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3,105 results for “vegetation”
Spectral albedo and summer ground temperature of herbaceous and shrub tundra vegetation at Bylot Island, Canadian High-Arctic
<p>These data are in support of a preprint: </p><p>Comparing spectral albedo and NDVI of herbaceous and shrub tundra vegetation at Bylot Island, Canadian High-Arctic</p><p>Florent Domine, Maria-Belke-Brea, Ghislain Picard, Laurent Arnaud, and Esther Lévesque</p><p>To be submitted in 2023. </p><p>The spectral albedo of several vegetation assemblages on Bylot Island and in Mala River valley on nearby Baffin Island were recorded between 10 and 18 July 2015. The spectral range covered was 346 to 2400 nm. Surfaces were classified according to the main vegetation types. Classes used are graminoids, moss, Salix arctica, soil, and Salix richardsonii. S. richardsonii is the only truly erect species on Bylot Island. Transmission spectra of radiation through the S. richardsonii canopy were also recorded. S. richardsonii spectra were different depending on the location where they were measured and we present spectra for sites in active parts of an alluvial fan (Salix-G2), an inactive part of an alluvial fan (Salix-D1) and in a mesic area on Mala River Valley (Salix-M). We also present typical relative solar irradiance spectra recorded at Bylot Island during the campaign, under clear and overcast conditions. In conjunction with spectral albedo data, these irradiance spectra allow the calculation of the broadband (BB) albedo of the vegetation types and to compare BB albedo values under identical irradiance conditions. 83 spectra were recorded: 39 for S. richardsonii and 44 for low vegetation and soil. 17 transmission spectra under S. richardsonii were recorded. We present here only averages for each vegetation type. We also present averages for all low vegetation types and for all S. richardsonii spectra, to allow the calculation of the radiative impact of erect shrubs at Bylot Island. </p><p>We also present soil temperature data at 15 cm depth for the spots GRASS (mostly Salix Arctica), TUNDRA (Mostly moss), SALIX-D1 (Salix richardsonii) and SALIX-F (Salix richardsonii). SALIX-F is similar to SALIX-G2. The data are during summer 2020. </p><p>The locations of the various spots investigated are: </p><p><strong>Spot name Latitude Longitude Vegetation types found</strong></p><p>TUNDRA 73.150° -80.004° Humid and moist polygons with low vegetation dominated by mosses, graminoids, S. arctica and S. herbacea.</p><p>PLAINE 73.167° -79.915° Low vegetation and bare soil patches caused by cryoturbation (mudboils) with mosses, graminoids and S. arctica.</p><p>GRASS 73.158° -79.907° Low vegetation between patches of S. richardsonii dominated by S. arctica, with litter, mosses, graminoids and occasional bare soil. </p><p>SALIX-D1 73.158° -79.907° Scattered patches of S. richardsonii <35 cm tall. Understory is mosses, graminoids, litter, S. arctica and bare soil.</p><p>SALIX-M 73.006° -80.685° Mesic area with patches of S. richardsonii 35 to 40 cm tall. Understory includes moss, graminoids and litter. Between patches: herb tundra with graminoids and mosses. The area is not within an alluvial fan.</p><p>SALIX-G2 73.168° -79.812° Extended area in an alluvial fan with S. richardsonii >40 cm. Understory includes litter, mosses, graminoids, bare soil, S. arctica and S. reticulata.</p><p>SALIX-F 73.182° -79.745° Similar to SALIX-G2. Ground temperature is monitored there. No spectral data were recorded at that site. </p><p> </p><p> </p>
GLAB-VOD: Global L-band AI-Based Vegetation Optical Depth Dataset Based on Machine Learning and Remote Sensing
<p>GLAB VOD is a Global L-band Ai-Based vegetation optical depth dataset with 18-day temporal and 25 km spatial resolution, covering 2002 to 2020. The dataset is created using a neural network with SMOS-SMAP-INRAE-BORDEAUX (SMOSMAP-IB) VOD product as a target (over 2015-2020) and brightness temperatures (TB) from the SMOS, AMSR-E, and AMSR-2 spaceborne missions alongside with a novel soil moisture dataset (CASM) as inputs. The GLAB-VOD dataset was created using a recently developed methodology previously used to create a long-term consistent soil moisture dataset CASM, adapted to the VOD retrievals. First, the TB and VOD signals were divided into fixed seasonal cycle and residuals, where the residual part of the signal contains sub-seasonal periodic signals, trends, extremes, and noise. Then, a multi-staged neural network training scheme was used to achieve internally consistent predictions by merging data from different sources without introducing biases or compromising data distribution. A side-product of this project is GLAB TB - a global long-term brightness temperature dataset that matches SMOS TB quality and spawns back to 2002. GLAB TB has daily temporal resolution and 25 km spatial resolution. </p>
BST/NOAA PSL Level 2 UAS Soil Moisture, Digital Elevation, Normalized Difference Vegetative Index, and Surface Temperature for SPLASH
<p>This dataset contains uncrewed aircraft systems (UAS) high-resolution data of soil moisture at the 0-5 cm soil depth, normalized difference vegetation index (NDVI), surface temperature, and digital elevation for the Study of Precipitation, the Lower Atmosphere, and Surface for Hydrology (SPLASH) campaign sponsored by the National Oceanic and Atmospheric Administration (NOAA). These data were collected near Avery Picnic (38.972425 degrees N,106.996855 degrees W) and Kettle Ponds (38.942005 degrees N,106.973006 degrees W) in the East River Watershed in Colorado from a series of flights starting on June 1st, 2022 and ending October 18th, 2023. Soil moisture measurements were retrieved using the Lobe Differencing Correlation Radiometer (LDCR) which is a L-Band (1-2 GHz) microwave radiometer and was flown on the E2 and S2 aerial platforms operated by Black Swift Technologies LLC. </p> <p> </p> <p>Each zip file contains a set of four Level 2 NetCDF files which provides the highest spatial resolution available for each of four products for a given flight location. With the Level 2 data, each flight location and variable can have different spatial resolutions depending on the sensor type, retrieval algorithm, and flight altitude. The file name convention for the zip files is as follows.</p> <p> </p> <p>uas_L2_yyyymmdd_hhmmss_vX.X.zip </p> <p>where</p> <p>L2 = Level 2 data </p> <p>yyyymmdd = year,month,day</p> <p>hhmmss = hour,minute,second</p> <p>vX.X = version number</p> <p>Time is the flight start time in UTC.</p> <p> </p> <p>The NetCDF file format contained in the zip files has a similar format to the zip files with convention</p> <p> </p> <p>uas_<var>_L2_yyyymmdd_hhmmss.nc </p> <p>where</p> <p><var> = vsm, dem, ndvi, or stmp</p> <p>vsm = volumetric soil moisture</p> <p>dem = digital elevation</p> <p>ndvi = normalized difference vegetation index</p> <p>stmp = surface temperature</p> <p> </p> <p>Note that each flight location using the E2 aerial platform required two flights so starting flight times for the soil moisture NetCDF files are different from the other three products.</p> <p><strong>November 2023 update</strong>: Version 2.0 added flight data from 2023. Version 2.0 includes an updated calibration of the soil moisture retrieval that has been applied to 2023 data, and a mask was applied to the soil moisture retrieval over water surfaces for both 2022 and 2023 data.</p> <p><strong>December 2023 update</strong>: Version 2.1 updated soil moisture data with a wet bias in v2.0 for flights #2 (17:40:35 UTC) and #3 (19:24:45 UTC) on July 27, 2022.</p>
Dataset from: Spatially heterogeneous shifts in vegetation phenology induced by climate change threaten the integrity of the avian migration network
<p>Original data and code for the study:</p> <p>Wei, J., Xu, F., Cole, E. F., Sheldon, B. C., de Boer, W. F., Wielstra, B., Fu, H., Gong, P., & Si, Y. (2024, Accepted). Spatially heterogeneous shifts in vegetation phenology induced by climate change threaten the integrity of the avian migration network. Global Change Biology.</p> <p>The dataset mainly contains data showing the climate change-induced heterogeneous shifts in vegetation phenology and the migration integrity change from 2000 to 2020 for 16 Asian herbivorous waterfowl species. These data were derived from the following resources available in the public domain.</p> <p>The Global Lakes and Wetlands Database is available from “https://www.worldwildlife.org/pages/global-lakes-and-wetlands-database”. The global land cover datasets are available from European Space Agency (ESA) Climate Change Initiative (CCI) products, “https://maps.elie.ucl.ac.be/CCI/viewer/download.php”. The Global Multi-resolution Terrain Elevation Data are available from “https://www.usgs.gov/centers/eros/science/terrain-monitoring-and-modeling”. The Moderate Resolution Imaging Spectroradiometer (MODIS) Terra surface reflectance product is available from “https://modis.gsfc.nasa.gov/data/dataprod/mod09.php”. The bird distribution maps are available from Birdlife International, “https://www.birdlife.org/”. The bird foraging attribute data are available from EltonTraits 1.0, “https://figshare.com”. The bird occurrence data are available from eBird Basic Dataset (EBD), “https://science.ebird.org/en/use-ebird-data/download-ebird-data-products”. The Hackett backbone phylogenetic trees are available from “https://birdtree.org/”.</p> <p>The code contains the R scripts and MATLAB scripts that we used for this study.</p> <p>For details please see the file “Readme.txt”, and the research paper.</p>
Mapping the global distribution of C4 vegetation using observations and optimality theory
<p>This dataset includes annual C4 vegetation distribution and its uncertainty from 2001 to 2019. We also provide the distribution of C4 natural grasses and C4 crops during the same period, as well as the code and interim dataset to generate the main figures. Please refer to manuscript for more details:</p> <p>Luo, X., Zhou, H., Satriawan, T.W., Tian, J., Zhao, R., Keenan, T.F., Griffith, D. M., Sitch, S. Smith, N.G. & Still, C.J. (2024). Mapping the global distribution of C4 vegetation using observations and optimality theory. <em>Nature Communications.</em> https://doi.org/10.1038/s41467-024-45606-3.</p> <p><strong>Update (Nov 2023): </strong>we have updated the observational constraint from a linear model to a non-linear model - logistic curve, to better depict how C4 photosynthetic advantage translates into C4 grass coverage changes (C4_distribution_NUS_v2.2.nc).</p> <p><strong>Update (August 2023): </strong>we corrected the issue caused by a bias in the remote sensing grassland base map, and released the version 2 of the C4 vmap (C4_distribution_NUS_v2.nc).</p> <p><strong>Update (June 2023): </strong>we noticed there is a critical issue in the version 1 of our C4 map, due to the quality of remote sensing grassland base map used. We are now working on providing a new version (V2) in the next few months (Jun 2023).</p>
Data: Cutting the costs of coastal protection by integrating vegetation in flood defences.
<p>File: levee_crest_height_reduction_per_country_version_July2021.nc<br>Fields: (1) Crest height reduction m per km along the populated coastline susceptible to flooding (return period = 100 years)<br> (2) Crest height reduction cost saving per country in million USD<sub>2005</sub> PPP along the populated coastline susceptible to flooding (return period = 100 years)<br> (3) Cost savings as percentage of GDP<sub>2005</sub> along the urban populated coastline susceptible to flooding (return period = 100 years)</p> <p>File: transectdata_version_July2021.nc<br> Transectdata of vegetated transects within the study area.<br>Fields: <br>(1) rps = return period <br>(2) fid = id of the transects<br>(3) centroids = coordinates of the transects<br>(4) inun = (1) in area susceptible to flooding<br>(5) urban = (1) in urban area, (0) not in urban area<br>(6) veg_width = derived coastal vegetation belt width along the foreshore<br>(7) veg_type = derived coastal vegetation type along the foreshore (1: salt marshes, 2: mangroves)<br>(8) hsig = Offshore significant wave heights (multiple return periods) corresponding to the transects<br>(9) wave period = Offshore peak wave period (multiple return periods) corresponding to the transects<br>(10) surge = Extreme water level combination of surge and tide (m +MSL) (multiple return periods)<br>(11) veg_z0 = elevation at the start of the vegetated zone (m +MSL)<br>(12) hrms_end_noveg = root mean square wave height at the end of the foreshore (without vegetation) (multiple return periods)<br>(13) hrms_endveg = root mean square wave height at the end of the foreshore (with vegetation) (multiple return periods) <br>(14) pdens_15km = population density derived using buffer of 15 kilometre radius</p>
Cover percentages of vegetation layers within the Landklif plots
<p><span>Cover percentages of vegetation layers within the Landklif plots, as assessed during the vegetation survey between mid-May and end of July 2019 (seven subplots, 10m2 sampling area per plot).</span> </p> <p>LandKlif is funded by the Bavarian State Ministry of Science and the Arts within the Bavarian Climate Research Network (bayklif). Within the five year funding period of bayklif, five interdisciplinary senior research associations and five junior research groups are be financed with a total sum of 18 million Euro. LandKliF, as one of the five interdisciplinary senior research associations, addresses the effects of climate change on biodiversity and ecosystem services in semi-natural, agricultural and urban landscapes.</p>
Data from: Effects of dispersal and geomorphology on riparian seedbanks and vegetation in a boreal stream
<p>SiteData: information that describes 20 riparian zones along Svartån, a boreal free-flowing stream, indicated per LocationID (column A). Coordinates are given in SWEREF 99 TM (column B and C) and degrees of longitude and latitude (column D and E). RPD refers to River Process Domain and takes one of three forms: lake, rapid or slow-flowing. Side of stream indicates plot placement when looking towards downstream. Data collection is described in the paper linked to below. </p> <p> </p> <p>LitterData: information that describes species lists of litter seedbanks from 20 riparian sites. Litter samples were taken in an unstandardised manner at each location. LocationID refers to locations as described in file SiteData, RPD refers to River Process Domain and takes one of three forms: lake, rapid or slow-flowing.</p> <p> </p> <p>SeedData: information that describes the soil seedbank composition from 20 riparian sites. LocationID refers to locations as described in file SiteData, RPD refers to River Process Domain and takes one of three forms: lake, rapid or slow-flowing. Layer refers to samples that are taken from from layer 0-1 cm in the soil, 1-5 cm or from 5-10 cm deep. Data collection is described in the paper linked to below. </p> <p> </p> <p>VegetationData: information that describes vegetation composition from 20 riparian sites. LocationID refers to locations as described in file SiteData, RPD refers to River Process Domain and takes one of three forms: lake, rapid or slow-flowing. Abundance is indicated following the categories in Table 1. Data collection is described in the paper linked to below. </p> <p> </p> <p>Table 1. Vegetation cover classes.</p> <table> <tbody> <tr> <td> <p><strong>Code</strong></p> </td> <td> <p><strong>Cover (%)</strong></p> </td> </tr> <tr> <td> <p>0</p> </td> <td> <p>0</p> </td> </tr> <tr> <td> <p>1</p> </td> <td> <p><1</p> </td> </tr> <tr> <td> <p>2</p> </td> <td> <p>1-3</p> </td> </tr> <tr> <td> <p>3</p> </td> <td> <p>3-5</p> </td> </tr> <tr> <td> <p>4</p> </td> <td> <p>5-15</p> </td> </tr> <tr> <td> <p>5</p> </td> <td> <p>15-25</p> </td> </tr> <tr> <td> <p>6</p> </td> <td> <p>25-50</p> </td> </tr> <tr> <td> <p>7</p> </td> <td> <p>50-75</p> </td> </tr> <tr> <td> <p>8</p> </td> <td> <p>75-100</p> </td> </tr> </tbody> </table> <p> </p> <p>For more information, help or collaboration, please contact Jacqueline.Hoppenreijs@kau.se. If you use the data here in your work or research, please cite the publication appropriately.</p>
Data from: Saltmarsh vegetation and secured woody debris facilitate mangrove re-colonization
<p>Does the presence of saltmarsh vegetation affect the long-term regeneration of the pioneer mangrove species <em>Avicennia germinans</em> in a degraded dwarf forest? Does immobilized coarse woody debris (CWD) affect regeneration similarly? Do larger trees suppress or facilitate intraspecific saplings? The study was conducted in a dwarf mangrove forest in the high intertidal zone on Bragança peninsula in northern Brazil. The spatial patterns of <em>A. germinans</em>, the herbaceous halophyte <em>Sesuvium portulacastrum</em>, and CWD were mapped in three sample plots (each 400 m<sup>2</sup>) during two consecutive vegetation surveys, conducted in 2011 and 2014. Inhomogeneous Poisson and Thomas point-process models were used to assess the distribution of <em>A. germinans</em> life-history stages (seedlings, saplings, and adult dwarf trees), conditioned on the presence of <em>S. portulacastrum</em> and CWD. In addition, intraspecific interactions between trees and regeneration were assessed based on crown projection mapping. Bivariate point pattern analyses were used to assess the dependence of advance regeneration on dwarf <em>A. germinans</em> trees and <em>S. portulacastrum</em>. <em>A. germinans</em> saplings and trees were positively associated with <em>S. portulacastrum</em> and CWD, whereas seedlings were located around tree crowns. The density of fruit-bearing trees was positively associated with sapling density, indicating that regeneration relied on locally dispersed propagules. Herbaceous vegetation and CWD have an important ecological function in degraded mangroves by retaining tidally dispersed propagules. Here, we show that herbaceous vegetation does not suppress the growth of seedlings but facilitates mangrove recolonization. Due to limited tidal dispersal, regeneration relies on local propagule supply. In addition to hydrological restoration, the observed vegetation patterns suggest that, in the absence of propagule-retaining vegetation, restoration of high-intertidal mangroves can be facilitated by establishing nuclei of planted trees and installing secured logs.</p>
Data used in the manuscript: "Influence of coastal vegetation on the 2004 tsunami wave impact in west Aceh"
<p>The data set presented accompanies the study by Laso Bayas et al. (2011) “Influence of coastal vegetation on the 2004 tsunami wave impact in west Aceh”. The data set contains all the observed (not transformed) variables used in the above mentioned study. The accompanying text file describes each of the variables included. A total of 180 transects were employed for the Laso Bayas et al (2011) study. The variables were further standardized and simplified to use them into the statistical models described in the paper.</p>
Can Artificial Intelligence help in the study of vegetative growth dynamics from herbarium collections? An evaluation of the tropical flora of the French Guiana forest
<p>Dataset was used for the article "Can Artificial Intelligence help in the study of vegetative growth dynamics from herbarium collections? An evaluation of the tropical flora of the French Guiana forest".</p> <p>The related work proposes to study to what extent the use of automated visual analysis techniques, based on deep learning, can help not only to detect relatively rare vegetative structures in herbarium collections but also to automatically classify them by type of growing shoot (continuous or rhythmic).</p> <p>Abstract of the paper:</p> <p>A better knowledge of tree vegetative growth patterns and their relationship to environmental variables is crucial in understanding forest growth dynamics and how climate change may affect them. Generally less studied than reproductive structures, the phenology of tree vegetative growth mainly focuses on the analysis of growing shoots, from vegetative buds development to leaf fall. This growth process usually strongly differs between temperate and tropical regions. In temperate regions, this pattern is quite well known. Low winter temperatures impose a stop of the vegetative growth shoots and lead to the typical expression of an annual growth cycle for the vast majority of tree species. In moist tropical regions, on the other hand, the seasonality is much less marked. In addition, these regions contain a much wider variety of tree species. These two aspects lead to a tremendous diversity of phenological patterns that are still poorly known and understood. In particular, not much is known on the periodicity and timing of growth at individual trees, population, or community levels.</p> <p>The work carried out in this study aims to advance knowledge in this area, focusing more particularly on herbarium scans, as herbarium collections offer the promise of monitoring plant phenology over long time periods. However, such a study requires the ability to detect a sufficiently large number of growing shoots in herbarium collections to draw statistically relevant conclusions, which can be very costly if the work is done manually. Furthermore, herbarium collections traditionally focus on reproductive organs, and herbarium specimens showing growing shoots are pretty rare.</p> <p>We propose in this paper to study to what extent the use of automated visual analysis techniques, based on deep learning, can help not only to detect these relatively rare vegetative structures in herbarium collections but also to automatically classify them by type of growing shoot (continuous or rhythmic). Our results show the relevance of using herbarium data for vegetative phenology research, as well as the potential of deep learning approaches for growth shoot detection.</p>
Vegetation Dynamics on Crete
<p>This dataset contains long-term vegetation dynamics assessments for the Island of Crete, Greece. 10+ years ago, Landsat time series analyses were inevitably limited to few expensive images from carefully selected acquisition dates. Yet, such a static selection may have introduced uncertainties when spatial or inter-annual variability in seasonal vegetation growth were large. As seminal pre-open-data-era papers are still heavily cited, variations of their workflows are still widely used, too. Thus, we here quantitatively assessed the level of agreement between an approach using carefully selected images, and a state-of-the-art analysis that uses all available images. Further details can be found in the corresponding paper.</p> <p><strong>Temporal Extent: </strong>1984-2006.</p> <p><strong>Spatial Extent:</strong> Crete, Greece</p> <p><strong>Data format: </strong>The data come in tiles of 30x30km. The projection is EPSG:3035. The images are compressed GeoTiff files (*.tif). There are mosaics in GDAL Virtual format (*.vrt), which can readily be opened in most Geographic Information Systems. </p> <p><strong>Sub-directories:</strong></p> <ul> <li>cso: Number of <em>Clear-Sky Observations </em>available for this study</li> <li>dem: <em>Digital Elevation Model</em> (SRTM filled with ASTER)</li> <li>vd-1.0: Vegetation Dynamics 1.0 (see paper) <ul> <li>bap: <em>Best Available Pixel</em> composites</li> <li>trend: monotonic trends fitted on BAPs</li> </ul> </li> <li>vd-2.0: Vegetation Dynamics 2.0 (see paper) <ul> <li>trend <ul> <li>monotonic trends fitted on <em>value of peak of season </em>phenometrics (VPS)</li> <li>monotonic trends fitted on value of <em>seasonal amplitude</em> phenometrics (VSA)</li> <li>change and piecewise monotonic trends fitted on <em>value of base level </em>phenometrics (VBL)</li> </ul> </li> <li>syndromes <ul> <li>syndrome classification for woody vegetation</li> <li>syndrome classification for herbaceous vegetation</li> <li>net cover change for woody vegetation</li> <li>net cover change for herbaceous vegetation</li> </ul> </li> </ul> </li> </ul> <p><strong>Further information:</strong><br> For further information, please see the publication.<br> A web-visualization of this dataset is available <a href="https://ows.geo.hu-berlin.de/webviewer/crete/">here</a>.</p> <p><strong>Publication:</strong><br> Frantz, D., Hostert, P., Rufin, P., Ernst, S., Röder, A., van der Linden, S. (2022): Revisiting the past: Replicability of a historic long-term vegetation dynamics assessment in the era of big data analytics. Remote Sensing 14(3), 597; https://doi.org/10.3390/rs14030597</p> <p><strong>Funding: </strong><br> This publication was financially supported by Geo.X, the Research Network for Geosciences in Berlin and Potsdam under grant number SO_087_GeoX, and by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 414984028 - SFB 1404.</p>
Locally adaptive temperature response of vegetative growth in Arabidopsis thaliana
<p>We investigated early vegetative growth of natural <em>Arabidopsis thaliana</em> accessions in cold, non-freezing temperatures, similar to temperatures these plants naturally encounter in fall at northern latitudes.</p> <p>Dataset includes:<br> - rosette area measurements over 3 weeks in a 16ºC and a 6ºC treatment. First phenoptying time point is at 14 days after stratification. Measurements were take twice per day.<br> These data are in file <a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/rawdata_combined_annotation.txt?versionId=7b707f81-723f-4059-b72b-9dfb9f5ddd2e">rawdata_combined_annotation.txt</a> and go together with <a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/outliers.csv?versionId=7287c919-1ed1-4b65-8e25-a75bb312c8fa">outliers.csv</a>, which contains outlying datapoints.</p> <p>- Seed Size measurements.<br> These data are in file <a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/seed_size_swedes_lab_updated.csv?versionId=fb739477-862b-45cb-8074-7a1d8e1650bb">seed_size_swedes_lab_updated.csv </a><br> </p> <p>The remainnig files are required to rerun the analyses and recreate figures.<br> Scripts to do so can be found in https://github.com/picla/growth_16C_6C/</p> <p><a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/1001genomes-accessions.csv?versionId=ee605038-bd9e-448f-9c96-1a8e980c1755">1001genomes-accessions.csv</a>: lists all accession from the 1001genomes project and their respective subpopulations.</p> <p><a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/2029_modified_MN_SH_wc2.0_30s_bilinear.csv?versionId=73c6c2bf-97bd-425f-bf7e-14b5a7cb162f">2029_modified_MN_SH_wc2.0_30s_bilinear.csv</a>: contains climate data for each accession, downloaded and prcocessed from www.worldclim.org</p> <p><a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/metabolic_distance.csv?versionId=8456f998-d0dc-4a80-b96f-c0c66c1c9731">metabolic_distance.csv</a>: contains the metabolic distance as calculated in Weiszmann et al. (https://www.biorxiv.org/content/10.1101/2020.09.24.311092v1)</p> <p><a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/RNAseq_samples.txt?versionId=6ae1518b-1a70-440d-b0bd-0ccdcb66665e">RNAseq_samples.txt</a>: sample description of the RNA-seq samples (data is downloadable from <a href="http://www.ncbi.nlm.nih.gov/bioproject/807069">http://www.ncbi.nlm.nih.gov/bioproject/807069)</a></p> <p><a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/ZAT12_downregulated_table10.csv?versionId=c6f7aa54-cb07-4378-a5a0-de12c6979b9b">ZAT12_downregulated_table10.csv</a>, <a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/ZAT12_upregulated_table9.csv?versionId=911a2aa2-f08f-4a20-85de-cfa7c58b73a8">ZAT12_upregulated_table9.csv</a>, <a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/CBF_regulon_DOWN_ParkEtAl2015.txt">CBF_regulon_DOWN_ParkEtAl2015.txt</a>, <a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/CBF_regulon_UP_ParkEtAl2015.txt?versionId=f7cacbda-eea6-4ac9-8f71-5ba74e3a67c4">CBF_regulon_UP_ParkEtAl2015.txt, </a><a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/CBF2_downregulated_table8.csv">CBF2_downregulated_table8.csv, </a><a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/CBF2_upregulated_table7.csv">CBF2_upregulated_table7.csv, </a><a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/HSFC1_regulon_ParkEtAl2015.txt">HSFC1_regulon_ParkEtAl2015.txt</a>: these files list genes that are involve din cold acclimation as described by Park et al. (https://onlinelibrary.wiley.com/doi/10.1111/tpj.12796), and Vogel et al.(https://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2004.02288.x).</p> <p><strong>Material and Methods</strong></p> <p><em><strong>Rosette growth</strong></em></p> <p>Seeds of 249 natural accessions (Suppl. Data 1) of <em>Arabidopsis thaliana</em> described in the 1001 genomes project <a href="https://paperpile.com/c/UDgV3V/DUBI">(1001 Genomes Consortium 2016)</a> were sown on sieved (6 mm) substrate (Einheitserde ED63). Pots were filled with 71.5 g ±1.5 g of soil to assure homogenous packing. The prepared pots were all covered with blue mats <a href="https://paperpile.com/c/UDgV3V/1WUv">(Junker et al. 2014)</a> to enable a robust performance of the high-throughput image analysis algorithm. Seeds were stratified (4 days at 4ºC in darkness) after which they germinated and left to grow for 2 weeks at 21ºC (relative humidity: 55 %; light intensity: 160 µmol m-2 s-1; 14 h light). The temperature treatments were started by transferring the seedlings to either 6 °C or 16 °C. To simulate natural conditions temperatures fluctuated diurnally between 16-21 °C, 0.5-6 °C and 8-16 °C for the 21 °C initial growth conditions and the 6 °C and 16 °C treatments, respectively (<a href="https://docs.google.com/document/d/1Bmr7p24ZMh4yPFVV5oPeH2-T5S41TOFDS3au8JhtwsU/edit#fig_design">Fig.2</a>). Light intensity was kept constant at 160 µmol m-2 s-1 throughout the experiment. Relative humidity was set at 55% but in colder temperatures it rose uncontrollably to maximum 95%. Daylength was 9h during the 16°C and 6°C treatments.</p> <p>Each temperature treatment was repeated in three independent experiments. Five replicate plants were grown for every genotype per experiment. Plants were randomly distributed across the growth chamber with an independent randomisation pattern for each experiment. During the temperature treatments (14 DAS – 35 DAS), plants were photographed twice a day (1 hour. after/before lights switched on/off), using an RGB camera (IDS uEye UI-548xRE-C; 5MP) mounted to a robotic arm. At 35 DAS, whole rosettes were harvested, immediately frozen in liquid nitrogen and stored at -80 °C until further analysis. Rosette areas were extracted from the plant images using Lemnatec OS (LemnaTec GmbH, Aachen, Germany) software.</p> <p><em><strong>Seed size</strong></em></p> <p>We used the seeds produced by <a href="https://paperpile.com/c/UDgV3V/Jqsd">(Kerdaffrec et al. 2016)</a> and limited our measurements to the set of 123 Swedish accessions that overlapped with our growth dataset. After seed stratification for four days at 4ºC in darkness, mother plants were grown for 8 weeks at 4ºC under long-day conditions (16h light; 8h dark) to ensure proper vernalization. Temperature was raised to 21ºC (light) and 16ºC (dark) for flowering and seed ripening. Seeds were kept in darkness at 16ºC and 30% relative humidity, from the harvest until seed size measurements. For each genotype three replicates were pooled and about 200-300 seeds were sprinkled on 12 x 12 cm square, transparent Petri dishes. Image acquisition was performed as described in <a href="https://paperpile.com/c/UDgV3V/WH1e">(Exposito-Alonso et al. 2018)</a> by scanning dishes on a cluster of eight Epson V600 scanners. The resulting 1200 dpi .tiff images were analyzed in the Fiji software. Images were converted to 8-bit binary images and thresholded with the <em>setAutoThreshold("Defaultdark”) </em>command, and seed area was measured in squared mm by running the <em>Analyse Particles</em> command (inclusion parameters: size=0.04-0.25 circularity=0.70-1.00).</p> <p> </p> <p> </p> <p> </p> <p> </p>
Supplementary material for "High semi-natural vegetation cover and heterogeneity of field sizes promote bird beta-diversity at larger scales in Ethiopian Highlands"
<p><strong>Abstract</strong></p> <ol> <li>The intensification of farming practices exerts detrimental effects on biodiversity. Most research has focused on declines in species richness at local scales (alpha-diversity) although species loss is exacerbated by biotic homogenization that operates at larger scales (i.e., affecting beta-diversity). The majority of studies have been conducted in temperate, industrialized countries while tropical areas remain poorly studied. Agricultural landscapes of sub-Saharan Africa are still largely dominated by small-scale subsistence farming, but strenuous efforts to intensify farming practices are currently spreading to meet a growing food demand. It is therefore crucial to understand how these intensified practices affect biodiversity to mitigate their negative impacts. </li> <li>We investigated how farming system (small- vs large-scale farming) and landscape complexity (semi-natural vegetation cover) drive bird species composition, community turnover, and beta-diversity patterns in Ethiopian Highlands’ agroecosystems. We evaluated the following hypotheses: (1) large-scale farming homogenizes bird communities, (2) community turnover is higher in small-scale farms, (3) interactive effects between landscape complexity and farming systems shape avian communities, (4) heterogeneity of field sizes increases community turnover at larger scales. </li> <li>Bird communities underwent greater compositional changes along the landscape complexity than along the agricultural intensity gradient. Contrary to our expectations, beta-diversity was not significantly lower within large-scale farms (no biotic homogenization), and complex landscapes that still offer a high amount of semi-natural vegetation promoted community turnover in both farming systems. </li> <li>Semi-natural vegetation cover mediated how avian communities responded to agricultural intensification: the compositional differences between small- and large-scale farms increased with vegetation cover, further promoting avian community heterogeneity at the landscape level.</li> <li>The heterogeneity in field sizes also enhanced bird community turnover, suggesting that a combination of both small- and large-scale farming systems within a given landscape unit would promote beta-diversity at larger scales, provided large-scale farms do not become dominant.</li> <li>Synthesis and applications: Landscape complexity shaped avian communities to a stronger degree than farming intensity, emphasizing the importance of semi-natural vegetation and landscape heterogeneity for the maintenance of diverse bird communities and for achieving multifunctional landscapes promoting biodiversity and associated ecosystem services on the High Ethiopian plateaus. <br> </li> </ol>
Periodic vegetation pattern classification in Sudan
<p>This archive contains features computed from satellites images in Kordofan State in Sudan. SPOT (Systeme Probatoire d’Observation de la Terre) images with a 10-m ground resolution and preprocessing level 2A were divided into non-overlapping square windows of 410 by 410 m. We calculated for each of these windows:</p> <ul> <li>skewness of the grayscale distribution of each window</li> <li>index of vegetation pattern anisotropy</li> <li>azimuthal angle in the first PCA plane, which directly correlates with the dominant frequency in the windows</li> <li>distance from PCA origin, which expresses the degree of scale dominance</li> <li>mean annual rainfall computed from gridded monthly estimates from the Tropical Rainfall Measuring Mission (TRMM, NASA/JAXA) 3B43 V6 product acquired from 1 January 1998 to 31 December 2007 and resampled to 410 by 410 m.</li> <li>slope computed from the Shuttle Radar Topography Mission (SRTM) digital elevation model with three arc seconds<br> horizontal (ca 92 m in this area) spatial resolution.</li> </ul> <p>The resulting pattern classification:</p> <ul> <li>1, spots</li> <li>2, labyrinthine</li> <li>3, gaps</li> <li>4, bands</li> <li>5, non-periodic</li> <li>Nodata, area not covered by SPOT images</li> </ul> <p>Data is provided as rasters in Arc/Info ASCII grid format (also known as Esri grid). The projection and datum for all datasets are UTM zone 35 N, WGS 1984.</p> <p>Details on the methods are availble in the following publication: Deblauwe, V., Couteron, P., Lejeune, O., Bogaert, J. & Barbier, N. (2011) Environmental modulation of self-organized periodic vegetation patterns in Sudan. Ecography, 34, 990-1001. <a href="https://doi.org/10.1111/j.1600-0587.2010.06694.x">https://doi.org/10.1111/j.1600-0587.2010.06694.x</a></p>
Data from: Vegetative phenologies of lianas and trees in two Neotropical forests with contrasting rainfall regimes
<ol> <li>Among tropical forests, lianas are predicted to have a growth advantage over trees during seasonal drought, with substantial implications for tree and forest dynamics. We tested the hypotheses that lianas maintain higher water status than trees during seasonal drought and that lianas maximize leaf cover to match high, dry-season light conditions while trees are more limited by moisture availability during the dry season.</li> <li>We monitored the seasonal dynamics of predawn and midday leaf water potentials and leaf phenology for branches of 16 liana and 16 tree species in the canopy of two lowland tropical forests with contrasting rainfall regimes in Panama.</li> <li>In a wet, weakly seasonal forest, lianas maintained higher water balance than trees and maximized their leaf cover during dry-season conditions, when light availability was high, while trees experienced drought stress. In a drier, strongly seasonal forest, lianas and trees displayed similar dry season reductions in leaf cover following strong decreases in soil water availability.</li> <li>Greater soil moisture availability and a higher capacity to maintain water status allow lianas to maintain the turgor potentials critical for plant growth in a wet and weakly seasonal forest but not in a dry and strongly seasonal forest.</li> </ol>
Dataset: Human-vegetation dynamics in Holocene South-Eastern Norway based on radiocarbon-dated charcoal from archaeological excavations
<p>The repository contains radiocarbon data used in the paper <em>Human-vegetation dynamics in Holocene South-Eastern Norway based on radiocarbon-dated charcoal from archaeological excavations</em>, written by By Axel Mjærum, Kjetil Loftsgarden, and Steinar Solheim (University of Oslo).</p> <p>The paper is accepted for publication in The Holocene.</p> <p>ABSTRACT: Charcoal from archaeological contexts differs from off-site pollen samples as it is mainly a product of intentional human action. As such, analysis of charcoal from excavations is a valuable addition to studies of past vegetation and the interaction between humans and the environment. In this paper, we use a dataset consisting of 6,186 dated tree species samples from 1,239 archaeological sites as a proxy to explore parts of the Holocene forest development and human-vegetation dynamics in South-Eastern Norway.</p> <p>From the middle of the Late Neolithic (from <em>c</em>. 2000 BC) throughout the Early Iron Age (to <em>c</em>. AD 550) the region’s agriculture is characterized by fields, pastures, and fallow. Based on our data, we argue that these practices, combined with forest management, clearly altered the natural distribution of trees, and favoured some species of broadleaved trees. The past distribution of hazel (<em>Corylus avellana</em>) is an example of human impact on the vegetation. Today, hazel is not even among the 15 most common tree species, while it is one of the most prevalent species in the archaeological record before AD 550. The data indicate that this species was favoured already by the region’s Mesolithic hunter-fisher-gatherers, and that it was among the species that thrived extremely well in the early farming landscape. Secondly, our analysis also indicates that spruce (<em>Picea abies</em>) first formed large stands in the south-eastern parts of Norway <em>c</em>. 500 BC, centuries earlier than previously assumed. It is argued that this event, and a further westward expansion of spruce, was partly a consequence of a specific historical event – the first millennium BC farming expansion.</p>
Supplemental data and code for "Global patterns in water flux partitioning: Irrigated and rainfed agriculture drives asymmetrical flux to vegetation over runoff"
<p>This dataset provides all data compiled and generated for the manuscript entitled "Global patterns in water flux partitioning: Irrigated and rainfed agriculture drives asymmetrical flux to vegetation over runoff" (https://doi.org/10.1016/j.oneear.2023.08.002). This includes the boundaries for 3614 hydrological catchments, the curated data used for analysis and modelling, the developed machine learning model, shapley values and area of applicability results, and data for global extrapolation</p> <p>It also contains a markdown file ('code.html') which shows how to access and use the data, and generic sample codes used to generate these results.</p> <p> </p> <p> </p> <p> </p>
Data on submerged aquatic vegetation and its water environment in Lake Saint-Pierre, Saint Lawrence River, from 2012 to 2016
<p>This dataset is the result of a large collaborative work lead by the GRIL from 2012 to 2015 on a submerged aquatic vegetation meadow located downstream of two agricultural tributaries (Saint-François and Yamaska rivers) in Lake Saint-Pierre, a fluvial lake of the Saint Lawrence River. The data describe plants (as rake biomass and echosounding) and their environment, including water chemistry, current velocity as well as light, temperature and instantaneous meteo. Only echosounding data are available in 2016 and sediments were collected in 2015. Data are organized as a relational database and the GRIL_LSP_database.png provides keys and links between tables as well as data format. Data are in the tables mesure_integree, mesure_spatiale, mesure_verticale, plante_biomass_taxon, plante_recolte, plante_in_situ. The other tables are metadata about spatiotemporal locations and reported measures. Additional data (e.g. zooplankton, sediments) should eventually be made available and associated to this overall GRIL dataset.</p>
A Tortonian (Late Miocene, 11.61–7.25 Ma) global vegetation reconstruction
<p>This contains the Tortonian data-model hybrid global map of vegetation (figure 6B of Pound et al., 2011). Please remember to cite the original journal article when using it.</p> <p>For full details on the construction of this global biome map for 11.6-7.25 million years ago, please see:</p> <p>Pound, M.J., Haywood, A.M., Salzmann, U., Riding, J.B., Lunt, D.J. and Hunter, S.J., 2011. A Tortonian (late Miocene, 11.61–7.25 Ma) global vegetation reconstruction. <em>Palaeogeography, Palaeoclimatology, Palaeoecology</em>, <em>300</em> (1-4), pp.29-45. https://doi.org/10.1016/j.palaeo.2010.11.029</p>
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.