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FIGURE 5 in Distribution and variation of the giant alpha anoles (Squamata: Dactyloidae) of the genus Dactyloa in the highlands of western Panama, with the description of a new species formerly referred to as D. microtus
FIGURE 5. Discriminant function analysis of the eight Dactyloa lineages using two morphometric and four pholidotic characters. See text for details.
FIGURE 2 in Distribution and variation of the giant alpha anoles (Squamata: Dactyloidae) of the genus Dactyloa in the highlands of western Panama, with the description of a new species formerly referred to as D. microtus
FIGURE 2. (A) Maximum likelihood consensus tree of 19 Panamanian anoles. Black bars demarcate smallest well-supported clusters. (B) Sampled individuals in life, with locality numbers referring to Fig. 1. (C) Taxonomic identity derived from morphology on the basis of available literature.
FIGURE 21 in Distribution and variation of the giant alpha anoles (Squamata: Dactyloidae) of the genus Dactyloa in the highlands of western Panama, with the description of a new species formerly referred to as D. microtus
FIGURE 21. Distribution of Dactyloa ibanezi and D. insignis in western Panama (main map) and Lower Central America (inset). Localities of specimens with 16S barcodes included in the molecular analyses are marked with an asterisk (*).
FIGURE 14 in Distribution and variation of the giant alpha anoles (Squamata: Dactyloidae) of the genus Dactyloa in the highlands of western Panama, with the description of a new species formerly referred to as D. microtus
FIGURE 14. Female specimens of Dactyloa insignis from western Panama: (A) juvenile female SMF 91477 from Willie Mazú; (B) adult female SMF 89482 from Cerro Mariposa at daytime, and (C) at night immediately after capture; (D–E) dewlaps of (D) SMF 89482 and (E) SMF 91477; (F) lateral and (G) dorsal views of head of SMF 89482; (H) dorsal and (I) ventral views of head of SMF 91477; ventral views of (J) entire specimen, (K) left foot, and (L) right hand of SMF 91477.
FIGURE 9 in Distribution and variation of the giant alpha anoles (Squamata: Dactyloidae) of the genus Dactyloa in the highlands of western Panama, with the description of a new species formerly referred to as D. microtus
FIGURE 9. Specimens of Dactyloa ginaelisae from Chiriquí and the Comarca Ngöbe-Buglé: (A) adult male MHCH 2237 from RFLF; (B) female SMF 89501 from RFLF in sleeping position and (C) the next day; (D) female SMF 91503 from Cerro Saguí in sleeping position and (E) the next day; (F) female SMF 89497 and (G) female MHCH 2234 from La Nevera; (H) uncollected female juvenile and (I) uncollected female from La Nevera; (J–M) dewlaps of (J) adult male SMF 89738 from RFLF, (K) male juvenile SMF 89737 from PNVB, (L) female SMF 89499 from RFLF, and (M) female SMF 89501; (N) lateral, (O) dorsal, and (P) ventral views of head of SMF 89501; (Q) ventral view of MHCH 2234; (R) enlarged postcloacal scales of SMF 89738; ventral views of (S) left foot and (T) left hand of male holotype SMF 91504 from Cerro Saguí.
FIGURE 11 in Distribution and variation of the giant alpha anoles (Squamata: Dactyloidae) of the genus Dactyloa in the highlands of western Panama, with the description of a new species formerly referred to as D. microtus
FIGURE 11. Specimens of Dactyloa casildae from the Comarca Ngöbe-Buglé: (A) adult male SMF 89454, and (B) adult female SMF 89453 in sleeping position, from La Nevera; (C) uncollected female from Río Flor; (D) female juvenile MHCH 2126 from La Nevera; (E–H) dewlaps of (E) adult male SMF 91454 and (F) male juvenile SMF 91453 from Río Flor; (G) female MHCH 2122 from La Nevera, and (H) female juvenile MHCH 2129 from Río Flor; (I) lateral, (J) dorsal, and (K) ventral views of head of preserved female SMF 89452 from La Nevera; enlarged postcloacal scales of (L) SMF 91454 and (M) SMF 91453; ventral views of (N) left foot and (O) left hand of MHCH 2129.
FIGURE 13 in Distribution and variation of the giant alpha anoles (Squamata: Dactyloidae) of the genus Dactyloa in the highlands of western Panama, with the description of a new species formerly referred to as D. microtus
FIGURE 13. Specimens of Dactyloa ibanezi from western Panama: (A) female SMF 91475 from Willie Mazú in sleeping position and (B) the next day; (C) male MHCH 2184 from Cerro Mariposa; (D) juvenile from Sendero Pianista, photo by Johannes J. Köhler; (E–G) dewlaps of (E) male paratype SMF 89459 from Cerro Mariposa, (F) male SMF 91476 from Willie Mazú, and (G) female SMF 91475; (H) lateral, (I) dorsal, and (J) ventral views of head of SMF 91475; enlarged postcloacal scales of (K) SMF 89459 and (L) MHCH 2184; ventral views of (M) left foot and (N) right hand of SMF 89459.
FIGURE 1 in Distribution and variation of the giant alpha anoles (Squamata: Dactyloidae) of the genus Dactyloa in the highlands of western Panama, with the description of a new species formerly referred to as D. microtus
FIGURE 1. Collection localities of Dactyloa specimens in western Panama (main map) and Lower Central America (inset). Black circles represent examined specimens and reliable photo records listed in the Appendix, gray circles stand for other localities that are mentioned in the text. One symbol may summarize several localities close to each other. See text for abbreviations and details. (1) Río Changena; (2) Bajo Mono, Sendero La Cascada; (3) Alto Chiquero; (4) Sendero El Pianista, Casa de Calixto; (5) Sendero Pianista, 1500 m; (6) Cerro Guayabo; (7) headwaters of Río Chiriquí Malí; (8) Quebrada Arena; (9) Willie Mazú; (10) Cerro Pata de Macho; (11) Cerro Saguí; (12) Río Flor; (13) Río Hacha; (14) W slope Cerro Santiago, La Nevera; (15) E slope Cerro Santiago, Quebrada Ardilla; (16) Cerro Mariposa; (17) Cerro Negro; (18) Río Chilagres; (19) Distrito de Donoso: between Botija, Brazo, Petaquilla, and Rio del Medio; (20) Camp Summit; (21) La Palma; (22) Cerro Dantas; (23) Parque Nacional Tapantí; (24) Sendero Quetzales on N slope Volcán Barú, 7000 ft = 2130 m; (25) Cerro Horqueta; (26) Boquete; (27) BPPS, transect of Hofer and Bersier (2001); (28) Smithsonian station at RFLF; (29) Quebrada Frank; (30) road to Almirante, 400 m; (31) PNGDOTH north of El Copé; (32) Valle de Antón; (33) Altos de Campana; (34) Isla Barro Colorado; (35) Nusagandí.
FIGURE 10 in Distribution and variation of the giant alpha anoles (Squamata: Dactyloidae) of the genus Dactyloa in the highlands of western Panama, with the description of a new species formerly referred to as D. microtus
FIGURE 10. Specimens of Dactyloa casildae from RFLF, Chiriquí (if not otherwise mentioned from western slope of Cerro Pata de Macho): (A) adult male SMF 89673 in sleeping position; (B) subadult male MHCH 2121; (C) female SMF 89458; (D) female MHCH 2120; (E) female juvenile MHCH 2123 in sleeping position and (F) the next day; (G) uncollected adult male exhibiting brown phase at night; (H) female juvenile MHCH 2127 in sleeping position; (I–L) dewlaps of (I) adult male SMF 89673, (J) subadult male MHCH 2121, (K) female SMF 90098 from Cerro Guayabo, and (L) female juvenile MHCH 2127; (M) lateral, (N) dorsolateral, and (O) ventral views of head of SMF 89458; cloacal regions of (P) uncollected male shown in G showing enlarged postcloacal scales, and of (Q) male SMF 89673 lacking enlarged postcloacal scales; (R) left foot and (S) left hand of SMF 89673.
FIGURE 8 in Distribution and variation of the giant alpha anoles (Squamata: Dactyloidae) of the genus Dactyloa in the highlands of western Panama, with the description of a new species formerly referred to as D. microtus
FIGURE 8. Holotype of Dactyloa ginaelisae sp. nov. (SMF 91504, adult male, SVL = 107 mm), (A–E) in life: (A) lateral view at time of capture; (B) portrait the next day; (C) dorsal view of entire specimen; (D) dewlap (width of forceps = 3 mm); (E) ventral view of cloacal region showing enlarged postcloacal scales; (F–M) specimen after approximately two years in preservative: (F) dorsal and (G) ventral view of entire specimen; (H) dorsal, (I) lateral, and (J) ventral view of head; (K) detail of dorsal scales at midbody, arrows indicate middorsal rows; (L) detail of subcaudal scales with one prominent keel; (M) detail of multicarinate scales on upper surface of right forearm. All arrows point posteriorly, scale bars = 1 mm.
FIGURE 20 in Distribution and variation of the giant alpha anoles (Squamata: Dactyloidae) of the genus Dactyloa in the highlands of western Panama, with the description of a new species formerly referred to as D. microtus
FIGURE 20. Distribution of Dactyloa casildae and D. frenata in western Panama (main map) and Lower Central America (inset). Localities of specimens with 16S barcodes included in the molecular analyses are marked with an asterisk (*). Records of D. frenata from Colombia, such as the type locality, are not shown.
FIGURE 17 in Distribution and variation of the giant alpha anoles (Squamata: Dactyloidae) of the genus Dactyloa in the highlands of western Panama, with the description of a new species formerly referred to as D. microtus
FIGURE 17. Hemipenes of Dactyloa from western Panama: (A–C) Dactyloa casildae, SMF 91454: (A) sulcate, (B) asulcate, and (C) lateral view; (D–F) Dactyloa frenata, SMF 89467: (D) sulcate, (E) asulcate, and (F) lateral view; (G–I) Dactyloa ginaelisae, SMF 89498: (G) sulcate, (H) asulcate, and (I) lateral view; (J–L) Dactyloa ibanezi, MHCH 2184: (J) sulcate, (K) asulcate, and (L) lateral view; (M–O) Dactyloa kunayalae, SMF 91484: (M) sulcate, (N) asulcate, and (O) lateral view; all scale bars equal 1 mm.
FIGURE 22 in Distribution and variation of the giant alpha anoles (Squamata: Dactyloidae) of the genus Dactyloa in the highlands of western Panama, with the description of a new species formerly referred to as D. microtus
FIGURE 22. Distribution of Dactyloa ginaelisae, D. kunayalae, and D. microtus in western Panama (main map) and Lower Central America (inset). Localities of specimens with 16S barcodes included in the molecular analyses are marked with an asterisk (*).
FIGURE 16 in Distribution and variation of the giant alpha anoles (Squamata: Dactyloidae) of the genus Dactyloa in the highlands of western Panama, with the description of a new species formerly referred to as D. microtus
FIGURE 16. Specimens of Dactyloa microtus from Río Changena, Bocas del Toro: young male SMF 91499 in (A) sleeping position and (B) the next day; (C) and (D) young male SMF 91500; (E–G) dewlaps of (E) young male SMF 91499, (F) young male SMF 91500, and (G) female hatchling SMF 91501; (H) lateral, (I) dorsal, and (J) ventral views of head of SMF 91500; enlarged postcloacal scales of (K) SMF 91500 and (L) SMF 91499; ventral views of (M) right foot and (N) right hand of SMF 91500.
Data from: Chromosome-scale reference genome and RAD-based genetic map of yellow starthistle (Centaurea solstitialis) reveal putative structural variation and QTLs associated with invader traits
<p>The data directory here includes all of the data and scripts necessary to recreate the results and plots for the manuscript titled "Chromosome-scale reference genome and RAD-based genetic map of yellow starthistle (Centaurea solstitialis) reveal putative structural variation and QTLs associated with invader traits". These data include a genetic map, QTL analysis, paleolog analysis, gene synteny analysis, and assembly validation for yellow starthistle (Centaurea solstitialis).</p>
Figure 1 in A new taxonomist-curated reference library of DNA barcodes for Neotropical electric fish (Teleostei: Gymnotiformes)
Figure 1. Percentages of 934 BOLD systems CO1 sequences (A) and 1015 GenBank CO1 sequences (B) categorized with respect to comparisons with reference library sequences. Minimum interspecific pairwise genetic divergence thresholds of 1.0% and 2.0% distinguish conspecifics (≤1.0/2.0%) and heterospecifics (>1.0/2.0%).
DPAM Domain Classification of Human Proteins against ECOD Reference
<p>Domain definitions of AlphaFold classifications of the human proteome (v1) from the AlphaFold Database. Also included are classifications of <em>Danio rerio</em>, <em>Mus musculus</em>, <em>Pan paniscus</em>, <em>Drosophila melanogaster</em>, <em>Caenorhabditis elegans </em>used for comparative analysis to human. See README file for descriptions of file formats.</p>
Target References dataset (TargetCall)
<p>Detailed description:</p> <p>Reference genomes used for the TargetCall as the target reference. All taken from NCBI RefSeq.</p>
Reference LES Simulations for Ocean Models Validation
<p>All Large-Eddy Simulations (LES) computations are conducted with the open-source PALM solver (<a href="https://palm.muk.uni-hannover.de/trac">https://palm.muk.uni-hannover.de/trac</a>) and version 5.0 of the Los Alamos National Laboratory (<a href="https://github.com/lanl/palm_lanl">https://github.com/lanl/palm_lanl</a>) branch. The simulations use a cubical domain with length L=128m, three grid resolutions (N=128<sup>3</sup>, 256<sup>3</sup>, or 512<sup>3</sup>), and mimic four single-column canonical oceanic regimes in which the surface flux and background stratification profiles are imposed. These simulations are named cooling (c), stratification (s), evaporation (e), and mixed (m):</p> <ul> <li><strong>cooling cases</strong> test different surface heat fluxes: Q<sub>h</sub>=-1.185x10<sup>-5</sup> (c<sub>01</sub>), -2.371x10<sup>-5</sup> (c<sub>02</sub>), -4.742x10<sup>-5</sup> (c<sub>04</sub>), and -18.966x10<sup>-5</sup> (c<sub>16</sub>) [K.m/s]. The background stratification is set through a vertical temperature gradient (T<sub>z</sub>) equal to 0.1 [K/m], and both the salinity surface flux (Q<sub>s</sub>) and the background stratification due to vertical salinity gradient (S<sub>z</sub>) are equal to zero.</li> <li><strong>stratification cases</strong> are similar to the cooling c<sub>02</sub> case, but Q<sub>h</sub>=-2.371x10<sup>-5</sup> [K.m/s], and T<sub>z</sub>=0.01 (s<sub>01</sub>), 0.1 (s<sub>10</sub>), or 0.2 (s<sub>20</sub>) [K/m].</li> <li><strong>evaporation cases</strong> define Q<sub>h</sub>=T<sub>z</sub>=0, S<sub>z</sub>=-0.025 [PSU/m], and Q<sub>s</sub>=3.115x10<sup>-6</sup> (e<sub>01</sub>) or 1.225x10<sup>-5</sup> (e<sub>04</sub>) [PSU/(m<sup>2</sup>.s)].</li> <li><strong>mixed cases</strong> combine heat and salinity surface fluxes, and the background stratification is imposed by both vertical temperature and salinity gradients. There are four mixed cases in which Q<sub>h</sub>=-1.185x10<sup>-6</sup> [K.m/s], T<sub>z</sub>=0.05 [K/m], S<sub>z</sub>=-0.025 [PSU/m], and Q<sub>s</sub> is either 0 (m<sub>01</sub>), 3.115x10<sup>-6</sup> (m<sub>02</sub>), 9.10x10<sup>-6</sup> (m<sub>03</sub>), or 4.55x10<sup>-5</sup> (m<sub>04</sub>) [PSU/(m<sup>2</sup>.s)].</li> </ul> <p>The simulations run 96h at a latitude of 43.29<sup>o</sup>, and utilize a linear equation of state where the reference temperature and salinity are 293.15 K and 35 PSU. The subgrid turbulent scales are modeled through the Moeng and Wyngaard SGS closure (see PALM documentation), and the flow is perturbed during the first 150 s of simulation with normally distributed fluctuations with a maximum amplitude of 10<sup>-4</sup>. The dataset provides 1D and 3D statistics. The 1D profiles are time-averaged during 3600 s and written every 3600 s. The 3D fields are not time-averaged and written every 3600 s, except those obtained with the grid having 512<sup>3</sup> points. In this case, the data are written every 21,600 s. The 3D fields are not in the tar file but can be requested by emailing the authors (fmsoarespereira@lanl.gov). The PALM input decks of the simulations are included in the shared files.<br> <br> <strong>Note:</strong> the PALM version used in this work requires the 1D salinity flux profiles to be normalized by the product of N<sub>x </sub>and<sub> </sub>N<sub>y </sub>(number of grid points in x and y)</p> <p> </p> <p><strong>LA-UR-22-32996</strong></p>
A chromosome-scale reference genome assembly of the great sand eel, Hyperoplus lanceolatus
<p><span>Despite increasing sequencing efforts, numerous fish families still lack a reference genome, which complicates genetic research. One such understudied family is the sand lances (Ammodytidae, literally: 'sand burrower'), a globally distributed clade of over 30 fish species that tend to avoid tidal currents by burrowing into the sand. Here, we present the first annotated chromosome-level genome assembly of the great sand eel (<em>Hyperoplus</em> <em>lanceolatus</em>). The genome assembly was generated using Oxford Nanopore Technologies long sequencing reads and Illumina short reads for polishing. The final assembly has a total length of 808.5 Mbp, of which 97.1% were anchored into 24 chromosome-scale scaffolds using proximity-ligation scaffolding. The assembly is highly contiguous with a scaffold and contig N50 of 33.7 Mbp and 31.3 Mbp, respectively, and has a BUSCO completeness score of 96.9%. The presented genome assembly is a valuable resource for future studies of sand lances, as they are of great ecological and commercial importance and may also contribute to studies aiming to resolve the suprafamiliar taxonomy of bony fishes.</span></p>
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.