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Data and code from: A spectral three-dimensional color space model of tree crown health
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Root crown images of soybean and wheat and statistical analysis for RhizoVision Crown
<p>This repository contains raw image data of root crowns imaged using the backlit RhizoVision Crown platform of soybean and wheat plants phenotyped in Missouri and Oklahoma, respectively, as described in the below manuscript. Data files and the R scripts are included for complete statistical analysis associated with the imaged root crown set as well as validation using images of copper wires and simulated root images. We request any reuse of this data to both cite this repository and also the publication given below.</p> <p><strong>Citation:</strong></p> <p>Seethepalli, A., Guo, H., Liu, X., Griffiths. M. G., Almtarfi, H., Li, Z., Liu, S., Zare, A., Fritschi, F., Blancaflor, E., Ma, X., and York, L. M. (2020). RhizoVision Crown: An integrated hardware and software platform for root crown phenotyping. <em>Plant Phenomics. doi:10.34133/2020/3074916</em></p> <p><strong>Link: </strong><a href="https://spj.sciencemag.org/plantphenomics/2020/3074916/">https://spj.sciencemag.org/plantphenomics/2020/3074916/</a></p> <p>Root crown images were acquired using the RhizoVision Imager software available at:</p> <p><a href="https://zenodo.org/record/2585882#.XWgOAeNKiUk">https://zenodo.org/record/2585882#.XWgOAeNKiUk</a></p> <p>Image analysis of physical wires, simulated dicot and monocot root systems, and soybean and wheat root crowns was originally conducted with RhizoVision Analyzer. However, Analyzer has been replaced by RhizoVision Explorer that uses the same underlying algorithms and the analysis can be recreated using the 'whole root' mode of Explorer, available here:</p> <p><a href="https://zenodo.org/record/4095629">https://zenodo.org/record/4095629</a></p> <p><strong>Image Files</strong></p> <p>physical_validation_wires.zip - A set for validation of physical units using 10 images of 2 individual wires of 5 gauges (10, 16, 22, 28, 32) in PNG format acquired using the RhizoVision Crown hardware platform. Includes a CSV file containing measured length and diameters as well as those from image analysis using RhizoVision Analyzer.</p> <p>Soybean_RVC_RootCrowns.zip - 2,778 greyscale images in PNG format of field excavated soybean root crowns.</p> <p>Wheat_RVC_RootCrowns.zip - 1,754 greyscale images in PNG format of field excavated wheat root crowns.</p> <p>metadata_Analyzer_allImageSets.zip - CSV files with the metadata files output by the RhizoVision Analyzer software for the physical validation, validation of simulated dicots and monocots (described in preprint), and the soybean and wheat root crown images. Useful to see thresholding and physical resolution settings.</p> <p>The simulated monocot and dicot root systems images and associated data are described in the preprint and available from Lobet et al. here:</p> <p>Lobet, Guillaume, Koevoets, Iko, Noll, Manuel, Tocquin, Pierre, Meyer, Patrick E, Pagès, Loic, & Périlleux, Claire. (2016). Library of simulated root images, with different noise levels [Data set]. Zenodo.</p> <p><a href="https://zenodo.org/record/208214">https://zenodo.org/record/208214</a></p> <p><strong>Statistical Analysis</strong></p> <p>Rcode_allData.zip - Contains a single .R text file with code to reproduce all statistics and data figures. Contains several .CSV data files used by the R code. Assumption for running is that R code and data files are in the same working directory and setwd() is set there. Also, libraries needed are called at the top of the script and need to be previously installed.</p> <p><strong>Hardware Plans</strong></p> <p>RhizoVision_Crown_Hardware_Plans_Details.pdf - For completeness, hardware plans for the RhizoVision Crown platform as described in the manuscript are included. Currently, we recommend the following camera and lens to use in this system:</p> <p>Basler 5472 monochrome usb camera</p> <p><a href="https://graftek.biz/products/basler-aca5472-17um">https://graftek.biz/products/basler-aca5472-17um</a></p> <p>This Moritex 25 mm lens:</p> <p><a href="https://graftek.biz/products/moritex-ml-u2515sr-18c?">https://graftek.biz/products/moritex-ml-u2515sr-18c?</a></p> <p><br> <br> ⇒ Version 2 of this repository includes updates based on peer-review of the manuscript. New versions of physical_validation_wires.zip and Rcode_allData.zip were uploaded.</p> <p>⇒ Version 3 of this repository includes updates based on peer-review of the manuscript. A new version of Rcode_allData.zip was uploaded.</p>
Figure 3 from: Aiello D, Vitale A, Polizzi G, Voglmayr H (2020) Ochraceocephala foeniculi gen. et sp. nov., a new pathogen causing crown rot of fennel in Italy. MycoKeys 66: 1-22. https://doi.org/10.3897/mycokeys.66.48389
Figure 3 Ochraceocephala foeniculi, holotype a culture on CMD (7d, 22 °C) b culture on MEA (21d, 22 °C) c conidiophores on aerial hyphae producing yellowish brown conidial masses in chains d–j, l, m unbranched (g–i) and verticillately branched (d–f, j, l, m) conidiophores (MEA, 21d, 22 °C) with phialides; in f with polyphialide (arrow) k, n, o phialides with collarettes (arrows) and young conidia p conidia. All microscopic preparations from MEA (21d, 22 °C) and mounted in water. Scale bars: 200 µm (c); 10 µm (d–j, l, m, p); 5 µm (k, n, o).
Figure 1 from: Aiello D, Vitale A, Polizzi G, Voglmayr H (2020) Ochraceocephala foeniculi gen. et sp. nov., a new pathogen causing crown rot of fennel in Italy. MycoKeys 66: 1-22. https://doi.org/10.3897/mycokeys.66.48389
Figure 1 Symptoms caused by Ochraceocephala foeniculi on fennel plants. a, b Necrotic lesions and crown rot on 'Narciso' cultivar. c, d Necrotic lesions and crown rot on 'Apollo' cultivar. e Symptoms on artificially inoculated seedlings of 'Pompeo' cultivar.
Figure 2 from: Aiello D, Vitale A, Polizzi G, Voglmayr H (2020) Ochraceocephala foeniculi gen. et sp. nov., a new pathogen causing crown rot of fennel in Italy. MycoKeys 66: 1-22. https://doi.org/10.3897/mycokeys.66.48389
Figure 2 Phylogram of the best ML tree (–lnL = 14211.5558) revealed by RAxML from an analysis of the combined SSU-ITS-LSU matrix of selected Leptosphaeriaceae, showing the phylogenetic position of Ochraceocephala foeniculi (bold red). Taxa in bold black denote new combinations proposed here. ML and MP bootstrap support above 50% are given above or below the branches.
Wildfire behaviour data for an experimental crown fire in thinned boreal black spruce, Alberta, Canada, 2019-05-11
<p>Data describing an experimental forest fire in Wabasca, Alberta, Canada in May 2019. The fire is described in detail in the paper: "Recent Crown Thinning in a Boreal Black Spruce Forest Does Not Reduce Spread Rate nor Total Fuel Consumption: Results from an Experimental Crown Fire in Alberta, Canada" https://doi.org/10.3390/fire3030028</p>
Within-crown variability in herbivore performance and leaf traits
<ol> <li>Functional trait variation within individual plants is predicted to have important ecological consequences. However, our understanding of the sources contributing to subindividual<i> </i>trait heterogeneity, and the ramifications thereof, is poor.</li> <li>In a common garden, we sampled multiple genotypes of mature trembling aspen (<i>Populus tremuloides</i>) at different vertical crown levels and quantified the contributions of genetic, spatial and biotic (herbivory) factors to subindividual morphological and chemical leaf trait variance. Bioassays using gypsy moth (<i>Lymantria dispar</i> L.) caterpillars were conducted to study impacts of spatial and genotypic factors on insect performance.</li> <li>Crown position was the primary source of subindividual variation in leaf morphology and explained more of the variance in morphological traits than tree genotype. Effects of spatial, genetic and biotic factors on within-crown chemistry were highly compound-specific. For many compounds, changes in within-crown concentrations differed among genotypes, revealing that genotypic variation not only contributes to phytochemical diversity among individuals of the same population, but also affects subindividual chemical trait heterogeneity. For many defense related compounds, total within-crown variance itself differed among genotypes and was in many cases a heritable trait. Bioassays revealed that effects of crown position on caterpillar performance varied among tree genotypes and caterpillar sexes.</li> <li>We demonstrate that even relatively small trees can express subtle but distinct levels of within-crown leaf-trait variation. In aspen, this variation is shaped not only by spatial factors, but also by genetics and to a lesser degree by herbivory. Within-crown variation in defense chemistry might itself provide a defensive phenotype against herbivores and contribute to the biological diversity of canopy insect communities.</li> </ol>
Figure 6 in Additions to the British list of Megaselia Rondani (Diptera: Phoridae), including two new species, from the crowns of ancient pollarded trees
Figure 6. Megaselia henrydisneyi female, details of abdomen. (A) Left cercus; (B) lobes at rear of sternum 8; (C) tergites 5–7. Scale bars: 0.1 mm.
Figure 5 in Additions to the British list of Megaselia Rondani (Diptera: Phoridae), including two new species, from the crowns of ancient pollarded trees
Figure 5. Megaselia henrydisneyi male. (A) Frons (with bristles represented by their basal sockets only); (B) right face of hypopygium; (C) left face of hypopygium. Scale bars: 0.1 mm.
Figure 2 in Additions to the British list of Megaselia Rondani (Diptera: Phoridae), including two new species, from the crowns of ancient pollarded trees
Figure 2. Megaselia crassipes male (synonym of M. basiturgida). (A) Left face of hypopygium; (B) posterior face of front tibia and basitarsus. Scale bar: 0.1 mm.
Wind creates crown shyness, asymmetry and orientation in a tropical montane oak forest
<p>In a cloud forest dominated by Quercus costaricensis the gap size between the crowns was consistent and crowns were asymmetrical, being elongated perpendicular to the prevailing wind direction. A wind storm of 20 m s-1 removed 1.5% of the leaves, consistent with the idea that wind abrasion shapes tree crowns.</p>
The Genome sequences of Calonectria ilicicola (anamorph Cylindrocladium parasiticum) causing Cylindrocladium black rot of peanut and red crown rot of soybean
<p>The fungus <em>Calonectria ilicicola</em> (anamorph <em>Cylindrocladium parasiticum</em>) is an important plant pathogen causing Cylindrocladium black rot (CBR) on peanut and Red crown rot (RCR) on soybean. CBR infection of peanuts cause symptoms such as chlorosis of leaves, blackening of taproots, and wilting, while RCR infection of soybeans lead to root and interveinal necrosis of soybean. In the present study, we sequenced the genome of four CBR-related<em> Ca. ilicicola</em> strains and three RCR-related<em> Ca. ilicicola</em> strains. The draft genome of <em>Ca. ilicicola</em>, ranged from 68.63 Mb to 70.35 Mb in genome size, containing 18536 to 19361 protein-coding genes. The described genome sequences will provide insights into factors that contribute to pathogenicity toward peanut and soybean and will be useful for future research in population genomics and molecular diagnostic marker development to quickly detect this pathogen.</p>
Data from: Tree species diversity promotes litterfall productivity through crown complementarity in subtropical forests
1. The role of niche complementarity for driving the positive biodiversity-ecosystem productivity relationship has been widely recognized, but there is scant evidence regarding the role of tree canopy structure on this relationship. Litterfall productivity is proportional to forest net primary productivity in natural forests, and we hypothesized that litterfall productivity would increase with tree species diversity via increased tree crown complementarity. 2. We investigated annual litterfall productivity, species diversity, tree crown architecture, soil moisture content, soil carbon content, and stand age across 28 subtropical forest plots in eastern Zhejiang province, China. Simple linear regression was used to examine bivariate relationships among rarified species richness, crown complementarity, total crown volume, soil moisture content, soil carbon content, stand age, and litterfall productivity. Structural equation modeling was employed to quantify the direct and indirect effects of species richness on litterfall productivity through tree crown complementarity. 3. Litterfall productivity increased with rarefied species richness via increasing crown complementarity rather than total crown volume. Species richness, crown complementarity, and litterfall productivity increased with soil moisture content, while crown complementarity and litterfall productivity increased with soil carbon content. Neither species richness nor crown complementarity increased with stand age, even though litterfall productivity increased with stand age. 4. Synthesis. Our study provides evidence for a strong role of tree crown assembly in shaping ecosystem function in complex natural forests. Our findings suggest that crown spatial complementarity among trees operates mechanistically to drive the positive tree species diversity-litterfall productivity relationship in subtropical forests. We argue that community and/or ecosystem ecology would benefit from more attention to crown variability among coexisting tree species.
FIGURE 1 in Honouring His Royal Highness the Crown Prince of Bhutan: Megalestes gyalsey (Odonata: Synlestidae)
FIGURE 1. Megalestes gyalsey represented in life (watercolour drawing by Albert Orr).
FIGURE 3 in Honouring His Royal Highness the Crown Prince of Bhutan: Megalestes gyalsey (Odonata: Synlestidae)
FIGURE 3. Holotype of Megalestes gyalsey.
Fig. 1 in Patterns of tooth crown wear in Dryomys nitedula (Mammalia, Rodentia): age-related variation in the light of annual cycle specifics based on museum collections
Fig. 1. Geographic details of the studied sample: record localities and the southern boundary of the forest dormouse's distribution.
Microsatellite genotyping data for habitat-linked genetic structure for white-crowned sparrow (Zonotrichia leucophrys): local factors shape population genetic structure
<p>Ecological, environmental, and geographic factors all influence genetic structure. Species with broad distributions are ideal systems because they cover a range of ecological and environmental conditions allowing us to test which components predict genetic structure. This study presents a novel, broad geographic approach using molecular markers, morphology, and habitat modelling to investigate rangewide and local barriers causing contemporary genetic differentiation within the geographical range of three white-crowned sparrow (<i>Zonotrichia leucophrys</i>) subspecies: <i>Z. l. gambelii, Z. l. oriantha, </i>and <i>Z. l. pugetensis</i>. Three types of genetic markers showed geographic distance between sampling sites, elevation, and ecosystem type are key factors contributing to population genetic structure. Microsatellite markers revealed white-crowned<i> </i>sparrows<i> </i>do not group by subspecies, but instead indicated four groupings at a rangewide scale and two groupings based on coniferous and deciduous ecosystems at a local scale. Our analyses of morphological variation also revealed habitat differences; sparrows from deciduous ecosystems are larger than individuals from coniferous ecosystems based on principal component analyses. Habitat modeling showed isolation by distance was prevalent in describing genetic structure, but isolation by resistance also had a small but significant influence. Not only do these findings have implications concerning the accuracy of subspecies delineations, they also highlight the critical role of local factors such as habitat in shaping contemporary population genetic structure of species with high dispersal ability.</p>
FIGURE 2 in Honouring His Royal Highness the Crown Prince of Bhutan: Megalestes gyalsey (Odonata: Synlestidae)
FIGURE 2. Habitat of Megalestes gyalsey.
Figure 2 from: Maxwell SJ, Dekkers AM, Rymer TL, Congdon Bradley C (2019) Recognising and defining a new crown clade within Stromboidea Rafinesque, 1815 (Mollusca, Gastropoda). ZooKeys 867: 1-7. https://doi.org/10.3897/zookeys.867.34381
Figure 2 The new phylogeny of StromboideaA and alternatives found from previous revisions B molecular analysis after Latiolais et al. (2006: 440, fig. 2) C anatomical analysis after Simone 2005: 261, fig. 388 D cladogram based on the nomenclature after MolluscaBase (2019).
Figure 1 from: Maxwell SJ, Dekkers AM, Rymer TL, Congdon Bradley C (2019) Recognising and defining a new crown clade within Stromboidea Rafinesque, 1815 (Mollusca, Gastropoda). ZooKeys 867: 1-7. https://doi.org/10.3897/zookeys.867.34381
Figure 1 The anatomy of representatives of the five families with Stromboidea Rafinesque, 1815 indicating the eye (e) eye stalk (es) and the tentacle (t) AStrutholariidae Gabb, 1868 – Tylospirascutulata (Gmelin, 1791) (Simone 2005, fig. 254) BAporrhaidae Gray, 1850 – Aporrhaisoccidentalis (Beck, 1836) (Simone 2005, fig. 297) CSeraphsidae Jung, 1974 – Terebellumterebellum (Linné, 1758) (Simone 2005, fig. 231) DRostellariidae Gabb, 1868 – Tibiainsulaechorab (Röding, 1798) (Simone 2005, fig. 249) EStrombidae Rafinesque, 1815 – Strombusgallus Linné, 1758 (Simone 2005, fig. 164).
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