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103 results for “DNA barcode library”
BAGS: an automated barcode, audit & grade system for DNA barcode reference libraries
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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>
Dataset from: A curated DNA barcode reference library for parasitoids of northern European cyclically outbreaking geometrid moths
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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: Establishing a community-wide DNA barcode library as a new tool for arctic research
DNA sequences offer powerful tools for describing the members and interactions of natural communities. In this study, we establish the to-date most comprehensive library of DNA barcodes for a terrestrial site, including all known macroscopic animals and vascular plants of an intensively studied area of the High Arctic, the Zackenberg Valley in Northeast Greenland. To demonstrate its utility, we apply the library to identify nearly 20 000 arthropod individuals from two Malaise traps, each operated for two summers. Drawing on this material, we estimate the coverage of previous morphology-based species inventories, derive a snapshot of faunal turnover in space and time and describe the abundance and phenology of species in the rapidly changing arctic environment. Overall, 403 terrestrial animal and 160 vascular plant species were recorded by morphology-based techniques. DNA barcodes (CO1) offered high resolution in discriminating among the local animal taxa, with 92% of morphologically distinguishable taxa assigned to unique Barcode Index Numbers (BINs) and 93% to monophyletic clusters. For vascular plants, resolution was lower, with 54% of species forming monophyletic clusters based on barcode regions rbcLa and ITS2. Malaise catches revealed 122 BINs not detected by previous sampling and DNA barcoding. The insect community was dominated by a few highly abundant taxa. Even closely related taxa differed in phenology, emphasizing the need for species-level resolution when describing ongoing shifts in arctic communities and ecosystems. The DNA barcode library now established for Zackenberg offers new scope for such explorations, and for the detailed dissection of interspecific interactions throughout the community.
Data from: A DNA barcode library for North American Pyraustinae (Lepidoptera: Pyraloidea: Crambidae)
Although members of the crambid subfamily Pyraustinae are frequently important crop pests, their identification is often difficult because many species lack conspicuous diagnostic morphological characters. DNA barcoding employs sequence diversity in a short standardized gene region to facilitate specimen identifications and species discovery. This study provides a DNA barcode reference library for North American pyraustines based upon the analysis of 1589 sequences recovered from 137 nominal species, 87% of the fauna. Data from 125 species were barcode compliant (>500bp, <1% n), and 99 of these taxa formed a distinct cluster that was assigned to a single BIN. The other 26 species were assigned to 56 BINs, reflecting frequent cases of deep intraspecific sequence divergence and a few instances of barcode sharing, creating a total of 155 BINs. Two systems for OTU designation, ABGD and BIN, were examined to check the correspondence between current taxonomy and sequence clusters. The BIN system performed better than ABGD in delimiting closely related species, while OTU counts with ABGD were influenced by the value employed for relative gap width. Different species with low or no interspecific divergence may represent cases of unrecognized synonymy, whereas those with high intraspecific divergence require further taxonomic scrutiny as they may involve cryptic diversity. The barcode library developed in this study will also help to advance understanding of relationships among species of Pyraustinae.
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.
Data from: Starting a DNA barcode reference library for shallow water polychaetes from the southern European Atlantic coast
Annelid polychaetes have been seldom the focus of dedicated DNA barcoding studies, despite their ecological relevance and often dominance, particularly in soft-bottom estuarine and coastal marine ecosystems. Here, we report the first assessment of the performance of DNA barcodes in the discrimination of shallow water polychaete species from the southern European Atlantic coast, focusing on specimens collected in estuaries and coastal ecosystems of Portugal. We analysed cytochrome oxidase I DNA barcodes (COI-5P) from 164 specimens, which were assigned to 51 morphospecies. To our data set from Portugal, we added available published sequences selected from the same species, genus or family, to inspect for taxonomic congruence among studies and collection location. The final data set comprised 290 specimens and 79 morphospecies, which generated 99 Barcode Index Numbers (BINs) within Barcode of Life Data Systems (BOLD). Among these, 22 BINs were singletons, 47 other BINs were concordant, confirming the initial identification based on morphological characters, and 30 were discordant, most of which consisted on multiple BINs found for the same morphospecies. Some of the most prominent cases in the latter category include Hediste diversicolor (O.F. Müller, 1776) (7), Eulalia viridis (Linnaeus, 1767) (2) and Owenia fusiformis (delle Chiaje, 1844) (5), all of them reported from Portugal and frequently used in ecological studies as environmental quality indicators. Our results for these species showed discordance between molecular lineages and morphospecies, or added additional relatively divergent lineages. The potential inaccuracies in environmental assessments, where underpinning polychaete species diversity is poorly resolved or clarified, demand additional and extensive investigation of the DNA barcode diversity in this group, in parallel with alpha taxonomy efforts.
FIGURE 37 in First record and five new species of Xylographellini (Coleoptera: Ciidae) from China, with online DNA barcode library of the family
FIGURE 37. Lower part of the Maximum Likelihood inference phylogram, upper part of which is depicted on Fig. 36. HT: holotype.
FIGURES 25 – 34 in First record and five new species of Xylographellini (Coleoptera: Ciidae) from China, with online DNA barcode library of the family
FIGURES 25 – 34. Syncosmetus stheno sp. nov., male holotype from Jizu Shan (Figs. 25 – 27): (25) dorsal view; (26) lateral view; (27) ventral view. Pregenital segment and aedeagus of a paratype from Jizu Shan (Figs. 28 – 30): (28) sternite VIII; (29) tegmen; (30) penis. Male paratype from Gaoligong Shan (Figs. 31 – 34): (31) dorsal view; (32) sternite VIII; (33) tegmen (left) still joined with basal piece (= phallobase; right) through membranes; (34) penis. The apices of sclerites of male abdominal terminalia are oriented to the left. Scale bars: 0.5 mm (Figs. 25 – 27, 31); 0.1 mm (Figs. 28 – 30, 32 – 34).
FIGURES 15 – 21 in First record and five new species of Xylographellini (Coleoptera: Ciidae) from China, with online DNA barcode library of the family
FIGURES 15 – 21. Syncosmetus medusa sp. nov., male holotype from Emei Shan (Figs. 15 – 17): (15) dorsal view; (16) lateral view, with arrow showing first two elytral keels diverging close to elytral base; (17) ventral view. Pregenital segment and aedeagus of a paratype from the type locality (Figs. 18 – 21): (18) sternite VIII; (19) tegmen; (20) basal piece (= phallobase); (21) penis. The apices of sclerites of male abdominal terminalia are oriented to the left. Scale bars: 0.5 mm (Figs. 15 – 17); 0.1 mm (Figs. 18 – 21).
FIGURES 7 – 14 in First record and five new species of Xylographellini (Coleoptera: Ciidae) from China, with online DNA barcode library of the family
FIGURES 7 – 14. Syncosmetus euryale sp. nov., male holotype (Figs. 7 – 8) from Gaoligong Shan: (7) dorsal view; (8) lateral view, with large arrow showing the first longitudinal elytral keel extending to about the middle of elytral edge, and small numbered arrows referring to the counting system of elytral keels used in the present work; (9) ventral view; (10) female paratype from Haba Shan. Pregenital segment and aedeagus of a paratype from the type locality (Figs. 11 – 14): (11) sternite VIII; (12) tegmen; (13) basal piece (= phallobase); (14) penis. The apices of sclerites of male abdominal terminalia are oriented to the left. Scale bars: 0.5 mm (Figs. 7 – 10); 0.1 mm (Figs. 11 – 14).
FIGURE 36 in First record and five new species of Xylographellini (Coleoptera: Ciidae) from China, with online DNA barcode library of the family
FIGURE 36. Upper part of the Maximum Likelihood inference phylogram obtained by using the Maximum Likelihood method based on the General Time Reversible model and using 185 DNA barcodes. The tree with the highest log likelihood is shown. The percentage of trees in which the associated taxa clustered together (= bootstrap) is shown next to the branches.
FIGURES 22 – 24 in First record and five new species of Xylographellini (Coleoptera: Ciidae) from China, with online DNA barcode library of the family
FIGURES 22 – 24. Syncosmetus perseus sp. nov., female holotype from Gongga Shan: (22) dorsal view; (23) lateral view, with arrow showing united apices of second and third elytral keels; (24) ventral view. Scale bar: 0.5 mm (Figs. 22 – 24).
FIGURES 1 – 6 in First record and five new species of Xylographellini (Coleoptera: Ciidae) from China, with online DNA barcode library of the family
FIGURES 1 – 6. Scolytocis danae sp. nov., male holotype from Gaoligong Shan: (1) dorsal view; (2) lateral view; (3) ventral view. Aedeagus of the holotype (Figs. 4 – 6): (4) tegmen; (5) basal piece (= phallobase); (6) penis. The apices of sclerites of male abdominal terminalia are oriented to the left. Scale bars: 0.5 mm (Figs. 1 – 3); 0.1 mm (Figs. 4 – 6).
FIGURE 35 in First record and five new species of Xylographellini (Coleoptera: Ciidae) from China, with online DNA barcode library of the family
FIGURE 35. Known distribution of Xylographellini beetles in the Palaearctic Region outside of Japan.
Supplementary material 1 from: Raupach MJ, Hannig K, Morinière J, Hendrich L (2016) A DNA barcode library for ground beetles (Insecta, Coleoptera, Carabidae) of Germany: The genus Bembidion Latreille, 1802 and allied taxa. ZooKeys 592: 121-141. https://doi.org/10.3897/zookeys.592.8316
Barcode analysis using the BOLD workbench : Explanation note: Molecular distances based on the Kimura 2-parameter model of the analyzed specimens of the analyzed species of the genera Asaphidion, Bembidion, Ocys and Sinechostictus. Divergence values were calculated for all studied sequences, using the Nearest Neighbour Summary implemented in the Barcode Gap Analysis tool provided by the Barcode of Life Data System (BOLD). Align sequencing option: BOLD aligner (amino acid based HMM), ambiguous base/gap handling: pairwise deletion. ISD = intraspecific distance. BINs are based on the barcode analysis from 01-02-2016. Asterisks indicate species not recorded from Germany. Species with intraspecific maximum pairwise distances >2.2% and species pairs with interspecific distances <2.2% are marked in bold. Country codes: A = Austria, B = Belgium, CZ = Czech Republic, D = Germany, F = France, I = Italy, S = Sweden and SLO = Slovenia.
Supplementary material 2 from: Raupach MJ, Hannig K, Morinière J, Hendrich L (2016) A DNA barcode library for ground beetles (Insecta, Coleoptera, Carabidae) of Germany: The genus Bembidion Latreille, 1802 and allied taxa. ZooKeys 592: 121-141. https://doi.org/10.3897/zookeys.592.8316
Neighbor joining topology : Explanation note: Neighbor joining topology of all analyzed carabid beetles based on Kimura 2-parameter distances. Specimens are classified using ID numbers from BOLD and species name. Numbers next to nodes represent non-parametric bootstrap values (1,000 replicates, in %).
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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.
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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
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