Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
38
datasets available to search
ShareScore release 0.9.0
Dataset results
38 results for “tree architecture”
Tree inventory data such as tree identity, position in the plot, height, architecture and biomass on Mt. Kilimanjaro
<p>This dataset describes position and sizes of all trees above 10 cm diameter at breast height in all plots, also fruiting and flowering events and if it is a canopy tree or not in KiLi project. -999999 represents NA in numeric variables. </p> <p>Within each plot, all trees wider than 10 cm diameter at breast height (dbh) were marked with aluminium tags and their dbh and height were measured. The dbh was measured with a diameter tape (Forestry Suppliers, USA) at 1.3 m for normally shaped trees and 20 cm below or above when branches or irregular shapes impeded measurement at that height. The 1.3 m height was measured from the highest ground level around the stem to standardize measurements taken on slopes. For trees which were strongly buttressed or too big to measure by hand, a laser dendrometer (Criterion RD 1000 with TruPulse 200/200, Centennial, USA) was used to measure the tree above the buttresses and at 1.3 m. Lianas above 10 cm in diameter were also marked and their dbh was measured. Tree height was measured using an ultra-sonic hypsometer (Vertex IV Hypsometer, Haglöf, Langsele, Sweden) or a laser rangefinder (TruPulse 200/200). The tree inventories were carried out between December 2010 and March 2013.</p> <p>The KiLi project (2010-2018) is a German Science Foundation (DFG) funded research unit (DFG research unit FOR1246) that focuses on biodiversity and ecosystem processes along altitudinal and disturbance gradients on Mt. Kilimanjaro (Tanzania, Africa), capitalizing on its world-wide unique range of climatic and vegetation zones. The research unit comprises 2 central projects and 7 subprojects from various disciplines. On a total of 60 study sites in both natural and human-disturbed ecosystems biodiversity (e.g. plants, soil arthropods, ants, bees, frogs, lizards, bats, birds), related ecosystem processes (decomposition, seed dispersal, pollination, herbivory, predation), and biogeochemical processes and properties of ecosystems (climate, soil properties and nutrient status, regulation of water and carbon fluxes, trace gas emissions, primary productivity, functional diversity) are analyzed.</p>
tree architectural traits in adult trees subjected to stemflow
<p>Dataset containing key tree architectural traits from tree individuals of Maple and Ash subjected to stemflow and stemflow-supression conditions</p>
Genetic architecture of disease resistance and tolerance in Douglas-fir trees
<p><span>Understanding the genetic architecture of tolerance and resistance to pathogens is important to monitor and maintain resilient tree populations. Here we investigate the genetic basis of tolerance and resistance to needle cast disease in Douglas-fir (<em>Pseudotsuga menziesii</em>) caused by two fungal pathogens: Swiss needle cast (SNC) caused by <em>Nothophaeocryptopus gaeumannii</em>, and Rhabdocline needle cast (RNC) caused by <em>Rhabdocline pseudotsugae</em>). We performed a case-control genome-wide association analysis (GWA) and found these traits to be polygenic and under selection.</span> <span>We showed that stomatal regulation as well as ethylene and jasmonic acid pathways are important for resisting SNC infection and secondary metabolite pathways play a role in tolerating SNC once the plant is infected. We identified a key upstream transcription factor of plant defence, ERF1, as the main candidate for RNC resistance. Our findings contribute to the understanding of the highly polygenic architectures underlying disease resistance and tolerance in Douglas-fir and have important implications for forestry and conservation as the climate changes.</span></p>
Network of reference tree-ring chronologies for forensic botanical (dendrochronological) examinations and dating of architectural structures in the Tyva Republic.
<p>The database consists of tables. First sheet - general description of tree-ring chronologies (general information: name of chronology, authors, data type, tree-ring parameter, notes, key words; description of sample collection site: site name, location, region, latitude, longitude, height; description of sample collection: collection code designation, number of series, year of first ring, year of last ring, maximum length of sample, average width of year ring; species affiliation - species; support - grant number). Second sheet, first column - years, second column - standardized growth value. The third sheet is a PDF document containing the results of independent testing in the program COFECA (the file is opened by the command: right-click/Acrobat Document object/open). The database is implemented in the OpenOffice.org Calc spreadsheet processor. The table file format is an internal OpenOffice.org Calc format, with the extension .ods. The data is accessed and structured using the standard tools "Sort", "Autofilter", etc. In the database, the integrity restriction control is not implemented, the user is invited to monitor the integrity of the database himself. Computer type: IBM PC. PC; OS: Windows 10.</p> <p>Type and version of the database management system: OpenOffice.org Calc.</p> <p>Database size: 5.6 MB</p>
Genetic architecture of disease resistance and tolerance in Douglas-fir trees
Open the record for dataset details and reuse information.
New insights into tree architecture from mobile laser scanning and geometry analysis
<p><span>The structure and dynamics of a forest are defined by the architecture and growth patterns of its individual trees. In turn, tree architecture and growth result from the interplay between the genetic building plans and environmental factors. We set out to investigate whether (i) latitudinal adaptations of the crown shape occur due to characteristic solar elevation angles at a species' origin, (ii) architectural differences in trees are related to seed dispersal strategies, and (iii) tree architecture relates to tree growth performance. We used Mobile Laser Scanning (MLS) to scan 473 trees and generated three-dimensional data of each tree. Tree architectural complexity was then characterized by fractal analysis using the box-dimension approach along with a topological measure of the top-heaviness of a tree. The tree species studied originated from various latitudinal ranges but were grown in the same environmental settings in the arboretum. We found that trees originating from higher latitudes had significantly less top-heavy geometries than those from lower latitudes. Therefore, to a certain degree, the crown shape of tree species seems to be determined by their original habitat. We also found that tree species with wind-dispersed seeds had a higher structural complexity than those with animal-dispersed seeds (p < 0.001). Furthermore, tree architectural complexity was positively related to the growth performance of the trees (p < 0.001). We conclude that the use of 3D data from MLS in combination with geometrical analysis, including fractal analysis, is a promising tool to investigate tree architecture.</span></p>
Data from: Architectural differences associated to functional traits among 45 coexisting tree species in central Africa
1. Architectural traits that determine the light captured in a given environment are an important aspect of the life-history strategies of tropical tree species. In this study, we examined how interspecific variation in architectural traits is related to the functional traits of 45 coexisting tree species in central Africa. 2. At the tree level, we measured tree diameter, total height and crown dimensions for an average of 30 trees per species (range 14–72, total 968 trees) distributed over a large range of diameters (up to 162 cm). Using log-log models, we fitted species-specific allometric relationships between tree diameter, height and crown dimensions. At the species level, we derived architectural traits (height and crown dimensions) at 15 cm and maximum diameters from species-specific allometries. The architectural traits were then related to functional traits, including light requirements, wood density, leaf habit, and dispersal mode. 3. Among the 45 coexisting tree species, we identified strong variations in height and crown allometries, along with architectural traits derived from these species-specific allometries. There was a positive correlation among architectural traits, suggesting that large-statured canopy species were taller and had larger and deeper crowns than small-statured understory species at all ontogenic stages. The relationships between architectural and functional traits highlighted a continuum of species between the large-statured canopy species and the small-statured understory species. In this moist and seasonal forest, large-statured canopy species tended to be light-demanding, wind-dispersed, deciduous and large contributors to forest biomass (high basal area), while small-statured understory species tended to be shade-tolerant, animal-dispersed, evergreen and most abundant in terms of stem density. 4. Our results highlighted strong architectural differences among coexisting tropical tree species in central Africa. The relationships between architectural and functional traits provided insights into the life-history strategy of tropical tree species.
Differences in architecture and performance between two sub-canopy congeneric tropical tree species
<p>We report architectural divergence between two congeneric tropical tree species coexisting in the same stratum which suggests different strategies: reducing self-shading and support costs, or maximizing light foraging. We found species-specific differential performance across light environments, suggesting that architectural differentiation could facilitate the coexistence of species with similar vertical habitat.</p>
New insights into tree architecture from mobile laser scanning and geometry analysis
Open the record for dataset details and reuse information.
Data from: Architectural differences associated to functional traits among 45 coexisting tree species in central Africa
Open the record for dataset details and reuse information.
Differences in architecture and performance between two sub-canopy congeneric tropical tree species
Open the record for dataset details and reuse information.
PhyloCNN: Improving tree representation and neural network architecture for deep learning from trees in phylodynamics and diversification studies
Open the record for dataset details and reuse information.
Data from: Plasticity in hydraulic architecture: Riparian trees respond to increased temperatures with genotype-specific adjustments to leaf traits
Open the record for dataset details and reuse information.
Data from: Effects of tree architecture on pollen dispersal and mating patterns in Abies pinsapo Boiss. (Pinaceae)
Plant architecture is crucial to pollination and mating in wind pollinated species. We investigate the effect of crown architecture on pollen dispersal, mating system and offspring quality, combining phenotypic and genotypic analyses in a low-density population of the endangered species Abies pinsapo. A total of 598 embryos from three relative crown height levels (bottom, middle, top) in five mother plants were genotyped using eleven nuclear microsatellite markers (nSSRs). Paternity analysis and mating system models were used to infer mating and pollen dispersal parameters. In addition, seeds were weighed (N = 16,110) and germinated (N = 736), and seedling vigour was measured to assess inbreeding depression. Overall, A. pinsapo shows a fat-tailed dispersal kernel, with an average pollen dispersal distance of 113–227 m, an immigration rate of 0.84–26.92%, and a number of effective pollen donors ranging between 3.5 and 11.9. We found an effect of tree height and relative crown height levels on mating parameters. A higher proportion of seeds with embryo (about 50%) and a higher rate of self-fertilization (about 60%) were found at the bottom level in comparison to the top level. Seed weight and seedling vigour are positively related. Nevertheless, no differences were found in seed weight or in seedling-related variables such as weight and length of aerial and subterranean parts among the different relative crown height levels, suggesting that seeds from the more strongly inbred bottom level are not affected by inbreeding depression. The different relative crown height levels also present a similar effective pollen dispersal distance and number of effective pollen donors, indicating vertical isotropy for outcross pollen. Our results thus suggest that self-pollen may compensate for the shortage of outcross pollen in low density populations.
Data from: A phylogenomic rodent tree reveals the repeated evolution of masseter architectures
Understanding the number of times a trait has evolved is a necessary foundation for comprehending its potential relationships with selective regimes, developmental constraints, and evolutionary diversification. Rodents make up over 40% extant of mammalian species and their ecological and evolutionary success has been partially attributed to the increase in biting efficiency that resulted from a forward shift of one or two portions of the masseter muscle from the zygomatic arch onto the rostrum. This forward shift has occurred in three discrete ways, but the number of times it has occurred has never been explicitly quantified. We estimated an ultrametric phylogeny, the first to include all rodent families, using thousands of ultraconserved elements. We examined support for evolutionary relationships among the five rodent suborders and then incorporated relevant fossils, fit models of character evolution, and used stochastic character mapping to determine that a portion of the masseter muscle has moved forward onto the rostrum at least seven times (with one reversal) during the ca. 70 MY history of rodents. Combined, the repeated evolution of this key innovation, its increasing prevalence through time, and the species diversity of clades with this character underscores the adaptive value of improved biting efficiency and the relative ease with which some advantageous traits arise.
Point clouds and QSM for 598 individually scanned tree branches to support "Terrestrial laser scanning to reconstruct branch architecture from harvested branches"
<p>A collection of 598 harvested branches scanned in high resolution using terrestrial LiDAR. Branches were collected from GEM forest plots in Malaysia, Australia and Brazil.</p> <p>Branch nomenclature is <em>PLOT</em>-<em>TREE</em>-B<em>N</em><S or SH> where <em>PLOT </em>codes can be found in the manuscript, <em>N</em> refers to the sample number of branch harvested from a tree, and S and SH refer to sun or shade branch respectivetly.</p> <p>For each branch there are 3 files: </p> <ul> <li>Unfiltered point clouds (raw_pc) are clipped from the original data only and have had no post processing applied</li> <li>Filtered point clouds (filtered_pc) have been filtered according to the steps in the manuscript</li> <li>QSMs were produced using <em>treegraph </em>(<a href="https://doi.org/10.5281/zenodo.5226212">https://doi.org/10.5281/zenodo.5226212</a>)</li> </ul> <p>Polygon File Format (.ply) files can be viewed in software such as CloudCompare.</p> <p>Full details of methods can be found in: Wilkes, P., Shenkin, A., Disney, M., Malhi, Y., Bentley, L. P., & Vicari, M. B. (2021). Terrestrial laser scanning to reconstruct branch architecture from harvested branches. <em>Methods in Ecology and Evolution</em>, 12, 2487–2500. <a href="https://doi.org/10.1111/2041-210X.13709">https://doi.org/10.1111/2041-210X.13709</a></p>
Architecture of the bronchial tree in Cuvier's dwarf caiman (Paleosuchus palpebrosus)
<p>We imaged the lungs of five Cuvier's dwarf caiman (<em>Paleosuchus palpebrosus</em>) via computed tomography (CT) and micro-computed tomography (μCT) and compared these data to the lungs of the American alligator (<em>Alligator mississippiensis</em>). These data demonstrate anatomical commonalities between the lungs of <em>P. palpebrosus</em> and <em>A. mississippiensis</em>, and a few notable differences. The structural similarities are (a) a proximally narrow, distally widened, hook-shaped primary bronchus; (b) a cervical ventral bronchus that branches of the primary bronchus and immediately makes a hairpin turn toward the apex of the lung; (c) a sequential series of dorsobronchi arising from the primary bronchus caudal to the cervical ventral bronchus; (d) intraspecifically highly variable medial sequence of secondary airways; (e) sac-like laterobronchi; and (f ) grossly dead-ended caudal group bronchi in the caudal and ventral aspects of the lung. The primary differences between the two taxa are in the overall number of large bronchi (fewer in <em>P. palpebrosus</em>), and the number of branches that contribute to the cardiac regions. Imaging data of both a live and deceased specimen under varying states (postprandial, fasting, total lung capacity, open to atmosphere) indicate that the caudal margin and position of the lungs shift craniocaudally relative to the vertebral column. These imaging data suggest that the smooth thoracic ceiling may be correlated to visceral movement during ventilation, but this hypothesis warrants validation. These results provide the scaffolding for future comparisons between crocodilians, for generating preliminary reconstructions of the ancestral crocodilian bronchial tree, and establishing new hypotheses of bronchial homology across Archosauria.</p>
Citrus Tree Root System Image Dataset: Effects of Propagation Methods on Root Architecture
<p>This dataset is composed of images from two different citrus rootstock trials designated "Field Trial 1" and "Field Trial 2". Each field trial was planted with trees of <em>Citrus sinensis</em> cv. 'Valencia' grafted onto 4 different, commercially available USDA citrus rootstocks: US-812, US-897, US-942, US-1516. The trees were excavated two years after planting, cleaned, dried, and imaged in two ways. First, the root systems were imaged radially as though you are looking down through the trunk of the tree with the roots radiating outward in all direction. Secondly, the root systems were imaged vertically in six different positions such that each image was a side view of the root system from a different angle. Additionally, the binary masks of the vertical root systems were included in each .tar file.</p> <p>All images were acquired with a Canon EOS Rebel T6 against a professional photography blue screen. A mapping of the image names to the experimental trial information is included in each .tar file, and a series of scaled images were taken before and after root system imaging to calculate the pixel to centimeter conversion for absolute measurements.</p> <p>This dataset is currently in beta as it may change at some point in the future, therefore until that time, this record will be set to restricted.</p>
Supplementary data: What drives grassland-forest boundaries? Assessing fire and frost effects on tree seedling survival and architecture
<ol> <li>Fire and frost represent two major hurdles for the persistence of trees in open grassy biomes and have both been proposed as drivers of grassland-forest boundaries in Africa.</li> <li>We assess the response of young tree seedlings, which represent a vulnerable stage in tree recruitment, to traumatic fire and frost disturbances.</li> <li>In a greenhouse experiment, we investigated how seedling traits predicted survival and resprouting ability in response to fire <i>vs</i> frost; we characterised survival strategies of seedlings in response to the two disturbances, and we documented how the architecture of surviving seedlings is affected by fire <i>vs</i> frost injury.</li> <li>Survival rates were similar under both treatments. However, different species displayed different levels of sensitivity to fire and frost. Seedling survival was higher for older seedlings and seedlings with more basal leaves. Survivors of a fire event lost more biomass than the survivors of a frost event. However, the architecture of recovered fire and frost treated seedlings were mostly similar. Seedlings that recovered from fire and frost treatments were often shorter than those that had not been exposed to any disturbance, with multiple thin branches, which may increase vulnerability to the next frost or fire event.</li> <li> <i>Synthesis</i>. Fire caused more severe aboveground damage compared to a single frost event, suggesting that fire is an important driver of tree distribution in these open grassland systems. However, the impact of repeated frost events may be equally severe, and needs to be investigated. Also, woody species composition may be influenced by phenomena that affect the timing and frequency of seedling exposure to damage, as mortality was found to be dependent on seedling age. Therefore, changes in fire regime and climate (esp. changes that bring about less frost and reduced fire intensity and frequency) are likely to result in changes in the composition and the structure of the woody components of these systems.</li> </ol>
Architecture of the bronchial tree in Cuvier’s dwarf caiman (Paleosuchus palpebrosus)
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
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.