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FIGURES 21–22 in Revision of the Nearctic species of Gimnomera Rondani (Diptera: Scathophagidae) with morphological phylogeny and DNA barcodes
FIGURES 21–22. Gimnomera vockerothi sp. nov., female. 21. Colour patterns on the occiput; 22. Colour pattern on scutellum.
Fig. 2 in Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator
Fig. 2. Last-instar caterpillars of 10 species in the A. fulgerator complex from the ACG. Interim names reflect the primary larval food plant and, in some cases, a color character of the adult.
Fig. 3 in Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator
Fig. 3. NJ tree based on Kimura-2-Parameter distances for COI DNA sequences from 466 individuals of the A. fulgerator complex from the ACG. Numbers in parentheses indicate the total sample size for each interim taxon, rectangles caricature caterpillar color patterns, and black backgrounds indicate groups of 10 conspecifics with identical sequences.
Fig. 1. Newly eclosed female A in Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator
Fig. 1. Newly eclosed female A. fulgerator (species LOHAMP, voucher code 02-SRNP-9770) from the ACG.
FIGURE 3 in First record of the West Nile virus bridge vector Culex modestus Ficalbi (Diptera Culicidae) in Belgium, validated by DNA barcoding
FIGURE 3. NJ tree based on COI sequences downloaded from BOLD, including Culex species recorded from Belgium (Boukraa et al. 2015) and sequences of Cx. modestus (Table 1). Bootstrap values are indicated above the branches. The blue square gives a zoom view of the un-collapsed tree.
FIGURE 2 in First record of the West Nile virus bridge vector Culex modestus Ficalbi (Diptera Culicidae) in Belgium, validated by DNA barcoding
FIGURE 2. The small vernal pond vegetated with common cattail (Typha latifolia) where the Cx. modestus larva was collected.
FIGURE 1 in First record of the West Nile virus bridge vector Culex modestus Ficalbi (Diptera Culicidae) in Belgium, validated by DNA barcoding
FIGURE 1. (A) Posterior part of the mounted Cx. modestus larva. Zoom on the diagnostic characteristic of the siphon, showing disarrayed insertion points of the ventral siphonal setae. (B) Posterior part of a mounted Cx. pipiens larva.
Data from: Plant DNA barcodes and the influence of gene flow
Success of species assignment using DNA barcodes has been shown to vary among plant lineages due to a wide range of different factors. In this study, we confirm the theoretical prediction that gene flow influences species assignment with simulations and a literature survey. We show that the genome experiencing the highest gene flow is, in the majority of the cases, the best suited for species delimitation. Our results clearly suggest that, for most angiosperm groups, plastid markers will not be the most appropriate for use as DNA barcodes. We therefore advocate shifting the focus from plastid to nuclear markers to achieve an overall higher success using DNA barcodes.
FIGURE 10 in DNA barcodes and morphology reveal two new species of Monodiamesa Kieffer (Diptera: Chironomidae: Prodiamesinae) in Tibetan Plateau
FIGURE 10. Monodiamesa bathyphila (Japanese population). Photos: (A–B) hypopygium. (Prodiamesa chuzenigra, from NMNS, No: 052:001); (C–D) hypopygium. (illustrated by Masaru Yamamoto). Scale bar: A–D, 100 μm.
FIGURE 9 in DNA barcodes and morphology reveal two new species of Monodiamesa Kieffer (Diptera: Chironomidae: Prodiamesinae) in Tibetan Plateau
FIGURE 9. Monodiamesa tibetica (Holotype, from Nankai University). Photos: (A–B) hypopygium, dorsal view, ventral view; (C) superior volsella; (D) median volsella; (E) basal median lobe. Scale bar: A–B, 50 μm; C–E, 25 μm.
FIGURE 7 in DNA barcodes and morphology reveal two new species of Monodiamesa Kieffer (Diptera: Chironomidae: Prodiamesinae) in Tibetan Plateau
FIGURE 7. Monodiamesa bonalpicola sp. n., female. Photos: (A) hypopygium, ventral view. Illustration. (B) antenna; (C) S VIII; (D) hypopygium, ventral view. Scale bar: A, 50μm; B–E, 100 μm.
FIGURE 8 in DNA barcodes and morphology reveal two new species of Monodiamesa Kieffer (Diptera: Chironomidae: Prodiamesinae) in Tibetan Plateau
FIGURE 8. Monodiamesa bonalpicola sp. n., immatures. Photos: (A–B) pharate, P/M, lateral view, dorsal view; (C) pupa, pedes spurii B; (D) pupa, segment VIII; (E) larva, procercus. (F) larva, head capsule, ventral view. Illustration: (G) larva, mentum. Scale bar: A–B, 50 μm; C–D, 20μm; E–G, 50 μm.
FIGURE 6 in DNA barcodes and morphology reveal two new species of Monodiamesa Kieffer (Diptera: Chironomidae: Prodiamesinae) in Tibetan Plateau
FIGURE 6. Monodiamesa bonalpicola sp. n., male. Photos: (A) hypopygium; (B) basal median lobe; (C) hind tibial comb. Illustration: (D) hypopygium, dorsal view; (E) hypopygium, ventral view. Scale bar: A–E, 50 μm.
FIGURE 2 in DNA barcodes and morphology reveal two new species of Monodiamesa Kieffer (Diptera: Chironomidae: Prodiamesinae) in Tibetan Plateau
FIGURE 2. Neighbor-joining tree based on the 146 COI barcodes of Prodiamesinae. Only bootstrap support (1000 replicates)> 70% are shown on the branches.
FIGURE 4 in DNA barcodes and morphology reveal two new species of Monodiamesa Kieffer (Diptera: Chironomidae: Prodiamesinae) in Tibetan Plateau
FIGURE 4. Monodiamesa secunditibetica sp. n., female. Photos: (A) hypopygium, ventral view. Illustration: (B) antenna; (C) S VIII; (D) dorsomesal lobe, apodeme and ventrolateral lobe; (E) hypopygium, ventral view. Scale bar: A–B, 100 μm; C–E, 50 μm.
FIGURE 3 in DNA barcodes and morphology reveal two new species of Monodiamesa Kieffer (Diptera: Chironomidae: Prodiamesinae) in Tibetan Plateau
FIGURE 3. Monodiamesa secunditibetica sp. n., male. Photos: (A) hypopygium; (B) clypeus; (C) MVo; (D) basal median lobe. Illustration: (E) hypopygium, dorsal view; (F) hypopygium, ventral view. Scale bar: A–B, 100 μm; C–F, 50 μm.
FIGURE 5 in DNA barcodes and morphology reveal two new species of Monodiamesa Kieffer (Diptera: Chironomidae: Prodiamesinae) in Tibetan Plateau
FIGURE 5. Monodiamesa secunditibetica sp. n., immatures. Photos: (A–B) pharate, P/M, lateral view, dorsal view; (C) pupa, thoracic horn; (D) pupa, anal lobe; (E) larva, head capsule, ventral view; (F) larva, ventromental plate. Illustration: (G) larva, mandible; (H) larva, mentum; (I) larva, antenna. Scale bar: A–B, 100 μm; C, 200 μm; D–F, 100 μm; G, 20 μm; H, 50 μm; I, 25 μm.
Data from: A preliminary framework for DNA barcoding, incorporating the multispecies coalescent
The capacity to identify an unknown organism using the DNA sequence from a single gene has many applications. These include the development of biodiversity inventories (Janzen et al. 2005), forensics (Meiklejohn et al. 2011), biosecurity (Armstrong and Ball 2005), and the identification of cryptic species (Smith et al. 2006). The popularity and widespread use (Teletchea 2010) of the DNA barcoding approach (Hebert et al. 2003), despite broad misgivings (e.g., Smith 2005; Will et al. 2005; Rubinoff et al. 2006), attest to this. However, one major shortcoming to the standard barcoding approach is that it assumes that gene trees and species trees are synonymous, an assumption that is known not to hold in many cases (Pamilo and Nei 1988; Funk and Omland 2003). Biological processes that violate this assumption include incomplete lineage sorting and interspecific hybridization (Funk and Omland 2003). Indeed, simulation studies indicate that the concatenation approach (in which these two processes are ignored) can lead to statistically inconsistent estimation of the species tree (Kubatko and Degnan 2007). However, recent developments make a barcoding approach that utilizes a single locus outdated. The cost of sequencing multiple gene fragments is no longer inhibitory, but more importantly, a range of analytical approaches have been developed that account for incomplete lineage sorting (Degnan and Salter 2005; Edwards et al. 2007; Liu et al. 2008; Kubatko et al. 2009; Heled and Drummond 2010; Yang and Rannala 2010). These approaches incorporate coalescent theory into the analysis of species trees and species delimitation (Fujita et al. 2012) and are conveniently accessible as software programs (e.g., BEST, BPP, *BEAST, MrBayes v. 3.2, STEM, and COAL). Although the general mixed Yule coalescent (GMYC) approach has also been developed for species delimitation (Pons et al. 2006), we do not consider it further here. It operates quite differently to the approaches outlined above (i.e., BEST, BPP, *BEAST, MrBayes v. 3.2, STEM, and COAL). The GMYC approach seeks to identify the shift in the rate of lineage branching that should be evident when interspecific evolutionary processes switch to population-level processes (Pons et al. 2006). Both empirical (Esselstyn et al. 2012) and simulation studies (Esselstyn et al. 2012; Fujisawa and Barraclough 2013) report that it performs poorly when effective population sizes and speciation rates are high, but within biologically relevant ranges. Ideally, a "next-generation" barcoding approach would (1) identify a minimal set of barcoding genes (perhaps specific to certain lineages), (2) generate a large and cladistically divergent database for comparisons, and (3) identify species using species delimitation approaches that incorporate the multispecies coalescent. The first two of these conditions are straightforward and require only discussion (requirement 1) and resources (requirement 2). However, the third requirement is much more problematic. Some of the recently developed approaches for species delimitation could not be used alone; for example, BPP requires a user-specified guide tree (Yang and Rannala 2010). All of the recently developed approaches are computationally intensive (Degnan and Rosenberg 2009), with many having practical limitations on the number of individuals that can be compared. By contrast, the current barcoding approach is able to compare enormous numbers of sequences in a very short time, primarily because the approach is analytically simple; a single sequence is compared with all sequences in the database by calculating all possible pairwise K2P distances. As long as exemplars exist within the database that have K2P distances below some predetermined threshold (usually 4%), the species is considered identified. The speed of analysis is due primarily to the use of distance-based measures. The purpose of this article is to initiate the development of a framework for "next-gen barcoding": one that incorporates the multispecies coalescent, but does so by comparing multiple gene sequences from an unknown taxon with a database of sequences.
Data from: Collecting in collections: a PCR strategy and primer set for DNA barcoding of decades-old dried museum specimens
Natural history museums are vastly underutilized as a source of material for DNA analysis because of perceptions about the limitations of DNA degradation in older specimens. Despite very few exceptions, most DNA barcoding projects, which aim to obtain sequence data from all species, generally use specimens collected specifically for that purpose, instead of the wealth of identified material in museums, constrained by the lack of suitable PCR methods. Any techniques that extend the utility of museum specimens for DNA analysis therefore are highly valuable. This study first tested the effects of specimen age and PCR amplicon size on PCR success rates in pinned insect specimens, then developed a PCR primer set and amplification strategy allowing greatly increased utilization of older museum specimens for DNA barcoding. PCR success rates compare favourably with the few published studies utilizing similar aged specimens, and this new strategy has the advantage of being easily automated for high-throughput laboratory workflows. The strategy uses hemi-nested, degenerate, M13-tailed PCR primers to amplify two overlapping amplicons, using two PCRs per amplicon (i.e. four PCRs per DNA sample). Initial PCR products are reamplified using an internal primer and a M13 primer. Together the two PCR amplicons yield 559 bp of the COI gene from Coleoptera, Lepidoptera, Diptera, Hemiptera, Odonata and presumably also other insects. BARCODE standard-compliant data were recovered from 67% (56 of 84) of specimens up to 25 years old, and 51% (102 of 197) of specimens up to 55 years old. Given the time, cost and specialist expertise required for fieldwork and identification, 'collecting in collections' is a viable alternative allowing researchers to capitalize on the knowledge captured by curation work in decades past.
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.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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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.