orange, blue and green, respectively. Lines representing interactions with parasitoids are coloured in blue, while lines involving hostplant interactions are coloured in green.
Figure 1 in Butterfly-parasitoid-hostplant interactions in Western Palaearctic Hesperiidae: a DNA barcoding reference library
Figure 1. Representation of the study system. Hesperiid larvae feeding on their hostplants can be attacked by a number of parasitoids, which can in turn be attacked by various hyperparasitoids. A, Spialia rosae on its hostplant Rosa sicula. B, third instar larva of Sp. rosae on a silk shelter. C, Microgaster australis parasitizing an L3 Sp. rosae larva. D, Gelis sp. parasitizing M. australis on its cocoon after emerging from the Sp. rosae larva. Drawings by Martí Franch.
Linked collectors and determiners for: A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library.
Natural history specimen data linked to collectors and determiners held within, "A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/6ea2cc5c-857b-4b47-8135-8bff7efbd1fc">https://bionomia.net/dataset/6ea2cc5c-857b-4b47-8135-8bff7efbd1fc</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/6ea2cc5c-857b-4b47-8135-8bff7efbd1fc">https://gbif.org/dataset/6ea2cc5c-857b-4b47-8135-8bff7efbd1fc</a>. Formatted as a Frictionless Data package.
BAGS: an automated barcode, audit & grade system for DNA barcode reference libraries
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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>
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>
Dataset from: A curated DNA barcode reference library for parasitoids of northern European cyclically outbreaking geometrid moths
<p><span>Large areas of forests are annually damaged or destroyed by outbreaking insect pests. Understanding the factors that trigger and terminate such population eruptions has become crucially important, as plants, plant-feeding insects, and their natural enemies may respond differentially to the ongoing changes in the global climate. In northernmost Europe, climate-driven range expansions of the geometrid moths <em>Epirrita autumnata</em> and <em>Operophtera brumata</em> have resulted in overlapping and increasingly severe outbreaks. Delayed density-dependent responses of parasitoids are a plausible explanation for the ten-year population cycles of these moth species, but the impact of parasitoids on geometrid outbreak dynamics is unclear due to a lack of knowledge on the host ranges and prevalences of parasitoids attacking the moths in nature. To overcome these problems, we reviewed the literature on parasitism in the focal geometrid species in their outbreak range, and then constructed a DNA barcode reference library for all relevant parasitoid species based on reared specimens and sequences obtained from public databases. The combined parasitoid community of<em> E. autumnata</em> and <em>O. brumata</em> consists of 32 hymenopteran species, all of which can be reliably identified based on their barcode sequences. The curated barcode library presented here opens up new opportunities for estimating the abundance and community composition of parasitoids across populations and ecosystems based on mass barcoding and metabarcoding approaches. Such information can be used for elucidating the role of parasitoids in moth population control, possibly also for devising methods for reducing the extent, intensity, and duration of outbreaks.</span></p>
Data from: Establishing community-wide DNA barcode references for conserving mangrove forests in China
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Dataset from: A curated DNA barcode reference library for parasitoids of northern European cyclically outbreaking geometrid moths
Open the record for dataset details and reuse information.
A new taxonomist-curated reference library of DNA barcodes for Neotropical electric fishes (Teleostei: Gymnotiformes)
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Data from: Untangling taxonomy: a DNA barcode reference library for Canadian spiders
Approximately 1460 species of spiders have been reported from Canada, 3% of the global fauna. This study provides a DNA barcode reference library for 1018 of these species based upon the analysis of more than 30 000 specimens. The sequence results show a clear barcode gap in most cases with a mean intraspecific divergence of 0.78% vs. a minimum nearest-neighbour (NN) distance averaging 7.85%. The sequences were assigned to 1359 Barcode index numbers (BINs) with 1344 of these BINs composed of specimens belonging to a single currently recognized species. There was a perfect correspondence between BIN membership and a known species in 795 cases, while another 197 species were assigned to two or more BINs (556 in total). A few other species (26) were involved in BIN merges or in a combination of merges and splits. There was only a weak relationship between the number of specimens analysed for a species and its BIN count. However, three species were clear outliers with their specimens being placed in 11–22 BINs. Although all BIN splits need further study to clarify the taxonomic status of the entities involved, DNA barcodes discriminated 98% of the 1018 species. The present survey conservatively revealed 16 species new to science, 52 species new to Canada and major range extensions for 426 species. However, if most BIN splits detected in this study reflect cryptic taxa, the true species count for Canadian spiders could be 30–50% higher than currently recognized.
Data from: DNA barcoding fishes from the Congo and the Lower Guinean provinces: assembling a reference library for poorly inventoried fauna
The Congolese and Lower Guinean ichthyological provinces are understudied hotspots of the global fish diversity. Here, we barcoded 741 specimens from the Lower and Middle Congo River and from three major drainage basins of the Lower Guinean ichthyological province, Kouilou-Niari, Nyanga and Ogowe. We identified 195 morphospecies belonging to 82 genera and 25 families. Most morphospecies (92.8%) corresponded to distinct clusters of DNA barcodes. Of the four morphospecies present in both neighbouring ichthyological provinces, only one showed DNA barcode divergence <2.5%. A small fraction of the fishes barcoded here (12.9% of the morphospecies and 16.1% of the barcode clusters representing putative species) were also barcoded in a previous large-scale DNA analysis of freshwater fishes of the Lower Congo published in 2011 (191 specimens, 102 morphospecies). We compared species assignments before and after taxonomic updates and across studies performed by independent research teams and observed that most cases of inconsistent species assignments were due to unknown diversity (undescribed species and unknown intraspecific variation). Our results report more than 17 putative new species and show that DNA barcode data provide a measure of genetic variability that facilitates the inventory of underexplored ichthyofaunae. However, taxonomic scrutiny, associated with revisions and new species descriptions, is indispensable to delimit species and build a coherent reference library.
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