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76 results for “reference libraries”
Reference libraries for execute the Annopipe software
<p>Libraries needed to run the software ANNOPIPE, available in the following link:</p> <p>https://github.com/celiosantosjr/annopipe</p>
BOLD curated data and reference library
<ul> <li>BOLD_Public.05-Apr-2024.BAGS.d39fc06c483ea4a7252b6a4e203ca15c6ce4dd24.tsv - BAGS ranking of BIN x species combinations</li> <li>BOLD_Public.05-Apr-2024.3c74c5e91daa2ddccce41d38881edc2e242e9c81.tsv.gz - BCDM rated with curation pipeline</li> <li>refdb.fa - COI-5P records with BAGS=(A,B,C), rating=(1,2,3) with <a href="https://github.com/naturalis/galaxy-tool-BLAST">galaxy-tool-BLAST</a>-compliant full lineage</li> <li>families-for-curation.tar.gz - TSVs of families with BCDM records for manual curation</li> </ul>
Bibliographic references extracted from theses and dissertations in the Electronic Theses and Dissertations Library of the Federal University of Paraná, Brazil
<p>Bibliographic references obtained from a <a href="https://doi.org/10.5281/zenodo.1169586">subset of PDF files in the Electronic Theses and Dissertations Library of the Federal University of Paraná, Brazil</a>, extracted through ParsCit.</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>
IDSL.CSA spectra annotation table for ST001000 CSA spectra annotated by ST000923 CSA library (reference)
<p>IDSL.CSA spectra annotation table for ST001000 CSA spectra annotated by ST000923 CSA library (reference)</p>
Mesopelagic fish reference specimen photographic library
<p>Mesopelagic fishes are a crucial component of the world's oceans in terms of their abundance, biomass, and ecosystem function. These fishes are important contributors to the biological carbon pump via their feeding and behaviors, whereby they facilitate the transfer of carbon from shallow waters to the deep sea. Several species undertake diel vertical migration, feeding in shallower waters at night and moving to deeper waters during the day. This process actively expedites the downward flux of carbon. However, carbon budgets and climate models require accurate information regarding the depth distributions and migration patterns of these fishes, and environmental DNA (eDNA) analyses can provide this information. Here, we utilize eDNA approaches, generating taxonomically-informative COI and 12S reference barcodes for 80 species of mesopelagic fishes, which can be used to for species-level identification of eDNA sequences. Using these, along with a publicly available barcode database, we compare results from eDNA analysis with traditional net sampling and explore the ability of eDNA techniques to detect diel vertical migration in fishes from samples collected in Northwest Atlantic Slope Water. We found that eDNA and net samples often resulted in different species identifications, demonstrating that eDNA can detect species that would otherwise be missed with traditional methods. In our eDNA samples, we also detected more species (12) in our shallowest depth category (0–100 m) from nighttime samples than from daytime samples (3). This is consistent with increased diversity in shallow waters at night due to diel vertical migration. Based on the variability observed in sample duplicates, we suggest that future mesopelagic eDNA studies incorporate larger sample volumes and scaled-up sampling efforts. We also note the potential for eDNA analysis to address ecological questions such as predator-prey relationships and identification of foraging hotspots, yielding insights into carbon flow through the ocean's midwaters.</p>
Mesopelagic fish reference specimen photographic library
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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: 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.
A tufA reference sequence library for the green algal genus Caulerpa (Bryopsidales)
<p>A 1230 nucleotide <em>tuf</em>A gene sequence alignment (in fasta format) of 89 <em>Caulerpa</em> species and nine '<em>Pseudochlorodesmis</em>' species, a Maximum Likelihood phylogeny (pdf file) based on this alignment, and an Excel file with listing details about all taxa included. These were first published in Draisma & Sauvage (2024): Jeju Journal of Islands Sciences 1: 1-11.</p> <p>https://www.jjis.or.kr/articles/xml/VxXM/</p> <p> </p>
PerSeq HMM reference libraries
<p>HMM reference libraries formatted for use with the PerSeq annotation tool.</p>
Supplementary material 9 from: Yi P, Yu P, Liu J, Xu H, Liu X (2018) A DNA barcode reference library of Neuroptera (Insecta, Neuropterida) from Beijing. ZooKeys 807: 127-147. https://doi.org/10.3897/zookeys.807.29430
Table S3. Intraspecific and interspecific divergence of Hemerobiidae based on COI barcode sequences (%) : Explanation note: Tthe range of interspecific distance = mean interspecific distance ± standard error. N/A indicates intraspecific distance not available because only one specimen was sequenced.
Supplementary material 8 from: Yi P, Yu P, Liu J, Xu H, Liu X (2018) A DNA barcode reference library of Neuroptera (Insecta, Neuropterida) from Beijing. ZooKeys 807: 127-147. https://doi.org/10.3897/zookeys.807.29430
Table S2. Intraspecific and interspecific divergence of Chrysopidae based on COI barcode sequences (%) : Explanation note: The range of interspecific distance = mean interspecific distance ± standard error. N/A indicates intraspecific distance not available because only one specimen was sequenced.
Supplementary material 4 from: Yi P, Yu P, Liu J, Xu H, Liu X (2018) A DNA barcode reference library of Neuroptera (Insecta, Neuropterida) from Beijing. ZooKeys 807: 127-147. https://doi.org/10.3897/zookeys.807.29430
Figure S4. Neighbor-joining tree based on the COI sequence dataset of Chrysopidae : Explanation note: Neighbor-joining tree based on the COI sequence dataset of Chrysopidae. Only bootstrap supports (1,000 replicates) > 0.95 are labelled.
Supplementary material 7 from: Yi P, Yu P, Liu J, Xu H, Liu X (2018) A DNA barcode reference library of Neuroptera (Insecta, Neuropterida) from Beijing. ZooKeys 807: 127-147. https://doi.org/10.3897/zookeys.807.29430
Table S1. Intraspecific and interspecific divergence of Coniopterygidae based on COI barcode sequences (%) : Explanation note: The range of interspecific distance = means interspecific distance ± standard error. N/A indicates intraspecific distance not available because only one specimen was sequenced.
Supplementary material 3 from: Yi P, Yu P, Liu J, Xu H, Liu X (2018) A DNA barcode reference library of Neuroptera (Insecta, Neuropterida) from Beijing. ZooKeys 807: 127-147. https://doi.org/10.3897/zookeys.807.29430
Figure S3. Photographs of male genitalia of species of Hemerobiidae newly recorded from Beijing : Explanation note: A. Drepanepteryxalgida (Erichson, 1851); B. Hemerobiusbispinus Banks, 1940; C. Hemerobiusexoterus Navás, 1936; D. Hemerobiushumulinus Linnaeus, 1758; E. Hemerobiusjaponicus Nakahara, 1915; F. Hemerobiusmarginatus (Stephens, 1836); G. Hemerobiussubtriangulus Yang, 1987; H. Sympherobiusmanchuricus Nakahara, 1960. Scale bar: 0.5 mm.
Supplementary material 10 from: Yi P, Yu P, Liu J, Xu H, Liu X (2018) A DNA barcode reference library of Neuroptera (Insecta, Neuropterida) from Beijing. ZooKeys 807: 127-147. https://doi.org/10.3897/zookeys.807.29430
Table S4. Intraspecific and interspecific divergence of Myrmeleontidae and Ascalaphidae based on COI barcode sequences (%) : Explanation note: The range of interspecific distance = mean interspecific distance ± standard error. N/A indicates intraspecific distance not available because only one specimen was sequenced.
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.