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32 results for “tree file”
Ground truth and raw hyperspectral files of olive trees for plant stress detection
<p>This dataset contains raw hyperspectral images from Cubert S-185 collected on 13 May 2021 from an olive field in Halkidiki, Northern Greece. Included is also a matrix containing the id of each recorded olive tree (the samples) that also appears in the hyperspectral images. QGIS (ver.3.28.0) software plugin 'zonal statistics multiband' was used to compute zonal statistics for each of the 138 spectral bands available for each sample. Accompanying each sample is also the ground truthing data recorded, which addresses the present stress of 3 stressors (<i>Verticillium dahliae, Pleospora herbarum </i>and 'other stressors').</p>
The Earth BioGenome Project Phase II: Illuminating the Eukaryotic Tree of Life. Data file underpinning Figure 2A and Figure 2B
<div>These datasheets accompany the article "The Earth BioGenome Project Phase II: Illuminating the Eukaryotic Tree of Life" in Frontiers in Science</div> <div>This file contains data processed from Catalog of Life on 31 December 2023. The catalog was downloaded and post-processed to</div> <div>remove prokaryotic taxa</div> <div>remove extinct and fossil taxa</div> <div>remove taxon names that were listed as junior synonyms</div> <div>remove taxon names listed as "invalid"</div> <div>Total living, valid eukaryotic genera 167,085</div> <div>The taxa were sorted by the nomenclatorial Code under which they were declared (to avoid namespace clashes)</div> <div>International Code for Algae, Fungi and Plants https://www.iapt-taxon.org/nomen/main.php</div> <div>Algal, Fungal, Plant code genera 31,076</div> <div>International Code of Zoological Nomenclature https://www.iczn.org/the-code/the-code-online/</div> <div>Zoological code genera 136,009</div> <div>The Code-sorted taxa were aggregated by the generic portion of their names, and two plots were generated:</div> <div>a plot aggregating the cumulative number of species in genera sorted by species number (Figure 2A)</div> <div>a plot illustrating the distribution of the size of genera (Figure 2B)</div> <div>This data file gives access to these processed data for</div> <div>Figure 2 A Data</div> <div>Figure 2 B Data</div> <div>The original data including the intermediate calculations of values, and the plotted graphs, are available as a GoogleDoc at https://docs.google.com/spreadsheets/d/1V-bTtWjIRasC3AgID0jGlyToKqI-H9h1aPeSxUpNrjk/edit?usp=sharing</div>
Conversion of measurements of tree ring gains: Canada, Africa, Mexico, South America from RWL- files to JSON format.
<p>The International Tree Rings Data Bank (ITRDB) is the most comprehensive tree growth database (https://www1.ncdc.noaa.gov/pub/data/paleo/treering).</p> <p>Shoudong Zhao, et al. (2019, 2018) analyzes the representativity of dendrochronological data (ITRDB) and proposes a corrected database with error indications. One of the bottlenecks of data use (ITRDB) is that the data is loaded as a collection of separate files in the Tucson positional format.</p> <p>The purpose of our data presentation is to change the Tucson data format to JSON format and combine the separate files into one.</p> <p>We convert the initial data for the <strong>Canada</strong>, <strong>Africa</strong>, <strong>Mexico</strong> and <strong>Southamerica</strong> rwl-files into Json format of data on tree growth in four files: <strong>canada.json</strong>, <strong>africa.json</strong>, <strong>mexico.json</strong> and <strong>southamerica.json</strong>. The data was converted using the R programming language and the dplR program library Bunn, A. (2008)</p> <p>The experience of developing the structure of dendroclimatic data in JSON format is described in the works of Kachaev A. (2016, 2017, 2020).</p> <p>Description of the structure of JSON data format is attached in the files ReadMe.pdf</p> <p> </p> <p>References</p> <p>Bunn, A. G. (2008). A dendrochronology program library in R (dplR). Dendrochronologia, 26, 115-124. https://doi.org/10.1016/j.dendro.2008.01.002</p> <p>Kachaev, Alexander (2020), "Compact dataset of dendrochronological data of pri-mary metric characteristics of tree rings of Asia.", Mendeley Data, V1, doi: 10.17632 / p9zhpmzgtk.1</p> <p>Kachaev A. V. (2017) Model for describing the structure of dendroclimatic data In the collection: Regional problems of remote sensing of the Earth Materials of the IV international scientific conference. Siberian Federal University, Institute of Space and Information Technologies. p. 120-122. (Russia)</p> <p>Kachaev A. V. (2016) NOSQL Approach for Development of Dendroclimatic Data Bank. In the collection: Regional problems of remote sensing of the Earth. Materials of the III International Scientific Conference. p. 89-91. (Russia)</p> <p>Shoudong Zhao, et al. (2019). The International Tree-Ring Data Bank (ITRDB) revisited: Data availability and global ecological representativity. Journal of Biogeography, 46 (2), 355-368. doi: 10.1111 / jbi.13488</p> <p>Zhao, Shoudong et al. (2018), Data from: The International Tree-Ring Data Bank (ITRDB) revisited: data availability and global ecological representativity, Dryad, Dataset, https://doi.org/10.5061/dryad.kh0qh06</p>
NEXUS file describing the taxonomic relationships of the 466 species for which genome sequencing was underway at Tree of Life, Wellcome Sanger Institute, at 31 December 2020
<p>This NEXUS file shows the taxonomic relationships of 466 species of eukaryote. The taxonomy derives from the NCBI TaxonomyDB. The species are those for which genome sequencing is underway at the Tree of Life programme, Wellcome Sanger Institute, as of 31st Decemnber 2020. The NEXUS file includes a figtree block generated in FigTree [<strong><a href="https://github.com/rambaut/figtree">https://github.com/rambaut/figtree</a>] </strong>that informs display of the data as a circular tree with species coloured by taxonomic Family, and Families with more than one species represented as triangles. The figure is used in publications and presentations describing the activities of the Tree of Life programme and the projects in which Tree of Life is involved, especially the Darwin Tree of Life project [https://darwintreeoflife.org].</p>
Raw data used for COI delineation of the Eupolybothrus species: Authors: Stoev et al. 2013 Data type: genomic The archive contains the following data: 1) fasta-Alignment as the basis for all analyses (.FASTA), 2) mega-file for the calculation of the genetic distances and the NJ tree (.MDSX), 3) NJ-tree in Newick format (.NWK), 4) graph of the TCS Software for the Statistical Parsimony method (.GRAPH) File: E_cavernicolus.rar from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
<p>Authors: Stoev et al. 2013 Data type: genomic The archive contains the following data: 1) fasta-Alignment as the basis for all analyses (.FASTA), 2) mega-file for the calculation of the genetic distances and the NJ tree (.MDSX), 3) NJ-tree in Newick format (.NWK), 4) graph of the TCS Software for the Statistical Parsimony method (.GRAPH) File: E_cavernicolus.rar</p>
Alignment and Tree file from: Two novel species of tropical Morchella (Ascomycota, Pezizales, Morchellaceae) discovered in the UNESCO Rinjani Lombok Biosphere Reserve, Indonesia
<p>Alignment and Tree file from: Two novel species of tropical Morchella (Ascomycota, Pezizales, Morchellaceae) discovered in the UNESCO Rinjani Lombok Biosphere Reserve, Indonesia</p>
Tree-Ring Measurement File: Lodgepole Pine Samples Collected at Steamboat Geyser, Yellowstone National Park
<p>Decade format (Tucson format) tree-ring measurement file (0.001 mm) for lodgepole pine core samples collected adjacent to Steamboat Geyser in Yellowstone National Park, Wyoming, USA.</p>
Molecular phylogeny and morphological perianth evolution in Corymbia (Myrtaceae), and the implications for generic delimitation: data and tree files
<p><strong>Premise:</strong> Eucalypts (Myrtaceae tribe Eucalypteae) are currently placed in seven genera. Traditionally,<em> Eucalyptus</em> was defined by its operculum but when phylogenies placed <em>Angophora</em>, with free sepals and petals, as sister to the operculate bloodwood eucalypts, the latter were segregated into a new genus, <em>Corymbia</em>. Yet generic delimitation in the tribe Eucalypteae remains uncertain. Here we address these problems using phylogenetic analysis with the largest molecular dataset to date.</p> <p><strong>Methods: </strong>We captured 101 low-copy nuclear exons from 392 samples representing 266 species. Our phylogenetic analysis used maximum likelihood (IQtree) and multi-species coalescent (Astral). At two nodes critical to generic delimitation, we tested alternative relationships among <em>Arillastrum</em>, <em>Angophora</em>, <em>Eucalyptus</em> and <em>Corymbia</em> using Shimodaira's AU test. Phylogenetic mapping was used to explore the evolution of perianth traits.</p> <p><strong>Results: </strong>Monophyly of <em>Corymbia</em> relative to <em>Angophora</em> was decisively rejected. All alternative relationships among the seven currently recognised Eucalypteae genera imply homoplasy in evolutionary origins of the operculum. Inferred evolutionary transitions in perianth traits are congruent with divergences between major clades except that expression of separate sepals and petals in <em>Angophora</em>, which is nested within the operculate genus <em>Corymbia</em>, appears to be a reversal to the plesiomorphic perianth structure.</p> <p><strong>Conclusions:</strong> Here we formally raise <em>Corymbia</em> subg. <em>Blakella</em> to genus rank and make the relevant new combinations. We also define and name three sections within <em>Blakella</em> (<em>B.</em> sect. <em>Blakella</em>, <em>B.</em> sect. <em>Naviculares</em> and <em>B.</em> sect. <em>Maculatae</em>), and two series within <em>Blakella</em> sect. <em>Maculatae</em> (<em>B.</em> ser. <em>Maculatae</em> and <em>B.</em> ser. <em>Torellianae</em>). <em>Corymbia</em> is reduced to the red bloodwoods.</p>
Alignments and tree files from: Phylogenetic relationships within tribe Hibisceae (Malvaceae) reveal complex patterns of polyphyly in Hibiscus and Pavonia
<p>The diverse and spectacular Hibisceae tribe comprises over 750 species. No studies, however, have broadly sampled across the dozens of genera in the tribe, leading to uncertainty in the relationships among genera. The non-monophyly of the genus <em>Hibiscus </em>is infamous and challenging, whereas the monophyly of most other genera in the tribe has yet to be assessed, including the large genus <em>Pavonia</em>. Here we significantly increase taxon sampling in the most complete phylogenetic study of the tribe to date. We assess monophyly of most currently recognized genera in the tribe and include three and thirteen newly sampled sections of <em>Hibiscus </em>and <em>Pavonia</em>, respectively. We also include five rarely sampled genera and 137 species previously unsampled. Our phylogenetic trees demonstrate that <em>Hibiscus</em>, as traditionally defined, encompasses at least 20 additional genera. The status of <em>Pavonia </em>emerges as comparable in complexity to <em>Hibiscus</em>. We offer clarity in the phylogenetic placement of several taxa of uncertain affinity (e.g., <em>Helicteropsis, Hibiscadelphus, Jumelleanthus, and Wercklea)</em>. We also identify two new clades and elevate them to the generic rank with the recognition of two, new monotypic genera: 1) <em>Blanchardia </em>M.M.Hanes & R.L.Barrett is a surprising Caribbean lineage that is sister to the entire tribe, and 2) <em>Astrohibiscus </em>McLay & R.L.Barrett represents former members of <em>Hibiscus caesius</em> s.l. <em>Cravenia </em>McLay & R.L.Barrett is also described as a new genus for the <em>Hibiscus panduriformis</em> clade which is allied to <em>Abelmoschus</em>. Finally, we introduce a new classification for the tribe and clarify the boundaries of <em>Hibiscus </em>and <em>Pavonia</em>.</p>
OTU-Taxid Mapping File for gg_13_5_99_otus tree
<p>File containing mapping information of 99_otus tree from gg_13_5. First column: OTU. Second column: Taxid. Third Column: accession.</p>
Files associated with: Migration-based simulations for Canadian trees show limited tracking of suitable climate under climate change
<p><strong>Aim</strong></p> <p>Species distribution models typically project climatically suitable habitat for trees in eastern North America to shift hundreds of kilometers this century. We simulated potential migration considering species' life history and traits for 10 tree species and their ability to track climatically suitable habitat.</p> <p><strong>Location</strong></p> <p>Eastern Canada, covering ~3.7 million km<sup>2</sup></p> <p><strong>Methods</strong></p> <p>We simulated migration-constrained range shifts through 2100 using a hybrid approach combining projections of climatically suitable habitat based on two Representative Concentration Pathways (RCP4.5, RCP8.5) for three time periods and two species distribution modelling approaches with process-based models parameterized using data related to <span>dispersal ability and generation time</span>. We developed a unique 'migration kernel' that uses seed dispersal traits and observed migration velocities to obtain kernel shape and dispersal probabilities. We then calculated lags between the migration-constrained range limits obtained through simulations and limits of climatically suitable habitat.</p> <p><strong>Results</strong></p> <p>All species demonstrated northward range shifts at the leading edge of their simulated distribution through 2100, but the magnitude and rate of that shift varied by species and time period. Climatically suitable habitat limits were found to be north of simulated distribution limits across both RCPs, with lags increasing through time. On average, the simulated distribution that remained within climatically suitable habitat showed higher decreases under RCP8.5 than RCP4.5, with large areas of the rear edge of the simulated distribution becoming partially or completely climatically unsuitable for many species.</p> <p><strong>Main conclusions</strong></p> <p><span>Climatically suitable habitat limits projected for 2100 far exceeded migration-constrained range limits for all 10 species, particularly for temperate species. This study underlines the limited extent to which species will track climate change via natural migration. Integrating observed migration velocities, seed dispersal and generation time with SDM outputs allows for more realistic evaluations of tree migration ability under climate change and may help orient forest conservation and restoration efforts.</span></p>
Alignment and tree files for archaeal NusA2 phylogeny
<p>These are the data underlying the phylogenetic analysis of archaeal NusA2 in Figure 3D in our manuscript:</p> <h1><strong>Archaeal NusA2 is the evolutionary ancestor of ribosomal protein eS7 in eukaryotes</strong></h1> <p>Duy Khanh Phung, Simona Pilotto, Dorota Matelska, Fabian Blombach, Nikos Pinotsis, Ladislav Hovan, Francesco Luigi Gervasio, and Finn Werner</p> <p>(under revision)</p>
Data and MATLAB files for: Timescale analyses of fluctuations in coexisting populations of a native and invasive tree squirrel
<p>1. Competition from invasive species is an increasing threat to biodiversity. In Southern California, the western gray squirrel (Sciurus griseus, WGS) is facing increasing competition from the fox squirrel (Sciurus niger, FS), an invasive congener.</p> <p>2. We used spectral methods to analyze 140 consecutive monthly censuses of WGS and FS within a 11.3 ha section of the California Botanic Garden. Variation in the numbers for both species and their synchrony was distributed across long timescales (> 15 months).</p> <p>3. After filtering out annual changes, concurrent mean monthly temperatures from nearby Ontario Airport (ONT) yielded a spectrum with a large semiannual peak and significant spectral power at long timescales (> 30 months). Squirrel-temperature cospectra showed significant negative covariation at long timescales (> 35 months) for WGS and smaller significant negative peaks at 6 months for both species.</p> <p>4. Simulations from a Lotka-Volterra model of two competing species indicates that the risk of extinction for the weaker competitor increases quickly as environmental noise shifts from short to long timescales.</p> <p>5. We analyzed the timescales of fluctuations in detrended mean annual temperatures for the time period 1915-2014 from 1218 locations across the continental USA. In the last two decades, significant shifts from short timescales to long timescales have occurred, changing from less than 3 years to 4-6 years.</p> <p>6. Our results indicate that (i) population fluctuations in co-occurring native and invasive tree squirrels are synchronous, occur over long timescales, and may be driven by fluctuations in environmental conditions; (ii) long timescale population fluctuations increase the risk of extinction in competing species, especially for the inferior competitor; and (iii) the timescales of interannual environmental fluctuations may be increasing from recent historical values. These results have broad implications for the impact of climate change on the maintenance of biodiversity.</p>
ITS phylogeny and tree file of Heterodontonyx species
<p><span><span>Here we used the DNA matrix of <em>Heterodontonyx</em> species to estimate their phylogenetic relationships and molecular distances. We used molecular data to inform the taxonomic revision of this Australian genus of spider wasps.</span></span></p>
Alignments and tree files from: Phylogenetic relationships within tribe Hibisceae (Malvaceae) reveal complex patterns of polyphyly in Hibiscus and Pavonia
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ITS phylogeny and tree file of Heterodontonyx species
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Files associated with: Migration-based simulations for Canadian trees show limited tracking of suitable climate under climate change
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Molecular phylogeny and morphological perianth evolution in Corymbia (Myrtaceae), and the implications for generic delimitation: data and tree files
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Data and MATLAB files for: Timescale analyses of fluctuations in coexisting populations of a native and invasive tree squirrel
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Sequence matrix and tree files for Spatial phylogenetics of the native California flora (Thornhill et al. BMC Biology)
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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