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389 results for “woodlands”
Natural Land Zones in New England in 2006 from 2010 Wildlands and Woodlands Report
This GIS dataset shows different Wildland and Woodland zones in New England and is intended to illustrate how the percentage of protected land could vary between New England landscapes while achieving the total acreage goals as expressed in the Wildlands and Woodlands 2010 Report. This is layer is intended to be conceptual and not prescriptive. The zones were created by expressing the percent natural landcover for a given 500m pixel using a 25 x 25-cell neighborhood. The landuse categories considered to be natural and the breakpoints for each zone are given in the Methods section of this document. The data are provided in vector format as an ESRI shapefile. The projection is NAD 1983 Albers. The Wildlands and Woodlands webpage, http://www.wildlandsandwoodlands.org/, includes a downloadable high-resolution copy of the report and an extensive set of resources that complement and support the arguments and facts presented in it. These include citations, metadata, and downloadable high-quality images of all the graphs and maps. The website will be updated to provide further information on many of the findings, activities, and recommendations provided in the report. Wildlands and Woodlands Report: Foster, D. R., Lambert, K. F., Kittredge, D. B., Donahue, B. M, Hart, C. M., Labich, W. G., Meyer, S., Thompson, J. , Buchanan, M., Levitt, J. N., Pershel, R., Ross, K., Elkins, G., Daigle, C., Hall, B., Faison, E. K., D'Amato, A. W., Forman, R. T. T., Del Tredici, P., Irland, L. C., Colburn, B. A., Orwig, D. A., Aber, J. D., Berger, A., Driscoll, C. T., Keeton, W. S., Lilieholm, R. J., Pederson, N., Ellison, A. M., Hunter, M. L., Fahey, T. J. 2017. Wildlands and Woodlands, Farmlands and Communities: Broadening the Vision for New England.
Wildlands and Woodlands Stewardship Science Vegetation Plots in New England 2009-2015
The Wildlands and Woodlands (W&W) initiative is a broad, collaborative effort to protect 70% of New England in forest over the next 50 years. At the heart of this initiative is the awareness that our wooded landscapes provide immeasurable economic, environmental, and cultural benefits and the conviction that we should understand these systems better, manage them wisely, and conserve them for the future. As part of W&W, Stewardship Science seeks to encourage widespread application of an accessible approach to monitoring forests that interested landowners or conservation-minded individuals can use to track changes in their woods over time. Whether the motivation is active management for timber, understanding how forests are being shaped by factors ranging from climate change and ice storms to insect pests, or simple pleasure in observing nature’s dynamics, anyone equipped with a notebook, tape measure, pencil, and the willingness to puzzle through a book of tree identification can readily develop a robust and valuable set of observations. This idea is not new. For over 150 years, leading conservationists and ecological thinkers beginning with Henry David Thoreau have argued that there is much to be learned through simple, long-term measurements of forest growth and change. Yet there are still remarkably few examples of private landowners, land trusts, timber companies, or conservation organizations that base their understanding and management practices on a regular system of observations and measurements. Because the vast majority of forestland in New England is privately owned, most of these lands remain unmonitored, and management plans are often drawn up from casual rather than systematic observation. For more background information on the project, please see the Wildlands & Woodlands Stewardship Science manual. This data package contains vegetation and environmental data on 64 20x20m plots set up in four areas across New England by staff and summer field crews fro
Land Zones in New England 1940-2070 from 2017 Wildlands and Woodlands Report
This dataset contains two GIS datalayers, one CSV file and an associated R script used to produce figures for the 2017 Wildlands and Woodlands report. The “wedge diagram” data (HF360-01-landcover-data.csv) shows actual percent landcover estimates across New England from 1940 to 2010 and straight-line trends needed between 2010 to 2070 to reach the Wildlands and Woodland vision by 2060. The published diagram can be seen in figure 1 of the 2017 Wildlands and Woodland report. In hf360-03-community-forests.zip, the GIS layer shows towns that contain community forests as determined by the authors of the report. In hf360-04-wildland-woodland-zones.zip, the GIS layer shows Wildland and Woodland Zones as illustrated in the report. It was created by starting with the Wildland and Woodland zones from the 2010 report and adding in areas with high agricultural land use. These types are meant to be conceptual and not prescriptive. Wildlands and Woodlands Report: Foster, D. R., Lambert, K. F., Kittredge, D. B., Donahue, B. M, Hart, C. M., Labich, W. G., Meyer, S., Thompson, J. , Buchanan, M., Levitt, J. N., Pershel, R., Ross, K., Elkins, G., Daigle, C., Hall, B., Faison, E. K., D'Amato, A. W., Forman, R. T. T., Del Tredici, P., Irland, L. C., Colburn, B. A., Orwig, D. A., Aber, J. D., Berger, A., Driscoll, C. T., Keeton, W. S., Lilieholm, R. J., Pederson, N., Ellison, A. M., Hunter, M. L., Fahey, T. J. 2017. Wildlands and Woodlands, Farmlands and Communities: Broadening the Vision for New England.
Ground Arthropod Community Survey in Grassland, Shrubland, and Woodland at the Sevilleta National Wildlife Refuge, New Mexico (1992-2004) (Reformatted to the ecocomDP Design Pattern)
This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-sev/29/175390. The abstract below was extracted from the Level 0 data package and is included for context: This data set contains records for the numbers of selected groups of ground-dwelling arthropod species and individuals collected from pitfall traps at 4 sites on the Sevilleta NWR, including creotostebush shrubland, both black and blue grama grasslands, and a pinyon/juniper woodland. Data collections begin in May of 1989, and are represented by subsequent sample collections every 2 months. One site (Goat Draw/Cerro Montosa) was discontinued in 2001, and a new site (Blue Grama) was initiated . Only three sites, creosotebush, black grama, and blue grama were continued between 2001-2004.
Carbon and water fluxes in a cork oak woodland in Central Portugal
<p>The Data set contains eddy covariance measurements of carbon and water fluxes and ancillary measurements observed at a cork oak woodland (<em>Quercus suber </em>L.) in central Portugal. The climate is Mediterranean, with mild, wet winters and hot, dry summers.</p> <p>Data are available in the file data.csv (UTF-8 encoding), the description of the variables and units are available in the file meta.csv (UTF-8 encoding).</p> <p>Further description of the site, methods and data processing can be viewed in the files metadata.pdf and metadata.csv</p> <p> </p>
DNA methylation dynamics during stress-response in woodland strawberry (Fragaria vesca)
<p><strong>Genome sequence and annotation of Fragaria vesca cv. Reine des Vallées</strong></p> <p>In order to generate a reference genome for Fragaria vesca cv. Reine des Vallées, we used MinIon long-read sequencing data to substitute the <em>F. vesca</em> genome v.4.0.a2 genome. The detailed method used to obtain these results were the following:</p> <p><em>Genome sequencing and assembly NIL Fb2</em></p> <p>Genomic DNA from strawberry plants was extracted by a Hexadecyltrimethylammonium bromide (Cetrimonium bromide, CTAB) modified protocol (Healey, Furtado, Cooper, & Henry, 2014) and purified with Agencourt AMPure XP beads (cat# A63880). Long-read sequencing was performed for the genome assembly; Genomic DNA by Ligation (Oxford Nanopore, cat# SQK-LSK109) library was prepared as described by the manufacturer and sequenced on a MinION for 72 h (Oxford Nanopore).</p> <p><em>Reference genome polishing</em></p> <p>Reads obtained from nanopore were filtered with Filtlong v0.2.1 (<a href="https://github.com/rrwick/Filtlong">https://github.com/rrwick/Filtlong</a>) using --min_mean_q 80 and --min_length 200. Cleaned reads were then aligned to the most recent version of the <em>F. vesca</em> genome v4.0.a2, downloaded from the Genome Database for Rosaceae (GDR) (<a href="https://www.rosaceae.org/species/fragaria_vesca/genome_v4.0.a2">https://www.rosaceae.org/species/fragaria_vesca/genome_v4.0.a2</a>), using minimap2 v2.21 (H. Li, 2018) with parameters -aLx map-ont --MD -Y. The generated BAM file was then sorted and indexed with samtools v1.11 (H. Li et al., 2009). We used mosdepth v0.3.1 (Pedersen & Quinlan, 2018) to verify that coverage on chromosomic scaffolds was over 50 X. Sniffles v1.0.12a (Sedlazeck et al., 2018) with parameters -s 10 -r 1000 -q 20 --genotype -l 30 -d 1000 was used to detect structural variations larger than 30 bp. The VCF files obtained from Sniffles was sorted and filtered with BCFtools v1.14 (Danecek et al., 2021) to keep only structural variants (SV) with smaller than 200,00 bp (we observed that larger SV were most of the time false positive caused by misalignments in regions with gaps or Ns), supported by 10 or more reads and with allelic frequencies above 0.8 (we were interested in homozygous changes). The complete filtering command used is “bcftools view -q 0.8 -Oz -i '(SVTYPE = "DUP" || SVTYPE = "INS" || SVTYPE = "DEL" || SVTYPE = "TRA" || SVTYPE = "INV" || SVTYPE = "INVDUP") && %FILTER = "PASS" && FMT/DV>9 && SVLEN>29 && SVLEN<200000' “</p> <p>From the VCF listing all the structural variants that we detected in our <em>F. vesca </em>accession, we generated a substituted genome version based on the reference <em>F. vesca</em> genome v.4.0.a2. The reference genome was first indexed with samtools faidx v1.11(Danecek et al., 2021) and a sequence dictionary was generated with Picard CreateSequenceDictionary v2.25.6 (<a href="https://broadinstitute.github.io/picard">https://broadinstitute.github.io/picard</a>). The VCF containing the SV produced from our Nanopore sequencing was also indexed with gatk (Van der Auwera GA & O'Connor BD, 2020) IndexFeatureFile v4.2.0.0 (<a href="https://gatk.broadinstitute.org/hc/en-us/articles/360037262651-IndexFeatureFile">https://gatk.broadinstitute.org/hc/en-us/articles/360037262651-IndexFeatureFile</a>). FastaAlternateReferenceMaker v4.2.0.0 (<a href="https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMaker">https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMaker</a>) was then run with the reference genome and the VCF file to generate a substituted genome representative of our <em>Fragaria</em> accession.</p> <p>As substituting our genome with the detected structural variants changes genomic coordinates, we also corrected the public GFF genome annotation of <em>F. vesca</em> (Y, Pi, Gao, Liu, & Kang, 2019) using liftoff v1.6.1 (Shumate & Salzberg, 2021). Liftoff also detects and annotates duplications within the substituted genome.</p> <p>Transposable elements annotation was carried out using the EDTA transposable element annotation pipeline v. 1.9.6 (S. Ou et al., 2019) on the substituted genome using default parameters<em>.</em></p> <p><strong>Differentially methylated regions</strong></p> <p>The file Stress_vs_control_DMRs.zip file contains the DMRs that were called using the reads submitted to ENA (ERP135585) and obtained as follows:</p> <p>First, bedGraph files from wgbs pipeline were pre-filtered for a minimum coverage of 5 reads using awk command. These output files were then used as input for the EpiDiverse/dmr bioinformatics analysis pipeline for non-model plant species to define DMRs (Nunn <em>et al</em>., 2021) with default parameters (minimum coverage threshold 5; maximum q-value 0.05; minimum differential methylation level 10%; 10 as minimum number of Cs; Minimum distance (bp) between Cs that are not to be considered as part of the same DMR is 146 bp). The pipeline uses metilene v.0.2.6.1 (<a href="https://www.bioinf.uni-leipzig.de/Software/metilene/">https://www.bioinf.uni-leipzig.de/Software/metilene/</a>) for pairwise comparison between groups and R-packages ggplot2 v.3.3.5 and gplots v.3.1.1, for visualization results (Fig. S1). Based on our <em>F. vesca</em> genome transcript annotation and methylation data (overlapped regions with DNA methylation cytosines and DMRs), we detected the methylated genes, promoters, 3’ UTRs, 5’UTR and transposable elements in strawberry. Global DNA methylation and DMR plots were performed with R-package ggplot2. Gene analyses by methylation patterns and analysis of per-family TE DNA methylation profiles were performed with deepTools v.3.5.0 (Ramírez <em>et al</em>., 2014). DMRs comparison between treatments were done by the Venn diagram v.1.7.0 R-package.</p> <p>We produced several genome browsers tracks with DMRs that we integrated in our local instance of JBrowse available at the following url: <a href="https://jbrowse.agroscope.info/jbrowse/?data=fragaria_sub">https://jbrowse.agroscope.info/jbrowse/?data=fragaria_sub</a></p>
Metabarcoding reveals a high diversity of woody host-associated Phytophthora spp. in soils at public gardens and amenity woodlands in Britain
<p>This is the demultiplexed Illumina MiSeq raw sequencing data from two 96-well plates from the following recent publication, shared with permission of the corresponding author, Sarah Green:</p> <p>Riddell <em>et al.</em> (2019). Metabarcoding reveals a high diversity of woody host-associated <em>Phytophthora</em> spp. in soils at public gardens and amenity woodlands in Britain. https://doi.org/10.7717/peerj.6931<br> <br> It consists of 244 gzipped compressed plain text FASTQ format sequence files, grouped into 122 pairs by the widely used R1 and R2 suffix. The files have been renamed to use the anonymised site numbers (1 to 14) as in the paper, see also supplementary table one for site metadata. Additionally there are two negative controls, and positive control DNA mixtures of 10 and 15 species as described in the paper.<br> </p>
Indicative distribution map for Ecosystem Functional Group T4.4 Temperate woodlands
<p>This archive contains indicative distribution maps and profiles for <strong>T4.4 Temperate woodlands</strong>, a ecosystem functional group (EFG, level 3) of the <a href="https://global-ecosystems.org/">IUCN Global Ecosystem Typology</a> (v2.0). Please refer to Keith <em>et al.</em> (2020) for details.</p> <p>The descriptive profiles provide brief summaries of key ecological traits and processes, maps are indicative of global distribution patterns, and are not intended to represent fine-scale patterns. The maps show areas of the world containing major (value of 1, coloured red) or minor occurrences (value of 2, coloured yellow) of each ecosystem functional group. Minor occurrences are areas where an ecosystem functional group is scattered in patches within matrices of other ecosystem functional groups or where they occur in substantial areas, but only within a segment of a larger region. Given bounds of resolution and accuracy of source data, the maps should be used to query which EFG are likely to occur within areas, rather than which occur at particular point locations. Detailed methods and references for the maps are included in the profile (xml format).</p>
Indicative distribution map for Ecosystem Functional Group T2.6 Temperate pyric sclerophyll forests and woodlands
<p>This archive contains indicative distribution maps and profiles for <strong>T2.6 Temperate pyric sclerophyll forests and woodlands</strong>, a ecosystem functional group (EFG, level 3) of the <a href="https://global-ecosystems.org/">IUCN Global Ecosystem Typology</a> (v2.0). Please refer to Keith <em>et al.</em> (2020) for details.</p> <p>The descriptive profiles provide brief summaries of key ecological traits and processes, maps are indicative of global distribution patterns, and are not intended to represent fine-scale patterns. The maps show areas of the world containing major (value of 1, coloured red) or minor occurrences (value of 2, coloured yellow) of each ecosystem functional group. Minor occurrences are areas where an ecosystem functional group is scattered in patches within matrices of other ecosystem functional groups or where they occur in substantial areas, but only within a segment of a larger region. Given bounds of resolution and accuracy of source data, the maps should be used to query which EFG are likely to occur within areas, rather than which occur at particular point locations. Detailed methods and references for the maps are included in the profile (xml format).</p>
Indicative distribution map for Ecosystem Functional Group T2.1 Boreal and temperate high montane forests and woodlands
<p>This archive contains indicative distribution maps and profiles for <strong>T2.1 Boreal and temperate high montane forests and woodlands</strong>, a ecosystem functional group (EFG, level 3) of the <a href="https://global-ecosystems.org/">IUCN Global Ecosystem Typology</a> (v2.0). Please refer to Keith <em>et al.</em> (2020) for details.</p> <p>The descriptive profiles provide brief summaries of key ecological traits and processes, maps are indicative of global distribution patterns, and are not intended to represent fine-scale patterns. The maps show areas of the world containing major (value of 1, coloured red) or minor occurrences (value of 2, coloured yellow) of each ecosystem functional group. Minor occurrences are areas where an ecosystem functional group is scattered in patches within matrices of other ecosystem functional groups or where they occur in substantial areas, but only within a segment of a larger region. Given bounds of resolution and accuracy of source data, the maps should be used to query which EFG are likely to occur within areas, rather than which occur at particular point locations. Detailed methods and references for the maps are included in the profile (xml format).</p>
Spectral library of vegetation from Mediterranean woodlands
<p>Site description:</p> <p>All reflectance measurements have been collected in Mediterranean oak woodland at <em>Herdade </em>da <em>Machoqueira do Grou</em>, located<em> </em>in Central Portugal (39° 08′ 18.9″ N, 9° 19′ 56.22″ W, 165-m height). The site is characterized by a Mediterranean climate with mild winters and hot dry summers. The average annual precipitation recorded at the climate station of Santarém (39° 12′ N, 8° 44′ W) for the period 1981–2010 was 652 mm, and mean daily temperature was 17°C (<a href="http://www.ipma.pt/pt/oclima/normais.clima/">www.ipma.pt/pt/oclima/normais.clima/</a>). Detailed meteorological measurements of radiation, temperature, and air humidity are also publicly available (Cerasoli et al., 2020). The soil is a cambisol (FAO) with 81% sand, 5% clay, and 14% silt. The tree layer is represented exclusively by cork oak trees (<em>Quercus suber</em> L.) with a tree density of 177 tree ha<sup>-1</sup> and leaf area index (LAI) of 1.5. The mean total tree height and height below the canopy are 7.9 and 3.1m respectively (Cerasoli et al., 2015). Tree canopy represents 36% of the soil cover fraction. The understorey is composed of a mixture of shrubs and herbaceous species. The site was plowed in 2013 (Correia et al., 2016), hence the cover fraction of shrubs changed across years. A field survey in 2017 estimated an 18% coverage of shrubs and 41% of herbaceous species, while the remaining 41% was represented by litter and bare soil (Heuschmidt et al., 2020). The most represented shrub species are <em>Cistus salvifolius</em> (cistus) and the <em>Ulex airensis</em> (ulex). In spite of occupying the same habitat, the two species have different growth habits and stress strategies. While the cistus is a semi-deciduous species with shallow roots, decreasing its canopy area during the summer period, the ulex has a deep root system and spine shaped leaves and shoots conferring high drought resistance (Correia et al., 2014). The herbaceous layer is composed of C3 species mainly grasses (44.5%) and legumes (28.7%) (Cerasoli et al., 2015).</p> <p> </p> <p>Reflectance measurements:</p> <p>All spectral observations were acquired with an ASD FieldSpec3 spectroradiometer (Malvern Panalytical, Boulder, USA) in the range of 350-2300nm. The visible and near-infrared region (350-1000nm) has a spectral resolution (full-width half maximum) of 3nm and a sampling interval of 1.4nm, while the mid infrared region (1000-2500nm) has a spectral resolution of 10nm and a sampling interval of 2.0nm. Canopy spectral data were collected by a fiber optic cable inserted into a pistol grip. A white reference of known reflectance (Spectralon panel, Labsphere, Inc., North Sutton, USA) was used to normalize for variation in atmospheric conditions and to convert the measurements into absolute reflectance. All targets were fully exposed to solar radiation at the time of the measurements. Measurements were performed on cork oak, cistus, and ulex canopies. Herbaceous plots were delimited by a 50X50 cm quadrat. Oak trees canopy measurements were done using a scaffold on the south side of the canopy. All canopy measurements were performed with a nadir view, a field of view angle of 25º, and a distance of about 90cm from the target, which resulted in a field of view of about 1256 cm<sup>2</sup>. All spectra were collected for 2 hours around solar noon, to minimize the effects of shadowing and solar zenith changes, with five replicates for each target, representing each the average of 25 spectra. All reflectance values in the range 1350-1400nm and 1800-1950nm were excluded, corresponding to the atmospheric water vapor absorption regions. A leaf clip including a white and a black standard was used for the measurement of the reflectance of cork oak leaf blades avoiding main veins.</p> <p> </p> <p>File description: </p> <p>The file "specveg_data_spectra" concerns all spectral data, the "specveg_metadata" covers the additional data of every single measured vegetation including photos (URL), and the "specveg_meta" describes all the existing variables.</p>
Ground Arthropod Community Survey in Grassland, Shrubland, and Woodland at the Sevilleta National Wildlife Refuge, New Mexico (1992-2004) (Reformatted to a Darwin Core Archive)
This data package is formatted as a Darwin Core Archive (DwC-A, event core). For more information on Darwin Core see https://www.tdwg.org/standards/dwc/. This Level 2 data package was derived from the Level 1 data package found here: https://pasta.lternet.edu/package/metadata/eml/edi/333/2, which was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-sev/29/175390. The abstract below was extracted from the Level 0 data package and is included for context: This data set contains records for the numbers of selected groups of ground-dwelling arthropod species and individuals collected from pitfall traps at 4 sites on the Sevilleta NWR, including creotostebush shrubland, both black and blue grama grasslands, and a pinyon/juniper woodland. Data collections begin in May of 1989, and are represented by subsequent sample collections every 2 months. One site (Goat Draw/Cerro Montosa) was discontinued in 2001, and a new site (Blue Grama) was initiated . Only three sites, creosotebush, black grama, and blue grama were continued between 2001-2004.
Comparative Bird Community Assessments in Grassland, Shrubland, and Woodland Habitats at the Sevilleta National Wildlife Refuge, New Mexico (1991-1997 and 2022-2023)
Across North America, avifauna abundance has declined by 30% since 1970 (Rosenberg, K.V. et al. 2019). Direct mortality from anthropogenic sources (pets, cars, collisions with building, power lines, wind turbines, etc.) and indirect mortality (habitat loss, disturbance, climate change, etc.) have both been major contributors to these declines (Loss, S.R. et al. 2015 and Calvert, A.M. et al. 2013). Variables such as migration patterns, family, breeding and non-breeding biomes show differing rates of decline (Rosenberg, K.V. et al. 2019). In New Mexico, there are three breeding biomes all classified with declining avian abundance. Avian abundance in grasslands has declined by 53.3% since 1970, western forests by 29.5% and arid lands by 17.0% (Rosenberg, K.V. et al. 2019). All three of these biomes also occur at the Sevilleta National Wildlife Refuge thus temporal declines in species richness and abundance are expected. This project was originally designed to sample the species richness and abundance of birds on the Sevilleta National Wildlife Refuge in three types of habitat: grassland, creosote shrubland and pinyon-juniper woodland. Surveys were conducted between January 1991 and May 1997 (Parmenter, R. 2016). Surveys were re-established in 2022 to document current species richness and abundance and to capture any temporal changes from the 90s data. Avian point count survey stations in grassland, creosote and pinyon-juniper habitats run through existing study sites which have all been subjected to intense research activity. Literature Cited A. M. Calvert, C. A. Bishop, R. D. Elliot, E. A. Krebs, T. M. Kydd, C. S. Machtans, G. J. Robertson, A synthesis of human-related avian mortality in Canada. Avian Conserv. Ecol. 8, art11 (2013). https://www.ace-eco.org/vol8/iss2/art11/ Loss, S. R., Will, T., Marra, P. P. 2015. Direct Mortality of Birds from Anthropogenic causes. Annu. Rev. Ecol. Evol. Syst. 46, 99–120. https://www.annualreviews.org/doi/10.1146/annurev-ecolsys-1124
Uncovering major types of deforestation frontiers across the world's tropical dry woodlands
<p>These datasets provide maps of deforestation frontier classsification into three themed typologies (severity, spatio temporal patterns and development stage) and archetypes of major frontier patterns. We do this for tropical dry woodland worldwide, for the period of 2000 to 2020, at ~3-km spatial resolution (Coordinate System: WGS_1984_Mollweide, float format). Datasets used for this analysis are publicly available, forest cover and loss data are available at: https://data.globalforestwatch.org/. Deforestation frontiers metrics were calculated and typologies developed in RStudio 1.3.1056. We share the code used to develop frontier metrics, frontier typologies, and archetypes, together with a sample dataset summarized from the originally publicly available dataset.</p> <p>Further details of the datasets can be found in Buchadas et. al. (2022): https://doi.org/10.1038/s41893-022-00886-9 </p> <p>For further questions or issues with the datasets, please contact Ana Buchadas at ana.buchadas@geo.hu-berlin.de.</p>
Supplementary material 3 from: Bongard C, Butler K, Fulthorpe R (2013) Investigation of fungal root colonizers of the invasive plant Vincetoxicum rossicum and co-occurring local native plants in a field and woodland area in Southern Ontario. Nature Conservation 4: 55-76. https://doi.org/10.3897/natureconservation.4.3578
Supplementary material 3 from: Bongard C, Butler K, Fulthorpe R (2013) Investigation of fungal root colonizers of the invasive plant Vincetoxicum rossicum and co-occurring local native plants in a field and woodland area in Southern Ontario. Nature Conservation 4: 55-76. https://doi.org/10.3897/natureconservation.4.3578
Detecting edge effects of geese grazing at the boundary of woodland and grassland
<p>The presence of geese on different areas of lawn was estimated by the length of droppings on the lawn. Geese defecate frequently and seemingly indiscriminately. Counting dropping is a well-known method for estimating their density on areas of land (Owen, 1971). However, we found it difficult to distinguish individual defecation events as the dropping tend to break apart as they are released. Therefore, we measured the total length of dropping in an area. Geese dropping are more or less cylindrical and we consider a measure related to the volume of droppings is more reliable than a count of their number.</p> <p>Observations were conducted in July 2014 and March and April 2015 at Meise Botanic Garden, Meise, Belgium. Rectangular plots were laid out perpendicular to a woodland-lawn boundary on sections of a Botanic Garden frequently used by geese. These plots are detailed in file DroppingsPlots.csv. The sites for these plots were chosen because they were well separated from each other; were away from other trees and faced different directions. The plots were marked out using bamboo canes and a tape measure. Then either 20 or 30 randomly chosen 1 m<sup>2</sup> square quadrats were surveyed within the rectangular plot. The cumulative length of dropping in a quadrat was measured to the nearest centimeter with a ruler.</p> <p>The results are found in file DroppingsMeasurements.csv.</p> <p>The columns of this file are as follows</p> <p>Plot - The identifying number given to the plot</p> <p>X - The distance parallel to the woodland-lawn boundary</p> <p>Y - The distance from the woodland-lawn boundary</p> <p>Length - The total length in centimeters of the dropping found in a 1m<sup>2</sup> quadrat</p> <p>Prunella - coverage of <em>Prunella vulgaris</em> L. in the 1m<sup>2</sup> quadrat on the DAFOR Scale (dominant 5, abundant 4, frequent 3, occasional 2, rare 1, absent 0)</p> <p>Renoncule - coverage of <em>Ranunculus</em> sp. in the 1m<sup>2</sup> quadrat on the DAFOR Scale (dominant 5, abundant 4, frequent 3, occasional 2, rare 1, absent 0)</p> <p>Bellis - coverage of <em>Bellis perennis</em> L. in the 1m<sup>2</sup> quadrat on the DAFOR Scale (dominant 5, abundant 4, frequent 3, occasional 2, rare 1, absent 0)</p> <p>Lotus - coverage of <em>Lotus</em> sp. in the 1m<sup>2</sup> quadrat on the DAFOR Scale (dominant 5, abundant 4, frequent 3, occasional 2, rare 1, absent 0)</p> <p>Glechoma - coverage of <em>Glechoma hederacea</em> L. in the 1m<sup>2</sup> quadrat on the DAFOR Scale (dominant 5, abundant 4, frequent 3, occasional 2, rare 1, absent 0)</p> <p>Four species of geese are present in the Botanic Garden and may have contributed droppings to the observations. These species are <em>Alopochen aegyptiaca</em> (L. 1766) (Egyptian geese), <em>Branta canadensis</em> (L. 1758) (Canada geese), <em>Anser anser</em> (L. 1758) (greylag geese) and <em>Branta leucopsis</em> (Bechstein, 1803) (barnacle geese).</p>
Epigenetic and transcriptional landscape of stress memory in woodland strawberry
<p>Bedfiles of differentially methylated regions (DMRs) that were detected in stressed mother plants (M) and their (themselves unstressed) clonal daughter plants that were formed <em>via</em> stolon formation (St1, St2, St3). The M plants were grown and sampled <em>in vitro</em> and the St1, St2, St3 plants in the green house. The DMRs were called using the the EpiDiverse/dmr bioinformatic analysis pipeline (Nunn et al., 2021).</p> <p><strong>Stress assays <em>in vitro</em></strong></p> <p>One-month-old seedlings were transferred to a fresh MS media and growth chambers at 24<sup>o</sup>C/21<sup>o</sup>C (day/night),16 h light/8 h dark, as control conditions<em>. </em>For heat-stress, plants were exposed to 30<sup>o</sup>C (day/night) for one week followed by 2 days of recovery (24<sup>o</sup>C/21<sup>o</sup>C) on fresh medium as well as the control plants. Then, the plates were transferred to 37<sup>o</sup>C (day/night) for 1 week with 2 recovery days (Figure 1A). We sampled aerial parts of plants for the molecular analyses. To reduce variability resulting from individual plants, three biological replicates of 5 pooled plants were collected per condition. Samples were harvested in 1.5 mL tubes between 9:00-11:00 a.m. and immediately frozen in liquid nitrogen and stored at -80<sup>o</sup>C until required.</p> <p><strong>Greenhouse propagation assays</strong></p> <p><em>In vitro</em> plants after heat and control treatment were transferred to soil (one plant per pot) in square plastic pots (size: 12x12x10 cm) and to a greenhouse with long day conditions (24<sup>o</sup>C/21<sup>o</sup>C day/night and 60%-70% humidity).</p> <p>Twelve mother plants (M) from control (CM; n=12) and heat-stress (HM; n=12) conditions were used for asexual propagation. From each mother plant, the two first stolons (St) were kept for producing the daughter plants of the first asexual propagation (St1) in individual pots. After two weeks, following root formation, the stolons were cut to get independent daughter plants from their mother plant (M). This process was continued until St3.</p> <p>The DMRs can also be visualized here: <a href="https://jbrowse.agroscope.info/jbrowse/?data=fragaria_sub">https://jbrowse.agroscope.info/jbrowse/?data=fragaria_sub</a></p> <p>And the raw bisulfite sequencing data can be found here: <a href="https://www.ebi.ac.uk/ena/browser/text-search?query=ERP135585">https://www.ebi.ac.uk/ena/browser/text-search?query=ERP135585</a></p> <p> </p> <p> How many daughter plants per stolon? One stolon produce a chain of daughter plants.</p>
Groundwater dependence of riparian woodlands and the disrupting effect of anthropogenically altered streamflow
This dataset includes data inputs from public sources, scripts and outputs to evaluate riparian vegetation reliance on groundwater across California from 2015 to 2020. This dataset accompanies the Rohde et al. paper titled, Groundwater dependence of riparian woodlands and the disrupting effect of anthropogenically altered streamflow. The provided scripts process groundwater, vegetation, climate, and streamflow input data from various sources. Further, all output data and statistical analyses are included.
Ecosystem-scale rainfall manipulation in a Pinon-Juniper Woodland: Volumetric Water Content (VWC) Profile Data (2009-2013 )
Climate models predict that water limited regions around the world will become drier and warmer in the near future, including southwestern North America. We developed a large-scale experimental system that allows testing of the ecosystem impacts of precipitation changes. Four treatments were applied to 1600 m2 plots (40 m × 40 m), each with three replicates in a piñon pine (Pinus edulis) and juniper (Juniper monosperma) ecosystem. These species have extensive root systems, requiring large-scale manipulation to effectively alter soil water availability. Treatments consisted of: 1) irrigation plots that receive supplemental water additions, 2) drought plots that receive 55% of ambient rainfall, 3) cover-control plots that receive ambient precipitation, but allow determination of treatment infrastructure artifacts, and 4) ambient control plots. Our drought structures effectively reduced soil water potential and volumetric water content compared to the ambient, cover-control, and water addition plots. Drought and cover control plots experienced an average increase in maximum soil and air temperature at ground level of 1-4° C during the growing season compared to ambient plots, and concurrent short-term diurnal increases in maximum air temperature were also observed directly above and below plastic structures. Our drought and irrigation treatments significantly influenced tree predawn water potential, sap-flow, and net photosynthesis, with drought treatment trees exhibiting significant decreases in physiological function compared to ambient and irrigated trees. Supplemental irrigation resulted in a significant increase in both plant water potential and xylem sap-flow compared to trees in the other treatments. This experimental design effectively allows manipulation of plant water stress at the ecosystem scale, permits a wide range of drought conditions, and provides prolonged drought conditions comparable to historical droughts in the past – drought events for which wide
Ecosystem-scale rainfall manipulation in a Pinon-Juniper woodland: Tree Sapwood and Leaf Area Data (2011)
Climate models predict that water limited regions around the world will become drier and warmer in the near future, including southwestern North America. We developed a large-scale experimental system that allows testing of the ecosystem impacts of precipitation changes. Four treatments were applied to 1600 m2 plots (40 m × 40 m), each with three replicates in a piñon pine (Pinus edulis) and juniper (Juniper monosperma) ecosystem. These species have extensive root systems, requiring large-scale manipulation to effectively alter soil water availability. Treatments consisted of: 1) irrigation plots that receive supplemental water additions, 2) drought plots that receive 55% of ambient rainfall, 3) cover-control plots that receive ambient precipitation, but allow determination of treatment infrastructure artifacts, and 4) ambient control plots. Our drought structures effectively reduced soil water potential and volumetric water content compared to the ambient, cover-control, and water addition plots. Drought and cover control plots experienced an average increase in maximum soil and air temperature at ground level of 1-4° C during the growing season compared to ambient plots, and concurrent short-term diurnal increases in maximum air temperature were also observed directly above and below plastic structures. Our drought and irrigation treatments significantly influenced tree predawn water potential, sap-flow, and net photosynthesis, with drought treatment trees exhibiting significant decreases in physiological function compared to ambient and irrigated trees. Supplemental irrigation resulted in a significant increase in both plant water potential and xylem sap-flow compared to trees in the other treatments. This experimental design effectively allows manipulation of plant water stress at the ecosystem scale, permits a wide range of drought conditions, and provides prolonged drought conditions comparable to historical droughts in the past – drought events for which wide
ScienceDex guides
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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.