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.
79
datasets available to search
ShareScore release 0.9.0
Dataset results
79 results for “genetic barcoding”
Genetic barcoding of museum eggshell improves data integrity of avian biological collections
Open the record for dataset details and reuse information.
Predation patterns on the tundra – genetic barcoding of scats from two sympatric fox species
Open the record for dataset details and reuse information.
Evaluating the genetic variation of the COI gene of Insecta: Implications for DNA barcoding, metabarcoding and species delimitation studies
Open the record for dataset details and reuse information.
Figure 4 from: Miller LA, Benefield TD, Lounsbury SA, Lohrmann V, Blaschke JD (2019) DNA barcoding of rhopalosomatid larvae reveals a new host record and genetic evidence of a second species of Rhopalosoma Cresson (Hymenoptera, Rhopalosomatidae) in America north of Mexico. Journal of Hymenoptera Research 74: 35-46. https://doi.org/10.3897/jhr.74.38276
Figure 4 Neighbor Joining phylogeny of Rhopalosoma with Olixon sp. as the outgroup. Consensus support shown for important nodes. Cricket photos by Carl Strang (Hapithus agitator), and Wil Hershberger/Lang Elliott (H. saltator and Anaxipha exigua s.g.).
Figure 3 from: Miller LA, Benefield TD, Lounsbury SA, Lohrmann V, Blaschke JD (2019) DNA barcoding of rhopalosomatid larvae reveals a new host record and genetic evidence of a second species of Rhopalosoma Cresson (Hymenoptera, Rhopalosomatidae) in America north of Mexico. Journal of Hymenoptera Research 74: 35-46. https://doi.org/10.3897/jhr.74.38276
Figure 3 Maximum Likelihood phylogeny of Rhopalosoma with Olixon sp. as the outgroup. Bootstrap support shown for important nodes. Cricket photos by Carl Strang (Hapithus agitator), and Wil Hershberger/Lang Elliott (H. saltator and Anaxipha exigua s.g.).
Figure 1 from: Miller LA, Benefield TD, Lounsbury SA, Lohrmann V, Blaschke JD (2019) DNA barcoding of rhopalosomatid larvae reveals a new host record and genetic evidence of a second species of Rhopalosoma Cresson (Hymenoptera, Rhopalosomatidae) in America north of Mexico. Journal of Hymenoptera Research 74: 35-46. https://doi.org/10.3897/jhr.74.38276
Figure 1 Adult female Rhopalosoma cf. nearcticum attracted to a mercury-vapor lamp in Fairfax County, VA, USA on July 29, 2018. Photo by Ashley Bradford, initially posted on bugguide.net.
Figure 2 from: Miller LA, Benefield TD, Lounsbury SA, Lohrmann V, Blaschke JD (2019) DNA barcoding of rhopalosomatid larvae reveals a new host record and genetic evidence of a second species of Rhopalosoma Cresson (Hymenoptera, Rhopalosomatidae) in America north of Mexico. Journal of Hymenoptera Research 74: 35-46. https://doi.org/10.3897/jhr.74.38276
Figure 2 Life stages and representative specimens of RhopalosomaA 5th instar larva prior to burrowing (MK991305) B pupal case extracted from soil (MK991302) C adult after failing to emerge properly from cocoon (MK991303) D disarticulated mandible from pupal case (MK991302) E pupal case extracted from dirt showing still living pre-pupa (MK991301) F pupal case awaiting adult emergence (MK991300) G–I early instar larvae attached to: GHapithus agitator adult (larva: MK991304) and HH. saltator nymph (larva: MK991307) IAnaxipha exigua species group (inset: detached larva: MK991302).
Figure 3 from: Raupach MJ, Rulik B, Spelda J (2022) Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea). ZooKeys 1082: 103-125. https://doi.org/10.3897/zookeys.1082.69851
Figure 3 Subtree of the Neighbor-joining topology based on Kimura 2-parameter distances of all analyzed specimens of Platyarthrus hoffmannseggii Brandt, 1833 and nearest neighbor. Branches with specimen ID-number from BOLD and sample localities. Numbers next to internal nodes are non-parametric bootstrap values (in %) with values higher than 80. BIN values are based on the barcode analysis from 05-06-2020. The isopod drawing by Christian Schmidt was obtained from Raupach (2005).
Supplementary material 2 from: Raupach MJ, Rulik B, Spelda J (2022) Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea). ZooKeys 1082: 103-125. https://doi.org/10.3897/zookeys.1082.69851
Neighbor-joining topology
Supplementary material 1 from: Raupach MJ, Rulik B, Spelda J (2022) Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea). ZooKeys 1082: 103-125. https://doi.org/10.3897/zookeys.1082.69851
Barcode analysis using the BOLD workbench
Figure 1 from: Raupach MJ, Rulik B, Spelda J (2022) Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea). ZooKeys 1082: 103-125. https://doi.org/10.3897/zookeys.1082.69851
Figure 1 Various woodlouse species of Germany AOniscus asellus Linnaeus, 1758 BArmadillidium nasatum Budde-Lund, 1885 CTrachelipus ratzeburgii (Brandt, 1833) DMesonicus alpicola (Heller, 1858) EPhiloscia muscorum (Scopoli, 1763) FHaplophthalmus mariae Strouhal, 1953 GArmadillidium opacum (C. Koch, 1841) HPlatyarthrus hoffmannseggii Brandt, 1833. Scale bar: 1 mm. Photograph credits: A–G Jörg Spelda H Armin Rose.
Supplementary material 3 from: Raupach MJ, Rulik B, Spelda J (2022) Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea). ZooKeys 1082: 103-125. https://doi.org/10.3897/zookeys.1082.69851
Neighbor-joining topology of the BOLD workbench including BIN analysis
Figure 2 from: Raupach MJ, Rulik B, Spelda J (2022) Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea). ZooKeys 1082: 103-125. https://doi.org/10.3897/zookeys.1082.69851
Figure 2 Neighbor-joining (NJ) topology of the analyzed isopod species based on Kimura 2-parameter distances. Triangles show the relative number of individual's sampled (height) and sequence divergence (width). Red triangles highlight terrestrial species with intraspecific maximum pairwise distances > 2.2%, whereas dark blue triangles indicate freshwater species with such distances. Numbers next to nodes represent non-parametric bootstrap values > 90% (1,000 replicates). Asterisks indicate species not recorded in Germany.
Supplementary material 2 from: Hernández-Triana LM, Brugman VA, Nikolova NI, Ruiz-Arrondo I, Barrero E, Thorne T, de Marco MF, Krüger A, Lumley S, Johnson N, Fooks AR (2019) DNA barcoding of British mosquitoes (Diptera, Culicidae) to support species identification, discovery of cryptic genetic diversity and monitoring invasive species. ZooKeys 832: 57-76. https://doi.org/10.3897/zookeys.832.32257
: Data type: molecular data
Supplementary material 1 from: Hernández-Triana LM, Brugman VA, Nikolova NI, Ruiz-Arrondo I, Barrero E, Thorne T, de Marco MF, Krüger A, Lumley S, Johnson N, Fooks AR (2019) DNA barcoding of British mosquitoes (Diptera, Culicidae) to support species identification, discovery of cryptic genetic diversity and monitoring invasive species. ZooKeys 832: 57-76. https://doi.org/10.3897/zookeys.832.32257
: Data type: molecular data
Figure 2 from: Hernández-Triana LM, Brugman VA, Nikolova NI, Ruiz-Arrondo I, Barrero E, Thorne T, de Marco MF, Krüger A, Lumley S, Johnson N, Fooks AR (2019) DNA barcoding of British mosquitoes (Diptera, Culicidae) to support species identification, discovery of cryptic genetic diversity and monitoring invasive species. ZooKeys 832: 57-76. https://doi.org/10.3897/zookeys.832.32257
Figure 2 Neighbor joining tree of COI DNA barcodes (658 bp) for mosquito species. A divergence of > 2% may be indicative of separate operational taxonomic units. Only bootstrap values higher than 70% are shown.
Figure 1 from: Hernández-Triana LM, Brugman VA, Nikolova NI, Ruiz-Arrondo I, Barrero E, Thorne T, de Marco MF, Krüger A, Lumley S, Johnson N, Fooks AR (2019) DNA barcoding of British mosquitoes (Diptera, Culicidae) to support species identification, discovery of cryptic genetic diversity and monitoring invasive species. ZooKeys 832: 57-76. https://doi.org/10.3897/zookeys.832.32257
Figure 1 Location of study sites in the United Kingdom. Key: 1 ADAS Arthur Rickwood; 2 Church Farm; 3 Coombelands Farms; 4 Elmley Nature Reserve; 5 Glendell Livery, Mill Lane; 6 Frimley; 7 Mudchute Farm; 8 Northney Farm, Hayling Island; 9 White Lodge, Bisley; 10 Bartley Heath; 11 Dee Marsh.
Fig. 1 in DNA barcoding and genetic variability of earthworms (Clitellata: Oligochaeta) with new records from Mizoram, India
Fig. 1 Location of sampling sites of earthworms from Mizoram, NER
Fig. 2 in DNA barcoding and genetic variability of earthworms (Clitellata: Oligochaeta) with new records from Mizoram, India
Fig. 2 Results from ABGD analysis showing stable count of 24 OTUs
Data from: Genetic barcoding of dark-spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies
Unicellular, eukaryotic organisms (protists) play a key role in soil food webs as major predators of microorganisms. However, due to the polyphyletic nature of protists, no single universal barcode can be established for this group, and the structure of many protistean communities remains unresolved. Plasmodial slime moulds (Myxogastria or Myxomycetes) stand out among protists by their formation of fruit bodies, which allow for a morphological species concept. By Sanger sequencing of a large collection of morphospecies, this study presents the largest database to date of dark-spored myxomycetes and evaluate a partial 18S SSU gene marker for species annotation. We identify and discuss the use of an intraspecific sequence similarity threshold of 99.1% for species differentiation (OTU picking) in environmental PCR studies (ePCR) and estimate a hidden diversity of putative species, exceeding those of described morphospecies by 99%. When applying the identified threshold to an ePCR data set (including sequences from both NGS and cloning), we find 64 OTUs of which 21.9% had a direct match (>99.1% similarity) to the database and the remaining had on average 90.2 ± 0.8% similarity to their best match, thus thought to represent undiscovered diversity of dark-spored myxomycetes.
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.