en: amphibians landscape wetlands occupancy-models connectivity conservation

en: Readme

en: Description of methods and datasets. Version 1.

en: Covariate data 1

en: This file contains covariate data that does not change over time for 856 ponds: the region the pond is in, whether the pond is old or new (constructed since 1991), elevation, water surface area, fluctuations of the water table (yes, no), the percent forest cover in 100m radius around the pond, the area or large (>6m wide) roads in 1km radius around the pond.

en: Model code 2

en: This R markdown file contains all code and descriptions necessary to load and format the provided data and to fit the dynamic occupancy models described in the second associated publication, including JAGS code for the fitted models.

en: Original raw data

en: This file contains the original raw monitoring data as provided by the canton of Aargau. Access is restricted and only considered upon request and in consultation with the canton of Aargau.

en: Potential population connectivity data

en: This file contains potential population connectivity data (three different metrics), calculated based on all existing and occupied ponds in each year, for each species, in long format. See Readme v2.0 for details. Required to run Model code 2.

en: Model code, description

media_type: text/html

en: This is the output of the R markdown file that provides JAGS model code and describes how to format the provided data and fit the dynamic occupancy models described in the associated publication, for a quick overview.

format: HTML

en: Observation data

en: This file contains detection/non-detection data for the 12 amphibian species between 1999 and 2019 for 3 annual visits. Detectable denotes whether or not a visit j was made to pond i in year t. ObservedID gives a unique ID for the observer collecting the data during visit j to pond i in year t.

en: Model code

en: This R markdown file contains all code and descriptions necessary to load and format the provided data and to fit the dynamic occupancy models described in the associated publication, including JAGS code for the fitted models.

en: Model code 2, description

en: This is the output of the R markdown file Model code 2 that provides JAGS model code and describes how to format the provided data and fit the dynamic occupancy models described in the second associated publication, for a quick overview.

en: Structural connectivity data

en: This file contains structural connectivity data (three different metrics), calculated based on all existing ponds in each year, in long format. See Readme v2.0 for details. Required to run Model code 2.

en: Readme, v 2.0

en: Description of methods and datasets. Version 2.0, including new datasets fro structural and potential population connectivity.

en: Covariate data 2

en: This file contains covariate data that changes over time for 856 ponds in 21 years (long format): whether or not a pond exists in year _t_, the age of constructed ponds in year _t_, structural connectivity of the pond in year _t_.

en:
In the canton of Aargau, hundreds of new ponds have been constructed since the 1990s to benefit declining amphibian populations. This dataset consists of monitoring data for all 12 pond-breeding amphibian species in the canton of Aargau from 1999 to 2019 in 856 ponds, and environmental variables that describe the ponds and the landscape surrounding the ponds. Species observation data is detection/non-detection data from repeat visits during survey years, during which all potentially suitable ponds in an area were surveyed. Environmental variables describing the ponds are whether the pond has been newly constructed since 1991 or not, pond age (if constructed), elevation a.s.l., the water surface area, and whether the water table fluctuates or not. Environmental variables describing the surroundings of the ponds are the percent area of forest within a circular buffer of radius 100m around the pond, the area of large (width ≥6m) roads within a circular buffer of radius 1km around the pond, as well as structural and potential population connectivity, quantified by three different metrics each.
The canton of Aargau is the owner of the monitoring data; the original datafile is only disclosed upon request and in consultation with the canton of Aargau.
The edited dataset contains cleaned observation data for the 12 amphibian species, as well as compiled and edited covariate data and code to fit dynamic occupancy models.

amphibians

display_name: amphibians

connectivity

display_name: connectivity

conservation

display_name: conservation

landscape

display_name: landscape

occupancy-models

display_name: occupancy-models

wetlands

display_name: wetlands

en: Amphibian observation and pond data (Aargau, Switzerland)


maintainer: EnviDat Support

en: habitat-heterogeneity conservation colonisation dead-wood sloss biodiversity habitat-availability saproxylic-beetles forest-management

state: active

type: dataset

en: Community matrix (all beetles)

en: Abundances of all beetle species for each branch bundle

format: XLS

en: Community matrix (saproxylic beetles)

en: Abundances of saproxylic beetle species for each branch bundle

en: Variable description

en: Detailed description of the forest and environmental variables

en: Forest and environmental variables

en: Data on the branch bundle, forest and environmental variables

en:
The data was generated during a landscape experiment performed on 69 plots in Sihlwald forest between 2016 and 2019. Branch bundles of different sizes consisting of beech branches were exposed in the forest for one year to be colonized by saproxylic beetles and later reared for one year in emergence traps. All beetles emerging from the branches were collected. Overall 244 branch bundles are included and we found 66 beetles species (23511 individuals) of which 43 were classified as saproxylic (20873 individuals).
 Species data (2 tables)
Two community matrices (including abundance): one for saproxylic beetles and one for all beetles. Beetles were classfied as saproxylic following an extended list of the list reported in Schmidl & Bussler (2004).
 Model data (1 table)
*Response variables*
Species richness and abundance of (saproxylic) beetles.
*Branch bundles*
Branch bundles consisted of 1, 3, 6 or 12 branches and each bundle size was installed at each of the 69 plots. The bundles consisted of standardized freshly cut beech branches (Fagus sylvatica) with a length of 80 cm and a diameter between 3 and 6 cm. Total surface and volume of each bundle is reported.
*Tree on which the bundle was installed*
Information on the tree to which the bundles were attached (tree species, dbh, distance and azimut from the plot center).
*Temperature and light availability*
Temperature (plot level) and light availability (bundle level) were calculated.
*Deadwood availability in the landscape*
Based on a map of lying dead wood, dead wood amount and isolation were calculated for concentric circles with a radius ranging from 20 to 200 m (in 10 m steps) around each branch bundle.
 Variable descriptions (1 table)

biodiversity

display_name: biodiversity

colonisation

display_name: colonisation

dead-wood

display_name: dead-wood

forest-management

display_name: forest-management

habitat-availability

display_name: habitat-availability

habitat-heterogeneity

display_name: habitat-heterogeneity

saproxylic-beetles

display_name: saproxylic-beetles

sloss

display_name: sloss

educ

fr: Éducation, culture et sport

de: Bildung, Kultur und Sport

en: Education, culture and sport

it: Istruzione, cultura e sport

envidat

fr: EnviDat: le portail de données environnementales

de: EnviDat: das Umwelt-Datenportal

en: EnviDat: the Environmental Data Portal

it: EnviDat: il portale dei dati ambientali

fr: EnviDat est le portail de données du WSL; il offre un accès uniformisé et réglementé aux données de surveillance et de recherche en matière d’environnement. Ce portail est capable d’héberger et de publier des ensembles de données précieuses et uniques, qui sont partagées aux quatre coins de la planète. Ce faisant, EnviDat favorise la recherche et contribue à l’avancement des sciences environnementales.

en: EnviDat is the WSL data portal providing unified and managed access to environmental monitoring and research data. The portal has the capability to host and publish data sets. Through the sharing of unique and high-value data sets worldwide, EnviDat fosters research and contributes to advancing environmental science.

de: EnviDat ist das Datenportal der WSL für einen einheitlichen und verwalteten Zugang zu Umweltdaten aus Monitoring- und Forschungsprojekten. Auf dem Portal können Datensätze gehostet und veröffentlicht werden. Durch die weltweite Bereitstellung einzigartiger und wertvoller Datensätze leistet EnviDat einen Beitrag zur Forschung im Bereich der Umweltwissenschaften.

it: EnviDat è il portale dati del WSL che fornisce un accesso unificato e gestito ai dati di monitoraggio ambientale e di ricerca. Il portale ha la capacità di ospitare e pubblicare serie di dati preziosi e unici che vengono condivisi in tutto il mondo. Così facendo, EnviDat promuove la ricerca e contribuisce al progresso della scienza ambientale.

political_level: other

wsl

capacity: public

type: organization

approval_status: approved

key: guid

key: uri

value: Envidat Harvester

en: Beetle communities reared from beech branches and associated forest and environmental variables


en: bacteria restoration plants fungi soil-chemistry soil-biodiversity soil-biology biodiversity topsoil-removal soil nematodes grassland

en: Fungi data

en:
Sample.data
Plot.ID	consecutive numbers for plots (in total 36 plots)
Treatment	One restoration treatment and two reference treatments. Topsoil+Propagules= Topsoil removal (upper 10-30 cm) combined with introduction of target plant species; Initial=intensively managed grasslands; Target= species-rich semi-wet to semi-dry grasslands
treat.yr	Treatment abbreviation. For restored grasslands: Treatment abbreviation + time since restoration; Initial + Target = NA
yr.trt	year when topsoil was removed; Initial + Target = NA
Age	time since restoration (sampling year 2018 - yr.trt); Initial + Target = NA
Age.class	restored sites of similar age grouped into four age classes. Y.4 = Year 3+4 (recently restored); Y.18 = Year 17+19 (mid-term); Y.24 = Year 23+25 (long-term); Y.30 = Year 27+32 (long-term); Initial + Target = NA
Cluster	clustered spatial arrangment of sites in the field (see Supporting Information Fig. S1)
Site	clustered spatial arrangment (replicates) of plots per site (see Supporting Information Fig. S1)

Taxonomy
OTU.ID	consecutive numbers for operational taxonomic units (OTUe 1-7794)
Taxonomic rank	Domain, Phylum, Class, Order, Family, Genus, Species

Abundance
columns	Plot.ID (see Sample.data)
rows	OTU.ID (see Taxonomy)

en: Ecosystem coupling_interactions

en:
Treatment	Treatment groups; Y.4-18 = restored grasslands; Initial = intensively managed grasslands; Target = species-rich semi-wet to semi-dry grasslands
Type	Interactions type; A.A = abiotic.abiotic; A.B = abiotic.biotic; B.B = biotic.biotic
Correlation	non-parametric Spearman rank correlations between biotic and abiotic parameters (ecological interactions)

en: Networks

en:
Treatment	Treatment groups; Y.4-18 = restored grasslands; Initial = intensively managed grasslands; Target = species-rich semi-wet to semi-dry grasslands
Correlation	non-parametric Spearman rank correlations
Vertex.1+2	Comparison between network components; N.pool = total soil nitrogen pool [kg ha-1 12 cm-1]; Corg.pool = soil organic carbon pool [kg ha-1 12 cm-1], pH = soil pH [CaCl2]; BD = bulk density [g cm-3]; FC = field capacity [%]
	PCoA 1 + 2 biotic communities [Veg = vegetation; Nem = nematoda; Fun = fungi; Prok = prokaryota]
Type	Interactions type; A.A = abiotic.abiotic; A.B = abiotic.biotic; B.B = biotic.biotic

en: Nematode data

en:
Sample.data
Plot.ID	consecutive numbers for plots (in total 36 plots)
Treatment	One restoration treatment and two reference treatments. Topsoil+Propagules= Topsoil removal (upper 10-30 cm) combined with introduction of target plant species; Initial=intensively managed grasslands; Target= species-rich semi-wet to semi-dry grasslands
treat.yr	Treatment abbreviation. For restored grasslands: Treatment abbreviation + time since restoration; Initial + Target = NA
yr.trt	year when topsoil was removed; Initial + Target = NA
Age	time since restoration (sampling year 2018 - yr.trt); Initial + Target = NA
Age.class	restored sites of similar age grouped into four age classes. Y.4 = Year 3+4 (recently restored); Y.18 = Year 17+19 (mid-term); Y.24 = Year 23+25 (long-term); Y.30 = Year 27+32 (long-term); Initial + Target = NA
Cluster	clustered spatial arrangment of sites in the field (see Supporting Information Fig. S1)
Site	clustered spatial arrangment (replicates) of plots per site (see Supporting Information Fig. S1)

Taxonomy
ASV.ID	unit number.letter code per amplicon sequence variant (in total 904)
Taxonomic rank	Phylum, Class, Order, Family, Genus, Species

Abundance
columns	Plot.ID (see Sample.data)
rows	ASV.ID (see Taxonomy)

en: Soil properties

en:
Plot.ID	consecutive numbers for plots (in total 36 plots)
Treatment	One restoration treatment and two reference treatments. Topsoil+Propagules= Topsoil removal (upper 10-30 cm) combined with introduction of target plant species; Initial=intensively managed grasslands; Target= species-rich semi-wet to semi-dry grasslands
treat.yr	Treatment abbreviation. For restored grasslands: Treatment abbreviation + time since restoration; Initial + Target = NA
yr.trt	year when topsoil was removed; Initial + Target = NA
Age	time since restoration (sampling year 2018 - yr.trt); Initial + Target = NA
Age.class	restored sites of similar age grouped into four age classes. Y.4 = Year 3+4 (recently restored); Y.18 = Year 17+19 (mid-term); Y.24 = Year 23+25 (long-term); Y.30 = Year 27+32 (long-term); Initial + Target = NA
Cluster	clustered spatial arrangment of sites in the field (see Supporting Information Fig. S1)
Site	clustered spatial arrangment (replicates) of plots per site (see Supporting Information Fig. S1)
N.pool	Soil nitrogen pool (June 2017); corrected for bulk density and 12 cm sampling depth [kg ha-1 12cm-1]
Corg.pool	Soil organic carbon pool (June 2017); corrected for bulk density and 12 cm sampling depth [kg ha-1 12cm-1]
pH	soil pH [CaCl2]
BD	Bulk density [g cm-3]
FC	Field capacity [%]
Veg.1	principle coordinate axis 1 (vegetation)
Veg.1	principle coordinate axis 2 (vegetation)
Nem.1	principle coordinate axis 1 (nematoda)
Nem.2	principle coordinate axis 2 (nematoda)
Fun.1	principle coordinate axis 1 (fungi)
Fun.2	principle coordinate axis 2 (fungi)
Prok.1	principle coordinate axis 1 (prokaryota)
Prok.2	principle coordinate axis 2 (prokaryota)
Veg.H	Shannon diversity (vegetation)
Nem.H	Shannon diversity (nematoda)
Fun.H	Shannon diversity (fungi)
Prok.H	Shannon diversity (prokaryota)

en: Vegetation data

en:
Plot.ID	consecutive numbers for plots (in total 36 plots)
Treatment	One restoration treatment and two reference treatments. Topsoil+Propagules= Topsoil removal (upper 10-30 cm) combined with introduction of target plant species; Initial=intensively managed grasslands; Target= species-rich semi-wet to semi-dry grasslands
treat.yr	Treatment abbreviation. For restored grasslands: Treatment abbreviation + time since restoration; Initial + Target = NA
yr.trt	year when topsoil was removed; Initial + Target = NA
Age	time since restoration (sampling year 2018 - yr.trt); Initial + Target = NA
Age.class	restored sites of similar age grouped into four age classes. Y.4 = Year 3+4 (recently restored); Y.18 = Year 17+19 (mid-term); Y.24 = Year 23+25 (long-term); Y.30 = Year 27+32 (long-term); Initial + Target = NA
Cluster	clustered spatial arrangment of sites in the field (see Supporting Information Fig. S1)
Site	clustered spatial arrangment (replicates) of plots per site (see Supporting Information Fig. S1)
column I-LW	Plant abundance per species (in total 327 plant species) expressed as cover percentage estimation according to van der Maarel (vdM 1979; 7 classes: 1-7); nomenclature according to Lauber & Wagner (1996)

en: Distance to target results

en:
Community	biotic community (vegetation, nematoda, fungi, prokaryota)
Treatment	Treatment groups; Y.4-30= restored grasslands (time since restoration); Initial=intensively managed grasslands (I)
Comparison	within- or between-community Bray-Curtis dissimilarity distance comparison
Label	within-community distances of initial/restored grasslands: treatment abbreviation; between-communities distances of initial/restored-to-target grasslands: treatment abbreviation plus Target (T; species-rich grasslands)
mean	Mean distance to Target (6 plots per treatment group)
sd	Standard deviation of distances to Target (6 plots per treatment group)

en:
This dataset contains all data, on which the following publication below is based.

Paper Citation:

_Resch, M.C., Schütz, M., Ochoa-Hueso, R., Buchmann, N., Frey, B., Graf, U., van der Putten, W.H., Zimmermann, S., Risch, A.C. (in review). Long-term recovery of above- and belowground interactions in restored grassland after topsoil removal and seed addition. Journal of Applied Ecology_

Please cite this paper together with the citation for the datafile.

Study area and experimental design
The study was conducted in and around two nature reserves, Eigental and Altläufe der Glatt, which were located approximately 5 km apart (47°27´ to 47°29´ N, 8°37´ to 8°32´ E, 417 to 572 m a.s.l., Canton of Zurich, Switzerland; Figure S1 and S2, Table S1). Mean annual temperature and precipitation are 9.8 ± 0.6 °C and 990 ± 168 mm (Kloten climate station 1988-2018; MeteoSchweiz, 2019). TFor this study, we used a space-for-time approach based on eight restoration sites that were between 3 and 32 years old. We measured recovery and restoration success by comparing the restored grasslands with intensively managed and semi-natural grasslands. Using a space-for-time approach requires high similarities in historical properties of the site, such as soil conditions and management regimes, to assure that temporal processes are appropriately represented by spatial patterns (Walker et al., 2010). This was the case in our study. The restored sites had similar soil conditions (i.e., soil type, structure, water availability) as the targeted semi-natural grasslands, while they shared the same agricultural legacy with intensively managed grasslands, i.e., biomass harvest and fertilization (manure and/or slurry) three to five times a year as well as tillage. We randomly established three 5 m x 5 m (25-m2) plots for plant identification and three 2 m x 2 m (4-m2) subplots for soil biotic and abiotic data collection at least 2 m away from the 25-m2 plots in each restoration site. Sites of similar age were grouped into four age classes: Y.4 (3 & 4 years after restoration), Y.18 (17 & 19 years), Y.24 (23 & 25 years), and Y.30 (27 & 32 years). Six intensively managed (Initial) and six semi-natural grassland (Target) sites complemented the experimental set-up, for a total of 36 plots. All plots were sampled under similar conditions, i.e., day of the year, air temperature, soil moisture, and time since last rain event, in June/July 2017 (intensively managed and semi-natural plots) and 2018 (restored plots).

Collection of plants and selected soil biota data
Plant species cover (in %) was visually estimated in each 25-m2 plot in mid-June (Braun-Blanquet, 1964; nomenclature: Lauber & Wagner, 1996). We calculated Shannon diversity and assessed plant community structure. We included soil microbial (fungi, procaryotes) and nematodes in our study as they represent the majority of soil biotic diversity and abundance (Bardgett & van der Putten, 2014), cover various trophic levels of the soil food web (Bongers & Ferris, 1999), and play key roles in soil functioning and ecosystem processes (Bardgett & van der Putten, 2014). In particular, soil nematodes were found to be well suited belowground indicators to evaluate recovery/development after restoration (e.g. Frouz, et al. 2008; Kardol et al., 2009; Resch et al., 2019). We randomly collected ten soil cores (2.2 cm diameter x 12 cm depths; sampler from Giddings Machine Company, Windsor, USA) in the 4-m2 subplots to assess soil nematode and microbial (fungal, prokaryotic) diversities and community structures. For soil nematodes, eight of the soil cores were combined and gently homogenized, placed in coolers and stored at 4 °C and transported to the laboratory (Netherlands Institute of Ecology, NIOO, Wageningen, Netherlands) within three days after collection. Free-living nematodes were extracted from 200 g of fresh soil using Oostenbrink elutriators (Oostenbrink, 1960). After extraction, each sample was divided into three subsamples, two for molecular identification and one to determine nematode abundance (see Resch et al., 2019). For the molecular work, two subsamples were stored in 70% ethanol (final volume 10 mL each) and transported to the laboratory at the Swiss Federal Research Institute WSL (Birmensdorf, Switzerland). Each subsample was reduced to roughly 200 μL by centrifugation and removal of the supernatant. The remaining ethanol was vaporized (65 °C for 3 h). Thereafter, 180 μL ATL buffer solution (Qiagen, Hilden, Germany) was immediately added and samples were stored at 4 °C until further processing. From these samples, nematode metagenomic DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany) according to the manufacturer`s protocol, except for the incubation step which was run at 56 °C for 4 h. PCR amplification of the V6-V8 region of the eukaryotic small-subunit (18S) was performed with 7.5 μL of genomic DNA template (ca. 1 ng/μL) in 25 μL reactions containing 5 μL PCR reaction buffer, 2.5 mM MgCL2, 0.2 mM dNTPs, 0.8 μM of each primer (NemF: Sapkota & Nicolaisen, 2015; 18Sr2b: Porazinska et al., 2009), 0.5 μL BSA, and 0.25 μL GoTaq G2 Hot Start Polymerase (Promega Corporation, Madison, USA). Amplification was using an initial DNA denaturation step of 95 °C for 2 min, followed by 35 cycles at 94 °C for 40 sec, 58 °C for 40 sec, 72 °C for 1 min, and a final elongation step at 72 °C for 10 min. Filtering, dereplication, sample inference, chimera identification, and merging of paired-end reads was implemented using the DADA2 pipeline (v.1.12; Callahan et al., 2016) to finally assign amplicon sequence variants (ASVs) as taxonomic units.
We combined and homogenized the remaining two soil cores to assess soil microbes, placed them in coolers (4 °C) and transported them to the laboratory at WSL. Metagenomic DNA was extracted from 8 g sieved soil (2 mm) using the DNAeasy PowerMax Soil Kit (Qiagen, Hilden, Germany) according to the manufacturer´s protocol. PCR amplification of the V3-V4 region of the small-subunit (16S) of prokaryotes (i.e., bacteria and archaea) and the ribosomal internal transcribed spacer region (ITS2) of fungi was performed with 1 ng of template DNA using PCR primers and conditions as previously described (Frey et al., 2016). PCRs were run in triplicates, pooled and sent to the Genome Quebec Innovation Centre (Montreal, QC, Canada) for barcoding using the Fluidigm Access Array technology (Fluidigm) and paired-end sequencing on the Illumina MiSeq v3 platform (Illumina Inc., San Diego, USA). Quality filtering, clustering into operational taxonomic units (OTUs, 97% similarity cutoffs) and taxonomic assignment were performed as previously described (Resch et al., 2021).Taxonomic classification of nematode, prokaryotic and fungal sequences was conducted querying against the most recent versions of PR2 (v.4.11.1; Guillou et al., 2013), SILVA (v.132; Quast et al., 2013), and UNITE (v.8; Nilsson et al., 2019) reference sequence databases. Taxonomic assignment cutoffs were set to confidence rankings ≥ 0.8 (below ranked as unclassified). Prokaryotic OTUs assigned to mitochondria or chloroplasts as well as OTUs or ASVs assigned to other than Fungi or Nematoda were manually removed prior to data analysis. The three datasets were filtered to discard singletons and doubletons. Taxonomic abundance matrices were rarefied to the lowest number of sequences per community to achieve parity of the total number of reads between samples (Prokaryotes: 10,929 reads; Fungi: 18,337 reads; Nematodes: 6,662 reads). We calculated Shannon diversity and assessed community structures for soil nematodes, prokaryotes and fungi based on their relative abundances of ASV or OTU at the taxon level.

Collection of soil physical and chemical properties
We randomly collected one undisturbed soil core (5 cm diameter, 12 cm depth) per 4-m2 subplot using a steel cylinder that fit into the soil corer. The cylinders were capped to avoid disturbance during transport and used to measure field capacity, rock content and fine earth density as previously described (Resch et al., 2021). We randomly collected another three soil cores (5 cm diameter, 12 cm depths) in each 4-m2 subplot to determine soil chemical properties. The cores were pooled, dried at 60 °C for 48 h and passed through a 2 mm sieve. We measured soil pH (CaCl2) on dried samples, total nitrogen (N) and organic carbon (C) concentration on dried and fine-ground samples (≤ 0.5 mm; for details see Resch et al., 2021). We calculated total N and organic C pools after correcting its concentration for soil depth, rock content and fine earth density.

bacteria

display_name: bacteria

fungi

display_name: fungi

grassland

display_name: grassland

nematodes

display_name: nematodes

plants

display_name: plants

restoration

display_name: restoration

soil

display_name: soil

soil-biodiversity

display_name: soil-biodiversity

soil-biology

display_name: soil-biology

soil-chemistry

display_name: soil-chemistry

topsoil-removal

display_name: topsoil-removal

en: Long-term recovery of above-and belowground interactions in restored grasslands


maintainer: Axel Volkwein

en: mass-movements trajectory field-tests experiments natural-hazards experiment rockfall field-data field-test

en: Overview of all tests

media_type: application/zip

en:
This table gives an overview on all tests performed including
- block used
- start & end position
- number of jumps
- etc.
-

format: ZIP

en: These data contain the point clouds obtained from laser scanning the test slope and the six test blocks used for the experiments. The coordinates of the slope are given in CH-1903 format. The coordinates of the block point clouds are kept in a lokal x/y/z coordinate system.

mimetype: application/zip

en: Block trajectories recorded from local positioning system

en: This file contains more than 80 rockfall trajectories projected onto the terrain, i.e. the positions of the single blocks over time during the single tests that were recorded by the local positioning system with about 10Hz. It contains the detected positions as well as a smoothened path (see Volkwein et al., Geosciences, 2018). The table also contains the derived velocities and accelerations along the slope (attention: these accelerations are the once that occur during an impact).

format: SERVICE

en: Jumps and impacts

en: This table contains data of more than 2200 of each jumps and impacts of the test blocks on a grassy slope. It gives there durations in combination with acting accerlartions and the rotational speed of the blocks. The data were retrieved using the block internal accelerometer and rotation sensors. The combination of these data with the measurement from the local positioning system allows the deduction of jump lengths, slope gradient etc.

en:
In summer 2014, 6 rock blocks between 20 and 80kg have been thrown in total 111 times down a slope at the Swiss Oberalppass close to the village Tschamut. The slope was mainly covered by grass and its lower part was flat and large enough to provide natural runouts of the single trajectories.

An extensive measurement program has been set up to measure the block trajectories: With surveyor's instruments the slope and the six used rock blocks were scanned and the start and end positions of each test were recorded. During the single events two cameras filmed the trajectories. A special sensor device located within the blocks recorded the acting accelerations and rotational speeds over time. Further, the device emitted a Wifi signal that got detected from eight receivers around the slope. Based on this signal the block position has been recorded over time.

The dataset contains all data that were gathered through above field campaign.

experiment

display_name: experiment

experiments

display_name: experiments

field-data

display_name: field-data

field-test

display_name: field-test

field-tests

display_name: field-tests

mass-movements

display_name: mass-movements

natural-hazards

display_name: natural-hazards

rockfall

display_name: rockfall

trajectory

display_name: trajectory

educ

en: Education, culture and sport

envidat

en: EnviDat: the Environmental Data Portal

en: EnviDat is the WSL data portal providing unified and managed access to environmental monitoring and research data. The portal has the capability to host and publish data sets. Through the sharing of unique and high-value data sets worldwide, EnviDat fosters research and contributes to advancing environmental science.

en: Repetitive trajectory testing in Tschamut 2014


maintainer: Camille Albouy

en: atlantic-region teleo edna fish-composition dna-metabarcoding bay-biscay chondrichthyes actinopterygii

en: Data access

en:
Environmental DNA complements scientific trawling in surveys of marine fish biodiversity (Dataset 2020)

In October 2020 we chose 16 sites from the 2020 EVHOE survey for eDNA sampling. The French international EVHOE bottom trawl survey is carried out annually during autumn in the BoB to monitor demersal fish resources. All sites were located on the continental shelf (26–170 m depth), except one on the upper slope with a depth of 1045 m. To perform eDNA sampling, we collected water samples at 15 sites (Figure 1a). At each site, we sampled seawater using Niskin bottles deployed with a circular rosette. There were nine bottles on the rosette, each of them able to hold ∼5 l of water. At each site, we first cleaned the circular rosette and bottles with freshwater, then lowered the rosette (with bottles open) to 5 m above the sea bottom, and finally closed the bottles remotely from the boat. The 45 l of sampled water was transferred to four disposable and sterilized plastic bags of 11.25 l each to perform the filtration on-board in a laboratory dedicated to the processing of eDNA samples. To speed up the filtration process, we used two identical filtration devices, each composed of an Athena® peristaltic pump (Proactive Environmental Products LLC, Bradenton, Florida, USA; nominal flow of 1.0 l min–1 ), a VigiDNA 0.20 μm filtration capsule (SPYGEN, le Bourget du Lac, France), and disposable sterile tubing. Each filtration device filtered the water contained in two plastic bags (22.5 l), which represent two replicates per sampling site. We followed a rigorous protocol to avoid contamination during fieldwork, using disposable gloves and single-use filtration equipment and plastic bags to process each water sample. At the end of each filtration, we emptied the water inside the capsule that we replaced by 80 ml of CL1 conservation buffer and stored the samples at room temperature following the specifications of the manufacturer (SPYGEN, Le Bourget du Lac, France). We processed the eDNA capsules at SPYGEN, following the protocol proposed by Polanco-Fernández et al., (2020). We performed library preparation and sequencing at Fasteris (Geneva, Switzerland). Specifically, we prepared four libraries using the MetaFast protocol (a ligation-based method) and sequenced them separately. We carried out paired-end sequencing using a MiSeq sequencer (2 × 125 bp, Illumina, San Diego, CA, USA) on two MiSeq Flow Cell Kits (v3; Illumina), following the manufacturer’s instructions. We analysed the sequence reads using the OBITools package (http:
//metabarcoding.org/obitools; Boyer et al., 2016), following the protocol described by Valentini et al. (2016).

Data content:
	* rawdata/: contains the raw reads for each individual sample. One archive contains the paired-end reads specified by the _R1 or _R2 suffix as well as individually tagged PCR replicates (if available) together with an archive containing all extraction and PCR blank samples of the library. Reads have been demultiplexed using cutadapt but not trimmed, individual demultiplexing tags and primers remain present in the sequences.
	* taxadata/: contains the table with all detected taxonomy for each sample after bioinformatic processing (see Polanco et al. 2020 for details; https://doi.org/10.1002/edn3.140) and associated field metadata.
	* metadata/: contains two metadata files, one related to the data collected in the field for each filter, and the second related to the sequencing process in the lab (including the tag sequence, library name, and marker information for each sample)

actinopterygii

display_name: actinopterygii

atlantic-region

display_name: atlantic-region

bay-biscay

display_name: bay-biscay

chondrichthyes

display_name: chondrichthyes

dna-metabarcoding

display_name: dna-metabarcoding

edna

display_name: edna

fish-composition

display_name: fish-composition

teleo

display_name: teleo

en: Environmental DNA Marine France Evhoe 2020


mosaic-snow-on-sea-ice-data

title_for_slug: mosaic-snow-on-sea-ice-data

en: spatial-variability drifting-and-blowing-snow surface-mass-balance snow-distribution arctic-sea-ice

en: SNOWPACK setup for MOSAiC

en:
 The zip file contains both input and output data as well as the model configuration as used in the submitted manuscript "Towards a fully physical representation of snow on Arctic sea ice using a 3D snow-atmosphere model".

The zip file contains 2 main folders:
* SNOWPACK_JGR_ALPHA1
* SNOWPACK_JGR_ALPHA3

In the SNOWPACK_JGR_ALPHA1 (reference "SP_R" simulation) and SNOWPACK_JGR_ALPHA3 (comparison "SP_C" scenario) folders you find the corresponding inputs, outputs and configuration as used in the paper, as well as the settings used - which only differ by the changed "SCHMIDT_DRIFT_FUDGE" value that is found in each SNOWPACK_JGR_ALPHA/setup/io.ini file. The input data is already linked accordingly in each io.ini file.

To reproduce the results, download and compile the source code for the adjusted SNOWPACK model first, which can be obtained from https://gitlabext.wsl.ch/snow-models/snowpack.git under the "snowpack_mosaic" branch. After installing, you can run the provided model setup uploaded here.

en: ALPINE3D setup for MOSAiC

en:
The zip file contains a folder structure that must be kept as it is in order to run the simulation in the current configuration.
The setup contains both input and output data as well as the model configuration as used in the submitted manuscript
"Towards a fully physical representation of snow on Arctic sea ice using a 3D snow-atmosphere model".

The zip file contains 3 main folders:
* base_setup_files
* a3d_jgr_alpha1
* a3d_jgr_alpha3

The "base_setup_files" contains all input files that are necessary to run the reference (R) simulation ("a3d_jgr_alpha1" folder) and the comparison "C" scenario ("a3d_jgr_alpha3") folder. In the a3d_jgr_alpha1 and a3d_jgr_alpha3 folders you find the corresponding outputs as used in the paper, as well as the settings used - which only differ by the changed "SCHMIDT_DRIFT_FUDGE" value that is found in each a3d_jgr_alphax/setup/io.ini file. The input data is already linked accordingly in each io.ini file.

a3d_jgr_alpha1 also contains the detailed snow profiles for each point along the transects.

To reproduce the results, download and compile the source code for the adjusted ALPINE3D model first, which can be obtained from https://gitlabext.wsl.ch/snow-models/alpine3d.git under the "alpine3d_mosaic" branch. After installing, you can run the provided model setup uploaded here.

en:
Data accompanying David Wagners' Dissertation.
Covers model results and various input from ALPINE3D and SNOWPACK adjusted for sea ice during MOSAiC.

arctic-sea-ice

display_name: arctic-sea-ice

drifting-and-blowing-snow

display_name: drifting-and-blowing-snow

snow-distribution

display_name: snow-distribution

spatial-variability

display_name: spatial-variability

surface-mass-balance

display_name: surface-mass-balance

en: MOSAIC Snow on Sea Ice Data


en: rainfall-simulation topsoil-interflow preferential-flow runoff-plot overland-flow velocity studibach celerity tracers alptal

en:
Description:
This dataset comprises the time series of overland flow (OF) and topsoil interflow (TIF) discharge, and tracer concentrations during artificial rainfall simulation experiments at two large (>80 m2) trenched runoff plots in the Studibach catchment in the Alptal, a typical pre-Alpine headwater catchment in Switzerland.
One plot is located in a natural clearing in an open mixed forest and the other in a grassland. Together, they represent the dominant land cover types in the region.
We applied streamwater to the surface of the plots using sprinklers and added tracers after OF and TIF had reached steady state. Deuterium enriched water was applied to the surface of the plots via the sprinklers, while Uranine and NaCl were applied as a line tracer at multiple distances from the trench. NaBr was injected into the topsoil at ~20 cm depth. Samples of overland flow and topsoil interflow were collected for several hours after tracer application, while the sprinklers continued to apply water to the surface. The runoff was collected into self-made "Upwelling Bernoulli Tubes" and the water level inside these tubes was measured using pressure sensors (DCX-22-CTD, Keller Druck, Switzerland) at a 1-min resolution during the day and 5-min resolution during the night. Uranine concentrations and electrical conductivity (EC) were recorded at a 1-minute interval. Samples for deuterium and Bromide were analysed in the lab.
The celerity of overland flow and topsoil interflow was determined during another experiment by temporarily adding more water to the surface of the plots at different distances from the trench after steady state conditions had been reached. The overland flow and topsoil interflow discharge were again measured using the Upwelling Bernoulli Tubes and pressure transducers.

alptal

display_name: alptal

celerity

display_name: celerity

overland-flow

display_name: overland-flow

preferential-flow

display_name: preferential-flow

rainfall-simulation

display_name: rainfall-simulation

runoff-plot

display_name: runoff-plot

studibach

display_name: studibach

topsoil-interflow

display_name: topsoil-interflow

tracers

display_name: tracers

velocity

display_name: velocity

en: Flow and tracer data for overland flow and topsoil interflow during rainfall simulation experiments in the Studibach catchment - Alptal - Switzerland


maintainer: Virginie Marques

en: edna fish-composition teleo mediterraneaen marine marseille

en: Please use cyberduck to download for the moment

en:
Description: Fish environmental DNA data set collected in 2022 in the Calanques National Park
The eDNA samples were collected in 2022 in two locations (Moyades, M−FPA and “Impérial du large”, I-LPA), during the winter (January- February), the summer (June to August)and fall (mid-September to November) seasons, with the sampling dates depending on the weather conditions. For the M−FPA, samples were collected between Moyades island and Riou island, while for the I-LPA, they were collected on the south side of the “Impérial du large” island. To account for the existing bathymetry, in the M−FPA the samples were taken at two sampling sites with depths of 20 and 40 m, while in the I-LPA they were taken at two sites with depths of 20 and 80 m.
At each site, in-situ filtration of seawater was performed using a double-head submersible pump (Subspace, Geneva, Switzerland; nominal flow of ca. 1 L/min) strapped to an underwater scooter with 2 VigiDNA 0.20 µm filtration capsules (SPYGEN, le Bourget du Lac, France), along with disposable sterile tubing. The samples were collected along two horizontal transects (up to 400 m in length) during each closed-circuit rebreather dive, enabling the filtration of a water volume of 15 L/filter per depth, as close as possible to the substrate. Two filter replicates were collected by two divers at each sampling site, except in two cases where bad weather conditions or logistical issues meant that only one replicate was sampled.
After the filtration, the remaining seawater was emptied from the capsule back on the boat and replaced by a 80 mL CL1 conservation buffer (SPYGEN, le Bourget du Lac, France). To prevent any contamination, a strict protocol was followed during the entire process, requiring disposable gloves and single-use filtration equipment. Finally, the samples were stored at room temperature. We followed a strict contamination control protocol in both field and laboratory stages. Each water sample processing included the use of disposable gloves and single-use filtration equipment to avoid any risk of contamination. Libraries were prepared with ligation using the MetaFast protocol (Fasteris).
Data content:
	* rawdata/: contains the raw reads for each individual sample. One archive contains the paired-end reads specified by the _R1 or _R2 suffix as well as individually tagged PCR replicates (if available) together with an archive containing all extraction and PCR blank samples of the library. Reads have been demultiplexed using cutadapt but not trimmed, individual demultiplexing tags and primers remain present in the sequences.
	* taxadata/: contains the table with all detected taxonomy for each sample after bioinformatic processing (see Polanco et al. 2020 for details; https://doi.org/10.1002/edn3.140) and associated field metadata.
	* metadata/: contains two metadata files, one related to the data collected in the field for each filter, and the second related to the sequencing process in the lab (including the tag sequence, library name, and marker information for each sample)

edna

display_name: edna

fish-composition

display_name: fish-composition

marine

display_name: marine

marseille

display_name: marseille

mediterraneaen

display_name: mediterraneaen

educ

en: Education, culture and sport

envidat

en: EnviDat: the Environmental Data Portal

en: Environmental DNA Marine France Calanques 2022


en: teleo senegal edna metabarcoding fish

en: Data access

en:
Monitoring fish diversity through eDNA metabarcoding along the Casamance river
In 2018, water samples were collected in 13 locations along the Casamance in Senegal. Samples were taken either from a boat or by filtering from the side of the river. At each station, two filtration replicates were performed using a peristaltic pump to conduct environmental DNA (eDNA) sampling. Each filtration targeted a maximum duration of 30 min, during which approximately 30 liters of water were filtered through each filtration capsule. After filtration, the water inside the capsules was removed, and the capsules were filled with 50 ml of conservation buffer for preservation at room temperature. We followed strict contamination control protocols throughout both the fieldwork and laboratory processes, adhering to the guidelines of Valentini et al. (2016). To prevent contamination, each sample was processed using disposable gloves and single-use filtration equipment. We use primers for eukaryote and fish. The MiSeq Reagent Kit v3 (2x75 bp) (Illumina, San Diego, CA, USA) was used for paired-end sequencing at a theoretical sequencing depth of 200,000 reads per sample.
Data content:
	* rawdata/: contains the raw reads for each individual sample. One archive contains the paired-end reads specified by the _R1 or _R2 suffix as well as individually tagged PCR replicates (if available) together with an archive containing all extraction and PCR blank samples of the library. Reads have been demultiplexed using cutadapt but not trimmed, individual demultiplexing tags and primers remain present in the sequences.
	* taxadata/: contains the table with all detected taxonomy for each sample after bioinformatic processing (see Polanco et al. 2020 for details; https://doi.org/10.1002/edn3.140) and associated field metadata.
	* metadata/: contains two metadata files, one related to the data collected in the field for each filter, and the second related to the sequencing process in the lab (including the tag sequence, library name, and marker information for each sample)

fish

display_name: fish

metabarcoding

display_name: metabarcoding

senegal

display_name: senegal

teleo

display_name: teleo

en: EnviDat is the WSL data portal providing unified and managed access to environmental monitoring and research data. The portal has the capability to host and publish data sets. Through the sharing of unique and high-value data sets worldwide, EnviDat fosters research and contributes to advancing environmental science.

en: Environmental DNA Freshwater Senegal Casamance 2018


photogrammetric-drone-data-schurlialp

maintainer: Yves Bühler

title_for_slug: photogrammetric-drone-data-schurlialp

en: wingtra photogrammetry dsm orthophoto drone-data uav

en: Data Access

en:
- 10 cm DSM
- 10 cm HS
- 3 cm orthophoto
- original RGB images
- Agisoft Metashape Processing Report

All of the products are also available as a cloud optimized geotiff.

en: The data was collected on 16.04.2021 and on 28.05.2021 with a Wingtra Gen II and a Sony RX1 II RGB sensor to obtain snow depth and distribution data. Following the data collection, the data was processed with Agisoft Metashape. A 10cm DSM, a 10cm snow depth raster, a 3mm orthophoto and the original drone images are available for download.

drone-data

display_name: drone-data

dsm

display_name: dsm

orthophoto

display_name: orthophoto

photogrammetry

display_name: photogrammetry

uav

display_name: uav

wingtra

display_name: wingtra

en: Photogrammetric Drone Data Schürlialp


en: python pattern-formation snow vapor-transport numerical-model

en:
Data and code v1.0 downloaded from the git.

Running the code requires an installation of FEniCS via docker.

en:
This python code uses the Finite Element library FEniCS (via docker) to solve the one dimensional partial differential equations for heat and mass transfer in snow. The results are written in vtk format.

The dataset contains the code and the output data to reproduce the key Figure 5 from the related publication:

_Schürholt, K., Kowalski, J., Löwe, H.; Elements of future snowpack modeling - Part 1: A physical
instability arising from the non-linear coupling of transport and phase changes, The Cryosphere, 2022_

The code and potential updates can be accessed directly through git via:

https://gitlabext.wsl.ch/snow-physics/snowmodel_fenics

numerical-model

display_name: numerical-model

pattern-formation

display_name: pattern-formation

python

display_name: python

snow

display_name: snow

vapor-transport

display_name: vapor-transport

en: A numerical solver for heat and mass transport in snow based on FEniCS


maintainer: Ariel Bergamini

en: functional-traits moss grassland pandiv bryophytes biodiversity-experiment species-richness fungicide biomass nitrogen

en: main data as used in Lin et al. 2025

en:
This dataset was used to analyse effects of different biodiversity and functional group treatments, fertilizer and fungicide applications as well as weeding of vascular plants on the species richness and species composition of bryophytes for the following publication: Lin M., Bergamini A., Pichon N.A., Allan E, Boch S. 2025. Nitrogen enrichment and vascular plant richness loss reduce bryophyte richness. Scientific Reports.
In this study we surveyed 96 of 216 2 m x 2 m experimental plots of the PaNDiv experiment, a large grassland field experiment in the Swiss lowlands (Pichon et al. 2020). In the PaNDiv experiment four experimental treatments were applied in a full-factorial design manipulating: (1) the nitrogen availability (through fertilization), (2) the presence of fungal pathogens (through fungicide application), (3) the functional composition of the vascular plant community (represented here by community-weighted mean (CWM) SLA), and (4) the vascular plant richness (sowing of either 1, 4, 8 or 20 species). To maintain the original sown vascular plant species richness and composition, one part of each plot (1.5 m × 2 m) was weeded, while the other part has been left unweeded since the beginning of the experiment (0.5 m × 2 m).
On each plot we surveyed two subplots, the unweeded subplot and a weeded subplot of the same area (0.5 m × 2 m). On each subplot we established a complete list of all bryophyte species together with an estimate of their cover.
The provided excel file contains three sheets:
1.	A sheet with raw species lists of all plots surveyed together with information on all treatments and an estimation of the percentage cover of vascular plants in a summer campaign in August 2022. Cover of bryophytes was estimated for each species in percent.
2.	A sheet with a list of all bryophyte species with its growth form (acroarpous/pleurocarpous)
3.	A sheet with some explantations
By means of the provided R code and the data in the excel file, all analyses can be repeated.
More details to the data sampled can be found in Lin et al (2025).

biodiversity-experiment

display_name: biodiversity-experiment

biomass

display_name: biomass

bryophytes

display_name: bryophytes

functional-traits

display_name: functional-traits

fungicide

display_name: fungicide

grassland

display_name: grassland

moss

display_name: moss

nitrogen

display_name: nitrogen

pandiv

display_name: pandiv

species-richness

display_name: species-richness

educ

en: Education, culture and sport

en: Data on bryophyte diversity and treatment factors in the PaNDiv experiment


maintainer: Merin Reji Chacko

en: biodiversity-assessment dna-metabarcoding spatial-ecology environmental-dna biomonitoring

en: Analysis and Figures

en: This zipped file includes R scripts and the datasets required to run the analyses. A README describes the columns in each dataset.

en: Field Metadata

en: Information concerning the locations and times of sampling, as well as the identity of the samplers and relevant comments.

en: Genomic data

en: Fastq files, primer descriptions and the final output dataset.

en: This dataset contains the results of a five-day field excursion which the extent to which eDNA sampling can capture the diversity of a region with highly heterogeneous habitat patches across a wide elevation gradient through multiple hydrological catchments of the Swiss Alps. Using peristaltic pumps, we filtered 60 L of water at five sites per catchment for a total volume of 1 800 L. Using an eDNA metabarcoding approach focusing on vertebrates and plants, we detected 86 vertebrate taxa spanning 41 families and 263 plant taxa spanning 79 families across ten catchments. This dataset includes two sets of data. The first (Genomic data) includes all the necessary data for the bioinformatic pipeline, whereas the second (Analysis Figures) contains tidied data and scripts for the reproduction of all figures/analyses in the article describing this study.

biodiversity-assessment

display_name: biodiversity-assessment

biomonitoring

display_name: biomonitoring

dna-metabarcoding

display_name: dna-metabarcoding

environmental-dna

display_name: environmental-dna

spatial-ecology

display_name: spatial-ecology

envidat

en: EnviDat: the Environmental Data Portal

en: Vertebrate and plant taxa recovered from 10 catchments in Vaud using an eDNA-metabarcoding approach


maintainer: Amelie Fees

en: avalanche-activity glide-snow-avalanche avalanche snowpack-simulation time-lapse-photography

en: SNOWPACK simulations

en: SNOWPACK simulations (.pro and .smet) covering season 2008/09 to 2021/22 at 10 virtual locations on Dorfberg. The locations correspond to the most common glide-snow avalanche paths.

en: Glide-snow avalanche activity

en: Table that contains all glide-snow avalanche events that were detected in time-lapse photographs (season 2008/09 to 2021/22). The columns are explained in the README.txt

en: README

en: README.txt explaining the dataset and columns of tables in more detail.

en: Glide distances for opening glide-cracks

en: This folder contains all glide-cracks where glide-distances were extracted from time-lapse photographs. Glide-distances were calculated in x-direction (width) and y-direction (downslope, length) by georeferencing the images.

en:
This dataset includes the processed data of the glide-snow avalanche activity and dynamics on Dorfberg (Davos, Switzerland) covering seasons 2008/09 to 2021/22. This dataset was described in the research article:

Fees, A., van Herwijnen A., Altenbach, M., Lombardo, M., Schweizer, J.: Glide-snow avalanche characteristics at different time-scales extracted from time-lapse photography, Annals of Glaciology, 91

We extracted the dynamics of opening glide-cracks and the glide-snow avalanche activity from time-lapse photographs. Glide-snow avalanches were separated into surface and interface events using the liquid water content which was simulated with SNOWPACK at 10 virtual stations on Dorfberg.

avalanche

display_name: avalanche

avalanche-activity

display_name: avalanche-activity

glide-snow-avalanche

display_name: glide-snow-avalanche

snowpack-simulation

display_name: snowpack-simulation

time-lapse-photography

display_name: time-lapse-photography

en: EnviDat is the WSL data portal providing unified and managed access to environmental monitoring and research data. The portal has the capability to host and publish data sets. Through the sharing of unique and high-value data sets worldwide, EnviDat fosters research and contributes to advancing environmental science.

en: Glide-snow avalanche activity on Dorfberg, Davos, Switzerland


data-konzeptionelles-systemmodell

maintainer: Matthias Bürgi

title_for_slug: data-konzeptionelles-systemmodell

en: scenarios qualitative-research policy-action landscape-change climate-change

media_type: application/pdf

format: PDF

en:
This folder contains documents relevant to the project step Konzeptionelles Systemmodell. It specifically contains the following documents:

1. 0201_Konzeptionelles Systemmodell_20221027: This document is the final version of the Konzeptionelles Systemmodell. The underlying structure of the Konzeptionelles Systemmodell is explained in chapter 4.4 of the document 0202_Masterarbeit Elena Siegrist_UniBern_Herbstsemester 2022 also deposited in this folder. The document contains 3 sheets. The sheet "Bausteine" shows the different possible options for table columns of the type Bausteine (see chapter 4.4 of Masterarbeit), the sheet "Direkte Effekte" contains identified direct impact pathways and the sheet "Indirekte Effekte" contains identified indirect impact pathways.

2. 0202_Masterarbeit Elena Siegrist_UniBern_Herbstsemester 2022: This document is the Master Thesis of Elena Grace Siegrist submitted to and accepted by the University of Bern in the Autumn Semester 2022. Chapter 4.4 of the document explains the underlying structure of the Konzeptionelles Systemmodell.

3. 0203_Literaturverzeichnis_konzeptionelles Systemmodell_20221026: This document lists all literature and documents cited in the Konzeptionelle Systemmodell.

climate-change

display_name: climate-change

landscape-change

display_name: landscape-change

policy-action

display_name: policy-action

qualitative-research

display_name: qualitative-research

scenarios

display_name: scenarios

educ

en: Education, culture and sport

en: Data Konzeptionelles Systemmodell


en: biological-control switzerland drosophila-suzukii population-genetics nuclear-microsatellite-markers trichopria-drosophilae simple-sequence-repeats multilocus-genotypes

media_type: text/csv

en: Multilocus genotypes (biallelic coding for 21 nuclear microsatellites) of Trichopria drosophilae described in Gugerli et al. Agrarforschung Schweiz 2019. Missing data denoted as '999'. Population codes (PopNo) are the following: 1, Vezia; 3, Contone ; 5, Davesco; 6, Corteglia; 7, Mezzana; 8, Stabio; 9, Gordola; 10, Sementina; 12, Brusata di Novazzano; 14, Monteggio; 16, Giubiasco; 17, ComoBP; 18, VD; 19, Weil_D; 20, Dossenheim; 21, BioPlanet_Como. Coordinates (CoordCH_E, CoordCH_N) refer to the Swiss coordinates system CH1903.

format: CSV

mimetype: text/csv

en: Table comprising all pertinent information for multiplex PCRs of species-specific nuclear microsatellite makers for Trichopria drosophilae, comprising all 21 newly developed markers, details on full sequences with GenBank accession numbers, primer sequences (including labeling and pig-tails), and repeat motives. PCRs with respective annealing temperatures (AnnealingTemp) refer to Type-It Multiplex PCR Kit (Qiagen, Hilden, Germany).

en:
 Nuclear microsatellite markers and genotype data for _Trichopria ddrosophilae_

This data set comprises (i) the characteristics of a set of 21 species-specific nuclear microsatellites for PCR amplification in _Trichopria drosophilae_ (ii) and genotype data for samples collected in southern Switzerland (Canton of Ticino), with few reference samples from Canton of Vaud, southern Germany, and northern Italy (lab-reared population).
Markers were developed by Ecogenics GmbH, Balgach (Switzerland), using MiSeq Nano 2x250 v2 format (on a mix of 10 individuals). Multiplex PCR assays for multilocus genotyping were established by Ecological Genetics (WSL Birmensdorf), and population genetic analyses are found in Gugerli et al., Agrarforschung Schweiz 2019.

biological-control

display_name: biological-control

drosophila-suzukii

display_name: drosophila-suzukii

multilocus-genotypes

display_name: multilocus-genotypes

nuclear-microsatellite-markers

display_name: nuclear-microsatellite-markers

population-genetics

display_name: population-genetics

simple-sequence-repeats

display_name: simple-sequence-repeats

switzerland

display_name: switzerland

trichopria-drosophilae

display_name: trichopria-drosophilae

envidat

en: EnviDat: the Environmental Data Portal

en: Nuclear microsatellite markers for Trichopria drosophilae, parasitoid wasp on Drosophila suzukii


maintainer: Yael Frischholz

en: snow-transport photovoltaic preferential-deposition alpine renewable-energy

en:
This file contains the snowBedFoam simulations carried out to produce the results presented in: _article not published yet_.
 Content
 1. /simulations
Groups all simulations folders organised by parameter (azimuth, groupsize, height, interspace) and by type of experiment (single_ref, group_ref).
 2. /simulations/[parameter]/
For each parameter multiple simulations were carried out. Each simulation folder follows the same naming systematic:
`helioplant_n#_h#_ARL#_BL#_az#_windDir#`
- n: number of Helioplant units
- h: height-above-surface
- sp: regular distance between the units
- ARL: additional refinement level
- BL: boundary layer first cell height
- windDir: wind direction
- stag: staggered arangement (suffix)
Here is an example of a folder content for a specific parameter
(simulations/azimuth/):
- `helioplant_n9_h07_sp10_ARL45_BL0015_az30_windDir5`: following the naming systematic this folder corresponds to a simulation with 9 aligned Helioplant units with 0.7m of height-above-surface, an inter-unit distance of 10m an azimuth of 30° and a wind direction of 5°.
 3. /simulations/[parameter]/[helioplant_n#_h#_ARL#_BL#_az#_windDir#]
Each simulation folder contains multiple sub-folders (0/, 100/, 300/, constant/ etc.) and files that define the experiment. For each simulation, the files used in the processing [scripts] are the following:
- 0/Cx: contains the x coordinates of sampling grid cells and of the Helioplants structures.
- 0/Cy: contains the y coordinates of sampling grid cells and of the Helioplants structures.
- 300/kinematicCloud-massCheckPatterns: contains the snow mass distribution values [kg/m2] for each grid cell.

[scripts]: https://github.com/frischwood/snowbed-helio.git

en: Browse simulation files

en:
This dataset groups numerical simulation outputs and validation measurement data produced in the context of the following [publication]: _not published yet_
The snow transport model [snowBedFoam] was used to analyse snow deposition around a specific type of Alpine PV structures named HELIOPLANT®.
The results of a sensitivity analysis of multiple key parameters that govern the spatial organisation of these structures are provided here. Measurements of snow distribution taken from the test-site of the [Gondosolar] project, are provided too.

To reproduce the results of the aforementioned publication, follow the instructions on this [repository].
[publication]: https://
[snowBedFoam]: https://www.doi.org/10.16904/envidat.223
[Gondosolar]: https://www.gondosolar.ch
[repository]: https://github.com/frischwood/snowbed-helio.git

alpine

display_name: alpine

photovoltaic

display_name: photovoltaic

preferential-deposition

display_name: preferential-deposition

renewable-energy

display_name: renewable-energy

snow-transport

display_name: snow-transport

en: Drifting and blowing snow distribution around structures for Alpine PV applications


maintainer: Varun Sharma

en: snow-atmosphere-interaction mesoscale-modelling antarctica blowing-snow alps

en: REPRODUCIBILITY_SIMULATION.zip contains all the extraneous files required to perform the simulations in associated manuscript (see Citations 3 in README.txt). The purpose of sharing these files apart from purposes of reproducibility is to also serve as templates for users to learn the workflow of CRYOWRF and perform simulations for their own purposes.

en:
REPRODUCIBILITY_POSTPROCESSING.zip contains data and scripts used to produce all figures from for the associated manuscript submitted for peer review ( see section on Citations below )

The folders stand for the three case studies presented in the manuscript. Two case studies (case Ia and case Ib) are on simulations in Antarctica and one case study
case II is for simulations in the Alps.

The associated data in the form of netcdf files or text files were produced using CRYOWRF v1.0

Apart from reproducibility, the intention of sharing these scripts is also to make it easy for new users to adopt CRYOWRF and be efficient, in particular in processing snowpack outputs.

The scripts were tested on multiple machines (different OSes) with the attached YAML file (wrf_analysis.yml) to setup the conda environment. All scripts were run using spyder as the IDE.

en:
This repository contains data required for reproducibility of the results to be published in the associated manuscript.

Apart from reproducibility, the attached datasets also serve as templates for new users to adopt CRYOWRF in their research.

The datasets consist of two folders organized in zip format:

1. REPRODUCIBILITY_SIMULATION:
  Consists of namelists for WPS, WRF and SNOWPACK to reproduce simulations published in the manuscript
  Additional files include datasets (from IMAU-FDM / RACMO, see "credits" below ) as well as helper python scripts to
  produce *.sno files
  which are used as initial conditions for SNOWPACK in CRYOWRF.

2. REPRODUCIBILITY_POSTPROCESSING:
   Includes outputs of CRYOWRF and python scripts used to prepare figures in the manuscript.

Each of the folders have their own readme files for more details.

 Code
citation: Varun Sharma. (2021, July 2). vsharma-next/CRYOWRF: CRYOWRF v1.0 (Version v1.0). Zenodo. http://doi.org/10.5281/zenodo.5060165

location: https://gitlabext.wsl.ch/atmospheric-models/CRYOWRF   (stable releases / institutional repo)
        https://github.com/vsharma-next/CRYOWRF            (dev branches / developer repo)

 Publication
**Introducing CRYOWRF v1.0: Multiscale atmospheric flow simulations with advanced snow cover modelling.**
Varun Sharma, Fraziska Gerber and Michael Lehning, Submitted to Geoscientific Model Development

 Acknowledgements
We thank Peter Kuipers Munneke (P.KuipersMunneke@uu.nl) for preparing and sharing outputs of IMAU-FDM and RACMO used for initial conditions for case Ia. The relevant citations for the methods through which these datasets were generated are:

* Kuipers Munneke, P., S. R. M. Ligtenberg, B. P. Y. Noël, I. M. Howat, J. E. Box, E. Mosley-Thompson, J. R. McConnell, K. Steffen, J. T. Harper, S. B. Das and M. R. van den Broeke. 2015. Elevation change of the Greenland ice sheet due to surface mass balance and firn processes, 1960-2014. The Cryosphere, 9, 2009-2025. doi:10.5194/tc-9-2009-2015

 * Ligtenberg, S. R. M., P. Kuipers Munneke, B. P. Y. Noël, and M. R. van den Broeke. 2018. Brief communication: Improved simulation of the present-day Greenland firn layer (1960-2016). The Cryosphere, 12, doi:10.5194/tc-12-1643-2018

alps

display_name: alps

antarctica

display_name: antarctica

blowing-snow

display_name: blowing-snow

mesoscale-modelling

display_name: mesoscale-modelling

snow-atmosphere-interaction

display_name: snow-atmosphere-interaction

envidat

en: EnviDat is the WSL data portal providing unified and managed access to environmental monitoring and research data. The portal has the capability to host and publish data sets. Through the sharing of unique and high-value data sets worldwide, EnviDat fosters research and contributes to advancing environmental science.

en: Reproducibility Dataset for CRYOWRF v1.0


en: colombia vert01 teleo magdalena edna metabarcoding fish

en: Data access

en: Please cyberduck to download for the moment

en:
Monitoring of vertebrates of the lower Magdalena river through eDNA metabarcoding
The Magdalena River basin harbors a large biodiversity of vertebrates, with numerous endemic species, many of which are threatened. Here, we used environmental DNA (eDNA) metabarcoding, with two primer sets targeting different regions of the mitochondrial DNA 12S ribosomal RNA gene, to detect vertebrate diversity in the Magdalena River. We detected a total of 159 vertebrate taxa, not only aquatic but also terrestrial, arboreal, and aerial. The diversity of these vertebrates increases in relation to the proximity to the river mouth with a change in the composition of the assemblage of aquatic vertebrates detected. We conclude that eDNA metabarcoding allows characterizing vertebrate assemblages in large rivers, assessing conservation status, and elucidating biodiversity patterns with minimal ecosystem disturbance. Samples were taken at the sides of the river or in the center using a boat. At each station, we performed two filtration replicates using a peristaltic pump to conduct environmental DNA (eDNA) sampling. Each filtration targeted a maximum duration of 1 hours, during which a maximum of 30 liters of water were filtered through each capsule. After filtration, the water inside the capsules was removed, and the capsules were filled with 50 ml of conservation buffer for preservation at room temperature. We followed strict contamination control protocols throughout both the fieldwork and laboratory processes, adhering to the guidelines of Valentini et al. (2016). To prevent contamination, each sample was processed using disposable gloves and single-use filtration equipment. The MiSeq Reagent Kit v3 (2x75 bp) (Illumina, San Diego, CA, USA) was used for paired-end sequencing at a theoretical sequencing depth of 200,000 reads per sample.
Data content:
	* rawdata/: contains the raw reads for each individual sample. One archive contains the paired-end reads specified by the _R1 or _R2 suffix as well as individually tagged PCR replicates (if available) together with an archive containing all extraction and PCR blank samples of the library. Reads have been demultiplexed using cutadapt but not trimmed, individual demultiplexing tags and primers remain present in the sequences.
	* taxadata/: contains the table with all detected taxonomy for each sample after bioinformatic processing (see Polanco et al. 2020 for details; https://doi.org/10.1002/edn3.140) and associated field metadata.
	* metadata/: contains two metadata files, one related to the data collected in the field for each filter, and the second related to the sequencing process in the lab (including the tag sequence, library name, and marker information for each sample)

colombia

display_name: colombia

edna

display_name: edna

fish

display_name: fish

magdalena

display_name: magdalena

metabarcoding

display_name: metabarcoding

teleo

display_name: teleo

educ

en: Education, culture and sport

en: Environmental DNA Freshwater Colombia Magdalena 2022