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Data from: Enriching the ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of ants and other Hymenoptera
1. Targeted enrichment of conserved genomic regions (e.g., ultraconserved elements or UCEs) has emerged as a promising tool for inferring evolutionary history in many organismal groups. Because the UCE approach is still relatively new, much remains to be learned about how best to identify UCE loci and design baits to enrich them. 2. We test an updated UCE identification and bait design workflow for the insect order Hymenoptera, with a particular focus on ants. The new strategy augments a previous bait design for Hymenoptera by (a) changing the parameters by which conserved genomic regions are identified and retained, and (b) increasing the number of genomes used for locus identification and bait design. We perform in vitro validation of the approach in ants by synthesizing an ant-specific bait set that targets UCE loci and a set of "legacy" phylogenetic markers. Using this bait set, we generate new data for 84 taxa (16/17 ant subfamilies) and extract loci from an additional 17 genome-enabled taxa. We then use these data to examine UCE capture success and phylogenetic performance across ants. We also test the workability of extracting legacy markers from enriched samples and combining the data with published data sets. 3. The updated bait design (hym-v2) contained a total of 2,590-targeted UCE loci for Hymenoptera, significantly increasing the number of loci relative to the original bait set (hym-v1; 1,510 loci). Across 38 genome-enabled Hymenoptera and 84 enriched samples, experiments demonstrated a high and unbiased capture success rate, with the mean locus enrichment rate being 2,214 loci per sample. Phylogenomic analyses of ants produced a robust tree that included strong support for previously uncertain relationships. Complementing the UCE results, we successfully enriched legacy markers, combined the data with published Sanger data sets, and generated a comprehensive ant phylogeny containing 1,060 terminals. 4. Overall, the new UCE bait design strategy resulted in an enhanced bait set for genome-scale phylogenetics in ants and likely all of Hymenoptera. Our in vitro tests demonstrate the utility of the updated design workflow, providing evidence that this approach could be applied to any organismal group with available genomic information.
Text-fig. 13. Enamel ultrastructure of I1, Equus hydruntinus (Kabazi 2). a: vertical sections, scale bar = 100 Μm; b: horizontal and vertical arrangement of prisms in the HSB structure, scale bar = 10 Μm; c: unstructured PLEX enamel at the end of the root, scale bar = 100 Μm. in The Ultrastructure Of The Tooth Enamel Of Small Equus Of The "Tarpan" Group And Their Possible Phylogenetic Connections
Text-fig. 13. Enamel ultrastructure of I1, Equus hydruntinus (Kabazi 2). a: vertical sections, scale bar = 100 Μm; b: horizontal and vertical arrangement of prisms in the HSB structure, scale bar = 10 Μm; c: unstructured PLEX enamel at the end of the root, scale bar = 100 Μm.
Text-fig. 12. HSB of first and second upper incisors of Equus przewalskii (Chornobyl Exclusion Zone). a, b: vertical section, scale bar = 100 Μm; c: horizontal cross-section, scale bar = 50 Μm. in The Ultrastructure Of The Tooth Enamel Of Small Equus Of The "Tarpan" Group And Their Possible Phylogenetic Connections
Text-fig. 12. HSB of first and second upper incisors of Equus przewalskii (Chornobyl Exclusion Zone). a, b: vertical section, scale bar = 100 Μm; c: horizontal cross-section, scale bar = 50 Μm.
Text-fig. 8. Enamel ultrastructure of M1, Equus przewalskii (Chornobyl Exclusion Zone). a, b: enamel row, scale bar = 100 and 20 Μm respectively; c: type I and III, scale bar = 20 Μm; d–f: first type enamel arrangement, scale bar d = 10, e = 3 Μm and f = 2 Μm; g, h: prisms of TZ, scale bar = 50 and 30 Μm respectively; i: type II near OES, scale bar = 20 Μm. in The Ultrastructure Of The Tooth Enamel Of Small Equus Of The "Tarpan" Group And Their Possible Phylogenetic Connections
Text-fig. 8. Enamel ultrastructure of M1, Equus przewalskii (Chornobyl Exclusion Zone). a, b: enamel row, scale bar = 100 and 20 Μm respectively; c: type I and III, scale bar = 20 Μm; d–f: first type enamel arrangement, scale bar d = 10, e = 3 Μm and f = 2 Μm; g, h: prisms of TZ, scale bar = 50 and 30 Μm respectively; i: type II near OES, scale bar = 20 Μm.
Text-fig. 4. Enamel ultrastructure of M1-2, Equus gmelini (Myrne). a: enamel row, scale bar = 30 Μm; b: type I and III, scale bar = 20 Μm; c: type II near OES border, scale bar = 2 Μm. in The Ultrastructure Of The Tooth Enamel Of Small Equus Of The "Tarpan" Group And Their Possible Phylogenetic Connections
Text-fig. 4. Enamel ultrastructure of M1-2, Equus gmelini (Myrne). a: enamel row, scale bar = 30 Μm; b: type I and III, scale bar = 20 Μm; c: type II near OES border, scale bar = 2 Μm.
Text-fig. 10. Enamel ultrastructure of I1 (a) and I2 (b, c), Equus gmelini, tarpan (Myrne). a: vertical section; b, c: horizontal cross-section, scale bar = 250 and 100 Μm respectively. in The Ultrastructure Of The Tooth Enamel Of Small Equus Of The "Tarpan" Group And Their Possible Phylogenetic Connections
Text-fig. 10. Enamel ultrastructure of I1 (a) and I2 (b, c), Equus gmelini, tarpan (Myrne). a: vertical section; b, c: horizontal cross-section, scale bar = 250 and 100 Μm respectively.
Text-fig. 5. Enamel ultrastructure of m1-2, Equus gmelini (Kamiana Mohyla). a: type I, scale bar = 2 Μm; b: type II, scale bar = 10 Μm; c: type II near the OES border, scale bar = 2 Μm. in The Ultrastructure Of The Tooth Enamel Of Small Equus Of The "Tarpan" Group And Their Possible Phylogenetic Connections
Text-fig. 5. Enamel ultrastructure of m1-2, Equus gmelini (Kamiana Mohyla). a: type I, scale bar = 2 Μm; b: type II, scale bar = 10 Μm; c: type II near the OES border, scale bar = 2 Μm.
Text-fig. 6. Enamel ultrastructure of M2, Equus gmelini (Hirzhevo). a: type I and III, scale bar = 20 Μm; b: IPM and PE first type prisms, scale bar = 3 Μm; c, d: wavy/decussated enamel of TZ, scale bar = 20 and 10 Μm respectively; e: type II near OES border, scale bar = 2 Μm; f: type III, scale bar = 2 Μm. in The Ultrastructure Of The Tooth Enamel Of Small Equus Of The "Tarpan" Group And Their Possible Phylogenetic Connections
Text-fig. 6. Enamel ultrastructure of M2, Equus gmelini (Hirzhevo). a: type I and III, scale bar = 20 Μm; b: IPM and PE first type prisms, scale bar = 3 Μm; c, d: wavy/decussated enamel of TZ, scale bar = 20 and 10 Μm respectively; e: type II near OES border, scale bar = 2 Μm; f: type III, scale bar = 2 Μm.
Text-fig. 7. Enamel ultrastructure of P3, Equus caballus (konik polski). a: enamel row, scale bar = 50 Μm; b: type I and III, scale bar = 50 Μm; c: type I, scale bar = 10 Μm; d, e: wavy enamel of TZ with decussations, scale bar = 100 and 50 Μm respectively; f: type II near OES, scale bar = 10 Μm. in The Ultrastructure Of The Tooth Enamel Of Small Equus Of The "Tarpan" Group And Their Possible Phylogenetic Connections
Text-fig. 7. Enamel ultrastructure of P3, Equus caballus (konik polski). a: enamel row, scale bar = 50 Μm; b: type I and III, scale bar = 50 Μm; c: type I, scale bar = 10 Μm; d, e: wavy enamel of TZ with decussations, scale bar = 100 and 50 Μm respectively; f: type II near OES, scale bar = 10 Μm.
Text-fig. 11. Enamel ultrastructure of first (a) and second (b, c) lower incisors, Equus caballus (konik polski), vertical sections. a: enamel row, scale bar = 100 Μm; b: arranging the prisms in the HSB structure, scale bar = 20 Μm; c: arranging the prisms in PI structure, scale bar = 20 Μm. in The Ultrastructure Of The Tooth Enamel Of Small Equus Of The "Tarpan" Group And Their Possible Phylogenetic Connections
Text-fig. 11. Enamel ultrastructure of first (a) and second (b, c) lower incisors, Equus caballus (konik polski), vertical sections. a: enamel row, scale bar = 100 Μm; b: arranging the prisms in the HSB structure, scale bar = 20 Μm; c: arranging the prisms in PI structure, scale bar = 20 Μm.
→ Fig. 2. Representative skeletal elements of ornithosuchid archosaur Dynamosuchus collisensis gen. et sp. nov. (CAPPA/UFSM 0248) from Janner outcrop, Carnian, Late Triassic. A. Selected skull bones in left lateral view. B. Reconstruction of the skull. C. Skull in ventral view. D. Left quadrate and quadratojugal in posterodorsal view. E. Parabasisphenoid in left lateral view. F. Neural arch of an anterior cervical vertebra in anterior view. G. Centrum of a cervical vertebra in left lateral view. H. Right osteoderm in dorsal view. I. Neural arch of an anterior dorsal vertebra in left lateral view. J. Left ilium in lateral view. L. Right humerus in anterior view. M. Right forearm in medial view. N. Left manus in dorsal view. O. Right (reversed) pubis in lateral view. P. Left femur in anterior view. Q. Left fibula in lateral view. Some unpreserved portions are modified from Baczko et al. in press, for the reconstruction of the skeleton of CAPPA/UFSM 0248 (preserved elements indicated in orange) (K). Scale bars 20 mm. in The first ornithosuchid from Brazil and its macroevolutionary and phylogenetic implications for Late Triassic faunas in Gondwana
→ Fig. 2. Representative skeletal elements of ornithosuchid archosaur Dynamosuchus collisensis gen. et sp. nov. (CAPPA/UFSM 0248) from Janner outcrop, Carnian, Late Triassic. A. Selected skull bones in left lateral view. B. Reconstruction of the skull. C. Skull in ventral view. D. Left quadrate and quadratojugal in posterodorsal view. E. Parabasisphenoid in left lateral view. F. Neural arch of an anterior cervical vertebra in anterior view. G. Centrum of a cervical vertebra in left lateral view. H. Right osteoderm in dorsal view. I. Neural arch of an anterior dorsal vertebra in left lateral view. J. Left ilium in lateral view. L. Right humerus in anterior view. M. Right forearm in medial view. N. Left manus in dorsal view. O. Right (reversed) pubis in lateral view. P. Left femur in anterior view. Q. Left fibula in lateral view. Some unpreserved portions are modified from Baczko et al. in press, for the reconstruction of the skeleton of CAPPA/UFSM 0248 (preserved elements indicated in orange) (K). Scale bars 20 mm.
Figure. The phylogenetic tree showing the relationship among Brevibacillus parabrevis strains SA2.2 and TJ2.3, Bacillus licheniformis MG4.2, and their phylogenetically closest type strains. The GenBank accession numbers of the type strains and studied strains are shown following species names. Distance matrix was calculated by Kimura's 2-parameter model. The scale bar indicates 0.02 substitutions per nucleotide position. Alicyclobacillus pohliae AJ564766 served as an out-group. in Distribution of extracellular enzyme-producing bacteria in the digestive tracts of 4 brackish water fish species
Figure. The phylogenetic tree showing the relationship among Brevibacillus parabrevis strains SA2.2 and TJ2.3, Bacillus licheniformis MG4.2, and their phylogenetically closest type strains. The GenBank accession numbers of the type strains and studied strains are shown following species names. Distance matrix was calculated by Kimura's 2-parameter model. The scale bar indicates 0.02 substitutions per nucleotide position. Alicyclobacillus pohliae AJ564766 served as an out-group.
Text-fig. 11. Protothymallus elongatus (KRAMBERGER, 1885): scale from the Caudale peduncle (SMMGD SaT161). in Revision Of The Cyprinids From The Early Oligocene Of The České Středohoří Mountains, And The Phylogenetic Relationships Of Protothymallus Laube, 1901 (Teleostei, Cyprinidae, Gobioninae)
Text-fig. 11. Protothymallus elongatus (KRAMBERGER, 1885): scale from the Caudale peduncle (SMMGD SaT161).
FIGURE 25 in Diverse new scale insects (Hemiptera: Coccoidea) in amber from the Cretaceous and Eocene with a phylogenetic framework for fossil Coccoidea
FIGURE 25. Diagram summarizing known fossil scale insects for each fossil deposit. Symbols indicates: grey circle = previously described taxa; dark star = herein described; white circle = undescribed.
FIGURE 21 in Diverse new scale insects (Hemiptera: Coccoidea) in amber from the Cretaceous and Eocene with a phylogenetic framework for fossil Coccoidea
FIGURE 21. Photomicrographs of (A) dorsal and (B) ventral surfaces of Rosahendersonia prisca, n. sp., holotype AMNH Bu-835. (C) Dorsal surface of Normarkicoccus cambayae, n. sp., holotype AMNH Tad-135.
FIGURE 23 in Diverse new scale insects (Hemiptera: Coccoidea) in amber from the Cretaceous and Eocene with a phylogenetic framework for fossil Coccoidea
FIGURE 23. Details of Normarkicoccus cambayae, n. sp. (A) Dorsal view of head. (B) Ventral view of head. (C) Leg. (D) Ventral view of penial sheath.
FIGURE 20 in Diverse new scale insects (Hemiptera: Coccoidea) in amber from the Cretaceous and Eocene with a phylogenetic framework for fossil Coccoidea
FIGURE 20. Details of Gilderius eukrinops, n. sp. (A) ventral view of head, (B) antenna, (C) leg, (D) dorsal view of penial sheath.
FIGURE 19 in Diverse new scale insects (Hemiptera: Coccoidea) in amber from the Cretaceous and Eocene with a phylogenetic framework for fossil Coccoidea
FIGURE 19. Details of Williamsicoccus megalops, n. sp. (A) Dorsal view of head. (B) Ventral view of head. (C) Dorsal mesothorax. (D) Wing. (E) Connection of the forewing and hamulohaltere. (F) Leg
FIGURE 18 in Diverse new scale insects (Hemiptera: Coccoidea) in amber from the Cretaceous and Eocene with a phylogenetic framework for fossil Coccoidea
FIGURE 18. Photomicrographs of (A) dorsal and (B) ventral surfaces of Williamsicoccus megalops, n. sp., holotype 1582. (C) Dorsal and (D) ventral surfaces of Gilderius eukrinops, n. sp., holotype AMNH Bu-1594.
FIGURE 22 in Diverse new scale insects (Hemiptera: Coccoidea) in amber from the Cretaceous and Eocene with a phylogenetic framework for fossil Coccoidea
FIGURE 22. Details of Rosahendersonia prisca, n. sp. (A) Ventral view of head. (B) Dorsal view of mesothorax. (C) Ventral pro- and mesothorax. (D) Antenna. (E) Leg from femur. (F) Ventral view of abdominal segments VII and VIII and penial sheath.
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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
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.