cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5285/e5bfac9b-0642-4b5b-a780-e5801b2dab8b
title: Source Attribution - deposition of nitrogen and sulphur to UK

description: This dataset contains 90 source footprints of nitrogen and sulphur deposition across the UK. Emission data from UK sources of nitrogen and sulphur for the year 2012 has been modelled using the FRAME (Fine Resolution Atmospheric Multi-Pollutant Exchange) atmospheric dispersion model on a 5 x 5 km grid. The data are split by into both wet and dry deposition, oxidised and reduced, as well as local vs long-range components.

Habitat-specific deposition data are provided also for (i) forest, (i) moorland (short semi-natural vegetation), and (iii) grid average (average of arable, grassland, urban, forest and moorland land cover types).
description: The FRAME (Fine Resolution Multi-pollutant Exchange) model was used to assess the long-term annual mean deposition of reduced and oxidised nitrogen and sulphur over the United Kingdom. Emissions of Sulphur and Nitrogen for input into the model were split into 160 different sub-sectoral emission categories. This included 22 individual point sources and background 'area' emissions of SO2, NOx and NH3 split into 11 SNAP sectors (Selected Nomenclature for Air Pollution, European Environment Agency, 2013), international shipping and European import emissions.

For each 5 km grid square across the domain, pollutant compounds for SOx, NOy and NHx deposition were calculated for all footprints. In addition the output deposition data was split into more detailed chemical species to provide an approximation of how much of each 'source attribution type (e.g. livestock, fertiliser, shipping, etc.) is a short or long range input.

Deposition data was output to three different ecosystem types: forest, moorland (representing short semi-natural vegetation) and a grid average (an average of arable, grassland, urban, forest and moorland). The resulting datasets were calibrated to CBED - Concentration Based Estimated Deposition for the three-year period 2011-2013.

The full methodology is available in the contextual metadata which can be found attached to this record.

The work in generating and compiling this dataset has been funded by the UK pollution and conservation agencies: Natural Resources Wales (NRW), the Environment Agency, Northern Ireland Environment Agency, Natural England, the Joint Nature Conservation Committee (JNCC), Scotland and Northern Ireland Forum for Environmental Research (SNIFFER), the Scottish Environment Protection Agency (SEPA), and Scottish Natural Heritage (SNH).
DOI: 10.5285/28880a9d-3d6b-4e8e-a1d3-8ed939222bdc
title: Chlorophyll fluorescence data collected on Mount Etna, Sicily, 2017

description: The dataset contains chlorophyll fluorescence data from different genotypes of two Senecio species on Mount Etna, Sicily. In 2017, multiple clones of c.40 genotypes for each of two Senecio species were transplanted at four elevations (500m, 1000m, 1500m, 2000m) on Mount Etna. For each species, five genotypes were chosen randomly and chlorophyll fluorescence was measured on four clones of each chosen genotype at each transplant elevation using an IMAGING-PAM fluorometer
description: The IMAGING-PAM fluorometer was used to estimate total photosynthetic capacity for each plant. Plants were dark adapted for 30minutes prior to measurements. To account for weather, timing and variation, four clones for each genotype and four leaves for each clone were measured. The measurements were also repeated on a second time on a different day. All measurements were taken within a five-day period.
DOI: 10.5285/78dba959-989b-43d4-b4da-efd2506e0c8e
title: Tree canopy data derived from LiDAR data for South West England, 2013

description: The data describe vegetation outlines and tree tops above 1m in height as polylines and points. Data have been processed from a digital terrain model (DTM) and digital surface model (DSM), converted from raw LiDAR data. The LiDAR dataset was acquired for Cornwall and Devon (all the land west of Exmouth) during the months of July and August 2013. The data were created as part of the Tellus South West project.
description: Data was downloaded in 25km squares and subdivided into a 5 x 5 grid for processing. The digital terrain model (DTM) was then subtracted from the digital surface model (DSM) to provide a Canopy Height Model (CHM) at the same 1m resolution. The data were then processed in R to provide canopy outlines for vegetation above 1m in height using the Forest Tools toolbox. Data was then filtered to exclude littoral, sub-littoral, and urban environments. However these data still exist and can be provided if requested.
DOI: 10.5285/c2fbd22c-1ce9-4435-b4b0-e333addef346
title: Palm frond damage from herbivory in Biodiversity and Ecosystem Function in Tropical Agriculture (BEFTA) plots, Kandista and Ujun Tanjung estates, Indonesia

description: Data comprise counts of damage to palm fronds in mature oil palm (2013-2015), and mature and replanted oil palm (2016-2017) plots as part of a large-scale ecological experiment programme (the Biodiversity and Ecosystem Function in Tropical Agriculture project, established in 2013). Herbivory was measured 17 times in total (every 3-4 months) between April 2013 and August 2017. Eighteen plots were examined across three estates - plots in Ujung Tanjung and Kandista estates were planted in 1987 to 1992 and are mature or over-mature oil palm, while Libo plots (2016-2017 data only) were replanted in 2014. Plots were organised in triplets; in Ujung Tanjung and Kandista, for each triplet one plot was assigned to each of three vegetation treatments: Reduced vegetation cover, normal vegetation management and enhanced vegetation cover. 

The data contain damage estimated in three ways: by eye for the whole crown, by eye for the 17th frond, and by image processing for 20 leaflets of the 17th frond. 
description: At each recording session, three palms were selected at random from within experimental plots. Random palm selection was done using the rnd function in excel before visiting the field, as each palm in the experimental plots has a unique identifying tag. In the replanted stands where palms are not tagged, the randomisation was done by counting steps from the corner of the plot, again using the rnd function in excel.

First the damage to the crown form herbivory was estimated visually from the ground. Then, counting from the youngest fully-opened frond, the 17th frond in the crown of the palm was cut and caught in a white cloth. Frond 17 represents a middle-aged frond (aged between 8.5 and 9 months) in mature palms and is commonly used by the oil palm industry as a standard to measure herbivory and herbivore load. The damage to the frond (in percent) was estimated visually. Then twenty paired leaflets, spaced evenly along the frond, were cut, placed flat on a white board and photographed (using a Nikon D90). Photography and visual damage estimates were always carried out by the same person, from the same angle (bottom left), to reduce sampling bias.

Photographs were pre-processed to remove noise and converted to binary images in Microsoft Paint. The total leaflet area was then measured in Fiji (https://fiji.sc/). A second image was prepared in Microsoft Paint, with all herbivory damage 'filled in', such that the leaflets appeared to be intact. Where leaflet tips were missing, a conservative estimate for the leaflet tip was drawn in, based on the length of neighbouring leaflets. This second image was measured in Fiji in the same way and the percent of the leaflet area consumed by herbivores was calculated. 

Basic data checks were carried out (checks for impossible values, such as an increase in leaf area after processing or extreme discrepancy between visual estimate and image processing values).
DOI: 10.5285/904af4a0-d66d-460d-82eb-c8965e161b3e
title:  European Monitoring and Evaluation Program Model for the UK (EMEP4UK) monthly atmospheric deposition of oxidised sulphur, oxidised nitrogen, and reduced nitrogen for 2002-2021

description: This dataset is a model output from the European Monitoring and Evaluation Programme (EMEP) model applied to the UK (EMEP4UK) driven by Weather and Research Forecast model meteorology (WRF). It provides UK estimates monthly averaged atmospheric deposition of oxidised sulphur, oxidised nitrogen, and reduced nitrogen at 3x3 km2 grid for the years 2002 to 2021.

The data consists of atmospheric deposition values of oxidised sulphur, oxidised nitrogen, and reduced nitrogen.
The EMEP4UK model version used here is rv4.36, and the WRF model version is the 4.2.2.

This work was supported by the Natural Environment Research Council award number NE/R016429/1 as part of the UK-SCAPE programme delivering National Capability.

description: The EMEP4UK atmospheric chemistry transport model calculated daily average concentrations for a model domain covering the UK with a resolution of about 3x3 km2. The model is evaluated using the UK Automatic Urban and Rural Network (AURN) monitoring stations (https://uk-air.defra.gov.uk/networks/network-info?view=aurn). R was used to access the AURN dataset to evaluate the EMEP4UK model output.
The data are processed from the full EMEP4UK model output to a subset containing essential variables only. The Climate Data Operators version 1.9.10 was used to subset the model output.

Your use of the content of this dataset is entirely at your own risk. We make no warranty or guarantee that the content is error free or fit for your intended use.
DOI: 10.5285/b01a4ec1-90b0-4690-924f-a408a3280149
title: Ecotoxicology data of Eisenia fetida earthworms exposed to four concentrations of bio-based teabags

description: This dataset contains ecotoxicology measurements of Eisenia fetida earthworms exposed to different types of bio-based teabags, at four concentration levels.

Variables measured include mortality, growth, reproductive output (number of egg cocoons and juveniles) and were collected over a 28-day period.

This research is part of the BIO-PLASTIC-RISK project, funded by Natural Environment Research Council through the grants NE/V007556/1 and NE/V007246/1.
description: The standard method OECD TG 222 earthworm reproduction test protocol was used; and standard LUFA 2.2 soil (LUFA Speyer, Germany). Earthworms were purchased from a commercial supplier (Blades Biological, Kent, UK). 

Four test replicates, each containing 10 worms were used per treatment (3 teabag types, each at 4 concentrations: none, 0.02% w/w, 0.04% w/w, 0.06% w/w). 

Survival and body weight were recorded on days 0 (start) and day 28 of the experiment. At the end of the experiment (28-days) the number of egg cocoons produced were quantified, and then each container was incubated for a further 28-days to examine fecundity, whereby the number and mass of juveniles were quantified.
DOI: 10.5285/d663aeb9-1e3e-40f7-ab9e-494e7646faeb
title: Spectral data for quaking aspen (Populus tremuloides) clones of different ploidy levels

description: Data comprise measurements of spectral reflectance for quaking aspen (Populus tremuloides Michx.) trees at a range of sites in southwestern Colorado near the town of Crested Butte. Spectra were measured in three different ways: hyperspectral measurements of leaves, hyperspectral measurements of bark, and multispectral measurements of canopies. The first two measurements were made using a handheld spectrometer, while the latter were made via airborne imaging from an unmanned aerial system.

In addition to these reflectance data, the dataset also includes information on the genotype and/or ploidy level of each sample, as determined by either DNA microsatellite analysis or flow cytometry. All samples are georeferenced.

The data include extracted data and raw imagery.

description: The hyperspectral data were filtered and averaged across multiple replicates to reduce sampling error. All spectra were hand-inspected, with samples that did not meet certain criteria (e.g. a near-infrared rise, or a green local maximum) were discarded. 

Multispectral data were calibrated against ground gray references and orthorectified using commercially available algorithms. 

Flow cytometry ploidy level data were validated against Hordeum vulgare standards; DNA microsatellite ploidy level data were validated using published algorithms described in more detail in the supplemental information.
DOI: 10.5285/6c58038e-f035-4ab5-8518-1f189eae3bf2
title: Groundwater temperatures and levels from a field experiment in the Conwy Valley, North Wales, UK (2013-2015)

description: Data showing groundwater temperature and levels from bore holes are presented. The data were collected from a field experiment in the Conwy catchment between December 2013 and June 2015. Data were recorded by pressure transducers installed in the bore holes. The data were collected by trained members of staff from Bangor University and the Centre for Ecology & Hydrology. The samples were taken to estimate the hydraulic pathways and velocities through an experimental hillslope.
The data were collected for the NERC project 'The Multi-Scale Response of Water quality, Biodiversity and Carbon Sequestration to Coupled Macronutrient Cycling from Source to Sea' (NE/J011991/1). The project is also referred to as Turf2Surf.

description: Three 75 metre long transects, 20 metres apart, were identified across a hillslope. Along each transect four boreholes were installed to bedrock. A pressure transducer with an integrated logger which recorded both water level and temperature was installed in each of the boreholes. These were periodically retrieved and logger data read into a laptop. 
Data were entered into an Excel spreadsheet and exported as a .csv file for ingestion into the EIDC.
DOI: 10.5285/e46dc740-2dc7-4f9f-b2b6-24748d86759a
title: Soil metrics, vegetation species and biomass data, and field management information from pasture fed livestock farms across Great Britain, 2019

description: This set of data includes records of vegetation species and characteristics, soil quality metrics and aspects of management relating to a single field on each sampled farm. Data were collected in 2019, from farms across Great Britain belonging to the Pasture Fed Livestock Association (PFLA).
The data were collected by the UK Centre of Ecology & Hydrology, during a project funded by the BBSRC, seeking to evidence the impacts of pasture fed livestock approaches on grassland parameters, in particular, sward composition and associated soil qualities.

description: Data were collected by trained members of UKCEH staff, according to standardised protocols in the summer of 2019. Vegetation and management records were collected on electronic recording devices. Soil samples were analysed at UKAS Accredited labs at UKCEH Lancaster. All data were transferred to secure databases at UKCEH Lancaster once collected.
DOI: 10.5285/6be00174-6544-4156-b1df-8678f6df2034
title: Family lineage and landscape quality data for wild bumblebee colonies across an agricultural landscape in Buckinghamshire, U.K.

description: Family lineage relationships between spring queens, daughter workers and sister queens of three bumblebee species (Bombus terrestris, B. lapidarius and B. pascuorum) collected across the Hillesden Estate, Buckinghamshire, UK, between spring 2011 and spring 2012. A combination of land-use and habitat surveys, molecular genetics and spatial modelling was used to estimate the locations of wild colonies represented by greater than 1 worker and to calculate the proportions of cover represented by different habitat quality and land-use variables within four spatial scales from each colony location. Data were collected as part of a project led by the Centre for Ecology & Hydrology, funded under the Insect Pollinators Initiative.
description: Bumblebee DNA was sampled non-lethally, stored, extracted and genotyped using recognised standard protocols (Dreier et al., 2014). The program COLONY v.2.0 was used to assign workers to full-sib groups and identify mother or sister queens from the same family lineages (with a genotyping error rate of 0-5% based on results of re-genotyping 10% of randomly selected individuals and scoring errors). Data were checked for errors at all stages by staff at the Centre for Ecology & Hydrology and at the Institute of Zoology. Analyses arising from the worker-only and landscape quality data have been peer reviewed and published in Molecular Ecology (Dreier et al., 2014; doi:10.1111/mec.12823) and Ecological Applications (Redhead et al., 2016; doi:10.1890/15-0546).
DOI: 10.5285/864434b7-2102-4edc-802d-ebdbfe9ff766
title: Dune migration measurements on the South Saskatchewan River, Canada, 2017

description: Data were collected in 2017, to provide information on spatial patterns of dune migration rates and associated water flow characteristics, at locations on the South Saskatchewan River, Canada. Dune migration rates were measured using repeat aerial imagery. Bedform crests were digitised in individual images, and average dune migration rates were calculated from the mean migration distance between image pairs, divided by the time between image collection. Water depth and velocity data were collected using a Sontek M9 acoustic Doppler current profiler (aDcp) mounted on a small zodiac boat. The position of the aDcp was recorded using a RTK dGPS system. Data were collected on 12th June 2017 as part of NERC project NE/L00738X/1
description: Data were collected to provide information on spatial patterns of dune migration rates and associated flow characteristics, at locations on the South Saskatchewan River, Canada. Dune migration rates were measured using repeat aerial imagery with flight lines completed on a grid pattern with 80% lateral and longitudinal overlap between images. Orthomosaics were constructed from these images using the SfM program Pix4D (https://pix4d.com/). Multiple flights were flown at 1 hour intervals (maximum of five epochs in a day) to allow tracking of bedforms. Image Ground Sampling Distance (GSD) was typically 0.025–0.03 m. Bedform crests were digitised in individual images, and average dune migration rates were calculated from the mean migration distance between image pairs, divided by the time between image collection. Data were collected on 12th June 2017.

Water depth and velocity data were collected using a Sontek M9 acoustic Doppler current profiler (aDcp) mounted on a small zodiac boat. The position of the aDcp was recorded using a RTK dGPS system.  Velocities are calculated relative to the instrument head and are corrected using the dGPS calculated boat speed and heading. The aDcp data were collected in pulse coherent mode, averaging 7 pings per second, and were averaged to 1 Hz to improve the signal-to-noise ratio. The M9 uses 9 transducers at frequencies between 0.5 and 3.0 MHz. Data were collected along cross-sections of the river that extended between both banks and were aligned approximately perpendicular to the downstream flow direction.
DOI: 10.5285/cbaa464a-ac18-42bf-8518-c746d8d97270
title: Scots pine single nucleotide polymorphisms (SNP) for Axiom array

description: This dataset contains  ~50,000 single nucleotide polymorphisms (SNPs, DNA mutations) for Scots pine (Pinus sylvestris) and closely related members of the Pinus mugo complex, which were selected for inclusion on a 50K SNP Axiom array
description: The array comprised 49,829 SNPs from several sources, as follows. The majority (N = 49,052) were obtained from transcriptome sequencing of four pine species: Pinus sylvestris, P. mugo, P. uncinata and P. uliginosa (Wachowiak et al., 2015). These included SNPs which were common to all species and also SNPs fixed in one species and polymorphic within and among others. The set of SNPs identified by Wachowiak et al. (2015) was filtered by the array manufacturer (Thermo Fisher) based on p-convert values signifying the SNP array quality, and a list of recommended and non-recommended SNP probes (avoiding SNPs with polymorphisms within 35 bp) was provided to the authors. A further set of SNPs (N = 578) were included from candidate genes (N = 279), which had been resequenced in previous population genetic studies of the pine species (Kujala & Savolainen, 2012; Mosca, Eckert, Di Pierro, et al., 2012; Palmé, Wright, & Savolainen, 2008; Wachowiak, Balk, & Savolainen, 2009; Wachowiak, Zaborowska, et al., 2018). Variation in mitochondrial DNA (mtDNA) was targeted using a set of SNPs (N = 14) which had been discovered by Donnelly et al. (2017). A set of SNPs putatively associated with susceptibility to Dothistroma needle blight (discovered in Pinus radiata, ENA accession numbers ERS1034542-53) were also included (N = 185).
DOI: 10.5285/2e9ad843-c5db-402a-8b47-de45bf7bbaf2
title: Pod and seed trait data for Moringa oleifera Lam. from Kenya 2019

description: This dataset comes from Moringa oleifera and M. stenopetala seed pod collections harvested from known provenances in Kenya. The data includes both pod and seed traits as well as canopy and coppicing information for the mother trees.
description: Pods were returned to Kenya Forestry Research Institute in Nairobi and Pods were air dried. The pods and seed were then measured and scored for traits in the laboratory. Provenance localities were measured using a hand held GPS.
DOI: 10.5285/f7ef2dc5-2bce-4436-8f65-90f7a99acff2
title: National Plant Monitoring Scheme survey data (2015-2022)

description: This data resource provides plot-level plant occurrence data for the first eight years (2015-2022) of the National Plant Monitoring Scheme (covering the UK, the Channel Islands, and the Isle of Man). Data consist of individual observations of plants, and other habitat characteristics, at the metre-scale; observations are accompanied by percentage cover information recorded according to the Domin frequency-abundance scale commonly used in plant community ecology. Other information provided includes the plot type (size, shape, according to the NPMS classification), the volunteer-recorded NPMS habitat, the date of sampling, and information regarding the spatial location of the plot. Information contained within the metadata file should allow users to reconstruct the sampling history (including gaps) of any plot that has been sampled within the NPMS scheme between 2015 and 2022.

This work was supported by the Natural Environment Research Council award number NE/R016429/1 as part of the UK-SCAPE programme delivering National Capability.

Please be aware that this dataset is updated annually and that more recent versions exist.


description: Data are collected directly from volunteers into a custom Indicia database system through the National Plant Monitoring Scheme website or app. The Indicia system is built on a PostgreSQL/PostGIS database, and the data presented here were extracted directly from this master database using appropriate SQL queries. See the associated documentation for more information on the broader Quality Assurance processes supporting the NPMS.