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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
Towards a DNA barcode library for Madagascar's threatened ichthyofauna
<p>Supplementary documents, trees and curated DNA barcode library dataset for freshwater and marine fishes from Madagascar, in XLSX, tab-delimited and Fasta formats.</p>
Supplemental files to "A COI DNA Barcode Library for Anastrepha Schiner (Diptera: Tephritidae)"
<p>The attached files are the supplemental material from Moore et al., "A COI DNA Barcode Library for <em>Anastrepha </em>Schiner (Diptera: Tephritidae)". They contain various DNA sequence alignments, calculation tables, tree files, taxonomic information on <em>Anastrepha</em>, and a R script.</p>
FIG. 4 in An updated checklist and a DNA barcode library for the earthworms (Crassiclitellata, Oligochaeta) of Corsica, France
FIG. 4. — Some examples of endemic earthworm species sampled in Corsica and their habitats (to their right): A, Scherotheca portonana L4 Qiu & Bouché, 1998; B, alpine pasture at Col de Vergio (Bouché#466); C, Scherotheca albomaculata Qiu & Bouché, 1998; D, open Mediterranean chaparral at Sainte-Lucie de PortoVecchio (Bouché#414); E, Eumenescolex emiliae L1 Qiu & Bouché, 1998; F, Pinus laricio L. forest at Zonza (Bouché#2932); G, Hormogaster insularis Bouché, 1970; H, Quercus suber L. open wood at Volpajola (Bouché#480). Scale bars: 5 cm.
FIG. 2 in An updated checklist and a DNA barcode library for the earthworms (Crassiclitellata, Oligochaeta) of Corsica, France
FIG. 2. — Bayesian inference of the phylogenetic relationships of earthworms from Corsica based on their COI sequences. Species-level genetic lineages (as delimited by ASAP, barcode gap analysis and morphological data) are shown as black triangles in order to facilitate visualization and to display the amount of intra-lineage genetic divergence (indicated by the height of the triangle). Green circles: posterior probability values over 90; all the species-level clades showed values close to 100.
FIG. 1 in An updated checklist and a DNA barcode library for the earthworms (Crassiclitellata, Oligochaeta) of Corsica, France
FIG. 1. — Distribution map of the sampling localities in Corsica Island. Locality codes refer to Table 1. Map base: Qgis.
FIG. 5 in An updated checklist and a DNA barcode library for the earthworms (Crassiclitellata, Oligochaeta) of Corsica, France
FIG. 5. — Observed and estimated species diversity of earthworms in the island of Corsica: A, incidence-based rarefaction and extrapolation curves of species numbers;B, Chao asymptotic estimator of species numbers. The figure compares the results obtained when considering all species-level lineages obtained with DNA barcodes (All), when considering non-cryptic lineages only (NC) and when considering all endemic lineages (End). Solid lines represent rarefaction curves, whereas dashed lines represent extrapolation curves; shaded areas are 95% and error bars confidence intervals based on a bootstrap with 200 replications.
FIG. 3 in An updated checklist and a DNA barcode library for the earthworms (Crassiclitellata, Oligochaeta) of Corsica, France
FIG. 3. — Graphical representation of the number of earthworm species known from Corsica. Rectangle surfaces are proportional to species numbers.
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.
Figure 3 in Endogean beetles (Coleoptera) of illustrated DNA barcode library Guatemala: deep soil sampling and
Figure 3. Neighbour Joining DNA barcode tree of 75 endogean beetles from Guatemala. Terminal names consist of the most detailed current taxonomic identification (genus, tribe, or subfamily), followed by specimen number, family name, sample number, length of the DNA barcode fragment [with the number of ambiguously read bases in square brackets], BIN number, and GenBank accession number.
Figure 2 in Endogean beetles (Coleoptera) of illustrated DNA barcode library Guatemala: deep soil sampling and
Figure 2. Sampling methods of the deep soil Guatemala beetles. (A–C) pits producing samples GT12, GT16, and GT25, respectively (note that sample GT16 is from an extremely dry habitat, while sample GT25 is twice as large in volume); (D) a floating soil sample in a barrel with water; (E) scooping floating organic foam containing live beetles on a fine mesh; (F) wet samples prior to specimen extraction; (G) two aluminium thermoeclectors of the novel larger and lighter design; (H) thermoeclectors exposed to the Sun.
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.
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