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FIGURE 5 in A new hybrid of Origanum (Lamiaceae) from the Aegean Island of Karpathos (Dodecanese, Greece): Origanum × karpathicum
FIGURE 5 Inflorescence of O. × karpathicum and its parents: A-Origanum onites, B, C-O. × karpathicum, D-O. vetteri (by Cattaneo and Dirmenci)
Interspecific hybridization and island colonization history, not rarity, most strongly affect the genetic diversity in a clade of Mascarene-endemic trees
<p>Many factors shape the genetic diversity of island-endemic trees, with important implications for conservation. Oceanic island-endemic lineages undergo an initial founding bottleneck during the colonization process and subsequently accumulate diversity following colonization. Moreover, many island endemics occur in small populations and are further threatened by anthropogenic factors that cause population declines, making them susceptible to losses in genetic diversity through genetic drift, inbreeding, and bottlenecks. <a name="_Hlk80963234"></a>However, life-history traits commonly found in trees, such as outcrossing mechanisms, long lifespans, and a propensity for interspecific hybridization, may help buffer against losses of genetic variation. To assess the relative importance of colonization history, rarity, and distribution in shaping genetic diversity of island-endemic trees, we conducted a<a name="_Hlk80964566"></a> comparative population genomic analysis of 13 species of <em>Diospyros</em> (Ebenaceae) endemic to the Mascarene Islands that differ in island colonization history, distribution, population size, and IUCN threat status. We genotyped 328 individuals across the islands using 2b-RADseq, compared genetic diversity both among and within species, and assessed patterns of genetic structure. <a name="_Hlk80965008"></a>Genetic diversity did not vary significantly by IUCN status, but we found that species that co-occur with others on the same intermediate-aged island (Mauritius) had much greater genetic diversity than those that occur solitarily on an island (Réunion and Rodrigues), likely because of greater interspecific hybridization among species with overlapping distributions and processes related to time since island colonization. Results presented here were used to <a name="_Hlk80991503"></a>determine priority localities for <em>in situ</em> and <em>ex situ</em> conservation efforts to maximize the genetic diversity of each Mascarene <em>Diospyros</em> species.</p>
Evidence that genomic incompatibilities and other multilocus processes impact hybrid fitness in a rattlesnake hybrid zone
<p>Hybrid zones provide valuable opportunities to understand the genomic mechanisms that promote speciation by providing insight into factors involved in intermediate stages of speciation. Here we investigate introgression in a hybrid zone between two rattlesnake species (<em>Crotalus viridis</em> and <em>C. oreganus concolor</em>) that have undergone historical allopatric divergence and recent range expansion and secondary contact. We use Bayesian genomic cline models to characterize genomic patterns of introgression between these lineages and identify loci potentially subject to selection in hybrids. We find evidence for a large number of genomic regions with biased ancestry that deviate from the genomic background in hybrids (i.e., excess ancestry loci), which tend to be associated with genomic regions with higher recombination rates. We also identify suites of excess ancestry loci that show highly correlated allele frequencies (including conspecific and heterospecific combinations) across physically unlinked genomic regions in hybrids. Our findings provide evidence for multiple multilocus evolutionary processes impacting hybrid fitness in this system.</p>
FIGURE 1 in Cymbidium ×shangrilaense (Orchidaceae; Epidendroideae), a new natural hybrid from China: evidence from morphology and molecular analyses
FIGURE 1. Phylogenetic relationships of C. ×shangrilaense based on the combined plastid DNA. Galeandra devoniana and Eulophia graminea were used as outgroups. The three numbers near the nodes are Bayesian posterior probabilities (PP), maximum likelihood bootstrap percentages (BP ML), and maximum parsimony bootstrap percentages (BP MP), respectively. "*" indicates that the node has BP=100 or PP=1.00. "-" indicates that the node is incongruent between the topology of the Bayesian and MP/ML trees.
FIGURE 4 in Cymbidium ×shangrilaense (Orchidaceae; Epidendroideae), a new natural hybrid from China: evidence from morphology and molecular analyses
FIGURE 4. Cymbidium ×shangrilaense S.Ke, Q.H.Zhang & S.R.Lan. A. Flowering plant. B. Flower, front view. C. Lip and column, side view. D. inflorescence. E. Structure of the flower. F. Lip, upper view. G. C. tracyanum flower. H. C. gaoligongense flower.
FIGURE 3 in Cymbidium ×shangrilaense (Orchidaceae; Epidendroideae), a new natural hybrid from China: evidence from morphology and molecular analyses
FIGURE 3. Cymbidium ×shangrilaense S.Ke, Q.H.Zhang & S.R.Lan. A. Flowering plant. B. Lateral sepal. C. Petal. D. Dorsal sepal. E. Lip. F. Pollinarium. G. Lip and column. H. Whole flower.
A hybrid structure determination approach to investigate the druggability of the nucleocapsid protein of SARS-CoV-2
<p><span>The ongoing pandemic caused by SARS-CoV-2 has called for concerted efforts to generate new insights into the biology of betacoronaviruses to inform drug screening and development. Here, we establish a workflow to determine the RNA recognition and druggability of the nucleocapsid N-protein of SARS-CoV-2, a highly abundant protein crucial for the viral life cycle. We use a synergistic method that combines NMR spectroscopy and protein-RNA cross-linking coupled to mass spectrometry to quickly determine the RNA binding of two RNA recognition domains of the N-protein. Finally, we explore the druggability of these domains by performing an NMR fragment screening. This workflow identified small molecule chemotypes that bind to RNA binding interfaces and that have promising properties for further drug development.</span></p> <p><span>This deposition contains the NMR data acquired to determine the structural features of RBDs- RNA recognition as well as selected relevant data regarding the characterization of promising molecular fragments to disrupt protein-RNA interaction.</span></p> <p><span>Furthermore, we included the molecular docking files used to obtain the reported structural model.</span></p>
Generation of hybrids in broadly sympatric ducks
<p>Although rare, hybrids are more common in broadly sympatric waterfowl than in any other avian family; yet, the behavioral ecology explaining their generation has remained controversial. Leading hypotheses are forced interspecific copulations, mis-imprinting caused by mixed broods, and scarcity of conspecific mates. Using a large sample of hybrid ducks solicited from North American hunters we evaluated these hypotheses by genetically determining the mother and father species of F1 hybrids. Based on abundances in areas where their breeding ranges overlap, the frequency of hybrids varied greatly from expectations, with hybrids between species within recently derived clades being much more frequent than those between more divergent clades. Forced copulations, as measured by large phallus length asymmetries between parentals, strongly predicted the father species of most F1 hybrids. Thus, most <em>Anas</em> <em>acuta</em> x <em>A</em>. <em>platyrhynchos</em> (Northern Pintail x Mallard) F1s were sired by <em>A</em>. <em>acuta</em>, and most <em>A.</em> <em>platyrhynchos</em> x <em>Mareca</em> <em>strepera</em> (Mallard x Gadwall) F1s were sired by <em>A</em>. <em>platyrhynchos</em>. Siring asymmetries were consistent with phallus length asymmetries in five additional parental combinations, but none had samples large enough to be individually statistically significant. The exception to this trend was our sample of nine <em>A</em>. <em>platyrhynchos</em> x <em>Mareca</em> <em>americana</em> (Mallard x Gadwall) F1s, for which a large phallus asymmetry failed to predict the father species. Hybrids were rare in brood parasitic species, suggesting mis-imprinting to be an unlikely cause of most hybrids; however, our samples of hybrids from regular brood parasites were inadequate to strongly address this hypothesis. We could test the scarcity of mates hypothesis for only a single hybrid combination and it contradicted our prediction: most F1 <em>M</em>. <em>Penelope</em> x <em>M</em>. <em>americana</em> (Eurasian x American Wigeon) were sired by <em>M</em>. <em>penelope</em>, strongly contradicting our prediction that female <em>M</em>. <em>penelope</em> wintering in enormous flocks of <em>M</em>. <em>americana</em> (American Wigeon) on the west coast of North America would have difficulty finding conspecific mates. In general, our results support interspecific forced copulations as the predominant behavioral mechanism generating hybrids in North temperate waterfowl.</p>
ZIKV in situ hybridization from full thickness placental center cuts, only positive samples included
<p>These data accompany the manuscript "Infection of the maternal-fetal interface and vertical transmission following low-dose inoculation of pregnant rhesus macaques (<em>Macaca mulattta</em>) with an African-lineage Zika virus" The included images are low magnification scans of full-thickness placental sections (placenta containing decidua, placental villi, and chorionic plate) evaluated with in situ hybridization against ZIKV RNA. Details of methods are provided in the manuscript. Only slides that were deemed positive are included. </p>
Second Harmonic Generation from Grating-Coupled Hybrid Plasmon-Phonon Polaritons - Experimental and Simulation Data
<p>Experimental and simulation data for "Second Harmonic Generation from Grating-Coupled Hybrid Plasmon-Phonon Polaritons" by Marcel Kohlmann et al., recently (10/22) accepted for publication in Applied Physics Letters. A preprint is available on the <a href="https://arxiv.org/abs/2209.00375">arXiv</a>. </p> <p>Content:<br> We provide matlab code to generate the figures from the experimental and simulated data.</p> <p>fig1.m: generates fig1c,d of the paper<br> fig2_4.m generates fig 2 and 4<br> fig3.m generates fig3</p> <p>experimental_data.zip contains all experimental data, please unzip before running the scripts<br> comsol_data.zip contains all Comsol simulation output data. Please unzip before running the scripts.</p> <p>The remaining matlab scripts are needed in the process. "passler_epsTarray_generator.m" is also part of the transfer matrix implementation available on <a href="https://doi.org/10.5281/zenodo.7034720">Zenodo</a>.</p> <p>Please contact <a href="mailto:alexander.paarmann@fhi-berlin.mpg.de">Alex Paarmann</a> for any questions.</p>
Temporally Programmable Hybrid MOPA Laser with Arbitrary Pulse Shape and Frequency Doubling
<p>Video S1: SBS pulse distortion_40kHz_40ns. Video S2: SBS pulse distortion_100kHz_168ns. Video S3: SBS_freqency shift_100 kHz_168ns.</p>
Supplementary material 1 from: Maddison WP, Evans SC, Hamilton CA, Bond JE, Lemmon AR, Lemmon EM (2017) A genome-wide phylogeny of jumping spiders (Araneae, Salticidae), using anchored hybrid enrichment. ZooKeys 695: 89-101. https://doi.org/10.3897/zookeys.695.13852
Supplementary table of assembly statistics : Explanation note: Statistics describing raw reads, loci, sequence lengths, and other aspects of sequencing assembly for each of the 34 salticid taxa and 12 outgroup taxa.
Data set for "Parametric Study of the Harmonic Structure of Lower Hybrid Waves Driven by Energetic Ions"
<p>After unzipping the zip file, you can produce the figures shown in our paper except Figure 9 by executing the Gnuplot scripts.</p>
Replication Data for: Unconventional superconductivity in chiral molecule-TaS2 hybrid superlattices
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Dataset supporting the submission to the journal "Ocean Dynamic" and titled "Hybrid covariance super-resolution data assimilation"
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Data from: D3.2. Multi-criteria decision analysis (MCDA) for selection and location of hybrid solutions
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Data from: Density-dependent unidirectional hybridization between the Japanese pond turtle, Mauremys japonica and the exotic Reeves' pond turtle, Mauremys reevesii in Japan, inferred from molecular and morphological analyses
<p>Hybridisation between the indigenous Japanese pond turtle, <em>Mauremys japonica</em>, and the exotic Reeves' pond turtle, <em>Mauremys reevesii</em>, is widespread in Japan. In this study, we examined this hybridisation using an analysis of mtDNA and 11 microsatellite markers (MS) combined with morphometry. In a Bayesian clustering analysis of MS, the admixture of two clusters equivalent to the two species was detected in the Seto Inland Sea and Ise Bay regions. While mtDNA showed reciprocal hybridisation between the two species, their hybrids tended to possess the mtDNA of the rarer species at each locality. Contrary to preceding studies, F2/later generations outnumbered F1 generations. In addition, the admixture of two mtDNA lineages (Chinese and Korean) of <em>M. reevesii</em> was widely observed in all regions, together with the range expansion of the recently introduced Chinese lineage. A significant correlation was observed between plastron morph and assignment probability of MS, showing that plastron morphology reflects the degree of introgression by <em>M. reevesii</em> in <em>M. japonica</em>. This finding means that the reproductive interference of the dominant species on a rarer species is a major factor driving the hybridisation of the two Mauremys species. In addition, the range expansion of the Chinese lineage of M. reevesii appears to enhance the introgression by <em>M. reevesii</em> in <em>M. japonica</em>.</p>
Data set for publication "Effect of milling atmosphere on stability and surface properties of ZnO/vermiculite hybrid nanocomposite powders"
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Annexes from the paper A Hybrid Methodology for the Facility Re-Layout Problem (FRLP) of Food Production Systems in Industry 5.0 Context
<p>In the attached dataset we present all the data collected and obtained in the case study of our model to improve the redistribution of food production plants. The importance of the attached data lies in the fact that they consist of real data collected in a small snack production plant located in the northern part of Ecuador, and were used to validate the methodology proposed in the article entitled: "A Hybrid Methodology for the Facility Re-Layout Problem (FRLP) of Food Production Systems in Industry 5.0 Context", which is currently in the publication stage.</p>
Enhancing Name Entity Recognition Through Hybrid Deep Learning in Natural Language Processing
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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.