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74 results for “tree research”
CO2 and CH4 fluxes from living and standing dead trees in Howland Research Forest, Maine USA, 2024
Methane (CH4) is the second-largest contributor to human-induced climate change, with significant uncertainties in its terrestrial sources and sinks. Tree stems, both living and dead, play crucial roles in forest ecosystem CH4 and carbon dioxide (CO2) flux dynamics, yet much remains unknown regarding the environmental drivers of fluxes. We measured CH4 and CO2 fluxes from 51 living trees (Picea rubens, Tsuga canadensis, Acer rubrum) along an upland-to-wetland gradient at Howland Research Forest, a net annual sink of CH4, in Maine USA. We also measured CH4 and CO2 fluxes from six standing dead red spruce stems (snags). We measured fluxes every two weeks throughout the growing season (April to November 2024) and at three heights (for a subset of red spruce stems) to capture a range of environmental conditions.
Forest tree, woody debris, root ingrowth, soil respiration and characterization data from long-term research plots for LTREB at the University of Michigan Biological Station
The NSF-funded project "LTREB: Drivers of temperate forest carbon storage from canopy closure through successional time" (2014-2024) supports research to meet the following goals: 1) elucidate mechanisms responsible for changes in C storage over decades to centuries; 2) link processes leading to persistence and resilience of forest C storage following disturbance; 3) quantify the effects of potential drivers such as forest structure, N availability, climate change, and atmospheric deposition on decadal and longer-term trajectories of C storage. Field activities for this research are conducted at the University of Michigan Biological Station (UMBS) on a pair of chronosequences and several old reference forests. Synthesis activities utilize data collected from these field sites in support of the LTREB project, as well as data synthesized from other sources (e.g., long-term UMBS plot data, AmeriFlux data, FIA data) all intended to address the core questions of the LTREB project. This dataset has been compiled and expanded over a series of versions, with new data types and observations appended periodically. Presently, the dataset includes observations from tree inventory censuses, woody debris sampling, fine root ingrowth cores, soil respiration measurements, and two sets of soil collections aimed at quantifying a range of physical, chemical, and biological properties of soil.
Long-term (1935-2019) tree population data from remeasurements of a large network of permanent study plots in old-growth forest, Dukes Research Natural Area, Marquette Co., MI, USA
The Dukes Research Natural Area (Hiawatha National Forest, Marquette Co., MI) amounts to ca. 100 ha of minimally disturbed original forests, including a mix of mesic 'hemlock-northern hardwood' types and peaty wetlands dominated by several species of swamp conifers and black ash (Fraxinus nigra). The RNA hosts a regular grid of 250 0.2-acre (~0.08 ha) permanent monitoring (CFI) plots. This package includes tree censuses for subsets of CFI plots conducted in 1935, 1948, and 1974-1980, and repeated censuses with mapped stems from 1989 to 2019. This 84-year record constitutes one of the longest repeated-measurement, permanent-plot data-sets for old-growth temperate forest.
Leslie Holdridge arboretum tree census, La Selva Research Station, Organization for Tropical Studies, Sarapiquí, Heredia, Costa Rica, 1972-2017.
This database is a collection of dendrometric and structural measurements for all the trees in the arboretum, it was compiled through the assessment of 10 census from 1972 to 2017 by O. Vargas and E. Castro for the Organization for Tropical Studies. The 3.5-hectare Holdridge Arboretum is located at La Selva Research Station. Leslie R. Holdridge, the original owner of the property, created the arboretum in 1968. Initially, it was a small cacao grove with an exceptionally rich overstory of native shade trees. To facilitate research in the arboretum, staff later removed the cacao. In 1970, Gary Hartshorn continued to plant seedlings of many native tree species. OTS continues to plant, tag, and measure trees. OTS maintains the arboretum by regular mowing and pruning to facilitate safe access. Courses, natural history visitors, students, and researchers use the arboretum for a wide range of observational studies, manipulations, dendrological practices, and taxonomy classes.
Bonanza Creek LTER: Tree Inventory Data from 1989 to present at Core research sites in Interior Alaska
This is the data from the periodic (3-10 yr interval) tree inventory monitoring of tree growth within the vegetation control plots. In 2013 and 2014, an initial tree inventory was done on each site belonging to the Regional Site Network (RSN). Some young RSN sites had no, or very few trees. In general, inventory is every 5 years presently; the most recent collection was in 2018 and next scheduled collection is for 2023.
Long-term (1993-2019) tree population measurements from a mapped 2.9-ha permanent plot in old-growth northern hardwood forest, Dukes Research Natural Area, Marquette Co., MI, USA
The Dukes Research Natural Area (Hiawatha National Forest, Marquette Co., MI) amounts to ca. 100 ha of minimally disturbed original forests, including a mix of mesic 'hemlock-northern hardwood' types and peaty wetlands dominated by several species of swamp conifers and black ash (Fraxinus nigra). The RNA hosts a regular grid of 250 permanent monitoring plots (data to be provided in a separate package). In 1993-95, a macroplot of 2.91 ha was established in a mixed mesic upland forest area within the RNA, in which all woody stems >2 cm diameter at breast height (DBH) were identified, measured, and mapped. In 1999 and again every five years subsequently through 2019, the macroplot was recensused; all stems were remeasured, stems newly recruited (>2 cm DBH) were measured and mapped, and any mortality since previous census was noted and described. A severe storm in 2002 resulted in extensive mortality throughout the RNA, particularly in the area in and around the macroplot.
Biomass accumulation in trees and downed wood at Bartlett Experimental Forest, Hubbard Brook Experimental Forest, the Bowl Natural Research Area, and the White Mountain National Forest, NH, USA
Standing trees and downed wood were inventoried in all of the chronosequence stands in the White Mountains, New Hampshire to characterize biomass. Live and standing dead trees were inventoried in the chronosequence stands in 1994, 2004, 2012, and 2021. Coarse (≥ 7.6 cm diameter) and fine woody debris (3.0 – 7.6 cm) were inventoried at the same stands in 2004 and 2020. Twigs (FWD < 3.0 cm) were inventoried in 2004 and 2020. The Bowl and Mt. Pond old-growth sites were inventoried (standing trees and downed wood) in 2021.
UAV outputs and associated field measurement of the herbaceous and tree of the Senegalese savanna of the Dahra Djoloff research center
<p>The dataset contains UAV outputs (mosaic , surface model and terrain) and the associated measurements of vegetation( herbaceous and woody) that were made within the research isra station of Dahra Djoloff.</p> <p>Sites</p> <p>The sites were 38 ha-1 plots across the research station. The UAV were collected on the same site at the same date in October 2018(end of the wet season and maximum of the biomass). The sites were the sites of previous studies (Raynal 1964, Ndiaye et al. 2014, Ndiaye et al. 2015). The plots were chosen based on several studies of vegetation dynamics and these plots were judged to be representative of the diversity of vegetation type within the research station.</p> <p>UAV flight plan</p> <p>We used a low-cost UAV with an RGB (Red Green Blue) captor integrated in the UAV. The plots were mapped using a Dji Spark UAV with the litchi application for the automatic flight. The flight plan was six 100 m transects each separated by 20 m was performed at an altitude of 80 m and at a speed of 5 m.s-1. Images were acquired in autofocus mode (ISO exposure were automatically adjusted) at two-second intervals throughout the flight. The angle of view was 80°. The frontal overlap was about 90% and the side overlap about 80% with 80° angle</p> <p>Field measurement.</p> <p>Herbaceous Biomass.</p> <p>For the Landscape dataset, 10 squares of 1 m² were sampled; All the aboveground biomass was cut and weighted in fresh. A composite sample was made for each site and weighted dry to evaluated the dry matter content and so the dry matter of each sample.</p> <p>The positions of the squared was mark r with a plastic bag on the ground.</p> <p>Tree measurement.</p> <p>For the landscape, we selected 10 trees on the UAV maps. The measurements were made after image analysis in January 2019 and January 2020. The trees were not measured on all the site.</p> <p>The measured variables were the maximum height of the tree (using a clinometer), the diameter of the tree crown in the north-south direction and in the west-east direction. Their tree crown area was calculated assuming that the crown was a circle. The trunk diameters were measured at 0.30 cm in both direction and the circumference were calculated. All woody species were identified at the species and genus levels.</p> <p>Image analysis.</p> <p>The images taken during each flight were processed using a PiX4D mapper (Pix4D SA, Lausanne, Switzerland). 3D mapping is the basic parameter proposed in the software. For each plot, an orthophotograph, a digital surface model, and a digital elevation model were computed and exported in GeoTIFF format.</p> <p>Data organization</p> <p>For each plot, we had</p> <ul> <li>DSM that contains the surface model in tiff</li> <li>DTM that contains the terrain model in tiff</li> <li>Mosaic that the orthomosaic in tiff.</li> </ul> <p>All the different geotiff can directly be download.</p> <p>Data are in a zip file that contains the shapefile with the position and table with the field measurements.</p> <p>The shapefile “Herbaceous.shp” contain the positions of the squared sample but also of squared that contains only soil (squared cut before the flight).</p> <p>The CSV “Herbaceous-landscape.csv” contains the measurement of Aboveground biomass. (FM fresh mass and DM dry mass). Both are in g (g.m-²). The biomass was available for 346 squared.</p> <p>The shapefile “tree.shp” contains the positions of the tree. Here the shapefile contains the positions of all the tree preselected on the map. Only a selection of theses tree was measured on the field.</p> <p>The file “Tree-landscape.csv” contains the tree measurements with the species, the height (in m), the trunk circumference (TC) in cm and the area of the crown(area) in m². The tree measurements were available for 240 trees.</p> <p> </p><p>reference</p> <p></p> <p>Ndiaye, O., A. T. Diop, L. E. Akpo, and M. Diène. 2014. Dynamique de la teneur en carbone et en azote des sols dans les systèmes d’exploitation du Ferlo: cas du CRZ de Dahra. Journal of Applied Biosciences <strong>83</strong>:7554-7569.</p> <p>Ndiaye, O., A. T. Diop, M. Diène, and L. E. Akpo. 2015. Étude comparée de la végétation de 1964 et 2011 en milieu pâturé: Cas du CRZ de Dahra. Journal of Applied Biosciences <strong>88</strong>:8235–8248.</p> <p>Raynal, J. 1964. Etude botanique de pâturages du Centre de Recherches Zootechniques de Dahra-Djoloff (Sénégal).</p> <p> </p>
Рис. 1. ФиΛогенетические Αеревья хантавируса AMRV и его прироΑного носитеΛя восточноазиатской мыши Apodemus peninsulae Thomas, 1906. А. ФиΛогенетическое Αерево восточноазиатской мыши Apodemus peninsulae, построенное метоΑом «максимаΛьного правΑопоΑобия» (ML) и поΛученное на основе анаΛиза участка гена цитохрома b мтΔНК (744 п.н.). В узΛах ветвΛения указаны бутстреп-поΑΑержки, рассчитанные ΑΛя 1000 повторов. Цветными Λиниями обозначены фиΛогенетические Λинии: Αве Китайские (зеΛеный), Корейская «Korea» (синий), Амурская «Amur» (красный). ПоΛужирным шрифтом выΑеΛены собственные образцы. Названия образцов из GenBank/NCBI быΛи сокращены; B. ФиΛогенетическое Αерево из работы Α. Н. Яшиной с ΑопоΛнениями, построенное метоΑом «бΛижайшего сосеΑа» (NJ) на основе посΛеΑоватеΛьностей фрагмента М-сегмента (2737–2980 н.п.) генома хантавирусов. В узΛах ветвΛения указаны бутстреппоΑΑержки, рассчитанные ΑΛя 1000 повторов. Жирным выΑеΛены иссΛеΑованные РНК изоΛяты (Яшина 2012; Яшина и Αр. 2019) Fig. 1. Phylogenetic trees of AMRV and its natural reservoir host — the Korean field mouse Apodemus peninsulae Thomas, 1906. A. Phylogenetic tree of the Korean field mouse Apodemus peninsulae constructed by the "maximum likelihood" method (ML). The data are obtained from the analysis of the cytochrome b mtDNA gene fragments (744 bp). Bootstrap supports calculated for 1,000 repeats are indicated in the branching nodes. Colored lines indicate phylogenetic lines: two Chinese (green), Korea (blue), and Amur (red). Own samples are highlighted in bold. The names of the samples from GenBank/NCBI have been shortened; B. Phylogenetic tree from L. N. Yashina's work with additions constructed by the neighbour joining method (NJ). It is based on the sequences of an M-segment fragment (2737–2980 bp) of the hantavirus genome. Bootstrap supports calculated for 1,000 repeats are indicated in the branching nodes. The researched RNA isolates are highlighted in bold (Yashina 2012; Yashina et al. 2019) in Variability of the gene cyt b in the Korean field mouse Apodemus peninsulae Thomas, 1906 - a reservoir host of AMRV in the Khasansky District of Primorsky Krai
Рис. 1. ФиΛогенетические Αеревья хантавируса AMRV и его прироΑного носитеΛя восточноазиатской мыши Apodemus peninsulae Thomas, 1906. А. ФиΛогенетическое Αерево восточноазиатской мыши Apodemus peninsulae, построенное метоΑом «максимаΛьного правΑопоΑобия» (ML) и поΛученное на основе анаΛиза участка гена цитохрома b мтΔНК (744 п.н.). В узΛах ветвΛения указаны бутстреп-поΑΑержки, рассчитанные ΑΛя 1000 повторов. Цветными Λиниями обозначены фиΛогенетические Λинии: Αве Китайские (зеΛеный), Корейская «Korea» (синий), Амурская «Amur» (красный). ПоΛужирным шрифтом выΑеΛены собственные образцы. Названия образцов из GenBank/NCBI быΛи сокращены; B. ФиΛогенетическое Αерево из работы Α. Н. Яшиной с ΑопоΛнениями, построенное метоΑом «бΛижайшего сосеΑа» (NJ) на основе посΛеΑоватеΛьностей фрагмента М-сегмента (2737–2980 н.п.) генома хантавирусов. В узΛах ветвΛения указаны бутстреппоΑΑержки, рассчитанные ΑΛя 1000 повторов. Жирным выΑеΛены иссΛеΑованные РНК изоΛяты (Яшина 2012; Яшина и Αр. 2019) Fig. 1. Phylogenetic trees of AMRV and its natural reservoir host — the Korean field mouse Apodemus peninsulae Thomas, 1906. A. Phylogenetic tree of the Korean field mouse Apodemus peninsulae constructed by the "maximum likelihood" method (ML). The data are obtained from the analysis of the cytochrome b mtDNA gene fragments (744 bp). Bootstrap supports calculated for 1,000 repeats are indicated in the branching nodes. Colored lines indicate phylogenetic lines: two Chinese (green), Korea (blue), and Amur (red). Own samples are highlighted in bold. The names of the samples from GenBank/NCBI have been shortened; B. Phylogenetic tree from L. N. Yashina's work with additions constructed by the neighbour joining method (NJ). It is based on the sequences of an M-segment fragment (2737–2980 bp) of the hantavirus genome. Bootstrap supports calculated for 1,000 repeats are indicated in the branching nodes. The researched RNA isolates are highlighted in bold (Yashina 2012; Yashina et al. 2019)
Data from: Provenance variation in functional traits of European forest trees: Meta-analysis reveals effects of taxa and age despite critical research gaps
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Data from: Variation in population structure and dynamics of montane forest tree species in Ethiopia guide priorities for conservation and research
The greatest extent of Afromontane environments in the world is found in Ethiopia. These areas support exceptional biodiversity, but forest cover and ecological integrity have declined sharply in recent decades. Conservation and management efforts are hampered in part by an inadequate understanding of the basic ecology of major tree species. We investigated population structure and inferred population dynamics from size frequency distributions of 22 forest tree species encountered in montane forests of Ethiopia. We collected new empirical data from four sites in the Bale Mountains, where some of the country's most extensive and least disturbed forests remain, and conducted a systematic review and analysis of all such studies that reported population structure for one or more of these species in Ethiopia. Thirteen widespread montane tree species showed a reverse-J size distribution, indicating a relatively stable population structure. Six other species had size-frequency distributions that indicate episodic recruitment and/or removal of certain size classes. Specific causes of these patterns are uncertain: they may involve timber harvesting, herbivory, fire, or natural disturbances, but patterns were inconsistent and locality dependent. For three other tree species, existing data are inadequate for any interpretation of population structure and dynamics. A species of particular conservation concern that emerged from this analysis was Hagenia abyssinica, which was found in all areas to consist only of larger individuals with no recent recruitment. For management and conservation purposes, the species in most urgent need of new research are those with inadequate or inconsistent data, and H. abyssinica..
Four historical tree-ring chronologies and underlying data derived from dendrochronological research on Batavia shipwreck timbers
<p>This dataset comprises four tree-ring chronologies and underlying tree-ring data derived from the dendrochronological research on the shipwreck timbers of the <em>Batavia</em> shipwreck. The undated tree-ring series have also been included.</p> <p>For context information about this dendrochronological dataset, please refer to the publication:</p> <p>Daly A, Domínguez-Delmás M, van Duivenvoorde W (2021) <em>Batavia</em> shipwreck timbers reveal a key to Dutch success in 17th-century world trade. PLOS ONE 16(10): e0259391. <a href="https://doi.org/10.1371/journal.pone.0259391">https://doi.org/10.1371/journal.pone.0259391</a> </p> <p> </p>
Aquatic islands in the sky: 100 years of research on water-filled tree holes
<p>Water-filled tree holes are unique ecosystems that may occur high up in tree crowns like aquatic islands in the sky. Insect larvae, mesofauna and other organisms colonize the waterbodies and feed on the accumulating detritus. Water-filled tree holes are not only important habitats for these species but have been used as model systems in ecology. Here we review more than 100 years of research on tree-hole inhabiting organisms and show that most studies focus on selected or even single species (most of which are mosquitoes) whereas only few studies examine groups other than insects, especially in the tropics. Using a vote counting of results and a meta-analysis of community studies, we show that the effects of tree-hole size and resources on abundance and richness were investigated most frequently. Both were found to have a positive effect, but effect sizes were modulated by site-specific environmental variables such as temperature or precipitation. We also show that parameters such as the height of the tree holes above ground, tree-hole density, predation and detritus type can be important drivers of organism abundance or richness but are less often tested. We identify several important research gaps and potential avenues for future research. Specifically, future studies should investigate the structure, functions and temporal dynamics of tree-hole food webs and their cross-system interactions, for example with terrestrial predators that act as a connection to their terrestrial surroundings in meta-ecosystems. Global observational or experimental tree-hole studies could contribute pivotal information on spatial variation of community structure and environmental drivers of community assembly. With a better understanding of these unique aquatic habitats in terrestrial ecosystems, natural and artificial tree holes can not only serve as model systems for addressing fundamental ecological questions but also as indicator systems of the impacts of environmental change on ecosystems.</p>
Research Data Management Decision Tree
<p>Researchers often face the same stumbling blocks. To support them, we have developed a <strong>RDM Decisional Tree</strong> starting from the fundamental bricks of the data lifecycle and posing a series of questions to help researchers navigate:</p> <p>1) the domain specific nature and origin of the data they are handling;</p> <p>2) Privacy/Ethics requirements (e.g. GDPR);</p> <p>3) Intellectual Property Rights;</p> <p>4) active data storage;</p> <p>5) long-term deposit and preservation.</p> <p><span>This diagram has been created by the team of data steward at the University of Bologna (UNIBO, Alma Mater Studiorum - Università di Bologna) in October 2022. </span>It has been developed in parallel to the Research Data Management: Data Lifecycle, available here: <a href="https://doi.org/10.5281/zenodo.7249050">10.5281/zenodo.7249050</a> </p>
Tabela 1. Wykaz stanowisk badawczych i występujących na nich platanów klonolistnych z obserwacjami Corythucha ciliata / Table 1. List of research sites and London plane trees with Corythucha ciliata observations].
<p>Wykaz stanowisk badawczych i występujących na nich platanów klonolistnych z obserwacjami<em> Corythucha ciliata / </em><em>List of research sites and London plane trees with Corythucha ciliata observations</em>.</p>
Aquatic islands in the sky: 100 years of research on water-filled tree holes
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Data from: Variation in population structure and dynamics of montane forest tree species in Ethiopia guide priorities for conservation and research
Open the record for dataset details and reuse information.
Crossett Experimental Forest site, station R. R. Reynolds Research Natural Area, study of plant density of hardwood trees in units of numberPerHectare on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Crossett Experimental Forest (CRO) contains plant density of hardwood trees measurements in numberPerHectare units and were aggregated to a yearly timescale.
Crossett Experimental Forest site, station R. R. Reynolds Research Natural Area, study of plant density of pine trees in units of numberPerHectare on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Crossett Experimental Forest (CRO) contains plant density of pine trees measurements in numberPerHectare units and were aggregated to a yearly timescale.
Supplementary material 1 from: Collins N, Schneider KR (2020) Oecanthus salvii sp. nov. (Orthoptera: Gryllidae: Oecanthinae): A new tree cricket species from Modoc County in northeast California. Journal of Orthoptera Research 29(1): 91-99. https://doi.org/10.3897/jor.29.50400
Supplementary material 1 from: Collins N, Schneider KR (2020) Oecanthus salvii sp. nov. (Orthoptera: Gryllidae: Oecanthinae): A new tree cricket species from Modoc County in northeast California. Journal of Orthoptera Research 29(1): 91-99. https://doi.org/10.3897/jor.29.50400
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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.