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9,204 results for “tree”
Metabolic profiling and antibacterial activity of tree wood extracts obtained under variable extraction conditions
<p>Scripts and dataset for Vinchira-Villarraga et al., 2024 "Metabolic profiling and antibacterial activity of tree wood extracts obtained under variable extraction conditions". The files label as A1, C6, H2/HCN2 and O1 correspond to the dataset obtained for Ash, Cherry, Horse-chestnut and Oak respectively. </p> <p>_batch.xml files contains the script for the pre-processing of .mzML mass spectrometry data created on MzMine 3.2.8. The file can be uploaded to newer versions of MzMine, but due to the addition of new modules, some parameters name have changed.</p> <p>_SIRIUS.mfg files contains the mass spectrometry data of each dataset for analysis in SIRIUS. The files were used for chemical formula prediction, classification and compound annotation using SIRIUS 5.0</p> <p>_quant.csv correspond to the output matrix as it was obtained from MzMine without noise, adducts and highly variable features filtering.</p> <p>_abundance.csv correspond to the output matrix after noise, adducts and highly variable features filtering.</p>
Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation
Open the record for dataset details and reuse information.
Climate Change Impacts for 14 Tree Species in Southwest Colorado
Forest management traditionally has been based on expectation of a steady climate. In the face of a changing climate, management requires projections of changes in the distribution of the climatic niche of the major species and strategies for applying the projections. We prepared climatic habitat models incorporating heatload as a topographic predictor for the 14 upland tree species of southwestern Colorado, USA, an area that has already seen substantial climate impacts. Models were trained with over 800,000 points of known presence and absence. Using 11 climate scenarios for the decade around 2060, we classified and mapped change for each species. Projected impacts are extensive. Except for the low-elevation woodland species, persistent habitat is rare. Most habitat is lost or threatened and is poorly compensated by emergent habitat. Three species may be locally extirpated. Nevertheless, strategies are described that can use the projections to apply management where it is likely to be most effective, to facilitate or assist migration, to favor species likely to be suited in the future, and to identify potential climate refugia.
Tree-ring width measurements and isotope data for riparian Populus species, Santa Clara River, 2019
This data set comprises tree-ring data collected from 114 cottonwood trees (Populus trichocarpa and Populus fremontii) within the floodplain of the Santa Clara River, CA. Tree-ring data include annual ring width measurements for all rings of each individual as well as semi-annual (earlywood and latewood) measurements of stable carbon and oxygen isotopes for pure alpha cellulose extracted from annual growth rings corresponding to calendar years 2010-2019 for a subset of 48 individuals. This data set is completed. Carbon and oxygen isotope ratios are reported using “delta” notation (i.e. δ13C and δ18O) calculated by the equation: δ13C (or δ18O) = (Rsample/Rstandard - 1) x1000 where R is the molar ratio of 13C/12C (or 18O/16O), with Rsample being that of tree ring cellulose and Rstandard that of Vienna Pee Dee Belemite (VPDB) for δ13C and Vienna Standard Mean Ocean Water (VSMOW) for δ18O. These data were used for the following publication: Williams, J., J.C. Stella, S.L. Voelker, A.M. Lambert, L. Pelletier, J.E. Drake, J.M. Friedman, D.A. Roberts, M.B. Singer. (2022). Local groundwater decline exacerbates response of dryland riparian woodlands to climatic drought. Global Change Biology.
University of Kansas Field Station: Forest demography, 1980 – 2015. On ten study plots established on three management units all live trees with a dbh > 7.5 cm (3 in) were identified to species, measured, and tagged. Trees were initially measured in 1980/1981 and re-measured in three successive time periods: 1993/95; 2002/03; and 2014/15. Trees will be measured again in 2025/26.
In 1980 researchers at the University of Kansas initiated a long-term experiment monitoring the composition of oak-hickory forest communities at the University’s field station near Lawrence, Kansas. The purpose of the study was to determine how forest species composition varied temporally across distinct habitats that varied in topography, elevation, sun exposure, management history and successional stage. Ten permanent sites were sampled approximately each decade with data collection periods of 1980/81, 1993/95, 2002/03, and 2014/15. Trees with a minimum diameter at breast height (dbh) of ≥ 7.5 cm were tagged, identified to species and measured. Trees will be measured again in 2025/26.
Soil extracellular enzyme activities in plots dominated by trees that associate with arbuscular mycorrhizal or ectomycorrhizal fungi in the N fertilized and reference watershed at the Fernow Experimental Forest, WV.
Our objective was to detect possible differences in N fertilization responses of soil extracellular enzymes in plots dominated by trees that associate with arbuscular mycorrhizal fungi (AM) or ectomycorrhizal fungi (ECM). To do this, we established a plot network of 6 AM and 6 ECM dominated 10 x 10 m plots in both the reference and N fertilized watersheds (N=24 plots) at the Fernow Experimental Forest, Parsons, WV. We assayed the potential activity of hydrolytic enzymes that release N (N-acetylglucosaminidase; NAG), phosphorus (acid phosphatase; AP), and simple carbon (ß-glucosidase; BG). In addition, we measured microbial allocation to complex C degrading oxidative enzymes phenol oxidase and peroxidase. The activities of these enzymes were measured separately in bulk mineral, rhizosphere, and organic horizon soils during the growing season in 2017.
Leaf temperature of northeastern US tree species
Leaf temperature measurements were collected during the summer of 2020 within forested areas at the Thompson Farm Earth Systems Observatory in Durham, New Hampshire, USA. Located within the property is a registered Ameriflux site, Thompson Farm Forest (US-TFF), as well as experimental throughfall exclusion plots that are part of DroughtNet (experiment running since 2015). Leaf temperature measurements were made within the footprint of the eddy covariance flux tower as well as within both control and throughfall exclusion treatment plots. Upper canopy foliage was accessed using a bucket lift and in situ measurements made using a handheld thermal IR sensor. All data were paired with concurrent meteorological measurements from US-TFF or data from a co-located NOAA CRN station (NH Durham 2 SSW). Additionally, leaf chemical, physical, structure, and physiological traits have been measured at this site as well as canopy scale measures of structure and UAV-based spectral, thermal, and lidar imagery. Specific to this leaf temperature dataset, leaf-level light, temperature, and vpd photosynthetic response curves were measured.
Leaf angle measurements for temperate tree species in northeastern USA
Leaf angle distribution (LAD) measurements were made during the growing season in 2021 at the Harvard Forest in Petersham, MA, USA, and in 2022 at the Thompson Farm Earth Systems Observatory in Durham, NH, USA. At both sites, a level-calibrated digital angle tool was used to measure LAD in upper canopy foliage of common northeastern temperate tree species accessed using a mobile canopy lift. Additionally, at Thompson Farm, measurements were made at multiple heights to characterize differences of LAD in high, middle, and low canopy positions. Here, we have published those measurements, including a summary table of species average leaf angles and calculated parameters for fitted beta distributions. Processing scripts can be made available upon request to the authors. Additionally, leaf chemical, physical, structure, optical and physiological traits have been measured at these site as well as canopy scale measures of structure and UAV-based spectral, thermal, and lidar imagery.
Xylem water oxygen and hydrogen isotopes of Ponderosa Pine trees and soil samples in the southwestern U.S. 2018 and 2021
Across seven sites in southern Utah and northern Arizona, we collected precipitation, xylem water, and soil water isotope samples during two years: 2018 and 2021. All xylem water samples were collected from mature Ponderosa pine forests. At each site, xylem water samples were collected from the same 15 trees during two periods during 2018, and three periods during 2021. Soil pits were dug close to the trees and soil samples were collected at 5, 25, and 45cm depth close to the tree xylem samples. In 2021, we also collected precipitation isotopes using a rain gauge that was topped with mineral oil to prevent evaporation.
Tree Survey Database of the WVU Forest Megaplot at Summit Bechtel Reserve
These are data from the initial tree census of the 18-hectare (400m x 500m, with 20m x 20m subplots) WVU Forest Megaplot at Summit Bechtel Reserve in Fayette County, West Virginia. West Virginia University (WVU) faculty and students completed the census during 2018-2022, recording the geographic position, diameter at breast height (DBH), and species of all trees greater than 5cm DBH. These data describing the initial census and analysis of spatial patterns in above ground carbon stocks are complete, and are fully described in the associated 2023 WVU thesis by Megan Ponczek, which is planned to be submitted for peer-reviewed publication. The WVU researchers plan to re-census the plot approximately every five years in order to monitor changes in carbon stocks.
canopy herbivory and leaf traits of tree communities in tropical montane rainforests of southern Ecuador
This dataset contains herbivory data estimated as leaf area loss [cm²] and [%] and several leaf traits measured either conventionally or via spectral sensing-based techniques from canopies of tree communities in tropical montane rainforests of the Andes in southern Ecuador between February and March in 2019. The data were used by Schön et al. (in prep) to evaluate whether leaf traits are valuable indicators of canopy herbivory mainly caused by arthropods and further, whether chemical leaf traits estimated via spectral sensing-based techniques have similar strong relations to herbivory as leaf traits measured conventionally. Herbivory was estimated with the software WinFOLIA ™ 2019a from scanned mature and sun-exposed leaves of tree canopies. Spectral sensing-based leaf traits comprising secondary plant metabolites and both structural and nutritional cell components were estimated from leaves with an OceanOptics spectrometer HDX. Conventionally measured leaf traits comprising morphological and nutritional traits were derived by applying both elemental and morphometrical analyses (e.g., ICP analysis, a digital micrometer and penetrometer). For detailed descriptions of the methodology see Schön et al. (in prep), Homeier et al. (2021), and Limberger et al. (2021). Research was conducted by the subprojects A1, B1, and B4 within the framework of the RESPECT project (Environmental changes in biodiversity hotspot ecosystems of South Ecuador: RESPonse and feedback effECTs) funded by the DFG with the grant numbers: BE1780/51-1, BE1780/51-2, Ho3296/6-1, FA 925/11-1, FA 925/11-2, FA 925/16-1, BR1293/17-1.
Comparison of Urban-Rural Tree Growth Response to Climate in the Eastern U.S. for the years 1990-2014
Climate is an important driver of tree growth in forests of the eastern U.S. Urbanization can augment the growing conditions of trees in ways that could change the sensitivity of radial growth to climate stressors such as excessive heat and water stress. This dataset include tree ring chronologies (1990-2014) in the form of basal area increment for canopy oak and maples trees from paired urban and nearby rural reference forest sites in Baltimore, Maryland, New York City, New York, and Boston, Massachusetts. Also included are metrics of heat stress and water stress from 1990-2014.
Tree species identity, diameter and qualitative canopy health measurements (full, partial or dead) from 2005 to 2023 on 12 experimental oak loss plots in Black Rock Forest, NY.
Black Rock Forest established a series of 12, 0.56 ha plots in 2005 to assess impacts of the loss of tree in the genus Quercus on the forest ecosystem (entitled the Future of Oak Forests experiment). Three trunk girdling treatments, with control plots were instituted in 2008. Each plot also contained an ~10m by ~15m deer exclosure to assess the impact of herbivory post-disturbance. Trees were measured twice per year from 2008 to 2013 (except 2009 when trees were measured once) and once per year from 2014 to 2023. Data include tree species identity, diameter at breast height (DBH), canopy health (a qualitative assessment of approximate cover as full, partial or dead), presence/absence of sprouts, and location within the plot. All live trees equal to or larger than 2.5 cm DBH are included in the dataset.
Tree species, size class, and DBH in the University of Michigan Biological Station (UMBS) Burn Chronosequence established in 1957 and remeasured in 1979 and 1998
A complete survey of overstory vegetation and saplings in the Bob Farmer plots within the UM Biological Station clearut and burn chronosequence. Surveys were completed in 1979 and 1998 to measure the change in biomass and forest composition in the burn plots with forest succession.
Distribution and abundance of canopy trees in floodplain forests of the Wisconsin River 1999 - 2001
The Wisconsin River Floodplain Project aimed to identify landscape indicators that are well correlated with specific aspects of ecological function. This is a crucial research need requiring an integrated approach that combines landscape monitoring with field studies. Large river-floodplain systems are among the most diverse and dynamic landscapes in the US, providing many important societal values, but relatively little effort has been devoted to development and testing of landscape indicators for these systems. We developed and tested ecological indicators for large river-floodplain landscapes along reaches of the Wisconsin River to determine which landscape metrics are most useful for monitoring population, community and ecosystem processes in large river-floodplain landscapes. Spatially extensive field sampling was combined with landscape analysis in nine reaches of the Wisconsin River sampling to quantify the ability of landscape indicators to predict ecological variables over broad scales. Landscape indicators were evaluated by their utility for detecting changes in the structure and function of the Wisconsin River floodplain landscape that were related to modification of the natural flow regime, historical land use, and current land-use patterns. Our field studies were concentrated in floodplain forest in nine 12 to 20-km reaches along the lower 400 km of the Wisconsin River.
Scale-dependent interactions between tree canopy cover and impervious surfaces reduce daytime urban heat during summer
As cities warm and the need for climate adaptation strategies increases, a more detailed understanding of the cooling effects of land-cover across a continuum of spatial scales will be necessary to guide management decisions. We asked how tree canopy cover and impervious surface cover interact to influence daytime and nighttime summer air temperature, and how effects vary with the spatial scale at which land-cover data are analyzed (10, 30, 60 and 90-m radii). A bicycle-mounted measurement system was used to sample air temperature every 5 m along 10 transects (about 7 km length, sampled 3-12 times each) spanning a range of impervious and tree canopy cover (0 to 100%, each) in a mid-sized city in the Upper Midwest, USA. Variability in daytime air temperature within the urban landscape averaged 3.5 degreeC (range 1.1 to 5.7 degreeC). Temperature decreased nonlinearly with increasing canopy cover, with the greatest cooling when canopy cover exceeded 40%. The magnitude of daytime cooling also increased with spatial scale, and was greatest at the size of a typical city block (60-90 m). Daytime air temperature increased linearly with increasing impervious cover, but the magnitude of warming was less than the cooling associated with increased canopy cover. Variation in nighttime air temperature averaged 2.1C (range 1.2 to 3.0 degreeC), and temperature increased with impervious surface. Effects of canopy were limited at night; thus, reduction of impervious surfaces remains critical for reducing nighttime urban heat. Results suggest strategies for managing urban land-cover patterns to enhance resilience of cities to climate warming.
American Residential Macrosystems - Tree Survey Data for six major metropolitan areas, 2012-2013
"This dataset contains measurements and iTree output (www.itreetools.org) of woody plant species observed in residential yards and nearby natural areas. Data were collected to assess biotic ecological homogenization in six cities across the U.S. that span major ecological biomes and climatic regions: Baltimore, MD, Boston, MA, Los Angeles, CA, Miami, FL, Minneapolis/St. Paul, MN, and Phoenix, AZ."
Species, DBH, and height of overstory trees in a chronosequence of reforested urban sites, Lexington, KY, USA
Urban reforested areas located in Lexington, Kentucky were evaluated over the course of summer 2020. This dataset contains information on tree species, height, DBH, and snag class across twenty urban reforestation sites planted as part of the Reforest the Bluegrass program in Lexington, KY. At least three plots (and up to nine plots) were established in each site, with additional plots added if forested patches were sufficiently large. At each plot, we established a 0.008-ha (0.02-ac) circular sampling plot and recorded the species, diameter at breast-height (DBH), and total height of each tree ≥2.5 cm (1 in) DBH. DBH was measured to the nearest 0.25 cm (0.1 in) using a DBH tape, and tree height was measured to the nearest 0.1 m using a laser hypsometer (Nikon Forestry Pro II) or telescoping height pole. These data provide a critical baseline for understanding tree growth on reforested urban sites.
Species and height of understory trees and shrubs in a chronosequence of reforested urban sites, Lexington, KY USA.
This dataset contains information on soil physical and chemical characteristics across twenty urban reforestation sites planted as part of the Reforest the Bluegrass program in Lexington, KY. Urban reforested areas located in Lexington, Kentucky were evaluated over the course of summer 2020. At least three plots (and up to nine plots) were established in each site, with additional plots added if forested patches were sufficiently large. At each plot, we established a 0.002-ha (0.005-ac) circular sampling plot to survey woody understory species, respectively. Height and species of all woody plants <2.5 cm DBH and ≥30 cm tall were tallied to the nearest 0.5 cm with a telescoping height pole. These data will contribute to understanding of understory stand dynamics in developing urban forests.
Extracellular enzyme activities in plots dominated by trees that associate with arbuscular mycorrhizal or ectomycorrhizal fungi in the nitrogen fertilized and reference watershed at the Bear Brook Watershed in Maine, USA during the final year of N fertilization (2016) and during the year after N fertilization ceased (2017).
Our objective was to detect possible differences in N fertilization responses of extracellular enzymes in plots dominated by trees that associate with arbuscular mycorrhizal fungi (AM) or ectomycorrhizal fungi (ECM). To do this, we established a plot network of 6 AM and 6 ECM dominated (>65% diameter at breast height) 10 x 10 m plots in the lower elevation hardwood zone of both the reference and N fertilized watersheds (N=24 plots) at Bear Brook Watershed, in Maine USA. We assayed the potential activity of hydrolytic enzymes that release N (N-acetylglucosaminidase; NAG), phosphorus (acid phosphatase; AP), and simple carbon (ß-glucosidase; BG). The activities of these enzymes were measured separately in bulk mineral, rhizosphere, and organic horizon soils in the final year of N fertilization at Bear Brook in 2016 and during the year after N fertilization ceased in 2017.
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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.