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FIGURE 4 in DNA barcode polymorphism within a common widespread rove beetle Quedius molochinus (Coleoptera: Staphylinidae)
FIGURE 4. Bayesian Inference phylogenetic tree of Quedius molochinus and allied species based on COI barcode. Specimens sequenced and morphologically examined here are designated with (*). Sequences obtained from BOLD or GenBank (**) were not examined here. Bars delimiting molecular clades 1–3 within Q. molochinus are colored as in Fig. 1. Numbers at nodes are Bayesian Posterior Probability (PP).
FIGURE 5 in DNA barcode polymorphism within a common widespread rove beetle Quedius molochinus (Coleoptera: Staphylinidae)
FIGURE 5. Haplotype network of Quedius molochinus and outgroups based on COI gene obtained with TCS using PopArt.
FIGURES 78–83 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 78–83. Immature stages of South African Gracillariidae. 78, Phodoryctis tephrosiella, mines on Tephrosia rhodesica (Fabaceae). Gauteng, Tshwane, A. Sharp leg. 79, Conopobathra carbunculata, mines on Peltophorum africanum (Fabaceae), Limpopo, York, A. & I. Sharp leg. 80, Phyllonorycter grewiella, mine on Grewia hexamita (Malvaceae), A. & I. Sharp leg. 81, P. pseudogrewiella sp. nov., mines on Grewia flavescens (Malvaceae), Limpopo, Hoedspruit, A. & I. Sharp leg. 82, P. pseudogrewiella sp. nov., larva, ibidem. 83, P. pseudogrewiella sp. nov., mines and pupae, ibidem.
FIGURES 67–72 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 67–72. Immature stages of South African Gracillariidae. 67, Conopomorphina aptata, mine on Schotia brachypetala (Fabaceae), Limpopo, Hoedspruit, A. & I. Sharp leg. 68, Acrocercops syzygiena, mine on Syzygium cordatum (Myrtaceae), Gauteng, Tshwane, A. & I. Sharp leg. 69, A. syzygiena, larva, ibidem. 70, A. combreticola, mine on Combretum zeyheri (Combretaceae) Gauteng, Tshwane, A. Sharp leg. 71, Cryptolectica capnodecta, larva on Syzygium cordatum (Myrtaceae), Limpopo, Hoedspruit, A. & I. Sharp leg. 72, C. terminalina, mine on Terminalia sericea (Combretaceae), A. & I. Sharp leg.
FIGURES 84−88 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 84−88. Immature stages of South African Gracillariidae species. 84, Cameraria melhaniella sp. nov., larva on Melhania acuminata (Malvaceae), Limpopo, Hoedspruit, A. & I. Sharp leg. 85, Metriochroa pergulariae, mine on Pergularia daemia (Apocynaceae), Limpopo, Hoedspruit, A. & I. Sharp leg. 86, Phyllocnistis allisonae, mine on Protea rubropilosa (Proteaceae), Limpopo, Lopez Vaamonde leg. 87, Phyllocnistis magalismontani sp. nov., mine on Englerophytum magalismontanum (Sapotaceae), Limpopo, Hoedspruit, leg. A. & I. Sharp. 88, Phyllocnistis faureae, mine on Faurea saligna (Proteaceae), Gauteng, Tshwane, leg. A. Sharp.
FIGURES 61−66 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 61−66. Immature stages of South African Gracillariidae. 61, Caloptilia sp., larva on Cryptocarya transvaalensis (Lauraceae), Limpopo, Lekgalameetse N. R., A. & I. Sharp leg. 62, C. cataractias, larva on Rhynchosia minima (Fabaceae), Limpopo, Hoedspruit, A. & I. Sharp leg. 63, Macarostola noellineae, larva on Syzygium cordatum (Myrtaceae), Limpopo, Hoedspruit, A. & I. Sharp leg. 64, Ectropina spirostachydis sp. nov., larva on Spirostachys africana (Euphorbiaceae), Limpopo, Hoedspruit, A. & I. Sharp leg. 65, Cuphodes melanostola, mine on Euclea divinorum (Ebenaceae), Limpopo, Hoedspruit, A. & I. Sharp leg. 66, Conopomorphina ochnivora, Gauteng, Magaliesburg, on Ochna pretoriensis, (Ochnaceae), H. Staude leg.
FIGURES 58–60 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 58–60. Female genitalia of South African Gracillariidae. 58-59, Phyllocnistis magalismontani sp. nov., paratype: 58, lateral view; 59, signa. 60, P. allisonae sp. nov., holotype: ventral view. (All scale bar 190 μm).
FIGURES 56–57 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 56–57. Female genitalia of South African Gracillariidae. 56, Telamoptilia cordati sp. nov., paratype: ventral view. 57, Phyllonorycter pseudogrewiella sp. nov., holotype: lateral view. (All scale bar 190 μm).
FIGURES 44–46 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 44–46. Male genitalia of South African Gracillariidae. Phodoryctis tephrosiella sp. nov.: 44, holotype, ventral view; 45, phallus with bulbus ejaculatorius; 46, segment VIII in ventral view (ae: aedeagus; pb: phallobase; be: bulbus ejaculatorius). (All scale bars 190 μm).
FIGURES 25−30 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 25−30. Forewing pattern of South African Gracillariidae. 25, Leucocercops curatellifoliae sp. nov., Limpopo. 26, Phodoryctis tephrosiella sp. nov., Gauteng. 27, Telamoptilia cordati sp. nov., South Africa, Limpopo. 28, Telamoptilia sp., Madagascar. 29, Cameraria melhaniella sp. nov., Limpopo. 30, Phyllonorycter pseudogrewiella sp. nov., Limpopo.
FIGURES 13–18 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 13–18. Adults of South African Gracillariidae. 13, Cryptolectica capnodecta, Limpopo, Hoedspruit, A. & I. Sharp leg. 14, C. terminalina, Limpopo, Hoedspruit, A. & I. Sharp leg. 15, Dialectica pyramidota, Limpopo, Hoedspruit, A. & I. Sharp leg. 16, Amblyptila cynanchi, Western Cape, Knysna, S. Mecenero leg. 17, Leucocercops dasmophora, Gauteng, Tshwane, A. & I. Sharp leg. 18, L. curatellifoliae sp. nov. Limpopo, Hoedspruit, A. & I. Sharp leg.
FIGURES 32–34 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 32–34. Forewing pattern of the South African Phyllocnistinae. 32, Phyllocnistis magalismontani sp. nov., drawn by holotype; 33, P. allisonae sp. nov., holotype; 34, P. faureae, holotype.
FIGURE 31 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURE 31. Forewing pattern of the Afrotropical Phyllocnistinae. A, Phyllocnistis pharetrucha; B, P. saligna; C, P. magalismontani sp. nov.; D, P. faureae sp. nov.; E, P. loxosticha; F, P. citrella; G, P. allisonae sp. nov..
FIGURES 1−6 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 1−6. Adults of South African Gracillariidae. 1, Caloptilia sp., Limpopo, Lekgalameetse N. R., A. & I. Sharp leg. 2, Caloptilia rhusina, Western Cape, Robberg Nature Reserve, S. Mecenero leg. 3, Macarostola noellineae, Limpopo, Hoedspruit, A. & I. Sharp leg. 4, Caloptilia cataractias, Limpopo, Hoedspruit, leg. A. & I. Sharp. 5, Ectropina spirostachydis sp. nov., Limpopo, Hoedspruit, A. & I. Sharp leg. 6, Graphiocephala barbitias, Gauteng, Tshwane, A. Sharp leg.
FIGURES 7–12 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 7–12. Adults of South African Gracillariidae. 7, Semnocera procellaris, Limpopo, Hoedspruit, A. & I. Sharp leg. 8, Conopomorphina ochnivora, Gauteng, Magaliesburg, A. & I. Sharp leg. 9, C. aptata, Limpopo, Hoedspruit, A. & I. Sharp leg. 10, Cuphodes melanostola, Limpopo, Hoedspruit, A. & I. Sharp leg. 11, Acrocercops syzygiena, Gauteng, Tshwane, A. Sharp leg. 12, A. combreticola, Gauteng, Tshwane, A. Sharp leg.
Data from: Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol
We report initial results from an ongoing effort to build a library of DNA barcode sequences for Dutch spiders and investigate the utility of museum collections as a source of specimens for barcoding spiders. Source material for the library comes from a combination of specimens freshly collected in the field specifically for this project and museum specimens collected in the past. For the museum specimens, we focus on 31 species that have been frequently collected over the past several decades. A series of progressively older specimens representing these 31 species were selected for DNA barcoding. Based on the pattern of sequencing successes and failures, we find that smaller-bodied species expire before larger-bodied species as tissue sources for single-PCR standard DNA barcoding. Body size and age of oldest successful DNA barcode are significantly correlated after factoring out phylogenetic effects using independent contrasts analysis. We found some evidence that extracted DNA concentration is correlated with body size and inversely correlated with time since collection, but these relationships are neither strong nor consistent. DNA was extracted from all specimens using standard destructive techniques involving the removal and grinding of tissue. A subset of specimens was selected to evaluate nondestructive extraction. Nondestructive extractions significantly extended the DNA barcoding shelf life of museum specimens, especially small-bodied species, and yielded higher DNA concentrations compared to destructive extractions. All primary data are publically available through a Dryad archive and the Barcode of Life database.
Data from: Evaluation of candidate DNA barcoding loci for economically important timber species of the mahogany family (Meliaceae)
There has been considerable debate regarding locus choice for DNA barcoding land plants. This is partly attributable to a shortage of comparable data from proposed candidate loci on a common set of samples. In this study, we evaluated main candidate plastid regions (rpoC1, rpoB, accD) and additional plastid markers (psbB, psbN, psbT exons and the trnS-trnG spacer) as well as the nuclear ribosomal spacer region (ITS1-5.8S-ITS2) in a group of land plants belonging to the mahogany family, Meliaceae. Across these samples, only ITS showed high levels of resolvability. Interspecific sharing of sequences from individual plastid loci was common. The combination of multiple loci did not improve performance. DNA barcoding with ITS alone revealed cryptic species and proved useful in identifying species listed in Convention on International Trade of Endangered Species appendixes.
Data from: Species-level para- and polyphyly in DNA barcode gene trees: strong operational bias in European Lepidoptera
The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service "Monophylizer" to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ∼23%, but with operational factors still being included. Within the operational factors, we separately assessed the frequency of taxonomic limitations (presence of overlooked cryptic and oversplit species) and identification uncertainties. We observed that operational factors are potentially present in more than half (58.6%) of the detected cases of non-monophyly. Furthermore, we observed that in about 20% of non-monophyletic species and entangled species, the lineages involved are either allopatric or parapatric—conditions where species delimitation is inherently subjective and particularly dependent on the species concept that has been adopted. These observations suggest that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors.
Data from: Using a comprehensive DNA barcode library to detect novel egg and larval host plant associations in a Cephaloleia Rolled-leaf Beetle (Coleoptera: Chrysomelidae)
To fully understand the ecology and evolution of plant-herbivore interactions, information regarding the life history of both immature and adult insect stages is essential. However, most knowledge of plant-herbivore associations is derived from observations of adults. One reason for this bias is that species identification of immature stages is usually challenging. DNA barcodes can be used to identify immature stages to the species-level. This technique compares short sequences of the appropriate DNA barcode loci (e.g., mitochondrial COI gene for insects) of an unidentified specimen to a known DNA barcode library. The accuracy of DNA-based identifications depends on the comprehensiveness of the DNA barcode library. We generated a comprehensive DNA barcode library for a community of Rolled-leaf Beetles (Coleoptera: Chrysomelidae) in a premontane tropical forest in Costa Rica. The DNA barcode COI accurately identified all beetle species included in this study. Using this DNA barcode library, we identified eggs and larvae of Cephaloleia histrionica Baly with 100% confidence. This new record of C. histrionica is unique in that this species completes its life cycle on a bromeliad, whereas most Cephaloleia species are associated with plants from the order Zingiberales. The life cycle, diet breadth, immature stages, and sexual dimorphism are described for C. histrionica.
Data from: Seeing is believing? comparing plant-herbivore networks constructed by field co-occurrence and DNA barcoding methods for gaining insights into network structures
Plant-herbivore interaction networks provide information about community organization. Two methods are currently used to document pairwise interactions among plants and insect herbivores. One is the traditional method that collects plant-herbivore interaction data by field observation of insect occurrence on host plants. The other is the increasing application of newly developed molecular techniques based on DNA barcodes to the analysis of gut contents. The second method is more appealing because it documents realized interactions. To construct complete networks, each technique of network construction is urgent to be assessed. We addressed this question by comparing the effectiveness and reliability of the two methods in constructing plant-Lepidoptera larval network in a 50 ha subtropical forest in China. Our results showed that the accuracy of diet identification by observation method increased with the number of observed insect occurrences on food plants. In contrast, the molecular method using three plant DNA markers were able to identify food residues for 35.6% larvae and correctly resolved 77.3% plant (diet) species. Network analysis showed molecular networks had three-fold more unique host plant species but fewer links than the traditional networks had. The molecular method detected plants that were not sampled by the traditional method, e.g., bamboos, bryophytes and lianas in the diets of insect herbivores. The two networks also possessed significantly different structural properties. Our study indicates the traditional observation of co-occurrence is inadequate, while molecular method can provide higher species resolution of ecological interactions.
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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.
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.