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3,878 results for “Molecular data”
Data from: Molecular sibship reconstruction reveals a promiscuous mating system in brood parasitic little bronze-cuckoos (Chalcites minutillus)
<p>In theory, emancipation from parental care is expected to favour promiscuous mating systems. However, in avian brood parasites monogamy is surprisingly widespread and it has been proposed that this may be favoured by factors such as low population density and territoriality. Correspondingly, our previous research revealed that brood parasitic Horsfield's bronze-cuckoos (<em>Chalcites basalis)</em>, which occur at low population densities and defend territories, are monogamous. Here, we contrast this study with the mating system of the congeneric little bronze-cuckoo (<em>C. minutillus)</em>, an obligate brood parasite that exploits more concentrated hosts and is therefore likely to occur at higher population densities. We use single nucleotide polymorphisms to characterise the reproductive patterns of unsampled adults by inferring sibling relationships among 30 offspring. We show that 1) little bronze-cuckoos occurred at high densities, 2) polygamy was the most common mating pattern found in this study in both sexes, and 3) where multiple cuckoo eggs are laid in the same nest, they were unrelated. These results indicate that females do not defend exclusive territories and males do not defend multiple females (polygyny). Instead, little bronze-cuckoos appear to have a non-territorial, promiscuous mating system. Our results are consistent with theoretical predictions that polygamy is more likely to evolve in species that are emancipated from parental care, where there are plenty of available mates and where home ranges are not defended.</p>
Data for "Probe molecular diffusivity in single ternary inorganic-organic microdroplets via interfacial ozonolysis of thiosulfate"
<p>ExpXX_YTZS/G.xlsx: Integrated Raman intensity time profiles of thiosulfate for Expt. XX</p> <p>Raman_spectra_ExpXX.xlsx: Raman spectra before and after thiosulfate depletion via O3 for Expt. XX</p>
Measuring the Total Photon Economy of Molecular Species through Fluorescent Optical Cycling: Raw Data
<p>Data acquired in the the paper titled: <br><br><a name="_Hlk150935558"></a><strong><span>Measuring the Total Photon Economy of Molecular Species through Fluorescent Optical Cycling </span></strong></p>
Morphological and molecular data sets from a taxonomic revision of the gecko Lygodactylus tolampyae
<p>Original data sets (raw morphological data, metadata of specimens, and alignments / treefiles of DNA data) for the paper:</p> <p><strong>Taxonomizing a truely morphologically cryptic complex of dwarf geckos from Madagascar: molecular evidence for new species-level lineages within <em>Lygodactylus tolampyae</em></strong></p> <p>Authors of original paper: Miguel Vences, Malte Multzsch, Milena V. Zerbe, Sven Gippner, Franco Andreone, Angelica Crottini, Frank Glaw, Jörn Köhler, Sandratra Rakotomanga, Solohery Rasamison, Achille P. Raselimanana</p>
The data for the work of 'Using non-adiabatic excitation transfer for signal transmission between molecular logic gates'
<p>There are input and output data for calculation of non-adiabatic transfer rates which was performed using the NATRC program. It was calculated rates for transfer and relaxation of an exciton in the molecule of 3H-thioxanthene-TTF-dibenzo-BODIPY. The study was carried out using three isomers of this molecule: 'Chain', 'Line' and 'S-line'</p>
Data from: Out of Africa to Madagascar - then back? Molecular phylogenetics and biogeography of tribe Tarchonantheae (Asteraceae: Tarchonanthoideae)
<p>Premise of research. Molecular data have revolutionized inferences of phylogenetic relationships and historical biogeography of flowering plants. Two small genera, Brachylaena and Tarchonanthus, are the only members of Asteraceae tribe Tarchonantheae (subfamily Tarchonanthoideae). The tribe is morphologically distinct within Asteraceae and is resolved as monophyletic with molecular markers. It is distributed in southern Africa and Madagascar. The purposes of the present study were to determine whether molecular data resolve the two genera as monophyletic and to infer the origin and dispersals that produced the current distribution of the tribe.</p> <p>Methodology. Sequences from the nuclear ribosomal ITS and ETS and plastid rpl16 intron were analyzed using maximum likelihood and Bayesian analyses to resolve phylogenetic relationships within the tribe. An ancestral trait reconstruction assessed the likely ancestral range for Tarchonantheae using BioGeoBEARS, and BEAST was used for dating divergence.</p> <p>Pivotal results. We resolved Tarchonanthus as a monophyletic group nested within Brachylaena, making the latter genus paraphyletic. All Malagasy species occurred within a strongly supported clade, but also resolved within the clade was the widely distributed African species Brachylaena huillensis. This indicates two dispersal events between Africa and Madagascar—either a single dispersal to Madagascar, followed by back dispersal to Africa, or two independent dispersals from Africa. </p> <p>Conclusions. Tarchonanthus is a monophyletic group nested within Brachylaena, rendering the latter genus paraphyletic. An initial dispersal of Brachylaena from Africa to Madagascar with subsequent speciation, followed by back dispersal to Africa, with minimal morphological divergence between the African species and its sister species in Madagascar could explain the current distribution of Brachylaena. Alternatively, there may have been two dispersal events to Madagascar from Africa during the Miocene, but all within the same subclade. Dispersal of flowering plants back to Africa from Madagascar is very rare, if not unprecedented. These dispersal events, and most diversification within the tribe, including the divergence of Tarchonanthus and Brachylaena, took place during the Miocene.</p>
Data from: Molecular phylogenetics of Distephanus supports the recognition of a new tribe, Distephaneae (Asteraceae)
<p>The genus <em>Distephanus</em> Cass. comprises 43 distinctive species of shrubs and small trees that have been placed historically within the ironweed tribe, Vernonieae (Asteraceae). Utilizing the most expansive sampling of <em>Distephanus </em>to date, this study aims to test the monophyly of this genus and facilitate its classification. Molecular phylogenetic analyses were conducted using four molecular markers from the nuclear and plastid genomes. These data also supported divergence dating analyses that were performed to understand the timing of diversification events within <em>Distephanus</em> and other related genera. Results from this study indicate that as currently circumscribed, Vernonieae is not monophyletic and that <em>Distephanus </em>is actually sister to a clade that comprises Vernonieae and another tribe, Moquinieae, which only includes two species restricted to Brazil. Based on these findings, <em>Distephanus </em>is recognized in a new tribe that we describe here, Distephaneae. This new tribe comprises 41 species of <em>Disptehanus</em> that are easily distinguished from Moquinieae and Vernonieae based on the presence of florets with yellow corollas and trinervate leaves.</p>
Collection data and molecular datasets for: Defining species-specific seed sourcing strategies for restoration: An example of how to use genetic data to inform seed collections for multiple co-occurring species
<p>Two files for each dataset are provided:</p> <p>Metadata files contain colelcting information for the samples in each molecular dataset as well as the group assignments (species, genetic neighbourhood and sites) used in analyses, saved as an excel spreadsheet.</p> <p>Molecular datasets containing samples and SNPs used in analyses. The data is formatted as a genlight object saved as an RData file that can be read into the R statisical environment and analysed using the 'dartR' package (Gruber et al. 2018).</p>
Fig. 1 in Evolution and systematics of Green Bush-crickets (Orthoptera: Tettigoniidae: Tettigonia) in the Western Palaearctic: testing concordance between molecular, acoustic, and morphological data
Fig. 1 Map showing the sampling sites for Tettigonia
Fig. 2 in Phylogeography and potential glacial refugia of terrestrial gastropod Faustina faustina (Rossmässler, 1835) (Gastropoda: Eupulmonata: Helicidae) inferred from molecular data and species distribution models
Fig. 2 Haplotype distribution for nuclear markers: ITS-2 (left) and 28S rRNA (right)
Data supplementing the article "Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of OTUs' ecological profiles" F. Keck, V. Vasselon, F. Rimet, A. Bouchez, and M. Kahlert submitted to Molecular Ecology Resources journal
<p>These data supplement the article "Enhancing DNA metabarcoding for biomonitoring with phylogenetic estimation of OTUs' ecological profiles" F. Keck, V. Vasselon, F. Rimet, A. Bouchez, and M. Kahlert submitted to Molecular Ecology Resources journal</p> <p>The directory contains the following files:</p> <p><strong>278 (139 x 2 replicates) samples fastq files.rar </strong>- contains the 278 fastq files provided by the sequencing platform with demultiplexed and contig DNA reads corresponding to the 139 samples with 2 sequencing replicates (A and B).</p> <p><strong>Counts_diatoms.xlsx </strong>- contains the morphological inventories with species list (Omnidia code) and valve abundances for the 139 samples.</p> <p><strong>Sites_list.xlsx </strong>- contains information regarding the 139 samples, including: River name, GPS coordinates, code used for molecular analysis and corresponding to sequencing fastq names.</p>
Data supporting Molecular Simulation of Hydrogen Storage and Transport in Cellulose
<p>Data support article accepted for publication in Molecular Simulation. Data includes inputs for crystal relaxation, absorption and diffusion simulations. All processed data required to reproduce plots included and outputs where practicable. Where impractical simulations can be rerun from the inputs provided.</p>
Data belonging to "Effect of molecular structure on the infrared signaturesof astronomically relevant PAHs"
<p>The data provided here form the basis of the publication titled:</p> <p>"Effect of molecular structure on the infrared signaturesof astronomically relevant PAHs"</p> <p>Which is published in Astronomy and Astrophysics</p> <p>The paper can be downloaded from:</p> <p>https://www.aanda.org/articles/aa/pdf/2019/01/aa34130-18.pdf</p> <p>The data contain raw spectra, both experimental and computational, mass spectrometric data and Cartesian coordinates of the optimized stuctures molecules studied in this work.</p> <p> </p>
Data supplementing the article "Diatom DNA metabarcoding for biomonitoring : strategies to avoid major taxonomical and bioinformatical biases limiting molecular indices capacities" K. Tapolczai, F. Keck, A. Bouchez, F. Rimet, M. Kahlert and V. Vasselon submitted to "Frontiers in Ecology and Evolution" journal
<p>These data supplement the article "Diatom DNA metabarcoding for biomonitoring : strategies to avoid major taxonomical and bioinformatical biases limiting molecular indices capacities" K. Tapolczai, F. Keck, A. Bouchez, F. Rimet, M. Kahlert and V. Vasselon submitted to "Frontiers in Ecology and Evolution" journal.</p> <p>The directory contains the following files:</p> <p><strong>464_samples_fastq_files_(mothur).rar </strong>- contains the 464 fastq files proceed together during the Mothur bioinformatics treatments to produce the OTUs and ISUs tables. As the contig and the demultiplexing steps were performed by the sequencing platform, there is 1 fastq file per sample. From this 464 samples OTU/ISU tables, only information regarding 76 samples were used in this study and are listed in the "<strong>76_samples_list_(mothur).xlsx" </strong>file<strong>.</strong></p> <p><strong>76_samples_list_(mothur).xlsx </strong>- contains the information regarding the 76 samples used to create the OTUs and ISUs tables presented in the paper.</p> <p><strong>76_samples_R1_R2_fastq_files(DADA2).rar - </strong>contains the raw demultiplexed fastq files (R1.fastq and R2.fastq) for each of the 76 samples used in this study to produce the ESVs table using the DADA2 bioinformatics pipeline.</p>
Speciation data for "Pressure-induced coordination changes in a pyrolitic silicate melt from ab initio molecular dynamics simulations"
<p>With <em>ab initio</em> molecular dynamics simulations on pyrolite melt, we examine the detailed changes in elemental coordination as a function of pressure and temperature. We consider the average coordination as well as the proportion and distribution of coordination environments at pressures and temperatures encompassing the conditions at which molten silicates may exist in present-day Earth and those of the Early Earth's magma ocean. At ambient pressure and 2000 K, we find that the average coordination of cations with respect to oxygen is 4.0 for Si-O, 4.0 for Al-O, 3.7 for Fe-O, 4.6 for Mg-O, 5.9 for Na-O and 6.2 for Ca-O. Although the coordination for iron with respect to oxygen is underestimated, the coordination number for all other cations are consistent with experiments. At the base of the upper mantle (~15 GPa and 2000 K), the average coordination for Si-O remains at 4.0, but increases to 4.1 for Al-O, 4.2 for Fe-O, 4.9 for Mg-O, 8.0 for Na-O and 6.8 for Ca-O. The coordination environment for Na-O remains approximately constant up to core-mantle boundary conditions (135 GPa and 4000 K), but increases to about 6 for Si-O, 6.5 for Al-O, 6.5 for Fe-O, 8 for Mg-O, 9.5 for Ca-O. Our results have implications for melt properties, such as viscosity, transport coefficients, thermal conductivities and electrical conductivities, and will help interpret experimental results on silicate glasses.</p> <p>Detailed speciation statistics for pyrolite melt were determined using <em>a</em><em>b initio</em> molecular dynamics simulations with the Vienna Ab Initio Simulation Package (VASP) (Kresse and Furthmuller, 1996). Simulations were performed with a time step of 0.5-2 femtoseconds for 10-50 picoseconds, depending on the temperature and density. The composition of the Bulk Silicate Earth was modeled with a pyrolite melt with the stoichiometry NaCa<sub>2</sub>Fe<sub>4</sub>Mg<sub>30</sub>Al<sub>3</sub>Si<sub>24</sub>O<sub>89</sub>. Bond distances were determined from the pair distribution functions, which describe the probability of finding an atom type at a given distance from the reference atom. We used the first peak in the pair distribution function to approximate the average bond length; the distance at which the first minimum occurs marks the radius of the first coordination sphere of atoms that are directly bonded to the reference atom. We used this value to define the bond criterion between two atom types. Additional computational details can be found in the manuscript.</p>
Fig. 5 in On Trimeresurus Fasciatus (Boulenger, 1896) (Serpentes: Crotalidae), With A Discussion On Its Relationships Based On Morphological And Molecular Data
Fig. 5. Strict consensus MP tree. Values above branches are boostrap proportions (1000 replicates).
Fig. 3 in On Trimeresurus Fasciatus (Boulenger, 1896) (Serpentes: Crotalidae), With A Discussion On Its Relationships Based On Morphological And Molecular Data
Fig. 3. Trimeresurus fasciatus, adult female in life. Photograph by Gernot Vogel.
Fig. 2 in On Trimeresurus Fasciatus (Boulenger, 1896) (Serpentes: Crotalidae), With A Discussion On Its Relationships Based On Morphological And Molecular Data
Fig. 2. Trimeresurus fasciatus, adult male in life. Photograph by Gernot Vogel.
Fig. 4 in On Trimeresurus Fasciatus (Boulenger, 1896) (Serpentes: Crotalidae), With A Discussion On Its Relationships Based On Morphological And Molecular Data
Fig. 4. Trimeresurus fasciatus, juvenile in life. Photograph by Gernot Vogel.
Fig. 3 in New data on Thelohanellus nikolskii Achmerov, 1955 (Myxosporea, Myxobolidae) a parasite of the common carp (Cyprinus carpio, L.): The actinospore stage, intrapiscine tissue preference and molecular sequence
Fig. 3. Thelohanellus cysts on the scales of an aged common carp specimen.
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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.