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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Thiergart, Thorsten; Landan, Giddy; Martin, William F.;

    BackgroundAnalyzed individually, gene trees for a given taxon set tend to harbour incongruent or conflicting signals. One popular approach to deal with this circumstance is to use concatenated data. But especially in prokaryotes, where lateral gene transfer (LGT) is a natural mechanism of generating genetic diversity, there are open questions as to whether concatenation amplifies or averages phylogenetic signals residing in individual genes. Here we investigate concatenations of prokaryotic and eukaryotic datasets to investigate possible sources of incongruence in phylogenetic trees and to examine the level of overlap between individual and concatenated alignments.ResultsWe analyzed prokaryotic datasets comprising 248 invidual gene trees from 315 genomes at three taxonomic depths spanning gammaproteobacteria, proteobacteria, and prokaryotes (bacteria plus archaea), and eukaryotic datasets comprising 279 invidual gene trees from 85 genomes at two taxonomic depths: across plants-animals-fungi and within fungi. Consistent with previous findings, the branches in trees made from concatenated alignments are, in general, not supported by any of their underlying individual gene trees, even though the concatenation trees tend to possess high bootstrap proportions values. For the prokaryote data, this observation is independent of phylogenetic depth and sequence conservation. The eukaryotic data show much better agreement between concatenation and single gene trees. LGT frequencies in trees were estimated using established methods. Sequence length in individual alignments, but not sequence divergence, was found to correlate with the generation of branches that correspond to the concatenated tree.ConclusionsThe weak correspondence of concatenation trees with single gene trees gives rise to the question where the phylogenetic signal in concatenated trees is coming from. The eukaryote data reveals a better correspondence between individual and concatenation trees than the prokaryote data. The question of whether the lack of correspondence between individual genes and the concatenation tree in the prokaryotic data is due to LGT or phylogenetic artefacts is remains unanswered. If LGT is the cause of incongruence between concatenation and individual trees, we would have expected to see greater degrees of incongruence for more divergent prokaryotic data sets, which was not observed, although estimated rates of LGT suggest that LGT is responsible for at least some of the observed incongruence. resourcesThe Zip-file include 8 Folders. Each containing phylogenetic trees and alignments for one dataset.

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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
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    Authors: Dylus, David; Czarkwiani, Anna; Blowes, Liisa; Elphick, Maurice; +1 Authors

    Details on fuzzy clustering. This file includes the data for Fig. 5. It shows the classification of TFs of A. filiformis and S. purpuratus into the four modes of expression. (XLSX 69 kb)

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    Authors: Horstmann, Jochen; Navarro, Wendy; Carrasco, Ruben; Brandt, Peter (ORCID: 0000-0002-9235-955X); +2 Authors

    During the Transatlantic Equatorial Cruise II (TRATLEQ II) with the R/V METEOR (M181) from 17. April to 28. May 2022 (Brandt, 2022), 44 Lagrangian drifters were deployed along the Equator (between 7°W and 37°W) to monitor the surface flow in the upper meter. The equatorial section covered the region of the Atlantic cold tongue that seasonally develops during boreal summer east of 23°W and the western equatorial Atlantic characterized by warmer surface waters and deeper mixed layer depths. In particular, the cruise M181 took place during the warm phase with relatively homogeneous warm surface layer in the whole equatorial Atlantic. Drifters were deployed every 1° longitude (~111 km) between 7°W and 37°W. The drifters were designed and built at Helmholtz-Zentrum Hereon to follow the upper surface flow (approx. 50 cm). The main body of these Hereon drifters consists of a 7.5 cm x 20 cm long tube with a floatation ring at the top. It is attached to a drogue of 35 cm in both length and diameter through a flexible cord within a distance of 20 cm to the tube. When deployed about 5 cm of the tube protrude from the water surface, resulting in a ratio of drag area inside to drag area outside the water of 21. The tube contains a battery pack and an electronic board, which acquires and reports the GPS position every 5 minutes via a global satellite network in near real time. Table 1 provides some information on the 44 deployed Hereon Drifters, which consists of deployment and working time, total covered distance and number of recorded GPS positions.

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    PANGAEA
    Dataset . 2023
    Data sources: B2FIND
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      PANGAEA
      Dataset . 2023
      Data sources: B2FIND
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Myroshnychenko, Volodymyr; Schaap, Dick; Schlitzer, Reiner;

    The SeaDataCloud Temperature and Salinity Historical Data Collection for the Black Sea (Version 2) includes open access in situ data on temperature and salinity of water column in the Black Sea (and a little in the Sea of Azov) for period 1868 – 2019. The data were retrieved from the SeaDataNet infrastructure at the end of 2019. The dataset format is Ocean Data View (ODV) binary collection. The quality control of the data has been performed with the help of ODV software. Data Quality Flags have been revised and set up using the elaborated by SeaDataNet2 and SeaDataCloud project QC procedures in conjunction with the visual expert check. Data duplicates have been identified and excluded from the dataset. The final number of the Temperature and Salinity profiles (stations) in the collection is 162626.For data access please register at http://www.marine-id.org/.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Ute Schuster;
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ PANGAEA - Data Publi...arrow_drop_down
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    Authors: Gibbin, Emma M; Gavish, Assaf; Krueger, Thomas; Kramarsky-Winter, Esti; +5 Authors

    We conducted two isotope experiments (described in Gibbin et al. 2018) to determine how the presence of pathogens influences resource partitioning in the coral holobiont. Specifically, we quantified: 1) 13C-assimilation in Symbiodinium and the amount of 13C-labelled photosynthates that are assimilated by the host; 2) the metabolic turnover of 13C in Symbiodinium and in their host and 3) the incorporation of bacterial-derived N within the tissues of the coral holobiont.NanoSIMS images (either 40×40 or 50×50 µm in size) were obtained by rasterizing a 16 keV Cs+ primary ion beam, focused to a spot-size of 150 nm, across the sample surface. Settings (dwell time = 5 ms; number of pixels = 256×256, layers = 5) were kept constant between images. Data was extracted from drift-corrected images using L'IMAGE (Dr. Larry Nittler, Carnegie Institution of Washington). Regions of interest (ROIs) were drawn around individual symbiont cells and the host gastrodermis (excluding symbionts), using the contour lines on the 12C14N- image. These ROIs were then used to quantify the average enrichment of 13C and 15N in each partner. Our measured values are expressed as Atom Percent Excess (APE, in %). Supplement to: Gibbin, Emma M; Gavish, Assaf; Krueger, Thomas; Kramarsky-Winter, Esti; Shapiro, Orr; Guiet, Romain; Jensen, Louise; Vardi, Assaf; Meibom, Anders (2018): Vibrio coralliilyticus infection triggers a behavioural response and perturbs nutritional exchange and tissue integrity in a symbiotic coral. The ISME Journal

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    Authors: Mortazavi, Bohayra;

    The energy minimized unit-cell by the DFT, the relaxed super-cell for the MD modelling, the script to load the model in LAMMPS THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOVE

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    Authors: Armendariz, Marcelo; Ban, Hiroshi; Welchman, Andrew E; Vanduffel, Wim;

    Electrophysiological evidence suggested primarily the involvement of area MT in depth cue integration in macaques, as opposed to human imaging data pinpointing area V3B/KO. To clarify this conundrum, we decoded monkey fMRI responses evoked by stimuli signaling near or far depths defined by binocular disparity, relative motion and their combination, and we compared results with those from an identical experiment previously performed in humans.Responses in macaque area MT are more discriminable when two cues concurrently signal depth, and information provided by one cue is diagnostic of depth indicated by the other. This suggests that monkey area MT computes fusion of disparity and motion depth signals, exactly as shown for human area V3B/KO. Hence, these data reconcile previously reported discrepancies between depth processing in human and monkey by showing the involvement of the dorsal stream in depth cue integration using the same technique, despite the engagement of different regions. data describing fig 1-8 and sfig 1-12data.zip

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    Authors: Reverdin, Gilles; Ólafsdóttir, Sólveig Rósa; Metzl, Nicolas;
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    Authors: Antonio, Jose; Butenschön, Momme; Frölicher, Thomas L.; Yool, Andrew;

    Marine enviromental data from Biogeochemical models in paper "Can we project changes in fish abundance and distribution in response to climate?" at Global Change Biology journal

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Thiergart, Thorsten; Landan, Giddy; Martin, William F.;

    BackgroundAnalyzed individually, gene trees for a given taxon set tend to harbour incongruent or conflicting signals. One popular approach to deal with this circumstance is to use concatenated data. But especially in prokaryotes, where lateral gene transfer (LGT) is a natural mechanism of generating genetic diversity, there are open questions as to whether concatenation amplifies or averages phylogenetic signals residing in individual genes. Here we investigate concatenations of prokaryotic and eukaryotic datasets to investigate possible sources of incongruence in phylogenetic trees and to examine the level of overlap between individual and concatenated alignments.ResultsWe analyzed prokaryotic datasets comprising 248 invidual gene trees from 315 genomes at three taxonomic depths spanning gammaproteobacteria, proteobacteria, and prokaryotes (bacteria plus archaea), and eukaryotic datasets comprising 279 invidual gene trees from 85 genomes at two taxonomic depths: across plants-animals-fungi and within fungi. Consistent with previous findings, the branches in trees made from concatenated alignments are, in general, not supported by any of their underlying individual gene trees, even though the concatenation trees tend to possess high bootstrap proportions values. For the prokaryote data, this observation is independent of phylogenetic depth and sequence conservation. The eukaryotic data show much better agreement between concatenation and single gene trees. LGT frequencies in trees were estimated using established methods. Sequence length in individual alignments, but not sequence divergence, was found to correlate with the generation of branches that correspond to the concatenated tree.ConclusionsThe weak correspondence of concatenation trees with single gene trees gives rise to the question where the phylogenetic signal in concatenated trees is coming from. The eukaryote data reveals a better correspondence between individual and concatenation trees than the prokaryote data. The question of whether the lack of correspondence between individual genes and the concatenation tree in the prokaryotic data is due to LGT or phylogenetic artefacts is remains unanswered. If LGT is the cause of incongruence between concatenation and individual trees, we would have expected to see greater degrees of incongruence for more divergent prokaryotic data sets, which was not observed, although estimated rates of LGT suggest that LGT is responsible for at least some of the observed incongruence. resourcesThe Zip-file include 8 Folders. Each containing phylogenetic trees and alignments for one dataset.

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    Authors: Dylus, David; Czarkwiani, Anna; Blowes, Liisa; Elphick, Maurice; +1 Authors

    Details on fuzzy clustering. This file includes the data for Fig. 5. It shows the classification of TFs of A. filiformis and S. purpuratus into the four modes of expression. (XLSX 69 kb)

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    Authors: Horstmann, Jochen; Navarro, Wendy; Carrasco, Ruben; Brandt, Peter (ORCID: 0000-0002-9235-955X); +2 Authors

    During the Transatlantic Equatorial Cruise II (TRATLEQ II) with the R/V METEOR (M181) from 17. April to 28. May 2022 (Brandt, 2022), 44 Lagrangian drifters were deployed along the Equator (between 7°W and 37°W) to monitor the surface flow in the upper meter. The equatorial section covered the region of the Atlantic cold tongue that seasonally develops during boreal summer east of 23°W and the western equatorial Atlantic characterized by warmer surface waters and deeper mixed layer depths. In particular, the cruise M181 took place during the warm phase with relatively homogeneous warm surface layer in the whole equatorial Atlantic. Drifters were deployed every 1° longitude (~111 km) between 7°W and 37°W. The drifters were designed and built at Helmholtz-Zentrum Hereon to follow the upper surface flow (approx. 50 cm). The main body of these Hereon drifters consists of a 7.5 cm x 20 cm long tube with a floatation ring at the top. It is attached to a drogue of 35 cm in both length and diameter through a flexible cord within a distance of 20 cm to the tube. When deployed about 5 cm of the tube protrude from the water surface, resulting in a ratio of drag area inside to drag area outside the water of 21. The tube contains a battery pack and an electronic board, which acquires and reports the GPS position every 5 minutes via a global satellite network in near real time. Table 1 provides some information on the 44 deployed Hereon Drifters, which consists of deployment and working time, total covered distance and number of recorded GPS positions.

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    Authors: Myroshnychenko, Volodymyr; Schaap, Dick; Schlitzer, Reiner;

    The SeaDataCloud Temperature and Salinity Historical Data Collection for the Black Sea (Version 2) includes open access in situ data on temperature and salinity of water column in the Black Sea (and a little in the Sea of Azov) for period 1868 – 2019. The data were retrieved from the SeaDataNet infrastructure at the end of 2019. The dataset format is Ocean Data View (ODV) binary collection. The quality control of the data has been performed with the help of ODV software. Data Quality Flags have been revised and set up using the elaborated by SeaDataNet2 and SeaDataCloud project QC procedures in conjunction with the visual expert check. Data duplicates have been identified and excluded from the dataset. The final number of the Temperature and Salinity profiles (stations) in the collection is 162626.For data access please register at http://www.marine-id.org/.

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    Authors: Ute Schuster;
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