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Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches
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An evaluation of the usefulness of morphological characters to infer higher-level relationships in birds by mapping them to a molecular phylogeny
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Data from: A worldwide molecular phylogeny provides new insight on cryptic diversity within the moonworts (Botrychium s. s., Ophioglossaceae)
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Figure 5 in Morphologyı morphogenesisı and molecular phylogeny of a soil ciliateı Gonostomum kuehnelti Foissnerı 1987 (Ciliophoraı Hypotrichia), from northwestern China
Figure 5. Photomicrographs of dividers of Gonostomum kuehnelti after protargol preparation. (a,b) Ventral views of early dividers showing oral primordium, arrow marks the formation of new membranelles; (c) ventral view of late divider, arrowheads mark the left frontal cirri (I/1), arrow denotes left marginal row anlage of proter, frontoterminal cirri are encircled; (d) dorsal view showing division of the macronuclear mass; (e) ventral view of opisthe of a late divider showing development of new cirri, arrowhead marks left marginal anlage, circle denotes the frontoterminal cirri; (f) dorsal view of late divider showing new dorsal kineties 1–3 of proter, inter alia, arrowheads mark new caudal cirri; (g,h) very late divider showing proter and opisthe (g); broken lines connect cirri which originated from the same anlage, arrowheads denote buccal cirrus, arrows indicate pretransverse ventral cirri, frontoventral cirri are encircled. AZM, adoral zone of membranelles; E, endoral; FC, frontal cirri; FTC, frontoterminal cirri; LMR, new left marginal row; Ma, macronuclear nodules; OP, oral primordium; P, paroral; PVC, postoral ventral cirri; RMA, right marginal anlagen; RMR, new right marginal row; TC, transverse cirri; II, III, V, VI, frontoventral-transverse cirral anlagen; 1–3, new dorsal kineties. Scale bars: a, c, e–g = 55 μm; h = 25 μm.
Figure 3 in Morphologyı morphogenesisı and molecular phylogeny of a soil ciliateı Gonostomum kuehnelti Foissnerı 1987 (Ciliophoraı Hypotrichia), from northwestern China
Figure 3. Photomicrographs of Gonostomum kuehnelti from life (a–g) and after protargol staining (h– k). (a) ventral view of a representative specimen; (b) ventral view of a different individual; (c) anterior body portion in ventral view showing adoral zone of membranelles; (d) dorsal view, showing the three caudal cirri; (e) loose arrangement of cortical granules on dorsal side (arrowheads) and the dorsal cilia (arrows); (f) dorsal view demonstrating single-celled ingested green algae (arrowheads); (g) resting cyst, showing the optical cross-section; (h) ventral view of the anterior portion showing the frontoventral ciliature (circled by dotted line) and buccal cirrus (arrowhead); (i) ventral view, showing transverse cirri (arrows), pretransverse ventral cirri (arrowheads) and macronuclear nodules; (j) dorsal view of anterior body portion showing the dorsal kineties (1–3); (k) posterior region of cell showing the caudal cirri (arrowheads). AZM, adoral zone of membranelles; CV, contractile vacuole; CC, caudal cirri; E, endoral; FC, frontal cirri; FT, frontoterminal cirri; FVC, frontoventral cirri; LMR, left marginal row; Ma, macronuclear nodules; P, paroral; PVC, postoral ventral cirri; RMR, right marginal row; 1–3, dorsal kineties. Scale bars: a, b, i = 40 μm; f = 7 μm; g = 20 μm.
Figure 2 in Morphologyı morphogenesisı and molecular phylogeny of a soil ciliateı Gonostomum kuehnelti Foissnerı 1987 (Ciliophoraı Hypotrichia), from northwestern China
Figure 2. Morphology of Gonostomum kuehnelti from life (a–d) and after staining with protargol (e– g). (a) Ventral view of a representative individual; (b,c) ventral views of other individuals showing different body shapes; (d) dorsal view, showing arrangement of cortical granules circular in crosssection; (e) ventral view to show the frontoventral ciliature, arrowhead denotes the buccal cirrus; (f, g) ventral and dorsal view of the same specimen, showing the infraciliature and macronuclear apparatus, black arrowheads indicate the pretransverse ventral cirri, white arrowheads indicate the transverse cirri, broken lines (f) connect cirri which originated from the same anlage, dashed circles (g) showing macronuclear nodules in two distinct groups, lying slightly left of median. AZM, adoral zone of membranelles; CC, caudal cirri; E, endoral; FC, frontal cirri; FTC, frontoterminal cirri; FVC, frontoventral cirri; I–VI, frontoventral-transverse cirral anlagen; LMR, left marginal row; Ma, macronuclear nodules; P, paroral; PVC, postoral ventral cirri; RMR, right marginal row; 1–3, dorsal kineties. Scale bars: a–c, f, g = 35 μm; d = 10 μm.
Figure 6 in Morphologyı morphogenesisı and molecular phylogeny of a soil ciliateı Gonostomum kuehnelti Foissnerı 1987 (Ciliophoraı Hypotrichia), from northwestern China
Figure 6. Maximum likelihood (ML) phylogenetic tree inferred from SSU rDNA sequences, showing the position of Gonostomum kuehnelti (in bold). Bootstrap values above 50 for ML (1000 replicates) and the posterior probabilities above 0.50 of Bayesian inference (BI, 1000 replicates) are given at the nodes, respectively. Clades with a different topology in the BI tree are indicated by '*'. '**', refers to species whose identification is unconfirmed. All branches are drawn to the scale bar, which corresponds to five substitutions per 100 nucleotide positions.
FIGURE 5. A in Morphology and Molecular Phylogeny of the Soil Ciliate Cyrtohymena seorakensis sp. n. (Ciliophora, Hypotricha, Oxytrichidae)
FIGURE 5. A maximum likelihood (ML) tree based on 18S rRNA genes, showing the phylogenetic position of Cyrtohymena seorakensis sp. n. Numbers at the nodes represent the maximum likelihood (ML) bootstrap values and the Bayesian inference (BI) posterior probabilities. Newly obtained sequence is in bold. Sequences belong to the genus Cyrtohymena are shaded in grey. GenBank accession numbers follow species names. Bootstrap values lower than 50% and posterior probabilities in BI lower than 0.5 were not shown. The scale bar represents two nucleotide substitutions per 100 nt.
FIGURE 3 in Morphology and Molecular Phylogeny of the Soil Ciliate Cyrtohymena seorakensis sp. n. (Ciliophora, Hypotricha, Oxytrichidae)
FIGURE 3. Line drawings of protargol-impregnated dividing specimens of Cyrtohymena seorakensis sp. n. Parental cirri and dorsal bristles drawn as outlines, newly formed structure are in black. A, B. Ventral and dorsal view of a mid-divider specimen, showing the frontal-ventral-transverse anlagen (arrows), the undulating membranes anlagen (arrowheads), and the dorsal kineties 1–3 anlagen. Note the fusion of the macronuclear nodules. C, D. Ventral and dorsal view of late divider, showing the frontal-ventral-transverse cirri migrate to their original locations, the dorsomarginal kineties (kineties 5 and 6) anlagen originate very close to the right marginal cirral row, and the new caudal cirri. Note the opisthe has 14 frontal-ventral-transverse cirri differing from all other cells in the preparations (~50 non-dividing cells). E, F. Ventral and dorsal view of very late divider, showing the frontal-ventral-transverse cirri already in their specific locations, the fragmentation of kinety 3 producing kinety 4 (arrows) posteriorly. CC—caudal cirri; DK1–6—dorsal kineties; DM—dorsomarginal kineties; LMR—left marginal row; MA—macronucleus; MI—micronucleus; OP—oral primordium; RMR—right marginal row; TC—transverse cirri. Scale bars: 30 μm.
FIGURE 1 in Morphology and Molecular Phylogeny of the Soil Ciliate Cyrtohymena seorakensis sp. n. (Ciliophora, Hypotricha, Oxytrichidae)
FIGURE 1. Line drawings of Cyrtohymena seorakensis sp. n. from life (A–C) and after protargol impregnation (D, E). A. A representative specimen showing the body shape and the arrangement of the ventral ciliature. B. Optical section of a resting cyst showing the thin, smooth wall (opposite arrowheads), the lipid droplets in the cytoplasm, and the fused macronuclear nodules. C. Dorsal view showing the randomly arranged cortical granules. D, E. Ventral and dorsal view of the holotype specimen showing the infraciliature and the nuclear apparatus. Dotted line in (E) connects dikinetids of dorsal kinety 4. AZM—adoral zone of membranelles; BC—buccal cirrus; CC—caudal cirri; CG—cortical granules; DK1–6—dorsal kineties; EM—endoral membrane; FC—frontal cirri; LD—lipid droplets; LMR—left marginal row; MA—macronucleus; MI—micronucleus; PF—pharyngeal fibers; PM—paroral membrane; PTC—pretransverse cirri; RMR—right marginal row; TC—transverse cirri. Scale bars = 30 μm (A, D, E), 10 μm (B).
FIGURE 51 in Revision of the bee group Anthophora (Micranthophora) (Hymenoptera: Apidae), with notes on potential conservation concerns and a molecular phylogeny of the genus
FIGURE 51. Male face of A) Anthophora hololeuca (101115), B) A. maculifrons (BBSL504449), C) A. mortuaria (BBSL504535), D) A. pachyodonta (BBSL504596), E) A. parkeri (BBSL311827), F) A. peritomae (BBSL504667). Scale=0.5 mm.
FIGURE 54 in Revision of the bee group Anthophora (Micranthophora) (Hymenoptera: Apidae), with notes on potential conservation concerns and a molecular phylogeny of the genus
FIGURE 54. Male habitus of A) Anthophora abroniae (BBSL502223), B) A. albata (10046), C) A. caudata (BBSLID92552), D) A. chihuahua (BBSL502617), E) A. cockerelli (72472), F) A. columbariae (BBSL853157). Scale=1 mm.
FIGURE 49 in Revision of the bee group Anthophora (Micranthophora) (Hymenoptera: Apidae), with notes on potential conservation concerns and a molecular phylogeny of the genus
FIGURE 49. Male face of A) Anthophora abroniae (BBSL502212), B) A. albata (BBSL504186), C) A. caudata (BBSLID98988), D) A. chihuahua (BBSL502617), E) A. cockerelli (BBSL502260), F) A. columbariae (BBSL853110). Scale=0.5 mm.
FIGURE 64. Male S7 in Revision of the bee group Anthophora (Micranthophora) (Hymenoptera: Apidae), with notes on potential conservation concerns and a molecular phylogeny of the genus
FIGURE 64. Male S7 of A) Anthophora abroniae (BBSL502216), B) A. albata (BBSL843758), C) A. caudata (BBSL506707), D) A. chihuahua (BBSL502617), E) A. cockerelli (BBSL502279), F) A. columbariae (BBSL502330). Scale=0.25 mm.
FIGURE 77 in Revision of the bee group Anthophora (Micranthophora) (Hymenoptera: Apidae), with notes on potential conservation concerns and a molecular phylogeny of the genus
FIGURE 77. Male genital capsule of A) Anthophora petrophila (BBSL504826), B) A. phenax (BBSL506626), C) A. rara (BBSL427007), D) A. rhodothorax (BBSL506666), E) A. salazariae (102053), F) A. squammulosa (BBSL841390). Scale=0.25 mm.
FIGURE 47 in Revision of the bee group Anthophora (Micranthophora) (Hymenoptera: Apidae), with notes on potential conservation concerns and a molecular phylogeny of the genus
FIGURE 47. Female habitus of A) Anthophora petrophila (BBSL853152), B) A. phenax (BBSL506654), C) A. rara (BBSL428146), D) A. rhodothorax (SDSHN_ENT_5393), E) A. salazariae (BBSL669804), F) A. squammulosa (BBSL852106). Scale=1 mm.
FIGURE 45 in Revision of the bee group Anthophora (Micranthophora) (Hymenoptera: Apidae), with notes on potential conservation concerns and a molecular phylogeny of the genus
FIGURE 45. Female habitus of A) Anthophora curta (BBSL502504), B) A. erythrothorax (UCRCENT335467), C) A. escalante (BBSL1048559), D) A. estebana (BBSL502610), E) A. exigua (82036), F) A. flavocincta (BBSL504157). Scale=1 mm.
FIGURE 43 in Revision of the bee group Anthophora (Micranthophora) (Hymenoptera: Apidae), with notes on potential conservation concerns and a molecular phylogeny of the genus
FIGURE 43. Female face of A) Anthophora striata (BBSL274662), B) A. timberlakei (BBSL275507). Scale=0.5 mm.
FIGURE 42 in Revision of the bee group Anthophora (Micranthophora) (Hymenoptera: Apidae), with notes on potential conservation concerns and a molecular phylogeny of the genus
FIGURE 42. Female face of A) Anthophora petrophila (BBSL506476), B) A. phenax (BBSL506652), C) A. rara (BBSLID92593), D) A. rhodothorax (UCRCENT335777), E) A. salazariae (BBSL676860), F) A. squammulosa (BBSL275509). Scale=0.5 mm.
FIGURE 41 in Revision of the bee group Anthophora (Micranthophora) (Hymenoptera: Apidae), with notes on potential conservation concerns and a molecular phylogeny of the genus
FIGURE 41. Female face of A) Anthophora hololeuca (BBSL504392), B) A. maculifrons (BBSL275403), C) A. mortuaria (BBSL504557), D) A. pachyodonta (BBSL907957), E) A. parkeri (BBSL919866), F) A. peritomae (BBSL504698). Scale=0.5 mm.
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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.