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3,878 results for “Molecular data”
Data from: Friends and Family: a software program for identification of unrelated individuals from molecular marker data. And from: Genetic diversity, relatedness and inbreeding of ranched and fragmented Cape buffalo populations in southern Africa
The identification of related and unrelated individuals from molecular marker data is often difficult, particularly when no pedigree information is available and the data set is large. High levels of relatedness or inbreeding can influence genotype frequencies and thus genetic marker evaluation, as well as the accurate inference of hidden genetic structure. Identification of related and unrelated individuals is also important in breeding programmes, to inform decisions about breeding pairs and translocations. We present Friends and Family, a Windows executable program with a graphical user interface that identifies unrelated individuals from a pairwise relatedness matrix or table generated in programs such as COANCESTRY and GenAlEx. Friends and Family outputs a list of samples that are all unrelated to each other, based on a user-defined relatedness cut-off value. This unrelated data set can be used in downstream analyses, such as marker evaluation or inference of genetic structure. The results can be compared to that of the full data set to determine the effect related individuals have on the analyses. We demonstrate one of the applications of the program: how the removal of related individuals altered the Hardy-Weinberg equilibrium test outcome for microsatellite markers in an empirical data set. Friends and Family can be obtained from https://github.com/DeondeJager/Friends-and-Family.
Data from: Molecular square dancing in CO-CO collisions
<p>Knowledge of rotational energy transfer (RET) involving carbon monoxide (CO) molecules is crucial for the interpretation of astrophysical data. As of now, our nearly perfect understanding of atom-molecule scattering shows that RET usually occurs by only a simple "bump" between partners. To advance molecular dynamics to the next step in complexity, we studied molecule-molecule scattering in great detail for collision between two CO molecules. Using advanced imaging methods and quasi-classical and fully quantum theory, we found that a synchronous movement can occur during CO-CO collisions, whereby a bump is followed by a move similar to a "do-si-do" in square dancing. This resulted in little angular deflection but high RET to both partners, a very unusual combination. The associated conditions suggest that this process can occur in other molecule-molecule systems.</p>
Data from: Host-plant use of a polyphagous mirid, Apolygus lucorum: molecular evidence from migratory individuals
While the host-plant use of insect herbivores is important for understanding their interactions and coevolution, field evidence of these preferences is limited for generalist species. Molecular diet analysis provides an effective option for gaining such information, but data from field-sampled individuals are often greatly affected by the local composition of their host plants. The polyphagous mirid bug Apolygus lucorum (Meyer-Dür) seasonally migrates across the Bohai Sea, and molecular analysis of migrant bugs collected on crop-free islands can be used to estimate the host-plant use of A. lucorum across the large area (northern China) from where these individuals come. In this study, the host-plant use of A. lucorum adults was determined by identifying plant DNA using a three-locus DNA barcode (rbcL, trnH-psbA and ITS) in the gut of migrant individuals collected on Beihuang Island. We successfully identified the host plant families of A. lucorum adults, and the results indicated that captured bugs fed on at least 17 plant families. In addition, gut analyses revealed that 35.9% of A. lucorum individuals fed on multiple host plants but that most individuals (64.1%) fed on only one plant species. Cotton, Gossypium hirsutum L., DNA was found in 35.8% of the A. lucorum bugs examined, which was much higher than the percentage of bugs in which other host plants were found. Our work provides a new understanding of multiple host-plant use by A. lucorum under natural conditions, and these findings are available for developing effective management strategies against this polyphagous pest species.
Data from: Molecular biogeography and host relations of a parasitoid fly
Successful geographic range expansion by parasites and parasitoids may also require host range expansion. Thus the evolutionary advantages of host specialization may trade off against the ability to exploit new host species encountered in new geographic regions. Here we use molecular techniques and confirmed host records to examine biogeography, population divergence, and host flexibility of the parasitoid fly, Ormia ochracea (Bigot). Gravid females of this fly find their cricket hosts acoustically by eavesdropping on male cricket calling songs; these songs vary greatly among the known host species of crickets. Using both nuclear and mitochondrial genetic markers, we (1) describe the geographical distribution and sub-division of genetic variation in O. ochracea from across the continental United States, the Mexican states of Sonora and Oaxaca, and populations introduced to Hawaii; (2) demonstrate that the distribution of genetic variation among fly populations is consistent with a single widespread species with regional host specialization, rather than locally differentiated cryptic species, (3) identify the more-probable source populations for the flies introduced to the Hawaiian islands; (4) examine genetic variation and sub-structure within Hawaii; (5) show that among-population geographic, genetic, and host song distances are all correlated, and (6) discuss specialization and lability in host-finding behavior in light of the diversity of cricket songs serving as host cues in different geographically separate populations.
N-ASW: Molecular Dynamics Data
<ul> <li> Description</li> </ul> <p>The data set was generated from ab-initio molecular dynamics simulations and was used to study the adsorption and desorption dynamics of nitrogen atoms on top of amorphous solid water (ASW) [1]. The data set contains structures with 3 to 378 atoms which result in 28,715 structures in total. The atomization energies and atomic forces are calculated at the PBEh-3c/def2-mSVP level of theory [2]. For more details, see Ref. 1.</p> <ul> <li> Format</li> </ul> <p>The data is stored in python compressed array format (.npz) with the atomization energy in kcal/mol and atomic forces in kcal/mol/Ang. The data set contains five numpy arrays</p> <p>import numpy as np<br> data = np.load('N-ASW.npz')<br> data['R'] # Cartesian coordinates of nuclei (Ang.)<br> data['E'] # Total energy (kcal/mol)<br> data['F'] # Atomic forces (kcal/mol/Ang.)<br> data['N'] # Number of atoms in each structure<br> data['Z'] # Nuclear charges</p> <ul> <li>References</li> </ul> <p>[1] Molpeceres G.; Zaverkin V.; and Kästner J. Neural-Network Assisted Study of Nitrogen Atom Dynamics on Amorphous Solid Water. I. Adsorption & Desorption. Mon. Not. R. Astron. Soc. 2020, submitted<br> [2] Grimme S.; Brandenburg J. G.; Bannwarth C.; Hansen A. Consistent structures and interactions by density functional theory with small atomic orbital basis sets. J. Chem. Phys. 2015, 143, 054107.</p>
FIGURE 4 in The unknown diversity of the genus Characidium (Characiformes: Crenuchidae) in the Chocó biogeographic region, Colombian Andes: Two new species supported by morphological and molecular data
FIGURE 4 Scale detail of C. tatama n. sp. IMCN 8924, Paratype, 36.3 mm LS, white arrows show the rounded point characteristic in the lateral line
FIGURE 2 in The unknown diversity of the genus Characidium (Characiformes: Crenuchidae) in the Chocó biogeographic region, Colombian Andes: Two new species supported by morphological and molecular data
FIGURE 2 Ultrametric tree using BEAST representing the phylogenetic relationships of the genus Characidium using COI sequences. Branch lengths were adjusted to a strict molecular clock. The black bars represent the UTOs obtained with the ABGD, GMYC and bPTP molecular delimitation methods and the majority consensus. Green dots posterior probability (>0.95)
FIGURE 1 in The unknown diversity of the genus Characidium (Characiformes: Crenuchidae) in the Chocó biogeographic region, Colombian Andes: Two new species supported by morphological and molecular data
FIGURE 1 Distribution map of the Characidium genus in the trans- Andean and cis-Andean regions of Colombia. Black triangle (HT)/yellow cicle, C. tatama n. sp.; red triangle (HT)/orange circle, C. dule n. sp.; red diamond, C. caucanum; red circle, C. phoxocephalum; white red mark (HT)/ purple circle, C. chancoense; white circle, C. cf. boavistae; blue diamond, C. cf. zebra; red-black star (HT)/grey circle, C. santcjohanni; HT, holotype
FIGURE 3 C. tatama n in The unknown diversity of the genus Characidium (Characiformes: Crenuchidae) in the Chocó biogeographic region, Colombian Andes: Two new species supported by morphological and molecular data
FIGURE 3 C. tatama n. sp., Holotype, IMCN 8925, 38.1 mm LS, Colombia, Chocó, San José Del Palmar. Scale bar = 1 cm
FIGURE 7 in The unknown diversity of the genus Characidium (Characiformes: Crenuchidae) in the Chocó biogeographic region, Colombian Andes: Two new species supported by morphological and molecular data
FIGURE 7 Detail of the composition of spots in C. dule n. sp. IMCN 8929, Paratype 38.24 mm LS, arrows show the detail. Scale bar = 1 cm
Data for the paper 'WISDOM Project - VI. Exploring the relation between supermassive black hole mass and galaxy rotation with molecular gas '
<p>This upload includes the data underlying the MNRAS paper Smith et al. (2020) entitled 'WISDOM Project - VI. Exploring the relation between supermassive black hole mass and galaxy rotation with molecular gas' (arXiv:2010.08565). The full author list is available from the paper, and we request that this paper is cited if this data is used in future publications.</p> <p>The upload includes machine-readable versions (csv) of Tables 3, 4, A1 and A2 of the paper. The upload also includes the calibrated spectra from the two observing programmes (191-18 at the IRAM 30m telescope and 2018-04a at the OSO 20m telescope), and the homogenised spectra used in the project. Full descriptions are given in the paper. </p> <p>Table 3: CubeData.csv; The table contains the determined line widths, inclinations, and SMBH masses used for the resolved sample of this project. The references from which the cubes were obtained, are listed in Table 3 of the paper.</p> <p>UnresolvedData.csv: Table 4; The table contains the determined line widths, inclinations, and SMBH masses used for the unresolved sample of this project. The references from which the spectra were obtained, are listed in Table 4 of the paper.</p> <p>IRAMData.csv: Table A1; The table contains a list of galaxies observed using the IRAM 30m telescope as part of project 191-18. For each galaxy the rms noise is listed, and for detected galaxies the spectrally-integrated line intensity measured over the specified velocity range given. The inferred molecular gas mass is also listed. </p> <p>OSO20mData.csv: Table A2; The table contains a list of galaxies observed using the OSO 20m telescope as part of project 2018-04a. For each galaxy the rms noise is listed, and for detected galaxies the spectrally-integrated line intensity measured over the specified velocity range given. The inferred molecular gas mass is also listed. </p> <p>IRAM30m_191-18.tar: Calibrated spectra from programme 191-18.</p> <p>OSO2018-04a.tar: Calibrated spectra from programme 2018-04a.</p> <p>ResolvedSample.tar: Homogenised spectra for the spatially-resolved sample. Note that some spectra were sourced from other works, the original references are given in the fits headers.</p> <p>UnresolvedSample.tar: Homogenised spectra for the spatially-unresolved sample. Note that some spectra were sourced from other works, the original references are given in the fits headers.</p>
FIGURES 14–17 in Vietnamella chebalingensis, a new species of the family Vietnamellidae (Ephemeroptera) from China based on morphological and molecular data
FIGURES 14–17. Vietnamella chebalingensis Tong, sp. nov. (14) Foreleg femur; (15) midleg; (16) hindleg; (17) foreleg claw.
FIGURES 8–13 in Vietnamella chebalingensis, a new species of the family Vietnamellidae (Ephemeroptera) from China based on morphological and molecular data
FIGURES 8–13. Mouthpart of Vietnamella chebalingensis Tong, sp. nov. (8) Labrum (dorsal view); (9) labium (ventral view); (10) hypopharynx; (11) left mandible; (12) right mandible; (13) maxilla.
FIGURES 18–21 in Vietnamella chebalingensis, a new species of the family Vietnamellidae (Ephemeroptera) from China based on morphological and molecular data
FIGURES 18–21. Vietnamella chebalingensis Tong, sp. nov. (18) Abdominal tergites I–X; (19) pronotum & mesonotum; (20) gill VI; (21) gill VII.
FIGURE 1 in Vietnamella chebalingensis, a new species of the family Vietnamellidae (Ephemeroptera) from China based on morphological and molecular data
FIGURE 1. Bayesian inference tree derived from DNA sequences of COI gene (number at nodes indicate posterior probabilities). Teloganella umbrata was used as outgroup. New sequences in red.
FIGURES 2–4 in Vietnamella chebalingensis, a new species of the family Vietnamellidae (Ephemeroptera) from China based on morphological and molecular data
FIGURES 2–4. Habitus of Vietnamella chebalingensis Tong, sp. nov. (2) Dorsal view; (3) ventral view; (4) dorsal view of immature larva.
FIGURES 5–7 in Vietnamella chebalingensis, a new species of the family Vietnamellidae (Ephemeroptera) from China based on morphological and molecular data
FIGURES 5–7. Vietnamella chebalingensis Tong, sp. nov. (5) Dorsal view of head, pronotum and forelegs; (6) ventral view of head, pronotum and forelegs; (7) abdominal tergites I–X.
FIGURE 16. Family Pilumnidae. A in Checklist of decapod crustaceans from the coast of the São Paulo state (Brazil) supported by integrative molecular and morphological data: III. Infraorder Brachyura Latreille, 1802
FIGURE 16. Family Pilumnidae. A) Pilumnus caribaeus Desbonne, in Desbonne & Schramm, 1867 (CCDB 5075). B) Pilumnus reticulatus Stimpson, 1860 (CCDB 5083). Animals from Brazil, São Paulo state, Ubatuba. Sex: females. Scale bars (mm): A—8; B—7. Photographs by R.C. Buranelli.
FIGURE 19. Family Trichodactylidae. A in Checklist of decapod crustaceans from the coast of the São Paulo state (Brazil) supported by integrative molecular and morphological data: III. Infraorder Brachyura Latreille, 1802
FIGURE 19. Family Trichodactylidae. A) Trichodactylus dentatus H. Milne Edwards, 1853 (CCDB 1775). B) Trichodactylus fluviatilis Latreille, 1828 (CCDB 2070). C) Trichodactylus petropolitanus (Göldi, 1886) (CCDB 2294). Animals from Brazil, São Paulo state: Ilha Comprida (A), São Sebastião (B), Caraguatatuba (C). Sex: females. Scale bars (mm): A—12; B—31; C—24. Photographs by R.C. Buranelli.
FIGURE 20. Families Panopeidae and Pseudorhombilidae. A in Checklist of decapod crustaceans from the coast of the São Paulo state (Brazil) supported by integrative molecular and morphological data: III. Infraorder Brachyura Latreille, 1802
FIGURE 20. Families Panopeidae and Pseudorhombilidae. A) Eurypanopeus abbreviatus (Stimpson, 1860) (CCDB 5764). B) Eurytium limosum (Say, 1818) (CCDB 6369). C) Hexapanopeus caribbaeus (Stimpson, 1871) (CCDB 5658). D) Hexapanopeus paulensis Rathbun, 1930 (CCDB 5546). E) Panopeus americanus Saussure, 1857 (CCDB 5657). F) Panopeus austrobesus Williams, 1983 (CCDB 5869). G) Panopeus harttii Smith, 1869 (CCDB 6207). H) Panopeus rugosus A. Milne-Edwards, 1880 [in A. Milne-Edwards, 1873-1880] (CCDB 5040). I) Tetraxanthus rathbunae Chace, 1939 (CCDB 5873). Animals from Brazil, São Paulo state: Ubatuba (A, C, D, E, G, H), Bertioga (B), Cananéia (F), RV Soloncy Moura Expedition, Point 14 (I). Sex: male (A, B, C, D, E, F, G), female (I), juvenile (H). Scale bars (mm): A—23; B—19; C—14; D—13; E—19; F—23; G—14; H—11; I—20. Photographs by R.C. Buranelli.
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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.