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Fig. 2 in Polyphasic classification of Nonomuraea strains isolated from the Karakum Desert and description of Nonomuraea deserti sp. nov., Nonomuraea diastatica sp. nov., Nonomuraea longispora sp. nov. and Nonomuraea mesophila sp. nov.
Fig. 2. Phylogenomic tree based on whole genome sequence data of strains KC201T, KC310T, KC401, KC712T, 6K102T and closely related type strains of the family Streptosporangiaceae reconstructed on the Type (Strain) Genome Server (TYGS). The tree was inferred with FastME 2.1.6.1 [51] from GBDP distances calculated from genome sequences. The branch lengths are scaled in terms of GBDP distance formula d5. The numbers above branches are GBDP pseudo-bootstrap support values from 100 replications, with an average branch support of 97.3 %. The tree was rooted at the midpoint [52].
Fig. 1 in Polyphasic classification of Nonomuraea strains isolated from the Karakum Desert and description of Nonomuraea deserti sp. nov., Nonomuraea diastatica sp. nov., Nonomuraea longispora sp. nov. and Nonomuraea mesophila sp. nov.
Fig. 1. Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showing relationships between strains KC201T, KC310T, KC401, KC712T, 6K102T and between them and type strains of closely related Nonomuraea species. Evolutionary distances were computed using the Jukes–Cantor method [76] and are in the units of the number of base substitutions per site. The analysis was based on 39 nucleotide sequences. Positions containing gaps and missing data were eliminated from the data set. There was a total of 1316 positions in the final dataset. Asterisks indicate corresponding nodes recovered in the maximum-likelihood and maximum-parsimony trees. Numbers at the nodes indicate percentage levels of bootstrap support, only values over 50 % are shown. Bar, 0.005 substitutions per nucleotide position.
Fig. 3 in Streptomyces aquilus sp. nov., a novel actinomycete isolated from a Chinese medicinal plant
Fig. 3. Neighbor-joining tree based on five-gene concatenated sequences (atpD, gyrB, recA, rpoB and trpB, 2458 nt) showing the relationships between the related members of the genus Streptomyces. Mycobacterium tuberculosis H37RvT was used as an outgroup. Bootstrap percentages over 50% derived from 1000 replications are shown at the nodes. Asterisks indicate branches that were also found using the maximum-likelihood method and the maximum-parsimony method. Bar, 0.05 substitutions per site.
Fig. 2 in Streptomyces aquilus sp. nov., a novel actinomycete isolated from a Chinese medicinal plant
Fig. 2. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences showing the relationship between selected species of the genus Streptomyces. Mycobacterium tuberculosis H37RvT was used as an outgroup. Bootstrap percentages over 50% derived from 1000 replications are shown at the nodes. Asterisks indicate branches also recovered in the maximum-likelihood and maximum-parsimony trees. Bar, 0.01 nucleotide substitutions per site.
Supplemental to Masterthesis: Comparative Genome analysis of borontolerant and -sensitive bacterial isolates
<p>Supplemental data and result files of the Masterthesis: Comparative Genome analysis of borontolerant and -sensitive bacterial isolates</p>
Using Seismic Noise Levels to Monitor Social Isolation: An Example from Rio de Janeiro, Brazil
<p>Paper</p> <p>Dias, F.L., M. Assumpção, P.S. Peixoto, M.B. Bianchi, B. Collaço, J. Calhau (2020), <strong>Using Seismic Noise Levels to Monitor Social Isolation: </strong><strong>An Example from Rio de Janeiro, Brazil. </strong><em>Geophysical Research Letters.</em></p> <p>1) Daily median particle velocity amplitudes for station ON.ON02. Each amplitude is the median of all values between 09 AM - 6 PM local time.</p> <p>median_VEL_4_14_Hz.csv = median daily velocity (m/s) in the 4-14Hz frequency band.</p> <p>median_VEL_8_14_Hz.csv = median daily velocity (m/s) in the 8-14Hz frequency band. Data used in Fig. 2.</p> <p>median_VEL_4_8_Hz.csv = median daily velocity (m/s) in the 4-8Hz frequency band. Data used in Fig. 4.</p> <p>The raw data from station ON.ON02 can be retrieved from the RSBR (Brazilian Seismic Network) database at www.rsbr.gov.br</p> <p>2) <em>In Loco</em> Isolation index for Rio de Janeiro city. Data provided by <em>In Loco</em> company on 2020 April 22.</p> <p>InLoco_IsolationIndex_RioDeJaneiroCity.txt = date and <em>Ik</em> index for Rio de Janeiro city.</p> <p>Data used in Figs. 2, 4 and 5.</p>
Resolution of the house mouse (Mus musculus) phylogeny by integration over isolation-with-migration histories
The three main subspecies of house mice, Mus musculus castaneus, Mus musculus domesticus , and Mus musculus musculus, are estimated to have diverged ~325-500KYA. Resolution of the details of their evolutionary history is complicated by their relatively recent divergence, ongoing gene flow among the subspecies, and complex demographic histories. Previous studies have been limited to some extent by the number of loci surveyed and/or by the scope of the method used. Here we apply a method (IMa3) that provides an estimate of a population phylogeny while allowing for complex histories of gene exchange. Results strongly support a topology with M. m. domesticus as sister to M. m. castaneus and M. m. musculus . In addition, we find significant evidence of reciprocal gene flow between all pairs of subspecies. Our estimates of another key set of parameters, effective population size ( N e ), support previous results that the N e of M. m. castaneus is larger than that of the other two subspecies.
Figure 4 in Temporal patterns of the calanoid copepod community in Veliko Jezero, an isolated marine lake (South Adriatic Sea): links to a larger-scale climate changes
Figure 4. Mean Margalef's species richness and Shannon–Wiener diversity index values per year; 90% confidence intervals are shown.
Figure 3 in Temporal patterns of the calanoid copepod community in Veliko Jezero, an isolated marine lake (South Adriatic Sea): links to a larger-scale climate changes
Figure 3. Seasonal and inter-annual patterns of total calanoid abundance (individuals per m3) (left scale and bars) and their contribution (%) to total mesozooplankton abundance (right scale and line) over the study period.
Figure 2 in Temporal patterns of the calanoid copepod community in Veliko Jezero, an isolated marine lake (South Adriatic Sea): links to a larger-scale climate changes
Figure 2. Seasonal and inter-annual patterns of hydrographic parameters (temperature and salinity) over the study period.
Supplementary material 2 from: Buzan E, Potušek S, Urzi F, Pokorny B, Šprem N (2020) Genetic characterisation of wild ungulates: successful isolation and analysis of DNA from widely available bones can be cheap, fast and easy. ZooKeys 965: 141-156. https://doi.org/10.3897/zookeys.965.54862
Microsatellite loci for muscle tissue samples and recent bone samples
Figure 1 from: Buzan E, Potušek S, Urzi F, Pokorny B, Šprem N (2020) Genetic characterisation of wild ungulates: successful isolation and analysis of DNA from widely available bones can be cheap, fast and easy. ZooKeys 965: 141-156. https://doi.org/10.3897/zookeys.965.54862
Figure 1 Micro-locations of sampling bone material for DNA isolation (see arrows) A roe deer mandibles B ethmoid bone of chamois C wild boar mandible D chamois skull.
Supplementary material 1 from: Buzan E, Potušek S, Urzi F, Pokorny B, Šprem N (2020) Genetic characterisation of wild ungulates: successful isolation and analysis of DNA from widely available bones can be cheap, fast and easy. ZooKeys 965: 141-156. https://doi.org/10.3897/zookeys.965.54862
Tables S1–S4
Figure 7 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069
Figure 7 BSPs showing NefT (Nef = effective population size; T = generation time) changes over time for P. minor based on Cytb sequences. The upper and lower limits of the blue line represent the 95% confidence intervals of highest posterior densities (HPD) analysis. The solid black line represents median estimates of NefT.
Figure 5 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069
Figure 5 Matrix of pairwise FST values between 11 P. minor populations based on Cytb sequences. * significant at p < 0.05 by the permutation test, ** extremely significant at p < 0.01 by the permutation test.
Figure 6 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069
Figure 6 The expected mismatch distributions under a sudden expansion model (solid gray line) and the observed pairwise difference (black bars) of Cytb haplotypes of P. minor.
Figure 4 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069
Figure 4 Unrooted minimum spanning tree showing the genetic relationships among the Cytb haplotypes of P. minor. Circle sizes are proportional to haplotype frequency. Perpendicular tick marks on the lines joining the haplotypes represent the number of nucleotide substitutions.
Figure 1 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069
Figure 1 Sampling locations of P. minor. Populations are marked by abbreviations that correspond to Table 1.
Figure 2 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069
Figure 2 Composition and distribution of 22 Cytb haplotypes in the Chinese and Malaysian populations.
Figure 3 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069
Figure 3 NJ tree and distribution of Cytb haplotypes among populations for P. minor. Bootstrap supports of > 50 in 1000 replicates are shown.
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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.