Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
4,144
datasets available to search
ShareScore release 0.9.0
Dataset results
4,144 results for “ITS barcode”
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.
Data from: Testing the potential of DNA barcoding in vertebrate radiations: the case of the littoral cichlids (Pisces, Perciformes, Cichlidae) from Lake Tanganyika
We obtained 398 cytochrome c oxidase subunit I barcodes of 96 morphospecies of Lake Tanganyika (LT) cichlids from the littoral zone. The potential of DNA barcoding in these fishes was tested using both species identification and species delineation methods. The best match (BM) and best close match (BCM) methods were used to evaluate the overall identification success. For this, three libraries were analysed in which the specimens were categorized into Operational Taxonomic Units (OTU) in three alternative ways: (A) morphologically distinct, including undescribed, species, (B) valid species and (C) complexes of morphologically similar or closely related species. For libraries A, B and C, 73, 73 and 96% (BM) and 72, 70 and 94% (BCM) of the specimens were correctly identified. Additionally, the potential of two species delineation methods was tested. The General Mixed Yule Coalescent (GMYC) analysis suggested 70 hypothetical species, while the Automatic Barcode Gap Discovery (ABGD) method revealed 115 putative species. Although the ABGD method had a tendency to oversplit, it outperformed the GMYC analysis in retrieving the species. In most cases where ABGD suggested oversplitting, this was due to intraspecific geographical variation. The failure of the GMYC method to retrieve many species could be attributed to discrepancies between mitochondrial gene trees and the evolutionary histories of LT cichlid species. Littoral LT cichlids have complex evolutionary histories that include instances of hybridization, introgression and rapid speciation. Nevertheless, although the utility of DNA barcoding in identification is restricted to the level of complexes, it has potential for species discovery in cichlid radiations.
Data from: Barcoding snakeheads (Teleostei, Channidae) revisited: discovering greater species diversity and resolving perpetuated taxonomic confusions
Snakehead fishes of the family Channidae are predatory freshwater teleosts from Africa and Asia comprising 38 valid species. Snakeheads are important food fishes (aquaculture, live food trade) and have been introduced widely with several species becoming highly invasive. A channid barcode library was recently assembled by Serrao and co-workers to better detect and identify potential and established invasive snakehead species outside their native range. Comparing our own recent phylogenetic results of this taxonomically confusing group with those previously reported revealed several inconsistencies that prompted us to expand and improve on previous studies. By generating 343 novel snakehead coxI sequences and combining them with an additional 434 coxI sequences from GenBank we highlight several problems with previous efforts towards the assembly of a snakehead reference barcode library. We found that 16.3% of the channid coxI sequences deposited in GenBank are based on misidentifications. With the inclusion of our own data we were, however, able to solve these cases of perpetuated taxonomic confusion. Different species delimitation approaches we employed (BIN, GMYC, and PTP) were congruent in suggesting a potentially much higher species diversity within snakeheads than currently recognized. In total, 90 BINs were recovered and within a total of 15 currently recognized species multiple BINs were identified. This higher species diversity is mostly due to either the incorporation of undescribed, narrow range, endemics from the Eastern Himalaya biodiversity hotspot or the incorporation of several widespread species characterized by deep genetic splits between geographically well-defined lineages. In the latter case, over-lumping in the past has deflated the actual species numbers. Further integrative approaches are clearly needed for providing a better taxonomic understanding of snakehead diversity, new species descriptions and taxonomic revisions of the group.
Data from: DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity
Documenting the diversity of marine life is challenging because many species are cryptic, small, and rare, and belong to poorly known groups. New sequencing technologies, especially when combined with standardized sampling, promise to make comprehensive biodiversity assessments and monitoring feasible on a large scale. We used this approach to characterize patterns of diversity on oyster reefs across a range of geographic scales comprising a temperate location [Virginia (VA)] and a subtropical location [Florida (FL)]. Eukaryotic organisms that colonized multilayered settlement surfaces (autonomous reef monitoring structures) over a 6-mo period were identified by cytochrome c oxidase subunit I barcoding (>2-mm mobile organisms) and metabarcoding (sessile and smaller mobile organisms). In a total area of ∼15.64 m2 and volume of ∼0.09 m3, 2,179 operational taxonomic units (OTUs) were recorded from 983,056 sequences. However, only 10.9% could be matched to reference barcodes in public databases, with only 8.2% matching barcodes with both genus and species names. Taxonomic coverage was broad, particularly for animals (22 phyla recorded), but 35.6% of OTUs detected via metabarcoding could not be confidently assigned to a taxonomic group. The smallest size fraction (500 to 106 μm) was the most diverse (more than two-thirds of OTUs). There was little taxonomic overlap between VA and FL, and samples separated by ∼2 m were significantly more similar than samples separated by ∼100 m. Ground-truthing with independent assessments of taxonomic composition indicated that both presence–absence information and relative abundance information are captured by metabarcoding data, suggesting considerable potential for ecological studies and environmental monitoring.
Mitochondrial DNA tree for COI sequences (DNA barcode) of the goby genus Trimma.
<p>Mitochondrial DNA tree for COI sequences (DNA barcode) of the goby genus Trimma</p>
FIGURE 4 in Use of DNA barcoding to distinguish the malaria vector An opheles neivai in Colombia
FIGURE 4. Dendrogram (K2P) for An. neivai specimens from Colombia, Panama, with other Kerteszia and Nyssorhynchus species (based on a 535 bp COI alignment. Branch support was provided by bootstrap resampling (10000 replicates).
FIGURE 5 in Use of DNA barcoding to distinguish the malaria vector An opheles neivai in Colombia
FIGURE 5. Haplotype network for An. neivai collected in Colombia and Panama (based on a 535 bp COI alignment).
FIGURE 2 in Use of DNA barcoding to distinguish the malaria vector An opheles neivai in Colombia
FIGURE 2. Genetic differences (K2P) among An. neivai collected specimens (A) and against other species from Kerteszia (B) and Nyssorhynchus from NCBI (C).
FIGURES 9–10 in Description of a new Oriental stonefly species, Phanoperla constanspina (Plecoptera: Perlidae) from Mindanao, Philippines and association of life stages using DNA barcoding
FIGURES 9–10. Phanoperla constanspina sp. nov. male nymph. (9) Right mandible. (10) Right foreleg. Scale = 0.5 mm.
FIGURE 12 in Description of a new Oriental stonefly species, Phanoperla constanspina (Plecoptera: Perlidae) from Mindanao, Philippines and association of life stages using DNA barcoding
FIGURE 12. Phanoperla constanspina sp. nov. male nymph. (A) Suture of anterolateral submental lobes. (B) Mesosternum posterior margin pointing fringes of hairs. (C) One pair of posterocoxal gill of hindleg.
FIGURE 7 in Description of a new Oriental stonefly species, Phanoperla constanspina (Plecoptera: Perlidae) from Mindanao, Philippines and association of life stages using DNA barcoding
FIGURE 7. Phenotypic variation of six adult male Phanoperla constanspina sp. nov. based on the shape and structure of hemitergites (HT) and unbranched anterior process (AP), adorned with variable short setae on tergum 9. (A) (Haplotype: A- G23.m) Medium-sized AP, body and slightly bent on the pointed apex, setal patches isolated from each other. (B) (Haplotype: A-H7.m) AP small and pointed, setae located above the apical tip adjacent to each other. (C) (Haplotype: A-H16.m) Plump base and small AP (Fig. 5), with slightly pointed tip, paired setal patches adjacent and overlapping. (D) (Haplotype: A-H12.m) Medium and longer AP, bent on the inner side near the apex, setal patches fused, distributed along and near the process. (E) (Haplotype: A-E23.m) AP blunt on the tip in a medium-sized body, setal patches adjacent. (F) (Haplotype: A-H11.m) HT and AP broad and plump, resembling a hook-like structure at the tip, setal patches adjacent.
FIGURE 2 in Description of a new Oriental stonefly species, Phanoperla constanspina (Plecoptera: Perlidae) from Mindanao, Philippines and association of life stages using DNA barcoding
FIGURE 2. Phanoperla constanspina sp. nov. male wing. (2A) Right forewing, showing the forking of Cu2 from Cu1. (2B) Right hindwing. Scale = 1.00 mm.
FIGURES 1 in Description of a new Oriental stonefly species, Phanoperla constanspina (Plecoptera: Perlidae) from Mindanao, Philippines and association of life stages using DNA barcoding
FIGURES 1. Phanoperla constanspina sp. nov. head and pronotum. (1A) Male adult, indicating occipital line. (1B) Female adult. Scale = 1.00 mm.
FIGURES 3–4 in Description of a new Oriental stonefly species, Phanoperla constanspina (Plecoptera: Perlidae) from Mindanao, Philippines and association of life stages using DNA barcoding
FIGURES 3–4. Phanoperla constanspina sp. nov. male. (3) Right foreleg. (4) Abdominal sternite showing hair brushes on each segment (S5–S8). Penial capsule visible on S9. Scale = 1.00 mm.
FIGURE 5 in Description of a new Oriental stonefly species, Phanoperla constanspina (Plecoptera: Perlidae) from Mindanao, Philippines and association of life stages using DNA barcoding
FIGURE 5. Phanoperla constanspina sp. nov. male dorsal terminalia showing the hemitergal (arrow) and paired clumps of short setae located on medial tergum 9. Scale = 1.00 mm.
FIGURE 12 in DNA barcoding and morphological studies confirm the occurrence of three Atarbolana (Crustacea: Isopoda: Cirolanidae) species along the coastal zone of the Persian Gulf and Gulf of Oman
FIGURE 12. Unrooted Neighbour-joining phylogram of the analyzed CO1 sequences of the three studied Atarbolana species. The optimal tree with the sum of branch length = 0.35376694 is shown. Numbers next to internal branches are non-parametric bootstrap values (in %). Only values above 90% are shown. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. Evolutionary distances were computed using the Kimura 2-parameter method and are in the units of the number of base substitutions per site. The analysis involved 28 nucleotide sequences. Codon positions included were 1st+2nd+3rd+Noncoding. All positions containing gaps and missing data were eliminated. There were a total of 658 positions in the final dataset.
FIGURE 10 in DNA barcoding and morphological studies confirm the occurrence of three Atarbolana (Crustacea: Isopoda: Cirolanidae) species along the coastal zone of the Persian Gulf and Gulf of Oman
FIGURE 10. Atarbolana setosa, male, (ZMSU 1014); A–C, pereopods 5–7 respectively; D, uropod dorsal view; E, uropod ventral view.
FIGURE 8 in DNA barcoding and morphological studies confirm the occurrence of three Atarbolana (Crustacea: Isopoda: Cirolanidae) species along the coastal zone of the Persian Gulf and Gulf of Oman
FIGURE 8. Atarbolana setosa, male, (ZMSU 1014); A, left mandible; B, maxillula; C, maxilla; D, maxilliped; E, maxilliped endite.
FIGURE 7 in DNA barcoding and morphological studies confirm the occurrence of three Atarbolana (Crustacea: Isopoda: Cirolanidae) species along the coastal zone of the Persian Gulf and Gulf of Oman
FIGURE 7. Atarbolana setosa, male, (ZMSU 1014); A, dorsal view; B, lateral view; C, pleotelson apex; D, female pleotelson; E, antennula; F, antenna.
FIGURE 5 in DNA barcoding and morphological studies confirm the occurrence of three Atarbolana (Crustacea: Isopoda: Cirolanidae) species along the coastal zone of the Persian Gulf and Gulf of Oman
FIGURE 5. Atarbolana exoconta, male, (ZMSU 1010); A–C, pereopods 5–7 respectively; D, uropod dorsal view; E, uropod ventral view.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.