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FIGURES 23–24 in The epigean Australasian species of Neobidessodes gen.n. diving beetles- a revision integrating morphology, cybertaxonomy, DNA taxonomy and phylogeny (Coleoptera: Dytiscidae, Bidessini)
FIGURES 23–24. Distribution of Neobidessodes: 23) N. flavosignatus; 24) N. samkrisi sp.n. (square) and N. grossus (dots).
FIGURES 13–17 in The epigean Australasian species of Neobidessodes gen.n. diving beetles- a revision integrating morphology, cybertaxonomy, DNA taxonomy and phylogeny (Coleoptera: Dytiscidae, Bidessini)
FIGURES 13–17. Median lobe of aedeagus in ventral (a) and lateral view (b), and right paramere in lateral view (c): 13) Neobidessodes thoracicus sp.n. (paratype); 14) N. thoracicus sp.n. ("light form"); 15) N. flavosignatus; 16) N. mjobergi and 17) N. samkrisi sp.n. (scale bar = 0.5 mm) (Photos: L. Hendrich).
FIGURES 9–12. 9 in The epigean Australasian species of Neobidessodes gen.n. diving beetles- a revision integrating morphology, cybertaxonomy, DNA taxonomy and phylogeny (Coleoptera: Dytiscidae, Bidessini)
FIGURES 9–12. 9) N. thoracicus sp.n. (paratype); 10) N. thoracicus sp.n. (paratype, "black specimen"); 11) N. thoracicus sp.n. ("light form", WA, Kimberley Region, 50 km S Wyndham, Black Flag Creek); 12) N. thoracicus sp.n. ("light form", NT, Kakadu N.P., Jim Jim District, Gungurul Lookout) (scale bar = 1 mm) (Photos: A. Riedel).
FIGURE 27 in The epigean Australasian species of Neobidessodes gen.n. diving beetles- a revision integrating morphology, cybertaxonomy, DNA taxonomy and phylogeny (Coleoptera: Dytiscidae, Bidessini)
FIGURE 27. Phylogram of the tree obtained using GARLI and cox1 and 16S data for Australasian Bidessini, Neotropical Bidessodes and outgroups. Node support, when above 50%: bold (GARLI bootstrap), italics (MrBayes posterior propablities>0.5, x100), normal font (TNT jackknife values). Note: "Clypeodytes migrator" will be transferred to Leiodytes in a forthcoming revision (Hendrich et al. in prep.).
FIGURES 30–35 in The epigean Australasian species of Neobidessodes gen.n. diving beetles- a revision integrating morphology, cybertaxonomy, DNA taxonomy and phylogeny (Coleoptera: Dytiscidae, Bidessini)
FIGURES 30–35. Habitats of Neobidessodes: 30) Slow flowing stream and rest pool in monsoonal rainforest at Gubara (Kakadu NP, NT), habitat of "black specimens" of Neobidessodes thoracicus sp.n.; 31) NT, Manton Dam Recreation Area, 46 km S Darwin (NT 1), habitat of N. denticulatus, N. flavosignatus and N. mjobergi; 32) NT, Finnis River 10 km W Batchelor (NT 2), habitat of N. mjobergi and N. denticulatus; 33) NT, Litchfield NP, Shady Creek, Florence Falls (NT 3), habitat of N. grossus; 34) NT, Nitmiluk NP, Edith Falls, Upper Pool (NT 12), habitat of N. grossus; 35) NT, Kakadu Hwy, Harriet Creek at Hwy Crossing (NT 14), habitat of N. grossus and N. thoracicus sp.n. (Photos: L. Hendrich).
FIGURES 5–8 in The epigean Australasian species of Neobidessodes gen.n. diving beetles- a revision integrating morphology, cybertaxonomy, DNA taxonomy and phylogeny (Coleoptera: Dytiscidae, Bidessini)
FIGURES 5–8. Habitus of 5) Neobidessodes samkrisi sp.n. (holotype, male); 6) N. grossus; 7) N. mjobergi; 8) Neobidessodes bilita (female) (scale bar = 1 mm) (Photos: A. Riedel).
FIGURES 1–4 in The epigean Australasian species of Neobidessodes gen.n. diving beetles- a revision integrating morphology, cybertaxonomy, DNA taxonomy and phylogeny (Coleoptera: Dytiscidae, Bidessini)
FIGURES 1–4. Habitus of 1) N. denticulatus (WA, Pilbara, Millstream Chichester National Park, Fortescue River side branch); 2) N. denticulatus (NT, Kakadu N.P., Jim Jim District, Gungurul Lookout); 3) N. flavosignatus (WA, East Kimberley, Gibb Range, Gibb River Road, Russ Creek Crossing); 4) N. flavosignatus (NT, Manton Dam Recreation Area, 46 km S Darwin) (scale bar = 1 mm), (Photos: A. Riedel).
FIGURES 18–20 in The epigean Australasian species of Neobidessodes gen.n. diving beetles- a revision integrating morphology, cybertaxonomy, DNA taxonomy and phylogeny (Coleoptera: Dytiscidae, Bidessini)
FIGURES 18–20. Median lobe of aedeagus in ventral (a) and lateral view (b), and right paramere in lateral view (c): 18) Neobidessodes bilita; 19) N. denticulatus and 20) N. grossus (scale bar = 0.5 mm) (Photos: L. Hendrich).
An Integrated Protocol for Exploring Molecular Mechanisms of Schizophrenia Using DNA Microarray Datasets
<p>The gene expression matrices, annotation information of probes and sample descriptions for GSE87610, GSE92538, GSE93577 and GSE93987. </p>
Integrative biodiversity inventories: characterizing lichen-forming fungal diversity in Glen Canyon National Recreation Area using DNA barcoding and vouchered specimens
<p>The Colorado River and its tributaries on the Colorado Plateau are home to unique desert river ecosystems and changing environmental conditions. Within this region, the Glen Canyon National Recreation Area (GCNRA) is comprised of rugged, high desert terrain and is managed by the United States National Parks Service as both a recreational and conservation area. Despite the ecological and economic importance of GCNRA, significant components of the ecological communities therein remain poorly characterized, including lichens. Accurately characterizing lichen-forming fungal diversity is challenging due to poorly known taxonomic groups, underexplored regions/habitats, and varying interpretations of morphological differences, including the recognition of environmentally modified forms. To better understand lichen diversity in GCNRA, we used an integrative taxonomic approach, incorporating both traditional morphology-based identification and information from the standard fungal DNA barcoding marker, the ITS, to compile a thorough inventory of lichen-forming fungi in Fifty-Mile Canyon. Vouchered lichen specimens were collected in 2019, and from these the ITS marker was sequenced. Candidate species-level lineages were delimited from family-level multiple sequence alignments using the Assemble Species by Automatic Partitioning web server. Specimens comprising DNA-based candidate species were then evaluated using traditional taxonomically diagnostic characters to link these, where possible, to currently described species. For Fifty-Mile Canyon, we document 100 putative species in 15 families, each represented by vouchered specimens, ITS sequence data, and photographic documentation. For comparison, a survey of historic records from GCNRA revealed a total of 124 documented lichen-forming fungal species throughout the NRA and adjacent land. Approximately 50% of the species documented in Fifty-Mile Canyon had not previously been found in GCNRA, and similar proportions of species diversity have been documented in GCNRA but not observed in our survey. We report three species new to North America – <em>Calogaya ferrugineoides</em> (H. Magn.) Arup, Froden & Sochting, <em>Endocarpon deserticola</em> T. Zhang, X. L. Wei & J. C. Wei and <em>Xanthocarpia ferrari</em> (Bagl.) Frödén, Arup & Søchting – verified using ITS sequencing data. In addition, <em>Circinaria squamulosa</em> sp. nov. is formally described here, currently known only from sandstone slabs in Fifty-Mile Canyon. However, the taxonomic identity of many of the candidate species from Fifty-Mile Canyon remained ambiguous at the species level, and some collections likely represent undescribed species-level lineages. Our results revealed unexpected, high species-level diversity of lichen-forming fungi at local scales and that overall lichen diversity across the entire GCNRA is likely vastly undercounted. These data – including DNA barcodes for the vast majority of lichen-forming fungi occurring in this canyon – provide an important resource that can be integrated into subsequent lichen biodiversity research in the southwestern United States and other semi-arid climates.</p>
Figure 3 in Detailed integrative taxonomic analysis reveals large-scale species misidentification of barnacles based on DNA barcoding data
Figure 3. Neighbour-joining tree for the three investigated barcode index numbers. Ŋe coloured sequences in each clade indicate our newly generated sequences of specimens with unequivocal morphological identification.
Figure 2 in Detailed integrative taxonomic analysis reveals large-scale species misidentification of barnacles based on DNA barcoding data
Figure 2. Morphology of unidentified Balanus sp. individuals of clade A (BOLD:AAG0069) (A), Balanus balanus (B), Balanus crenatus
Figure 1 in Detailed integrative taxonomic analysis reveals large-scale species misidentification of barnacles based on DNA barcoding data
Figure 1. Bubble plot of the correspondence between species assignments and the barcode index number (BIN; genetic clade). Ŋe size of the bubbles corresponds to the number of sequences contained in each combination of BIN and species assignment. Vertical lines highlight BINs that contain more than one species assignment, and horizontal lines highlight species assignments that are present in more than one BIN. Grey bubbles indicate a one-to-one match between BIN and species assignment. Coloured bubbles represent the three BINs that were investigated further by integrative taxonomic analysis.
Supplemental Data: Differential roles of kinetic on- and off-rates in T-cell receptor signal integration revealed with a modified Fab'-DNA ligand
<p>Microscopy data and associated code for analysis. For more information refer to https://doi.org/10.1101/2024.04.01.587588.</p>
Data from: Integrating three comprehensive datasets shows that mitochondrial DNA variation is linked to species traits and paleogeographic events in European butterflies.
Understanding the dynamics of biodiversity, including the spatial distribution of genetic diversity, is critical for predicting responses to environmental changes, as well as for effective conservation measures. This task requires tracking changes in biodiversity at large spatial scales and correlating with species functional traits. We provide three comprehensive resources to understand the determinants for mitochondrial DNA differentiation represented by i) 15,609 COI sequences and ii) 14 traits belonging to 307 butterfly species occurring in Western-Central Europe and iii) the first multi-locus phylogenetic tree of all European butterfly species. By applying phylogenetic regressions we show that mitochondrial DNA spatial differentiation (as measured with Gst, G'st, D and Dst) is negatively correlated with species traits determining dispersal capability and colonization ability. Thanks to the high spatial resolution of the COI data, we also provide the first zoogeographic regionalization maps based on intraspecific genetic variation. The overall pattern obtained by averaging the spatial differentiation of all Western-Central European butterflies shows that the paradigm of long-term glacial isolation followed by rapid pulses of post-glacial expansion has been a pervasive phenomenon in European butterflies. The results and the extensive datasets we provide here constitute the basis for genetically-informed conservation plans for a charismatic group in a continent where flying insects are under alarming decline.
Figure 7. Mitochondrial DNA gene tree estimated for Acanthocercus atricollis using a in Lifting the blue-headed veil - integrative taxonomy of the Acanthocercus atricollis species complex (Squamata: Agamidae)
Figure 7. Mitochondrial DNA gene tree estimated for Acanthocercus atricollis using a portion of the 16S gene. The support for branches from BI and ML are shown on each branch, respectively. The *BEAST species tree is shown in the top left with posterior probability values on branches.
FIGURE 2 in DNA barcoding and integrative taxonomy of Macrobiotus hufelandi C.A.S. Schultze 1834, the first tardigrade species to be described, and some related species
FIGURE 2. Animal and egg morphology by LM of paragenophores and hologenophores of Macrobiotus vladimiri from St. Ulrich (Germany). A: Macroplacoids (Faure-Berlese fluid, phase contrast); B: egg shell (hologenophore HM136934, Faure- Berlese fluid, DIC); C: egg shell (paragenophore, Faure-Berlese fluid, phase contrast). Scale = 10 µm.
FIGURE 5 in DNA barcoding and integrative taxonomy of Macrobiotus hufelandi C.A.S. Schultze 1834, the first tardigrade species to be described, and some related species
FIGURE 5. Animal and egg morphology by LM of paragenophores and hologenophores in Macrobiotus hufelandi. A-B: Specimens from Monte Rondinaio (Italy) (polyvinyl lactophenol, phase contrast). A: Placoids; B: egg shell (paragenophore). C-E: Specimens from Gotthard Pass (Faure-Berlese fluid). C: Macroplacoids (phase contrast); D: distal dishes in the egg shell (hologenophore HQ876594, DIC); E: egg shell reticulation (same hologenophore, phase contrast). Scale = 10 µm.
FIGURE 3 in DNA barcoding and integrative taxonomy of Macrobiotus hufelandi C.A.S. Schultze 1834, the first tardigrade species to be described, and some related species
FIGURE 3. Egg morphology by SEM of paragenophores. A: Macrobiotus hufelandi from St. Ulrich (Germany); B: M. hufelandi from Gotthard Pass (Switzerland); C: Macrobiotus vladimiri from St. Ulrich; D: Macrobiotus sandrae from St. Ulrich. Scale = 5 µm.
FIGURE 7 in DNA barcoding and integrative taxonomy of Macrobiotus hufelandi C.A.S. Schultze 1834, the first tardigrade species to be described, and some related species
FIGURE 7. Neighbor joining dendrogram computed on Kimura 2-parameters distances. Numbers in bold indicate bootstrap values. Acronyms as in Tables 2 and 3. Asterisks indicate hologenophore specimens (sensu Pleijel et al. 2008).
ScienceDex guides
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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.