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Figure 5 from: Kodada J, Jäch MA, Freitag H, Čiamporová-Zaťovičová Z, Goffová K, Selnekovič D, Čiampor Jr F (2020) Ancyronyx lianlabangorum sp. nov., a new spider riffle beetle from Sarawak, and new distribution records for A. pulcherrimus Kodada, Jäch & Čiampor based on DNA barcodes (Coleoptera, Elmidae). ZooKeys 1003: 31-55. https://doi.org/10.3897/zookeys.1003.55541
Figure 5 Habitats of Ancyronyx lianlabangorum sp. nov. (A–C) and A. pulcherrimus (D) A type locality, Pa' Ramudu River B Pa' Masia River C Pa' Kasi River D shaded shallow creek in primary forest, Gunung Mulu NP.
FIGURE 5 in Hyperxiphia hirashimai, comb. n. (Hymenoptera, Xiphydriidae) from southern Japan: remarkable sexual dimorphism revealed by DNA barcodes and new distribution records
FIGURE 5. Distribution of Hyperxiphia hirashimai, black dots showing collection records.
Figure 1 from: Ruiz C, Suárez D, Naranjo M, De la Rúa P (2020) First record of the carpenter bee Xylocopa pubescens (Hymenoptera, Apidae) in the Canary Islands confirmed by DNA barcoding. Journal of Hymenoptera Research 80: 169-175. https://doi.org/10.3897/jhr.80.59649
Figure 1 Pictures of Xylocopa pubescens (male left; female right) in the Parque de La Ballena (Las Palmas de Gran Canaria). Photos: M. Naranjo.
Figure 2 from: Ruiz C, Suárez D, Naranjo M, De la Rúa P (2020) First record of the carpenter bee Xylocopa pubescens (Hymenoptera, Apidae) in the Canary Islands confirmed by DNA barcoding. Journal of Hymenoptera Research 80: 169-175. https://doi.org/10.3897/jhr.80.59649
Figure 2 Localities where Xylocopa pubescens has been recorded in Gran Canaria island (red dots). A detailed distribution in Las Palmas de Gran Canaria city is presented, showing urban areas (grey) and the port of Las Palmas (in blue).
Data from: Applying plant DNA barcodes to identify species of Parnassia (Parnassiaceae)
DNA barcoding is a technique to identity species by using standardized DNA sequences. In the present study, a total of 105 samples, representing 30 Parnassia species were collected to test the effectiveness of four proposed DNA barcodes (rbcL, matK, trnH-psbA and ITS) for species identification. Our results demonstrated that all four candidate DNA markers have a maximum level of primer universality and sequencing success. As single DNA marker, ITS region provided the highest species resolution with 86.7%, followed by trnH-psbA with 73.3%. The combination of the core barcode, matK + rbcL, gave the lowest species identification success (63.3%) among any combination of multiple markers, and was found unsuitable as DNA barcode for Parnassia. The combination of ITS + trnH-psbA achieved the highest species discrimination with 90.0% resolution (27 out of 30 sampled species), equal to the four-marker combination; ITS combined with matK, rbcL or matK + rbcL did not improve species discrimination. Therefore, matK and rbcL should not be used as DNA barcode for species identification of Parnassia. Based on the overall performance, the combination of ITS + trnH-psbA, is proposed as the most suitable DNA barcode for identifying Parnassia species. DNA barcoding is a useful technique to providing a reliable and effective mean for the discrimination of Parnassia species, and in combination with morphology based taxonomy can be a robust approach for tackling taxonomically complex groups. In the light of our findings, we found among the three species not identified a possible cryptic speciation event in Parnassia.
FIGURE 1 in DNA barcodes and morphology reveal two new species of Monodiamesa Kieffer (Diptera: Chironomidae: Prodiamesinae) in Tibetan Plateau
FIGURE 1. Distribution of sampling sites.
Data from: DNA barcoding meets molecular scatology: short mtDNA sequences for standardized species assignment of carnivore noninvasive samples
Although species assignment of scats is important to study carnivoran biology, there is still no standardized assay for the identification of carnivores worldwide, which would allow large-scale routine assessments and reliable cross-comparison of results. Here we evaluate the potential of two short mtDNA fragments (ATP6 [126 bp] and COI [187 bp]) to serve as standard markers for the Carnivora. Samples of 66 species were sequenced for one or both of these segments. Alignments were complemented with archival sequences, and analyzed with three approaches (tree-based, distance-based and character-based). Intraspecific genetic distances were generally lower than between-species distances, resulting in diagnosable clusters for 86% (ATP6) and and 85% (COI) of the species. Notable exceptions were recently diverged species, most of which could still be identified using diagnostic characters, uniqueness of haplotypes, or by reducing the geographic scope of the comparison. In silico comparative analyses were also performed with a 110-bp cytochrome b (cytb) segment, whose identification success was lower (70%), possibly due to the smaller number of informative sites and/or the influence of misidentified sequences obtained from GenBank. Finally, we performed case-studies with faecal samples, which supported the suitability of our two focal markers for poor-quality DNA, and allowed an assessment of prey-DNA co-amplification. No evidence of prey DNA contamination was found for ATP6, while some cases were observed for COI and subsequently eliminated by the design of more specific primers. Overall, our results indicate that these segments hold good potential as standard markers for accurate species-level identification in the Carnivora.
Data from: DNA barcodes from century-old type specimens using next generation sequencing
Type specimens have high scientific importance because they provide the only certain connection between the application of a Linnean name and a physical specimen. Many other individuals may have been identified as a particular species, but their linkage to the taxon concept is inferential. Because type specimens are often more than a century old and have experienced conditions unfavorable for DNA preservation, success in sequence recovery has been uncertain. The present study addresses this challenge by employing next generation sequencing (NGS) to recover sequences for the barcode region of the cytochrome c oxidase 1 gene from small amounts of template DNA. DNA quality was first screened in more than 1800 century-old type specimens of Lepidoptera by attempting to recover 164bp and 94bp reads via Sanger sequencing. This analysis permitted the assignment of each specimen to one of three DNA quality categories – high (164bp sequence), medium (94bp sequence), or low (no sequence). Ten specimens from each category were subsequently analyzed via a PCR-based NGS protocol requiring very little template DNA. It recovered sequence information from all specimens with average read lengths ranging from 458bp to 610bp for the three DNA categories. By sequencing ten specimens in each NGS run, costs were similar to Sanger analysis. Future increases in the number of specimens processed in each run promise substantial reductions in cost, making it possible to anticipate a future where barcode sequences are available from most type specimens.
Data from: Understanding the spectacular failure of DNA barcoding in willows (Salix): Does this result from a trans-specific selective sweep?
Willows (Salix: Salicaceae) form a major ecological component of Holarctic floras, and consequently are an obvious target for a DNA-based identification system. We surveyed two to seven plastid genome regions (~3.8 kb; ~3% of the genome) from 71 Salix species across all five subgenera, to assess their performance as DNA barcode markers. Although Salix has a relatively high level of interspecific hybridization, this may not sufficiently explain the near complete failure of barcoding that we observed: only one species had a unique barcode. We recovered 39 unique haplotypes, from more than 500 specimens, that could be partitioned into six major haplotype groups. A unique variant of group I (haplotype 1*) was shared by 53 species in three of five Salix subgenera. This unusual pattern of haplotype sharing across infrageneric taxa is suggestive of either a massive non-random coalescence failure (incomplete lineage sorting), or of repeated plastid capture events, possibly including a historical selective sweep of haplotype 1* across taxonomic sections. The former is unlikely as molecular dating indicates that haplotype 1* originated recently, and is nested in the oldest major haplotype group in the genus. Further, we detected significant non-neutrality in the frequency spectrum of mutations in group I, but not outside group I, and demonstrated a striking absence of geographic structure to the haplotype distributions in this group. The most likely explanation for the patterns we observed involves recent repeated plastid capture events, aided by widespread hybridization and long-range seed dispersal, but primarily propelled by one or more trans-species selective sweeps.
Data from: Identification of North Sea molluscs with DNA barcoding
Sequence-based specimen identification, known as DNA barcoding, is a common method complementing traditional morphology-based taxonomic assignments. The fundamental resource in DNA barcoding is the availability of a taxonomically reliable sequence database to use as a reference for sequence comparisons. Here, we provide a reference library including 579 sequences of the mitochondrial cytochrome c oxidase subunit I for 113 North Sea mollusc species. We tested the efficacy of this library by simulating a sequence-based specimen identification scenario using Best Match, Best Close Match (BCM) and All Species Barcode (ASB) criteria with three different threshold values. Each identification result was compared with our prior morphology-based taxonomic assignments. Our simulation resulted in 87.7% congruent identifications (93.8% when excluding singletons). The highest number of congruent identifications was obtained with BCM and ASB and a 0.05 threshold. We also compared identifications with genetic clustering (Barcode Index Numbers, BINs) computed by the Barcode of Life Datasystem (BOLD). About 68% of our morphological identifications were congruent with BINs created by BOLD. Forty-nine sequences were clustered in 16 discordant BINs, and these were divided in two classes: sequences from different species clustered in a single BIN and conspecific sequences divided in more BINs. Whereas former incongruences were probably caused by BOLD entries in need of a taxonomic update, the latter incongruences regarded taxa requiring further investigations. These include species with amphi-Atlantic distribution, whose genetic structure should be evaluated over their entire range to produce a reliable sequence-based identification system.
Data from: Molecular diversity of Germany's freshwater fishes and lampreys assessed by DNA barcoding
This study represents the first comprehensive molecular assessment of freshwater fishes and lampreys from Germany. We analysed COI sequences for almost 80% of the species mentioned in the current German Red List. In total, 1056 DNA barcodes belonging to 92 species from all major drainages were used to (i) build a reliable DNA barcode reference library, (ii) test for phylogeographic patterns, (iii) check for the presence of barcode gaps between species and (iv) evaluate the performance of the barcode index number (BIN) system, available on the Barcode of Life Data Systems. For over 78% of all analysed species, DNA barcodes are a reliable means for identification, indicated by the presence of barcode gaps. An overlap between intra- and interspecific genetic distances was present in 19 species, six of which belong to the genus Coregonus. The Neighbour-Joining phenogram showed 60 nonoverlapping species clusters and three singleton species, which were related to 63 separate BIN numbers. Furthermore, Barbatula barbatula, Leucaspius delineatus, Phoxinus phoxinus and Squalius cephalus exhibited remarkable levels of cryptic diversity. In contrast, 11 clusters showed haplotype sharing, or low levels of divergence between species, hindering reliable identification. The analysis of our barcode library together with public data resulted in 89 BINs, of which 56% showed taxonomic conflicts. Most of these conflicts were caused by the use of synonymies, inadequate taxonomy or misidentifications. Moreover, our study increased the number of potential alien species in Germany from 14 to 21 and is therefore a valuable groundwork for further faunistic investigations.
Data from: Species diversity can be overestimated by a fixed empirical threshold: insights from DNA barcoding of the genus Cletus (Hemiptera: Coreidae) and the meta-analysis of COI data from previous phylogeographical studies
The use of genetic distances to identify species within the framework of DNA barcoding has to some extent improved the development of biodiversity studies. However, using a fixed empirical threshold to delimit species may lead to overestimating species diversity. In this study, we use a new data set of COI sequences for 366 specimens within the genus of Cletus as well as conduct an analysis on the same genetic data for collected morphologically defined species from previous phylogeographical studies, to test whether high intraspecific genetic divergences are common with the premises of comprehensive sampling. The results indicate C. graminis Hsiao & Cheng 1964, is the same species with C. punctiger (Dallas, 1852) and should be synonymized and that the distributional record of C. pugnator (Fabricius, 1787) in China is correct. High intraspecific genetic differentiations (0%–4.35%) were found in C. punctiger. Furthermore, as to the mined data, the maximum intraspecific K2P distances of 186 species (48.44% of 384) exceed 3%, and 101 species (26.30%) can be divided into two or more clusters with a threshold of 3% in cluster analysis. If genetic distance is used to delimit species boundaries, the minimum interspecific K2P distance of the congeneric species should be considered rather than only using the fixed empirical value; otherwise, the species richness may be overestimated in some cases.
Data from: A fuzzy-set-theory-based approach to analyze species membership in DNA barcoding
Reliable assignation of an unknown query sequence to its correct species remains a methodological problem for the growing field of DNA barcoding. While great advances have been achieved recently, species identification from barcodes can still be unreliable if the relevant biodiversity has been insufficiently sampled. We here propose a new notion of species membership for DNA barcoding - fuzzy membership, based on fuzzy set theory - and illustrate its successful application to four real datasets (bats, fishes, butterflies and flies) with more than 5000 random simulations. Two of the datasets comprise especially dense species/population level samples. In comparison with current DNA barcoding methods, the newly proposed minimum distance (MD) plus fuzzy set approach, and another computationally simple method, "best close match", outperform two computationally sophisticated Bayesian and BootstrapNJ methods. The new method proposed here has great power in reducing false positive species identification compared with other methods when conspecifics of the query are absent from the reference database.
Data from: Known knowns, known unknowns, unknown unknowns and unknown knowns in DNA barcoding: a comment on Dowton et al.
In a recent commentary, Dowton et al. (2014) propose a framework for "next-generation" DNA barcoding, whereby multi-locus datasets are coupled with coalescent-based species delimitation methods to make specimen identifications. They claim single-locus DNA barcoding is outdated, and a multilocus approach superior, with their assertions supported by an analysis of 33 species of Sarcophaga flesh flies. Here, we reanalyse their data and show that a standard DNA barcode analysis is in fact capable of identifying 99.8% (all but one) of their Sarcophaga specimens, and that their conclusions misrepresent their data. We also discuss the benefits and drawbacks to their vision of "next-gen" barcoding.
Data from: COI is better than 16S rRNA for DNA barcoding Asiatic salamanders (Amphibia: Caudata: Hynobiidae)
The 5' region of the mitochondrial DNA (mtDNA) gene cytochrome c oxidase I (COI) is the standard marker for DNA barcoding. However, because COI tends to be highly variable in amphibians, sequencing is often challenging. Consequently, another mtDNA gene, 16S rRNA gene, is often advocated for amphibian barcoding. Herein, we directly compare the usefulness of COI and 16S in discriminating species of hynobiid salamanders using 130 individuals. Species identification and classification of these animals, which are endemic to Asia, is often based on morphology only. Analysis of Kimura 2-parameter genetic distances (K2P) documents the mean intraspecific variation for COI and 16S rRNA genes to be 1.4% and 0.3%, respectively. Whereas COI can always identify species, sometimes 16S cannot. Intra- and interspecific genetic divergences occasionally overlap in both markers thus reducing the value of a barcoding gap to identify genera. Regardless, COI is the better DNA barcoding marker for hynobiids. In addition to the comparison of two potential markers, high levels of intraspecific divergence in COI (>5%) suggest that both Onychodactylus fischeri and Salamandrella keyserlingii might be composites of cryptic species.
FIGURE 3 in Use of DNA barcoding to distinguish the malaria vector An opheles neivai in Colombia
FIGURE 3. DNA barcode threshold optimization for An. neivai.
FIGURE 11 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 11. Atarbolana setosa, male, (ZMSU 1014); A–E, pleopods 1–5; F, penes.
FIGURE 9 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 9. Atarbolana setosa, male, (ZMSU 1014); A–D, pereopods 1– 4 respectively.
FIGURE 6 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 6. Atarbolana exoconta, male, (ZMSU 1010); A–E, pleopods 1–5; F, penes.
FIGURE 4 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 4. Atarbolana exoconta, male, (ZMSU 1010); A–D, pereopods 1–4 respectively.
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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.
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DANDI Archive for NWB datasets
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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.