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2,052 results for “Species tree”
Supplementary material 8 from: Collins N, Lightfoot DC (2022) A new species of tree cricket (Orthoptera, Gryllidae, Oecanthinae) from Chihuahuan Desert gypsum dunes in the United States and a key to the nigricornis species group. Journal of Orthoptera Research 31(2): 181-189. https://doi.org/10.3897/jor.31.79036
Supplementary material 8 from: Collins N, Lightfoot DC (2022) A new species of tree cricket (Orthoptera, Gryllidae, Oecanthinae) from Chihuahuan Desert gypsum dunes in the United States and a key to the nigricornis species group. Journal of Orthoptera Research 31(2): 181-189. https://doi.org/10.3897/jor.31.79036
Supplementary material 5 from: Collins N, Lightfoot DC (2022) A new species of tree cricket (Orthoptera, Gryllidae, Oecanthinae) from Chihuahuan Desert gypsum dunes in the United States and a key to the nigricornis species group. Journal of Orthoptera Research 31(2): 181-189. https://doi.org/10.3897/jor.31.79036
Supplementary material 5 from: Collins N, Lightfoot DC (2022) A new species of tree cricket (Orthoptera, Gryllidae, Oecanthinae) from Chihuahuan Desert gypsum dunes in the United States and a key to the nigricornis species group. Journal of Orthoptera Research 31(2): 181-189. https://doi.org/10.3897/jor.31.79036
Supplementary material 6 from: Collins N, Lightfoot DC (2022) A new species of tree cricket (Orthoptera, Gryllidae, Oecanthinae) from Chihuahuan Desert gypsum dunes in the United States and a key to the nigricornis species group. Journal of Orthoptera Research 31(2): 181-189. https://doi.org/10.3897/jor.31.79036
Supplementary material 6 from: Collins N, Lightfoot DC (2022) A new species of tree cricket (Orthoptera, Gryllidae, Oecanthinae) from Chihuahuan Desert gypsum dunes in the United States and a key to the nigricornis species group. Journal of Orthoptera Research 31(2): 181-189. https://doi.org/10.3897/jor.31.79036
Supplementary material 2 from: Collins N, Lightfoot DC (2022) A new species of tree cricket (Orthoptera, Gryllidae, Oecanthinae) from Chihuahuan Desert gypsum dunes in the United States and a key to the nigricornis species group. Journal of Orthoptera Research 31(2): 181-189. https://doi.org/10.3897/jor.31.79036
Supplementary material 2 from: Collins N, Lightfoot DC (2022) A new species of tree cricket (Orthoptera, Gryllidae, Oecanthinae) from Chihuahuan Desert gypsum dunes in the United States and a key to the nigricornis species group. Journal of Orthoptera Research 31(2): 181-189. https://doi.org/10.3897/jor.31.79036
Supplementary material 1 from: Erdélyi A, Hartdégen J, Malatinszky Á, Vadász C (2023) Historical reconstruction of the invasions of four non-native tree species at local scale: a detective work on Ailanthus altissima, Celtis occidentalis, Prunus serotina and Acer negundo. One Ecosystem 8: e108683. https://doi.org/10.3897/oneeco.8.e108683
Derived data of Ailanthus altissima, Celtis occidentalis, Prunus serotina and Acer negundo from the National Forestry Database and its archives.
Supplementary material 3 from: Collins N, Lightfoot DC (2022) A new species of tree cricket (Orthoptera, Gryllidae, Oecanthinae) from Chihuahuan Desert gypsum dunes in the United States and a key to the nigricornis species group. Journal of Orthoptera Research 31(2): 181-189. https://doi.org/10.3897/jor.31.79036
Supplementary material 3 from: Collins N, Lightfoot DC (2022) A new species of tree cricket (Orthoptera, Gryllidae, Oecanthinae) from Chihuahuan Desert gypsum dunes in the United States and a key to the nigricornis species group. Journal of Orthoptera Research 31(2): 181-189. https://doi.org/10.3897/jor.31.79036
Supplementary material 4 from: Collins N, Lightfoot DC (2022) A new species of tree cricket (Orthoptera, Gryllidae, Oecanthinae) from Chihuahuan Desert gypsum dunes in the United States and a key to the nigricornis species group. Journal of Orthoptera Research 31(2): 181-189. https://doi.org/10.3897/jor.31.79036
Supplementary material 4 from: Collins N, Lightfoot DC (2022) A new species of tree cricket (Orthoptera, Gryllidae, Oecanthinae) from Chihuahuan Desert gypsum dunes in the United States and a key to the nigricornis species group. Journal of Orthoptera Research 31(2): 181-189. https://doi.org/10.3897/jor.31.79036
Supplementary material 7 from: Collins N, Lightfoot DC (2022) A new species of tree cricket (Orthoptera, Gryllidae, Oecanthinae) from Chihuahuan Desert gypsum dunes in the United States and a key to the nigricornis species group. Journal of Orthoptera Research 31(2): 181-189. https://doi.org/10.3897/jor.31.79036
Supplementary material 7 from: Collins N, Lightfoot DC (2022) A new species of tree cricket (Orthoptera, Gryllidae, Oecanthinae) from Chihuahuan Desert gypsum dunes in the United States and a key to the nigricornis species group. Journal of Orthoptera Research 31(2): 181-189. https://doi.org/10.3897/jor.31.79036
FIGURE 1. Phylogenetic tree generated from a in Xenoacremonium palmarum sp. nov., a novel species associated with Phoenix dactylifera in Iran
FIGURE 1. Phylogenetic tree generated from a maximum likelihood (ML) analysis based on the combined tub2, tef1α and ITS sequences of Xenoacremonium strains. The tree was rooted using Stachybotrys chartarum CBS 129.13 as the out-group taxon. Bootstrap values obtained in maximum likelihood (ML) analysis equal or greater than 50% and Bayesian posterior probability values (BYPP) equal or greater than 0.5 are shown at the nodes, respectively.
Developing a global biodiversity standard certification for tree-planting and restoration: Tutorials for standardizing species names with WorldFlora
<p>This archive provides <a href="https://rmarkdown.rstudio.com/lesson-1.html">R Markdown files (.Rmd files)</a> containing scripts used to standardize tree species names downloaded from the <a href="https://www.bgci.org/resources/bgci-databases/globaltree-portal/">GlobalTree Portal</a> for different countries with national hubs for the <a href="https://www.darwininitiative.org.uk/project/DAREX001/">Developing a global biodiversity standard certification for tree-planting and restoration</a> project.</p> <p>The R Markdown files were modified from <a href="https://rpubs.com/Roeland-KINDT/1134151">a recent Rpub</a> where I standardized tree species names from <a href="https://tools.bgci.org/global_tree_search.php">GlobalTreeSearch</a> version 1.7. One of my objectives during a training workshop held in January 2024 with national hub partners at the <a href="https://sitioduascachoeiras.org.br/">Jardim Botânico Araribá, Sítio Duas Cachoeiras</a>, site in Brazil was to show how R Markdown files can be easily modified to analyse different data sets.</p> <p> </p> <p>This publication was generated after conducting training for a <strong>Darwin Initiative project</strong> (<a href="https://www.darwininitiative.org.uk/project/DAREX001/">DAREX001</a>) that develops a <a href="https://www.biodiversitystandard.org/">Global Biodiversity Standard for tree planting</a>. Recently the <a href="https://www.nature.com/articles/s41598-023-39552-1">GlobalUsefulNativeTrees</a> and <a href="https://onlinelibrary.wiley.com/doi/10.1111/gcb.16914">Tree Globally Observed Environmental Ranges</a> databases were released from this project. With scripts such as the ones shown here, when the Global Biodiversity Standard scheme becomes operational, tree planting projects can crosscheck lists of species before applying.</p>
FIGURE 2. Bayesian inference tree for 8,074 in Terrestrial predatory leeches of the genus Orobdella (Hirudinea: Erpobdelliformes: Orobdellidae) endemic to the Southern Russian Far East: a new species of the genus from Primorsky Krai, Russia
FIGURE 2. Bayesian inference tree for 8,074 bp of nuclear 18S rRNA, 28S rRNA, and H3, and mitochondrial COI, tRNACys, tRNAMet, 12S rRNA, tRNAVal and 16S rRNA, tRNALeu and ND1 markers. Numbers on nodes indicate bootstrap (BS) values for maximum likelihood ≥ 60% and Bayesian posterior probabilities (PP) ≥ 0.90. Double asterisks denote nodes with BS = 100%, PP = 1.0; single asterisks denote nodes with BS ≥ 80%, PP ≥ 0.95. Numbers in parentheses represent the mid-body somite annulation of each species.
Allometric regression statistics for 285 North American tree species
<p>Scaling patterns in plants have long interested biologists, particularly whether different species share similar patterns of growth, and whether differences in growth trajectories depend on plant size. Using 8,794,737 measurements for 285 species from the U.S. Forest Inventory and Analysis database, we test several predictions emerging from a recently published "flow similarity" model for plant growth and allometry. We show that the model's predicted curvature for intraspecific relationships between height, DBH and biomass is found in 88.1% of examined cases, and empirical slopes fall as predicted between the elastic similarity and flow similarity predictions in 71.1% of cases. We also find a strong size dependence in observed intraspecific allometric exponents, with large species, particularly gymnosperms, converging near the expectation for elastic similarity, and the central tendency among small species approaching the expectations for flow similarity in most cases. Our results support the idea that differences in growth patterns across plant species depend on plant size and their attendant hydraulic and/or biomechanical demands and helps to delineate the bounds of the theoretical morphospace in which they occur.</p>
FIGURE 5. Circular maximum parsimony phylogenetic tree with all sequenced recognised Thai Aleiodes species with a in A turbo-taxonomic study of Thai Aleiodes (Aleiodes) and Aleiodes (Arcaleiodes) (Hymenoptera: Braconidae: Rogadinae) based largely on COI barcoded specimens, with rapid descriptions of 179 new species
FIGURE 5. Circular maximum parsimony phylogenetic tree with all sequenced recognised Thai Aleiodes species with a number of named, primarily Palaearctic taxa included. Species groups that are characterizable morphologically and discussed are indicated in different colours. The tree is rooted using Heterogamus species.
Fig. 4 in Big trees of small baskets: phylogeny of the Australian genus Spyridium (Rhamnaceae: Pomaderreae), focusing on biogeographic patterns and species circumscriptions
Fig. 4. Distributions of samples of S. phylicoides, S. sp. Red Dots (J.Kellermann 689) and S. sp. Dwarf (J.Kellermann 579) used in this study. For S. phylicoides, samples are coloured by the clades in which they are placed in the nrDNA tree (Fig. 2), with the distribution of the species, on the basis of the records in the Atlas of Living Australia (2020), also shown (grey dots).
Fig. 2 in Big trees of small baskets: phylogeny of the Australian genus Spyridium (Rhamnaceae: Pomaderreae), focusing on biogeographic patterns and species circumscriptions
Fig. 2. Nuclear rDNA (nrDNA) phylogeny of Spyridium, based on Bayesian inference (BI) analysis. Bayesian posterior probabilities (PP) and ultrafast bootstrap (UFBS) values are shown at nodes when <95%; values ≥95% are not shown. Where one value for a node is supported (≥95%) and the other for that node is unsupported (<95%), only the unsupported value is shown. Where a hyphen (-) is provided at a node, this node varied in resolution in the ML tree and was therefore not transferable to the BI phylogeny. Colour coding of clades and taxa in the bar to the right of the tree matches that used on maps in Fig. 3, 4. Labels are given for some clades (A–J) and subclades (A1–J3) discussed in text. Species polyphyletic across clades are highlighted in red text. Monophyletic taxa with supported nodes are highlighted in green text. Note: S. eriocephalum is polyphyletic, but var. eriocephalum is monophyletic (and therefore coloured half red and half green). Dashed lines associated with S. tricolor, S. glaucum, S. phlebophyllum and S. subochreatum E.D.Adams 21/0907 are provided as reference points connecting taxa to the sidebar.
Fig. 1 in Big trees of small baskets: phylogeny of the Australian genus Spyridium (Rhamnaceae: Pomaderreae), focusing on biogeographic patterns and species circumscriptions
Fig. 1. Distribution of Spyridium in Australia. Dots represent filtered records accessed from Atlas of Living Australia (2020). States and territories are also high-lighted as follows: WA, Western Australia; SA, South Australia; NT, Northern Territory; Qld, Queensland; NSW, New South Wales; ACT, Australian Capital Territory; Vic., Victoria and Tas., Tasmania.
Fig. 5 in Big trees of small baskets: phylogeny of the Australian genus Spyridium (Rhamnaceae: Pomaderreae), focusing on biogeographic patterns and species circumscriptions
Fig. 5. Chloroplast genome (cpDNA) phylogeny of Spyridium, based on Bayesian inference (BI) analysis. Bayesian posterior probabilities (PP) <0.95 and ultrafast bootstrap (UFBS) values are shown at nodes when <95%; values ≥95% are not shown. Where one value for a node is supported (≥95%) and the other for that node is unsupported (<95%), only the unsupported value is shown. Where a hyphen (-) is provided at a node, this node varied in resolution in the ML tree and was therefore not transferable to the BI phylogeny. Coloured bar to the right of the tree indicates placement of samples in the nrDNA phylogeny (i.e. matching the coloured bar on Fig. 2). Labels are given for some clades (K–Q) and subclades (M1–Q2) discussed in text. Species polyphyletic across clades are highlighted in red text. Monophyletic taxa with>0.95 PP support are highlighted in green. Dashed lines associated with S. tricolor, S. glaucum, S. phlebophyllum and S. subochreatum E.D.Adams 21/0907 are provided as reference points connecting taxa to the sidebar.
Fig. 3 in Big trees of small baskets: phylogeny of the Australian genus Spyridium (Rhamnaceae: Pomaderreae), focusing on biogeographic patterns and species circumscriptions
Fig. 3. Distributions of nrDNA clades of Spyridium, colour-coded to match groups shown in Fig. 2. Clade distributions are based on those of included species, using records in the Atlas of Living Australia (2020). Distributions of S. phylicoides, S. sp. Dwarf (J.Kellermann 579) and S. sp. Red Dots (J.Kellermann 689) have been omitted from these maps and are provided in Fig. 4. (a) Distribution of Clade A1 (mid blue), Clade A2 (royal blue), S. tricolor (light blue) and S. glaucum (dark blue). The location of sample CC545 (S. tricolor) is highlighted. (b) Distribution of Clade C. The general location of the southern transition zone is also highlighted. (c) Distribution of Clade D. (d) Distribution of Clade E. (e) Distribution of S. phlebophyllum. (f) Distribution of S. eriocephalum var. eriocephalum from Clade F. (g) Distribution of Clade G. The location of sample CC566 (S. sp. Wollar) is highlighted. (h) Distribution of Clade H. (i) Distribution of Clade I, excluding S. phylicoides and S. sp. Dwarf (J.Kellermann 579). (j) Distribution of Clade J1 (bright pink), Clade J2 (deep pink) and Clade J3 (light pink). The location of sample E.D.Adams 21/0907 (S. subochreatum) is highlighted (dark grey). Spyridium phylicoides and S. sp. Red Dots (J.Kellermann 689) have been excluded from this map.
FIGURE. Bayesian tree based on nuclear (ITS) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches. in Hedysarum sunhangii (Fabaceae, Hedysareae), a new species from Pamir-Alay (Babatag Ridge - Uzbekistan)
FIGURE. Bayesian tree based on nuclear (ITS) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches.
FIGURE. Bayesian tree based on combined plastid (matK, trnL-trnF) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches in Hedysarum sunhangii (Fabaceae, Hedysareae), a new species from Pamir-Alay (Babatag Ridge - Uzbekistan)
FIGURE. Bayesian tree based on combined plastid (matK, trnL-trnF) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches
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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.