en: soil-biodiversity decomposition bacteria detritus wolf biogeochemical-cycling fungi carrion yellowstone carcass

en:
Site	ID for different carcasses across the Yellowstone Landscape
Location	Sampling location, either under carcass or control plot
Species	Indicating whether carcass was from bison or elk
Gender	Gener of carcass; F = female, M = male, ? = unknown
Lat	Latitude
Long	Longitude
DSK	Days since kill; in days
Soil.N	Soil N concentration (%)
Soil.C	Soil C concentration (%)
Veg.C	Vegetation C concentration (%); dominant grasses sampled
Veg.N	Vegetation N concentration (%); dominant grasses sampled
Veg.CtoN	Vegetation C to N ratio; dominant grasses sampled
Soil.resp	Soil respiration (g m-2 h-1)
soil.temp	Soil temperature (°C)
Soil.moist	Soil moisture (volumentric; %)
CRR	Cotton rotting rate
bacteria.richness	Bacteria richness
bacteria.diversity	Bacteria diverstiy
fungi.richness	Fungi richness
fungi.diversity	Fungi diversity
bacteria.abundance	Bacteria abundance
fungi.abundance	Fungi abundance

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

Paper Citation:

Risch, A.C., Frossard, A., Schütz, M., Frey, B., Morris, A.W., Bump, J.K. (accepted) Effects of elk and bison carcasses on soil microbial communities and ecosystem functions in Yellowstone, USA. (accepted). Functional Ecology
doi: ...

Methods
Study area and study sites
This study was conducted in YNP’s Northern Range (NR), located in north-western Wyoming and south-western Montana, USA (~44.9163° N, 110.4169° W). The NR expands over ~1000 km2 and features long cold winters and short dry summers. Grasslands and shrublands dominate the NR that is the home of large migratory herds of bison (winter counts 2017: ~3919 individuals; Geremia, Wallen, & White, 2017) and elk (~5349 individuals) as well as their main predators, approximately five packs of wolves with a total of 33 individuals (Smith et al., 2017). As part of a long-term research program within YNP, wolf predation has been studied since their reintroduction in 1995.
For our study, we received ground-truthed coordinates of bison and elk carcasses from winter 2016/17 (November 2016 through April 2017) from the YNP Wolf Project. Between June 20 and July 1, 2017, we visited 24 carcasses in total. At five sites, we could not sample as the carcasses were no longer found. In total we located remains (hairmats, rumen content, bones, teeth) of 19 adult male and female carcasses (7 bison, 12 elk; Supplementary Table 1). Live body weights of adult bison and elk are approximately 730 kg (male bison), 450 kg (female bison), 330 kg (male elk), and 235 kg (female elk, Meagher, 1973; Quimby & Johnson, 1951).
The kills and subsequent consumption happened between 34 and 173 days prior to our sampling (hereafter “days since kill”, DSK), for which we accounted in our statistics. Note that wolves and other scavengers consumed the soft tissue of the carcasses quickly, hence, there is close to no soft tissue left for decomposition as compared to an intact body left on the soil surface. The 19 carcass sites covered the extent of YNP’s NR, with both bison and elk carcasses showing similar distributions; elevation ranged from 1703 to 2884 m a.s.l. (Supplementary Fig 1 & Supplementary Table 1). The carcasses were all located in grassland or sage-brush shrubland, with or without sparsely scattered trees, and both bison and elk carcasses showed the same distribution of DSK. At each study site, we selected a reference plot (hereafter “control”) that was of comparable size, slope aspect and vegetation to the carcass location (hereafter “carcass”). The control was at least 10 m away (Danell, Berteaux, & Brathen, 2002; Melis et al., 2007) from the carcass itself to ensure the absence of potential direct and indirect carcass effects (paired design; (Bump, Webster, et al., 2009; Bump, Peterson, et al., 2009).

Ecosystem functions and soil properties
We randomly collected 50 g of mineral soil from three locations on both control and carcass plots to a depth of 5 cm with sterile techniques and gently mixed the material to obtain a composite sample. Half the soil sample was immediately bagged in plastic bags (whirl packs), stored in a cooler with ice packs (~5 ºC), sieved (2-mm) and frozen within 4-6 hours of collection to assess soil microbial communities. For this purpose, we extracted total genomic DNA from 0.5 g soil using the PowerSoil DNA Isolation Kit (Qiagen, Hilden, Germany). DNA concentrations were measured using PicoGreen (Molecular Probes, Eugene, OR, USA). PCR amplifications of partial bacterial small-subunit ribosomal RNA genes (region V3–V4 of 16S rRNA) and fungal ribosomal internal transcribed spacers (region ITS2) were performed as described previously (Frey et al., 2016). Each sample consisting of 40 ng DNA was amplified in triplicate and pooled before purification with Agencourt AMPure XP beads (Beckman Colter, Berea, CA, USA) and quantified with the Qubit 2.0 fluorometric system (Life Technologies, Paisley, UK). Amplicons were sent to the Genome Quebec Innovation Center (Montreal, Canada) for barcoding using the Fluidigm Access Array technology and paired-end sequencing on the Illumina MiSeq v3 platform (Illumina Inc., San Diego, CA, USA).
Quality control of bacterial and fungal reads was performed using a customized pipeline (Supplementary Table 2; Frey et al., 2016). Paired-ends reads were matched with USEARCH (Edgar & Flyvbjerg, 2015), substitution errors were corrected using Bayeshammer (Nikolenko, Korobeynikov, & Alekseyev, 2013) and PCR primers were trimmed (allowing for 1 mismatch, read length >300 bp for 16S and >200 bp for ITS primers) using Cutadapt (M. Martin, 2011). Sequences were dereplicated and singleton reads removed prior to clustering into operational taxonomic units (OTUs) at 97% identity using USEARCH (Edgar, 2013). The remaining centroid sequences were tested for the presence of ribosomal signatures using Metaxa2 (Bengtsson-Palme et al., 2015) or ITSx (Bengtsson-Palme et al., 2013). Taxonomic assignments of the OTUs were obtained using Bayesian classifier (Wang, Garrity, Tiedje, & Cole, 2007) with a minimum bootstrap support of 60% implemented in mothur (Schloss et al., 2009) by querying the bacterial and fungal reads against the SILVA Release 128 (Quast et al., 2013) and UNITE 8.0 (Abarenkov et al., 2010) reference databases for 16S and ITS OTUs, respectively.
Abundances of the bacterial 16S rRNA gene and fungal ITS amplicon were determined by quantitative real-time PCR (qPCR) on an ABI7500 Fast Real-Time PCR system (Applied Biosystems, Foster City, CA, USA) as described previously (Frossard et al., 2018). The same primers (without barcodes) and cycling conditions as for the sequencing approach were used for the 16S and ITS qPCR. Three standard curves per target region were obtained using tenfold serial dilutions of plasmids generated from cloned targets (Frey, Niklaus, Kremer, Lüscher, & Zimmermann, 2011). Data were converted to represent mean copy number of targets per gram of soil (dry weight).
The other half of the soil sample was bagged in paper, dried to constant weight at 60°C, passed through a 2 mm sieve and analyzed for total C and N concentration with a CE Instruments NC 2100 soil analyzer (CE Elantech Inc., Lakewood NJ, USA). We also collected 20 mature and undamaged leaves of the dominant grass species growing on control and carcass sites, but taxa were not recorded. The plant material was dried at 60°C, finely ground till homogenized and also analyzed to obtain total C and N concentrations. Soil temperature (10 cm depth) was measured with a waterproof digital thermometer (Barnstead International, Dubuque IA, USA) at three locations each at the control and carcass site. Soil moisture (0 – 10 cm depth) was measured with time domain reflectometry (Field-Scout TDR-100; Spectrum Technologies, Plainfield IL, USA) at five randomly chosen points on control and carcass sites. We measured soil respiration at five randomly chosen points at both control and carcass sites with a PP-Systems SRC-1 soil respiration chamber (closed circuit) attached to a PP-Systems EGM-4 infrared gas analyzer (PP-Systems, Amesbury, MA, USA). For each measurement the soil chamber (15 cm high; 10 cm diameter) was tightly placed on the soil surface, after clipping plants to avoid measuring plant respiration or photosynthesis. Measurements were conducted over 120 s.
In addition, we assessed the decomposition rates of standardized OM using the cotton strip assay (Latter & Howson, 1977; Latter & Walton, 1988). Cotton cloth tensile strength loss (CTSL) is a measure of decomposition, and an index to express the combined effect of soil microclimatic, physical, chemical and biological properties on decomposition while accounting for OM quality (Latter & Walton, 1988; Risch, Jurgensen, & Frank, 2007; Withington & Sanford Jr., 2007). We placed five 20 cm wide x 13 cm long sheets of 100% unbleached cotton cloth (American Type SM 1/18’’, Warp: 34/1, Weft: 20/1, Weave plain, 29.5 picks/cm warp, 22 picks/cm weft, 237 g/m2; Daniel Jenny & Co., Switzerland;) at each carcass and control site vertically into the soil by making slits with a flat spade to a depth of 12 cm. We inserted each cloth with the spade, and then pushed the slit closed to assure tight contact with the soil. The cloths were retrieved after 18 to 27 days. After retrieval, the cloths were air-dried, remaining soil gently removed by hand, and 1.5 cm wide strips were cut at the 3.5-5.0 cm (top) and the 9-10.5 cm (bottom) soil depth. The strips were equilibrated at 50 % relative humidity and 20°C for 48 hours (climate chamber) prior to strength testing (Scanpro Awetron TH-1 tensile strength tester; AB Lorentzen and Wettre, Kista, Sweden). Cotton rotting rate (CRR) = (CTScontrol - CTSfinal/CTSfinal)1/3 * (365/t), where CTScontrol is the cotton tensile strength of a control cloth and CTSfinal the cotton tensile strength of the incubated sample, t is the incubation period in days. Control cloths were inserted into the ground and immediately retrieved to account for tensile strength loss associated with cloth insertion. We averaged the CRR of top and bottom strips for further analyses as no difference was found between the two. All sampling and cloth insertion took place between June 20 and July 1, 2017, cloths were retrieved between July 17 and 20, 2017. Soil respiration, average CRR, vegetation N concentration and vegetation C:N ratio are defined as ecosystem functions, soil C and N concentration, soil temperature and moisture as soil abiotic properties, and bacterial and fungal richness (number of taxa), diversity (Shannon) and abundance as soil biotic properties.

Statistical analyses
Univariate analyses for ecosystem functions, soil biotic and abiotic properties
We tested whether individual ecosystem functions, soil biotic and abiotic properties differed between carcass and control (“Location”), bison and elk (“Species”) and days since kill (“DSK”). For this purpose, we used linear mixed effect models (LMM, “nlme” package v 3.1 – 131.1 in R v 3.4.4; Pinheiro, Bates, DebRoy, & Sarkar, 2018; R Core Team, 2019) with Location, Species, Location x Species and DSK as fixed effects. Site was included as random effect to account for the paired design. We developed a separate model for all dependent variables. All but bacterial richness, fungal richness, fungal diversity and vegetation N concentration were natural-log transformed to meet model assumptions. For each LMM, we calculated contrasts to assess the specific comparisons we were interested in with the “lsmeans” package v 2.27-62 (Lenth & Love, 2018): 1) carcass vs control, 2) carcass bison vs control bison, and 3) carcass elk vs control elk. We also tested whether we had differences between bison and elk carcasses or the sites where bison and elk were killed and included contrasts 4) carcass bison vs carcass elk and 5) control bison vs control elk.
We calculated the log response ratio (LRR = ln[carcass/control]) to obtain carcass effects for all variables for both species separately. LRR < 0 indicates higher value at control compared to carcass, LRR > 0 indicates higher values at carcass compared control. We used LRRs for visualization and to assess spatial patterns in carcass effects across YNP. For this purpose we calculated the Moran’s I statistic for each ecosystem function, soil biotic and abiotic property based on a latitude-longitude matrix with the “moran.test” function in the “spdep” package version 1.1-3 (Bivand et al., 2019).
Multivariate analyses
Rare OTUs, defined as OTUs with a low abundance of reads, were retained in multivariate methods because they only marginally influence these analyses (Gobet, Quince, & Ramette, 2010). Bray–Curtis dissimilarity matrices were generated based on square-root-transformed matrices. We used Principal Coordinate Analyses (PCoA) to assess how soil bacterial and fungal communities differed between control and carcass of bison and elk (“vegan” package v 2.5-4, Oksanen et al., 2019). We then extracted PCoA axes scores 1 and 2 and used LMM (“nlme” package) with Location, Species, Location x Species and DSK as fixed effects. Site was, again, included as random effect. We again calculated the contrasts as described above using the “lsmeans” package. We also assessed how ecosystem functions, and soil abiotic and biotic properties were related to the soil bacteria and fungi community structure associated with bison and elk control and carcasses using the “envfit” function in the “vegan” package (Oksanen et al., 2019).
Indicator species analyses were performed using the multipatt function implemented in the “indicspecies” package version 1.7.6 with 100000 permutations (De Caceres & Jansen, 2016). This step allowed to identify OTUs that led to changes in multivariate patterns between control and carcass of both bison and elk separately (De Cáceres, Legendre, & Moretti, 2010). The multipatt function uses a point biserial correlation coefficient statistical test. Indicator OTUs were defined as bacterial and fungal OTUs with more than 50 sequences, i.e., removing rare taxa and taxa with low abundances containing little indicator information (Rime et al., 2015) and that were significantly correlated with Location (p < 0.05, correlation coefficient > 0.3). A heatmap of these OTUs were generated with the vegan and ggplot2 packages. The indicator analyses were performed in R version 3.3.3 (R Core Team, 2017).

References
Abarenkov, K., Henrik Nilsson, R., Larsson, K.-H., Alexander, I. J., Eberhardt, U., Erland, S., … Kõljalg, U. (2010). The UNITE database for molecular identification of fungi – recent updates and future perspectives. New Phytologist, 186(2), 281–285. doi:10.1111/j.1469-8137.2009.03160.x
Bengtsson-Palme, J., Hartmann, M., Eriksson, K. M., Pal, C., Thorell, K., Larsson, D. G. J., & Nilsson, R. H. (2015). metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. Molecular Ecology Resources, 15(6), 1403–1414. doi:10.1111/1755-0998.12399
Bengtsson-Palme, J., Ryberg, M., Hartmann, M., Branco, S., Wang, Z., Godhe, A., … Nilsson, R. H. (2013). Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods in Ecology and Evolution, 4(10), 914–919. doi:10.1111/2041-210X.12073
Bivand, R., Altman, M., Anselin, L., Assuncao, R., Berke, O., Blanchet, G., … Yu, D. (2019). spdep: Spatial dependence, weighthing schemes, statistics. R package version 1.1-3.
Bump, J. K., Peterson, R. O., & Vucetich, J. A. (2009). Wolves modulate soil nutrient heterogeneity and foliar nitrogen by configuring the distribution of ungulate carcasses. Ecology, 90(11), 3159–3167.
Bump, J. K., Webster, C. R., Vucetich, J. A., Peterson, R. O., Shields, J. M., & Powers, M. D. (2009). Ungulate carcasses perforate ecological filters and create biogeochemical hotspots in forest herbaceous layers allowing trees a competitive advantage. Ecosystems, 12(6), 996–1007. doi:10.1007/s10021-009-9274-0
Danell, K., Berteaux, D., & Brathen, K. A. (2002). Effect of muskox carcasses on nitrogen concentration in tundra vegetation. Arctic, 55(4), 389392.
De Caceres, M., & Jansen, F. (2016). indicspecies: relationship between species and groups of species. R package version 1.7.6.
De Cáceres, M., Legendre, P., & Moretti, M. (2010). Improving indicator species analysis by combining groups of sites. Oikos, 119(10), 1674–1684. doi:10.1111/j.1600-0706.2010.18334.x
Edgar, R. C. (2013). UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods, 10, 996.
Edgar, R. C., & Flyvbjerg, H. (2015). Error filtering, pair assembly and error correction for next-generation sequencing reads. Bioinformatics, 31(21), 3476–3482. doi:10.1093/bioinformatics/btv401
Frey, B., Niklaus, P. A., Kremer, J., Lüscher, P., & Zimmermann, S. (2011). Heavy-machinery traffic impacts methane emissions as well as methanogen abundance and community structure in oxic forest soils. Applied and Environmental Microbiology, 77(17), 6060–6068. doi:10.1128/AEM.05206-11
Frey, B., Rime, T., Phillips, M., Stierli, B., Hajdas, I., Widmer, F., & Hartmann, M. (2016). Microbial diversity in European alpine permafrost and active layers. FEMS Microbial Ecology, 92(3), fiw018.
Frossard, A., Donhauser, J., Mestrot, A., Gygax, S., Bååth, E., & Frey, B. (2018). Long- and short-term effects of mercury pollution on the soil microbiome. Soil Biology and Biochemistry, 120, 191–199. doi:https://doi.org/10.1016/j.soilbio.2018.01.028
Geremia, C., Wallen, R., & White, P. J. (2017). Status report of the Yellowstone bison population, September 2017. Yellowstone National Park, Mammoth, WY, USA: National Park Service, Yellowstone Center for Resources.
Gobet, A., Quince, C., & Ramette, A. (2010). Multivariate cutoff level analysis (MultiCoLA) of large community data sets. Nucleic Acids Research, 38(15), e155–e155. doi:10.1093/nar/gkq545
Latter, P., & Howson, G. (1977). The use of cotton strips to indicate cellulose decomposition in the field. Pedobiologia, (17), 145–155.
Latter, P., & Walton, D. (1988). The cotton strip assay for cellulose decomposition studies in soil: history of the assay and development. In Cotton strip assay: an index for decomposition in soils (pp. 7–9). ITE Symposium, Institute of Terrestrial Ecology, Natural Environment Research Council, UK.
Lenth, R., & Love, J. (2018). lsmeans: least-squares means. R package version 2.27-62.
Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.Journal, 17(1), 10–12.
Meagher, M. M. (1973). The bison of Yellowstone National Park. NPS Scientific Monograph (Vol. 1). National Park Service, Yellowstone Center for Resources.
Melis, C., Selva, N., Teurlings, I., Skarpe, C., Linnell, J. D. C., & Andersen, R. (2007). Soil and vegetation nutrient response to bison carcasses in Białowieża Primeval Forest, Poland. Ecological Research, 22(5), 807–813. doi:10.1007/s11284-006-0321-4
Nikolenko, S. I., Korobeynikov, A. I., & Alekseyev, M. A. (2013). BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics, 14(1), S7. doi:10.1186/1471-2164-14-S1-S7
Oksanen, J., Blanchet, F. G., Friendly, M., Kindt, R., Legendre, P., McGlinn, D., … Wagner, H. H. (2019). vegan: community ecology package. R package version 2.5-4.
Pinheiro, J., Bates, D., DebRoy, S., & Sarkar, D. (2018). nlme: Linear and nonlinear mixed effect models. R package version 3.1-131.1.
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., … Glöckner, F. O. (2013). The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research, 41(Database issue), D590–D596. doi:10.1093/nar/gks1219
Quimby, D. C., & Johnson, D. E. (1951). Weights and measurements of Rocky Mountain elk. Journal of Wildlife Management, 15, 57–62.
R Core Team. (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Zurich, Switzerland.
R Core Team. (2019). R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing.
Rime, T., Hartmann, M., Brunner, I., Widmer, F., Zeyer, J., & Frey, B. (2015). Vertical distribution of the soil microbiota along a successional gradient in a glacier forefield. Molecular Ecology, 24(5), 1091–1108. doi:10.1111/mec.13051
Risch, A. C., Jurgensen, M. F., & Frank, D. A. (2007). Effects of grazing and soil micro-climate on decomposition rates in a spatio-temporally heterogeneous grassland. Plant and Soil, 298(1–2), 191–201. doi:10.1007/s11104-007-9354-x
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., … Weber, C. F. (2009). Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology, 75(23), 7537–7541. doi:10.1128/AEM.01541-09
Smith, D., Stahler, D., Cassidy, K., Stahler, E., Metz, M., Cassidy, B., … Cato, E. (2018). Yellowstone National Park wolf project annual report 2017. Yellowstone National Park, Mammoth, WY, USA: National Park Service, Yellowstone Center of Resources.
Wang, Q., Garrity, G. M., Tiedje, J. M., & Cole, J. R. (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 73(16), 5261–5267. doi:10.1128/AEM.00062-07
Withington, C., & Sanford Jr., R. (2007). Decomposition rates of buried substances increase with altitude in a forest-alpine tundra ecotone. Soil Biology and Biochemistry, (39), 68–75.

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

bacteria

display_name: bacteria

biogeochemical-cycling

display_name: biogeochemical-cycling

carcass

display_name: carcass

carrion

display_name: carrion

decomposition

display_name: decomposition

detritus

display_name: detritus

fungi

display_name: fungi

soil-biodiversity

display_name: soil-biodiversity

wolf

display_name: wolf

yellowstone

display_name: yellowstone

en: Elk and bison carcasses in Yellowstone, USA


maintainer: EnviDat Support

en: climate-change-impact discharge model water-temperature hydrology

state: active

type: dataset

en: Data access

format: SERVICE

en:
This work presents the first extensive study of climate change impacts on rivers temperature in Switzerland. Results show that even for low emissions scenarios, water temperature increase will lead to adverse effect for both ecosystems and socioeconomic sectors (such as nuclear plant cooling) throughout the 21st century. For high emissions scenarios, the effect will be worsen. This study also shows that water warming in summer will be more important in Alpine regions than in lowlands.
This material is distributed under CC BY 4.0 license (https://creativecommons.org/licenses/by/4.0/legalcode).

climate-change-impact

display_name: climate-change-impact

discharge

display_name: discharge

hydrology

display_name: hydrology

model

display_name: model

water-temperature

display_name: water-temperature

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: Dataset for: Future water temperature of rivers in Switzerland under climate change investigated with physics-based models


maintainer: Lisa Hülsmann

en: inventory-data empirical-mortality-models tree-mortality forest-reserves tree-growth

en: Calibration data

media_type: text/csv

en:
A set of three consecutive inventories was used to generate records for the calibration of mortality models based on trees that were alive in the first and second inventory and either dead or alive in the third inventory.

 Meta data
Reserve: Name of the forest reserve

Plot: Permanent plot number

 Tree data
Species: Latin species name (or species group, cf. _Quercus_ spp.)

y: Status of the tree with 0 = alive and 1 = dead

dt: Length of the mortality period (years)

DBH: Diameter at breast height (mm) of the second inventory

relBAI: Annual relative basal area increment (-) calculated based on the first and the second DBH measurement as the compound annual growth rate of the trees basal area

 Stand data
_All stand variables were calculated for the second inventory._

mDBH: Mean diameter at breast height (mm)

iqrDBH: Interquartile range of diameter at breast height (mm)

BA: Basal area per hectare (m2 ha-1)

N: Number of trees per hectare (ha-1)

 Climate data
_Both climate variables were calculated for the period between the second and the third inventory._

P: Mean annual precipitation sum (mm)

mT: Mean annual air temperature (°C)

format: CSV

mimetype: text/csv

en:
The dataset comprises > 90 000 records from inventories in 54 strict forest reserves in [Switzerland](https://www.wsl.ch/de/wald/biodiversitaet-naturschutz-urwald/naturwaldreservate.html) and [Lower Saxony / Germany](http://naturwaelder.de/) along a considerable environmental gradient. It was used to develop parsimonious, species-specific mortality models for 18 European tree species based on tree size and growth as well as additional covariates on stand structure and climate.

 Inventory data
Measurements had been conducted repeatedly on up to 14 permanent plots per reserve for up to 60 years with re-measurement intervals of 4 - 27 years. The permanent plots vary in size between 0.03 and 3.47 ha. The inventories provide diameter measurements at breast height (DBH) and information on the species and status (alive or dead) of trees with DBH ≥ 4 cm for Switzerland and ≥ 7 cm for Germany.

 Data selection
We excluded three permanent plots where at least 80 % of the trees died during an interval of 10 years, and mortality could be clearly assigned to a disturbance agent. Mortality in the remaining stands was rather low, with a mean annual mortality rate of 1.5 % and strong variation between plots from 0 to 6.5 % (assessed for trees of all species with DBH ≥ 7 cm).
We only used data from permanent plots with at least 20 trees per species to obtain reliable plot-level mortality rates even for species with low mortality rates (about 5 % during 10 years), and selected tree species occurring on at least 10 plots to cover sufficient ecological gradients. This led to a dataset of 197 permanent plots and 18 tree or shrub species: _Abies alba_ Mill., _Acer campestre_ L., _Acer pseudoplatanus_ L., _Alnus incana_ Moench., _Betula pendula_ Roth, _Carpinus betulus_ L., _Cornus mas_ L., _Corylus avellana_ L., _Fagus sylvatica_ L., _Fraxinus excelsior_ L., _Picea abies_ (L.) Karst, _Pinus mugo_ Turra, _Pinus sylvestris_ L., _Quercus pubescens_ Willd., _Quercus_ spp. (_Q. petraea_ Liebl. and _Q. robur_ L.; not properly differentiated in the Swiss inventories), _Sorbus aria_ Crantz, _Tilia cordata_ Mill. and _Ulmus glabra_ Huds..

 Predictors of tree mortality
We considered tree size and growth as key indicators for mortality risk. Radial stem growth between the first and second inventory and DBH at the second inventory were used to predict tree status (alive or dead) at the third inventory. To this end, the annual relative basal area increment (relBAI) was calculated as the compound annual growth rate of the trees basal area. Additional covariates on stand structure and climate comprise mean annual precipitation sum (P), mean annual air temperature (mT), the mean and the interquartile range of DBH (mDBH, iqrDBH), basal area (BA) and the number of trees (N) per hectare.

 Further information
For further information, refer to Hülsmann _et al_. (in press) How to kill a tree – Empirical mortality models for eighteen species and their performance in a dynamic forest model. _Ecological Applications_.

empirical-mortality-models

display_name: empirical-mortality-models

forest-reserves

display_name: forest-reserves

inventory-data

display_name: inventory-data

tree-growth

display_name: tree-growth

tree-mortality

display_name: tree-mortality

en: Calibration data for empirical mortality models of 18 European tree species


en: snow-hydrology avalanches snow-depth-distribution photogrammetry davos dischma

en: Snowdepth maps

format: GeoTIFF

en:
The available datasets are snow depth maps with a spatial resolution of 0.5 m derived from images of the survey camera Vexcel Ultracam mounted on a piloted airplane. Image acquisition was carried out during the approximately peak of winter (time when the thickest snowpack is expected) in spring. The snow depth maps are calculated by the subtraction of a summer-DTM from the processed winter- DSM of the corresponding date. The summer-DTM used was derived from a point cloud of an airborne laser scanner from 2020.

Due to the occurrence of inaccuracies of the calculated snow depth values caused by the photogrammetric method, we applied different masks to significantly increase the reliability of the snow depth maps. We masked out settled areas, high-frequented streets and technical constructions, pixels with high vegetation (height > 0.5 m) , outliers and unrealistic snow depth values. In addition, we modified the snow depth values of snow-free pixels to 0.
The information on buildings and infrastructure comes from the exactly classified ALS point cloud and the TLM dataset from Swisstopo (https://www.swisstopo.admin.ch/de/geodata/landscape/tlm3d.html#links). High vegetation is also derived from the classification and the calculated object height from the point cloud.
Outliers and unrealistic snow depth values are defined as negative snow depth values and snow depths exceeding 10 m. The classification of each pixel of the corresponding orthophoto into snow-covered or snow-free is based on the application of a threshold of the NDSI or manually determined ratios of the RGB values.

An extensive accuracy assessment proves the high accuracy of the snow depth maps with a root mean square error of 0.25 m for the year 2017 and 0.15 m for the following snow depth maps.

The work is published in:

avalanches

display_name: avalanches

davos

display_name: davos

dischma

display_name: dischma

photogrammetry

display_name: photogrammetry

snow-depth-distribution

display_name: snow-depth-distribution

snow-hydrology

display_name: snow-hydrology

en: Snow depth mapping by airplane photogrammetry (2017 -  ongoing)


maintainer: Leonie Schönbeck

en: fluorescence gas-exchange drought vpd acclimation pinus-sylvestris photosynthesis

en: Methods survey

en: Parameters and methods for point measurements / survey measurements

en: Methods light response

en: Methods and parameters for light response curves

en: Variable names and units

en: Variable names, description and units for the Pfynwald Gas exchange data

format: XLS

en: Instrument details

en:
Instrument details for all LiCor instruments used during collection of dataset.

Metatdata created following guidelines from
Ely et al (2021). A reporting format for leaf-level gas exchange data and metadata. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2021.101232

en: Pfynwald gas exchange

en:
Full dataset of Pfynwald gas exchange data taken in the period from June 2013 to October 2020.
All metdata can be found in attached documents.
Data uploaded after quality control using guidelines by Ely et al (2021). A reporting format for leaf-level gas exchange data and metadata. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2021.101232

en: Methods fluorescence

en:
Parameters and methodology for Fluorescence measurements

Metadata format from
Ely et al (2021). A reporting format for leaf-level gas exchange data and metadata. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2021.101232

en: Methods diurnal measurements

en:
Parameters and methodology for diurnal measurements

Metadata format from
Ely et al (2021). A reporting format for leaf-level gas exchange data and metadata. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2021.101232

en: Methods ACi curves

en:
Parameters and methods for CO2 response curves of Photosynthesis.

Metatdata format by
Ely et al (2021). A reporting format for leaf-level gas exchange data and metadata. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2021.101232

en:
Gas exchange was measured on control, irrigated and irrigation-stop trees at the irrigation experiment Pfynwald, during the years 2013, 2014, 2016-2020. The measurement campaigns served different purposes, resulting in a large dataset containing survey data, CO2 response curves of photosynthesis, light response curves of photosynthesis, and fluorescence measurements. Measurements were done with LiCor 6400 and LiCor 6800 instruments. Until 2016, measurements were done on excised branches or branches lower in the canopy. From 2016 onwards, measurements were done in the top of the canopy using fixed installed scaffolds.
All metadata can be found in the attached documents.

acclimation

display_name: acclimation

drought

display_name: drought

fluorescence

display_name: fluorescence

gas-exchange

display_name: gas-exchange

photosynthesis

display_name: photosynthesis

pinus-sylvestris

display_name: pinus-sylvestris

vpd

display_name: vpd

en: 2013-2020 gas exchange at Pfynwald


greenland-shrubs-and-microclimate

maintainer: Nathalie Chardon

title_for_slug: greenland-shrubs-and-microclimate

en: arctic field-data climate accessible-shrub-forest validation sdm

en: Kangerluarsunnguaq

en:
 Collected August 2020 (PI: Nathalie Isabelle Chardon)

These data collected August 2020 (PI: Nathalie Isabelle Chardon). Please contact N. I. Chardon (nathalie.chardon_at_gmail.com) for individual quadrat (i.e. 1 m x 1 m) data, which are averaged at the 90 m spatial grid here.

 COLUMN ABBREVIATIONS

 Metadata for 90 m spatial grid

id: sampling zone and unique 90 m grid identifier

long: WGS84 longitude

lat: WGS84 latitude

x_stere: longitude in Polar Stereographic (EPSG 4326)

y_stere: latitude in Polar Stereographic (EPSG 4326)

date: sampling day.month.year

 Species presence [1] or absence [0] at grid level

alcr: _Alnus crispa_

bena: _Betula nana_

dila: _Diapensia lapponica_

emni: _Empetrum nigrum_

hahy: _Harimanella hypoides_

lopr: _Loiseleuria procumbens_

oxpa: _Oxycoccus palustre_

phca: _Phyllodoce caerulea_

rhod: _Rhododendron_ sp.

saar: _Salix arctica_

sagl: _Salix glauca_

sahe: _Salix herbacea_

vaul: _Vaccinium uliginosum_

drin: _Dryas integrifolia_

thpr: _Thymus praecox_

 Habitat characteristics [% cover]

shrub: all shrub species

gram: graminoids

forb: forbs

bryo: bryophytes

lich: lichens

litt: litter

bare: bare ground

stone: stones (> 2 cm)

org: organic crust

 Shrub species height (maximum vegetative height) [mm] and cover (estimated in 1x1 m quadrat) [%]

alcr_c: _Alnus crispa_ cover

alcr_h: _Alnus crispa_ height

bena_c: _Betula nana_ cover

bena_h: _Betula nana_ height

dila_c: _Diapensia lapponica_ cover

dila_h: _Diapensia lapponica_ height

emni_c: _Empetrum nigrum_ cover

emni_h: _Empetrum nigrum_ height

hahy_c: _Harimanella hypoides_ cover

hahy_h: _Harimanella hypoides_ height

lopr_c: _Loiseleuria procumbens_ cover

lopr_h: _Loiseleuria procumbens_ height

oxpa_c: _Oxycoccus palustre_ cover

oxpa_h: _Oxycoccus palustre_ height

phca_c: _Phyllodoce caerulea_ cover

phca_height: _Phyllodoce caerulea_ height

rhod_c: _Rhododendron_ sp. cover

rhod_h: _Rhododendron_ sp. height

saar_c: _Salix arctica_ cover

saar_h: _Salix arctica_ height

sagl_c: _Salix glauca_ cover

sagl_h: _Salix glauca_ height

sahe_c: _Salix herbacea_ cover

sahe_h: _Salix herbacea_ height

vaul_c: _Vaccinium uliginosum_ cover

vaul_h: _Vaccinium uliginosum_ height

drin_c: _Dryas integrifolia_ cover

drin_h: _Dryas integrifolia_ height

 Community characteristics

rich_pa: shrub species richness at grid level

rich: shrub species richness averaged across 3 1x1 m sampling quadrats per grid

shan: Shannon diversity (‘vegan’ package; Oksanen et al. 2019)

comp_bena: shrub competition on _Betula nana_ (i.e. summed cover of non-_B. nana_ species) [% cover]

comp_sagl: shrub competition on _Salix glauca_ (i.e. summed cover of non-_S. glauca_ species) [% cover]

ht_cwm: maximum shrub canopy height (i.e. community weighted mean by abundance of maximum shrub height) [mm]

 Topography and terrain wetness (calculated from)

tcws: Tasseled Cap Wetness component (Sentinal images)

slope: slope angle (MEaSUREs Greenland Ice Mapping Project Digital Elevation Model v. 1; Howat et al., 2014, 2015) [º]

twi: SAGA wetness index (MEaSUREs Greenland Ice Mapping Project Digital Elevation Model v. 1; Howat et al., 2014, 2015)

asp: aspect (MEaSUREs Greenland Ice Mapping Project Digital Elevation Model v. 1; Howat et al., 2014, 2015) [º]

 Downscaled climate (time series 1984 – 2013)

insoljja: average June-August insolation [MJ cm-2 yr-1]

precipmam: cumulative March-May precipitation [mm]

tempcont: yearly maximum – minimum temperature [ºC]

tempmin: yearly minimum temperature [ºC]

precipjja: cumulative June-August precipitation [mm]

tempjja: average maximum June-August temperature [ºC]

tempmax: yearly maximum temperature [ºC]

en: Nuup Kangerlua

en:
 Collected July-August 2011-2013 (PI: Jacob Nabe-Nielsen)

These data collected July-August 2011-2013 (PI: Jacob Nabe-Nielsen). Please contact J. Nabe-Nielsen (jnn_at_ecos.au.dk) to request access to data on all surveyed shrub species. Available here are only data used in Chardon et al. 2022.

 COLUMN ABBREVIATIONS

 Metadata for 90 m spatial grid

year: sampling year

alt: average altitude of grid as recorded during field surveys [m]

long: WGS84 longitude

lat: WGS84 latitude

x_stere: longitude in Polar Stereographic (EPSG 4326)

y_stere: latitude in Polar Stereographic (EPSG 4326)

 Species presence [1] or absence [0] at grid level

pa_bena: _Betula nana_

pa_sagl: _Salix glauca_

 Shrub species cover (calculated from pin hits in 0.7 x 0.7 m frame, based on total of 25 hits) [%]

cov_bena: _Betula nana_ cover

cov_sagl: _Salix glauca_ cover

 Downscaled climate (time series 1984 – 2013)

tempjja: average maximum June-August temperature [ºC]

tempmax: yearly maximum temperature [ºC]

tempmin: yearly minimum temperature [ºC]

tempcont: yearly maximum – minimum temperature [ºC]

precipmam: cumulative March-May precipitation [mm]

precipjja: cumulative June-August precipitation [mm]

insoljja: average June-August insolation [MJ cm-2 yr-1]

 Topography and terrain wetness (calculated from)

twi: SAGA wetness index (MEaSUREs Greenland Ice Mapping Project Digital Elevation Model v. 1; Howat et al., 2014, 2015)

slope: slope angle (MEaSUREs Greenland Ice Mapping Project Digital Elevation Model v. 1; Howat et al., 2014, 2015) [º]

asp: aspect (MEaSUREs Greenland Ice Mapping Project Digital Elevation Model v. 1; Howat et al., 2014, 2015) [º]

tcws: Tasseled Cap Wetness component (Sentinal images)

 Community characteristics

rich: shrub species richness averaged across pin-point frames per grid

shan: Shannon diversity (‘vegan’ package; Oksanen et al. 2019)

comp_bena: shrub competition on Betula nana (i.e. summed cover of non-_B. nana_ species) [% cover]

comp_sagl: shrub competition on Salix glauca (i.e. summed cover of non-_S. glauca_ species) [% cover]

en: GitLab Repository

en: Zip drive of GitLab repository contents (https://gitlab.com/nathaliechardon/gl_microclim).

en:
 Study Aim

We collected these data to alternatively train and validate high resolution (~ 90 m) Species Distribution Models (SDMs) and Species Abundance Models (SAMs) for _Betula nana_ L. (dwarf birch, Betulaceae) and _Salix glauca_ L. (grey willow, Salicaceae) in Southwest Greenland to assess how well such models can predict local-scale patterns.

 Data Description

Individual (presence-absence, abundance, maximum vegetative height) and community (species composition, maximum canopy height) shrub data for two fjords near Nuuk, Southwest Greenland. Also provided are corresponding downscaled climate data as well as calculated topographic and terrain wetness indicator variables.

 Nuup Kangerlua (Godthåbsfjord)

_Betula nana_ and _Salix glauca_ presence-absence, abundance, community species richness

 Kangerluarsunnguaq (Kobbefjord)

Shrub presence-absence, abundance, maximum vegetative height, community composition, maximum shrub canopy height

 Methods

 Field survey in Nuup Kangerlua

We conducted a stratified systematic plant survey along the length of Nuup Kangerlua (NK) fjord in Soutwesth Greenland (Fig. 1 in Chardon et al. 2022; following Nabe-Nielsen et al., 2017). At five distinct sites, we sampled along elevational gradients to collect data on presences, absences, abundance, and species composition of all woody species using a 0.7 x 0.7 m pin-point frame (Fig. 1e in Chardon et al. 2022). For model training, we converted these pin-point data to percent cover estimates based on the number of pins dropped (n = 25 per plot) and averaged them across the 119 spatio-climatic grids (see next section) corresponding to the plot locations (for details see Appendix S2 in Chardon et al. 2022).

 Field survey in Kangerluarsunnguaq

We conducted a random stratified plant survey in Kangerluarsunnguaq (K) fjord in Southwest Greenland. We used a preliminary Species Abundance Model trained with summed pin counts of _Betula nana_ in NK fjord (see Fig. S1.3 in Chardon et al. 2022) to stratify the ~ 27 x 17 km fjord landscape into low, medium, and high abundances classes. We randomly selected 90 x 90 m spatio-climatic grids to survey in each class for a total of 200 grids, ensuring that they were accessible by foot or boat (for details see Appendix S2 in Chardon et al. 2022). Within each grid, we sampled within three 1 m2 quadrats arranged in a randomly rotated equilateral triangle centered on the mid-point of the cell. We used a gridded sampling quadrat with 1% delineations (Fig. 1h in Chardon et al. 2022) to record woody species presences, absences, and composition, estimated percent cover, and measured maximum shrub species vegetatitve height. At every plot, we also visually scanned the area in a 20 m radius from the plot and recorded the presence of any additional shrub species to estimate grid-level species richness. As in NK fjord, we averaged these data at the grid level (for details see Appendix S2 in Chardon et al. 2022).

 Biotic variables

We calculated biotic microscale variables from the plant survey data collected in NK and K fjords. We calculated shrub species richness, diversity, and competition (i.e. sum of non-B. nana or non-S. glauca pin hits or percent cover). In K fjord, we also calculated canopy height as the community weighted mean (by abundance) of maximum vegetative shrub height.

 Climate variables

We computed high resolution temperature, precipitation, and insolation for local scale data for the study area by statistically downscaling climate time series (1982 - 2013) from the monthly CHELSA data (Karger et al. 2017). We downscaled these data from 30 arc sec (~ 400 m at the latitude of our study) to our target grid size of ~ 90 m with geographic weighted regression and using the MEaSUREs Greenland Ice Mapping Project (GIMP) Digital Elevation Model (DEM) v. 1 (Howat et al., 2014, 2015). We then calculated 30-year averages of the climate parameters: average summer (June – August) maximum temperature, yearly maximum temperature, yearly minimum temperature, temperature continentality (yearly max. - min. temperatures), cumulative Spring (March – May) precipitation, cumulative summer precipitation, and average summer incident solar radiation (henceforth, insolation) (for calculation details see Appendices S2, S3 in Chardon et al. 2022 and Appendix S2 in von Oppen et al. 2021).

 Topography and terrain wetness indicator variables

We calculated several topographic and terrain wetness indices at a local scale. We derived slope, aspect, and the SAGA wetness index (hereafter TWI; Boehner et al., 2002; Boehner and Selige, 2006) from the GIMP DEM. TWI is a measure of how ‘wet’ an area is, based on water drainage from the surrounding landscape. We also calculated the tasseled cap wetness component (hereafter TCW, Crist and Cicone 1984) from satellite images (for details see Appendices S2, S3 in Chardon et al. 2022) as an alternative measure of wetness.

 Computer code

Attached as zip file and available on GitLab (https://gitlab.com/nathaliechardon/gl_microclim)

 Third-party data

Data used to calculate climate, topography, and terrain wetness indicator variables are publicly available (see Appendix S2 in Chardon et al. 2022 for all data references).

accessible-shrub-forest

display_name: accessible-shrub-forest

arctic

display_name: arctic

climate

display_name: climate

field-data

display_name: field-data

sdm

display_name: sdm

validation

display_name: validation

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: Greenland shrubs and microclimate


lidar-davos-wolfgang

maintainer: Patric Seifert

title_for_slug: lidar-davos-wolfgang

en: raclets clouds lidar polly tropos

en: Raman Lidar Davos

en: A portable Raman lidar system (Polly) from Leibnitz Institute for Tropospheric Research (Tropos) was deployed at Davos Wolfgang (LON: 9.853594, LAT: 46.835577). Please use this [link](http://polly.tropos.de/?p=lidarzeit&Ort=39), to be directly forwarded to the Davos location and select the date of interest from the calendar (bold numbers). The data can be requested directly at the Polly team.

clouds

display_name: clouds

lidar

display_name: lidar

polly

display_name: polly

raclets

display_name: raclets

tropos

display_name: tropos

en: LIDAR Davos Wolfgang


snow-depth-mapping

maintainer: Mauro Marty

title_for_slug: snow-depth-mapping

en: snow-hydrology snow-depth dsm image-matching snow-water-equivalent aerial-imagery avalanche

en: Snow depth map 20120320

media_type: image/tiff

en: Snow depth map generated from ADS 80 imagery (CIR). GSD of imagery = 0.25 m

format: TIFF

mimetype: image/tiff

en: Snow depth map 20100416

en: Snow depth map 20160126

en:
Snow depth map generated from ADS 100 imagery (CIR). GSD of imagery = 0.16 m
Because of very diffuse light conditions at time of image acquisition the quality of the resulting snow depth values are in some regions quite poor.

media_type: application/pdf

format: PDF

mimetype: application/pdf

en: Snow depth map 20150415

en: Snow depth map 20160309

en: Snow depth map 20160420

en: Snow depth map 20130415

en: Snow depth map 20140417

en: Snow depth map generated from ADS 100 imagery (CIR). GSD of imagery = 0.18 m

en:
The available datasets are snow depth maps with a spatial resolution of 2m generated from image matching of ADS 80/100 data. Image acquisition took place at peak of winter (time when the thickest snowpack is expected). The snow depth maps are the difference of a summer DSM from the winter DSM of the corresponding date . The summer DSM used is a product of image matching of ADS 80 data from summer 2013. In the available products buildings, vegetation and outliers were masked (set to NoData).
For the elimination of buildings the TLM layer (swisstopo) was used, because this layer might not represent exactly the
state of infrastructure at time of image acquisition, it is possible that mainly in dense settlement some buildings were not successfully masked. For the relevant area above treeline the masking of buildings showed good results. Vegetation got masked for a height above ground > 1m and was detected in a combination of summer and winter data sets. As Outliers were considered unrealistic snow depths caused by a failure of the image matching algorithm. Snow depths > 15m and smaller than < -15m were classified as outliers. Negative snow depth were kept, because of an uncertainty in image orientation accuracy. It is expected that in regions with negative snow depth also positive snow depth are underestimated by the same amount, which means that an estimation of snow volume should be carried out summing up the absolute values of snow depth (also the negative ones). For volume estimation in small regions the user has to take into account, that orientation accuracy of the images is roughly around 1-2 GSD (30cm), which propagates directly to the snow depth product. Areas which are not covered by snow got assigned a value of 0 as snow depth.

The work is published in:

Bühler, Y.; Marty, M.; Egli, L.; Veitinger, J.; Jonas, T.; Thee, P.; Ginzler, C., (2015). Snow depth mapping in high-alpine catchments using digital photogrammetry. Cryosphere, 9 (1), 229-243. doi: 10.5194/tc-9-229-2015

aerial-imagery

display_name: aerial-imagery

avalanche

display_name: avalanche

dsm

display_name: dsm

image-matching

display_name: image-matching

snow-depth

display_name: snow-depth

snow-hydrology

display_name: snow-hydrology

snow-water-equivalent

display_name: snow-water-equivalent


en: relative-humidity meteo long-term climate-change temperature par swiss-forest-lab meteorology wind-speed precipitation

en: Data plot of the field station (SCF)

en: Data overview for air temperature, relative humidity, precipitation, PAR, wind speed.

en: Site photo of the field station (SCF)

en: Site photo of the field station from above (viewing downwards the slope).

en: Field station data (SCF)

en: Data file.

en: Site aerial photo (Schänis)

en: Site aerial photo from both Schänis stations. Source: Google. 2016. Site aerial photo from both Schänis stations. Retrieved November 11, 2016, from https://www.google.ch/maps

en: Forest station data (SCB)

en: Further details on the data repository

en: Meta data documentation.

en: Data plot of the forest station (SCB)

en: Site photo of the forest station (SCB)

en: Site photo of the forest station from below (viewing upwards the slope).

en: High quality meteorological data are needed for long-term forest ecosystem research, particularly in the light of global change. The long-term data series published here comprises almost 20 years of measurements for two meteorological stations in Schänis in Switzerland where one station is located within a natural mixed forest stand (SCB) with European beech (_Fagus sylvatica_; 130-150 yrs), European silver fir (_Abies alba_; 130-150 yrs) and European ash (_Fraxinus excelsior_; 130-150 yrs) as dominant tree species. A second station is situated in the very vicinity outside of the forest (field station, SCF). The meteorological time series are presented in hourly time resolution of air temperature, relative humidity, precipitation, photosynthetically active radiation (PAR) and wind speed. Schänis is part of the Long-term Forest Ecosystem Research Programme (LWF) established and maintained by the Swiss Federal Research Institute WSL.

climate-change

display_name: climate-change

long-term

display_name: long-term

meteo

display_name: meteo

meteorology

display_name: meteorology

par

display_name: par

precipitation

display_name: precipitation

relative-humidity

display_name: relative-humidity

swiss-forest-lab

display_name: swiss-forest-lab

temperature

display_name: temperature

wind-speed

display_name: wind-speed

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: Schänis, Switzerland: Long-term forest meteorological data from the Long-term Forest Ecosystem Research Programme (LWF), from 1998 onwards


en: snow-hydrology meteorological-data snowpack catchment-data rain-on-snow

media_type: application/zip

en: The file contains all data needed to run simulations with the snow cover model SNOWPACK.

format: ZIP

mimetype: application/zip

media_type: text/plain

format: TXT

mimetype: text/plain

en: Meteorological data used to run SNOWPACK for 58 catchments in the Swiss Alps. The data consists of a 2 km grid of "virtual meteorological stations" for each catchment. It was used to simulate snow cover processes during rain-on-snow events, therefore meteorological data of each catchment contains at least one rain-on-snow event. Further information can be found in the attached readme.txt and in Würzer & Jonas et al. (2017), currently under review in Hydrological Processes.

catchment-data

display_name: catchment-data

meteorological-data

display_name: meteorological-data

rain-on-snow

display_name: rain-on-snow

snowpack

display_name: snowpack

en: Meteorological data for investigation of rain-on-snow events in 58 catchments in Switzerland


maintainer: Peter Bebi

en: vegetation climate-change carbon-dioxide stillberg experiment soil-temperature

en: Metadata FACE Stillberg Data File Description

en: List of descriptions for each of the .csv FACE data files.

en: Metadata FACE Stillberg Experimental Design

en: Schematic illustration and tabular listing of the FACE experimental design.

en: Data FACE Stillberg

en: Folder in .zip format containing the FACE datasets.

en: Project Description FACE Stillberg

media_type: text/html

en: Link to FACE project description on the WSL website.

format: HTML

en:
 Background information

High elevation ecosystems are important in research about environmental change because shifts in climate associated with anthropogenic greenhouse gas emissions are predicted to be more pronounced in these areas compared to most other regions of the world. This project involved a Free Air CO2 Enrichment (FACE) and soil warming experiment located in a natural treeline environment near Davos, Switzerland (Stillberg, 2200 m a.s.l.). Elevated atmospheric CO2 concentrations (+200 ppm) were applied from 2001 until 2009, and a soil warming treatment (+4 °C) was applied from 2007 until 2012. The combined CO2 enrichment and warming treatment reflects conditions expected to occur in this region in approximately 2050. A broad range of ecological and biogeochemical research was carried out as part of this environmental change project.

 Experimental design

The experiment consisted of 40 hexagonal 1.1 m² plots, 20 with a *Pinus mugo* ssp. *uncinata* (mountain pine, evergreen) individual in the centre and 20 with a *Larix decidua* (European larch, deciduous) individual in the centre. A dense cover of understorey vegetation surrounded the tree in each plot, including the dominant dwarf shrub species *Vaccinium myrtillus* (bilberry), *Vaccinium gaultherioides* (group *V. uliginosum agg.*, northern bilberry) and *Empetrum nigrum* ssp. *hermaphroditum* (crowberry) plus several herbaceous and non-vascular species.
At the beginning of the experimental period, the 40 plots were assigned to ten groups of four neighbouring plots (two larch and two pine trees per group) in order to facilitate the logistics of CO2 distribution and regulation. Half of these groups were randomly assigned to an elevated CO2 treatment, while the remaining groups served as controls and received no additional CO2. In spring 2007, one plot of each tree species identity was randomly selected from each of the 10 CO2 treatment groups and assigned a soil warming treatment, yielding a balanced design with a replication of five individual plots for each combination of CO2 level, warming treatment and tree species.

 Data description

Soil and air conditions have been monitored closely throughout the study period, with most measurements made during the combined CO2 x warming experiment (2007-2009). The data comprise of air temperature, soil temperature, soil moisture, sapflow, tree diameter and CO2 measurements.

carbon-dioxide

display_name: carbon-dioxide

experiment

display_name: experiment

soil-temperature

display_name: soil-temperature

stillberg

display_name: stillberg

vegetation

display_name: vegetation

en: FACE: Stillberg CO2 enrichment and soil warming study


en: weissfluhjoch longwave-radiation incoming shortwave-radiation outgoing

en: DATA ACCESS

en: Metadata

en: Parameter file

en: Processing doc

en:
Corrected incoming and outgoing shortwave and longwave 2 min radiation measurements at the Weissfluhjoch summit, Davos, CH.

 References
1. Marty, C., Philipona, R., Frohlich, C., Ohmura, A.. Altitude dependence of surface radiation fluxes and cloud forcing in the alps: results from the alpine surface radiation budget network. 2002. Theoretical and Applied Climatology. Volume 72. Issue 3-4. 137-155. http://dx.doi.org/10.1007/s007040200019. 10.1007/s007040200019.
2. Christoph Marty. Surface Radiation, Cloud Forcing and Greenhouse Effect in the Alps. 2000. Institute fuer Klimaforschung ETH. Zuercher Klima-Schriften. Volume 79. http://e-collection.library.ethz.ch/eserv/eth:23491/eth-23491-01.pdf.

incoming

display_name: incoming

longwave-radiation

display_name: longwave-radiation

outgoing

display_name: outgoing

shortwave-radiation

display_name: shortwave-radiation

weissfluhjoch

display_name: weissfluhjoch

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: ASRB_WFJ: Shortwave and longwave radiation measurements (2 min) at the Weissfluhjoch research site, Davos


maintainer: Adam Winstral

en: jules-investigation-model snow-depth snow snow-simulation jim

en: HS and SWE observations

en: Automated (HS) and manual (SWE) data used to evaluate model simulations

en: Station forcing data

en: All forcing data need to run JIM at HS and SWE stations. These are data downscaled directly from COSMO NWP data (WY14, WY15) and further enhanced by additional station observations of snow depth (HS) and air temperature (Ta) in WY17. Further information can be found in README file. Note that in WY14 and WY15, shortwave radiation was not split into direct and diffuse (not necessary for JIM) and that the default method in JIM for splitting precipitation phase was used. In WY 17, direct and diffuse were combined as input to JIM and JIM was forced with pre-processed liquid and solid precipitation phases.

en: DEM

en: 1-km resolution DEM used for downscaling gridded NWP data to stations and for distributing BDE evaluations at HS-stations to SWE-stations

en: File/data descriptor

en: These data were used to drive and evaluate Jules Investigation Model (JIM) snow simulations. The data provided are the forcing data used for the "deterministic" runs as described in Winstral et al., 2019. The bias-detecting ensemble (Winstral et al., 2019) used observed snow depths (HS) to detect biases in these deterministic simulations related to precipitation and energy inputs to JIM. Simulations that included the BDE evaluations substantially improved JIM simulations.

jim

display_name: jim

jules-investigation-model

display_name: jules-investigation-model

snow

display_name: snow

snow-depth

display_name: snow-depth

snow-simulation

display_name: snow-simulation

en: Meteorological data used to develop and validate the bias-detecting ensemble (BDE)


maintainer: Virginie Marques

en: fish marine fjord biodiversity plankton environmental-dna dna-metabarcoding

en: Metabarcoding data

en: Raw metabarcoding data for both primers (teleo and 18S) and corresponding file to perform the demultiplexing and primer trimming

en: Code, data and figures

en: Here there are all the data and code to reproduce the figures and analysis presented in the paper, with a README.md file

en:
This dataset contains the raw environmental DNA data associated with the publication *Environmental drivers of eukaryotic plankton and fish biodiversity in an Arctic fjord* in the journal Polar Biology (2023).

 Methods

**Sampling**
We sampled the Lilliehöök fjord on the west coast of Spitsbergen (Svalbard, Norway) over 3 days from 3 to 5 of August 2021. Samples were taken from the glacier front up to the fjord mouth of the Krossfjorden system, around 30 km long, after the Lilliehöök fjord merged with the mouth of Möller fjord. The fjord’s maximum depth has been recorded at 373 m (Svendsen et al. 2002) and has no sill at its entrance, thereby facilitating water exchange with the open ocean of the West Spitsbergen Current. We used a research vessel to sample 5 sites for a total of 15 samples, sampling 3 depths per site (3-m, chlorophyll a maximum and 85-m, unless sea floor was shallower). Shallow and intermediate samples between 3-m and 12-m represent ~35-L of water filtered in-situ using long tubing and a peristaltic pump, and all other deeper samples were taken from a total of 3 Niskin bottles (General Oceanics), representing 22-L of water sampled per sample. Water was filtered through a VigiDNA filtration capsule (SPYGEN) with a 0.20-µm pore size using an Athena peristaltic pump (Proactive Environmental Products, Bradenton, Florida) with a flow rate of ~1-L/min. Each sample was handled with single use tubing and gloves.

**Molecular**
To perform the amplification, we used two sets of primers: teleo (forward: ACACCGCCCGTCACTCT, reverse: CTTCCGGTACACTTACCATG; Valentini et al. 2016) and the universal eukaryotic 1389F/1510R primer pair, amplifying the V9-18S rDNA gene (Amaral-Zettler et al. 2009) (forward: TTGTACACACCGCCC, reverse: CCTTCYGCAGGTTCACCTAC).

 Data content:

+ Metabarcoding data: This zip file contains the 2 sequencing libraries filtered to only retain the samples used in the present study.
+ Code, data and figure: This zip file contains all data and code to reproduce the figures and the analysis in the study, with an associated README explaining the content of each folder.

 Additional informations
For more details, please see the Methods in the associated publication: DOI: 10.1007/s00300-023-03187-9.

biodiversity

display_name: biodiversity

dna-metabarcoding

display_name: dna-metabarcoding

environmental-dna

display_name: environmental-dna

fish

display_name: fish

fjord

display_name: fjord

marine

display_name: marine

plankton

display_name: plankton

en: Data: Environmental drivers of eukaryotic plankton and fish biodiversity in an Arctic fjord


maintainer: Merin Reji Chacko

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

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: Genomic data

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

spatial-ecology

display_name: spatial-ecology

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


backward-trajectories

maintainer: Michael Sprenger

title_for_slug: backward-trajectories

en: raclets atmospheric-dynamics backward-trajectories complex-topopgraphy alps lagrangian-analysis cosmo

en: Backward Trajectories

en: The trajectories are started from surface up to 5000 m altitude, with an equidistant vertical spacing of 200 m, and calculated 120 h backward in time. As long as the trajectories stay in the COSMO1 domain (essentially the Alpine region), as run operationally at MeteoSwiss, the COSMO analysis wind fields are used. When the trajectories leave this domain, they are extended further backward in time based on ECMWF analysis data. The following fields are traced along the trajectories: longitude, latitude, geopotential height, pressure, specific humidity, temperature and surface topography. Furthermore, it is indicated for each trajectory time instance on which model data, COSMO or ECMWF, the trajectory time is based. Finally, the trajectories are started every hour in the specified time period, and positions and fields are available every 10 min. Each day is saved as a separate file. The last 8 digits of the file names indicate the starting date of the trajectories.

en: Backward trajectories were calculated from two positions: Davos Wolfgang (LON: 9.85361, LAT: 46.83551) and Weissfluhjoch (LON: 9.80646 LAT: 46.83304) for the time period February 2 until March 27 2019 using COSMO or ECMWF, respectively.

alps

display_name: alps

atmospheric-dynamics

display_name: atmospheric-dynamics

backward-trajectories

display_name: backward-trajectories

complex-topopgraphy

display_name: complex-topopgraphy

cosmo

display_name: cosmo

lagrangian-analysis

display_name: lagrangian-analysis

raclets

display_name: raclets

en: Backward  Trajectories


en: stream-water spatially-distributed-sampling precipitation stable-water-isotopes geochemical-solutes

en: The dataset contains daily measurements of volumes, isotopes and solutes of stream water as well as precipitation measured several locations; meteorological variables are added. Date: 18.07.2019

en:
This dataset contain measurements of solute and stable water isotopes in stream water and precipitation in the Alp catchment and two of its tributaries (between 2015 -2018) . The river Alp is a snow-dominated catchment situated in Central Switzerland characterized by an elevation range from 840 to 1898 m a.s.l. The dataset provides solutes (major anions and cations, trace metals) and stable water isotopes and water fluxes (precipitation rates, discharge) at daily intervals from several sampling locations.
An updated version of the isotope dataset is available here: https://www.doi.org/10.16904/envidat.242

geochemical-solutes

display_name: geochemical-solutes

precipitation

display_name: precipitation

spatially-distributed-sampling

display_name: spatially-distributed-sampling

stable-water-isotopes

display_name: stable-water-isotopes

stream-water

display_name: stream-water

en: Daily data of solute and stable water isotopes in stream water and precipitation in the Alp catchment, Central Switzerland


en: single-tree forest-inventory tree-volume terrestiral-laserscanning lidar biomass

en: Individual tree parameters and volume estimates based on TLS point clouds and allometric models

en:
"ASM" denotes volume estimates calculated by allometric scaling models (as used in Swiss NFI), based on tree height, DBH and D7.
"QSM" denotes volume estimates derived from TLS point clouds by quantitative structure models (QSM).
The remaining variables are geometrical features directly calculated from single tree TLS point clouds.
For more detailed variable descriptions see related publication.

en:
 Dataset
This dataset is based on terrestrial laser scanning (TLS) data acquired during winter 2020/2021 in leaf-off conditions, with a Leica BLK 360 instrument following a tree-centric scanning pattern.
The data was acquired on two sites (47.42°N 8.49°E and 47.504°N, 7.78°E), both of which were managed mixed temperate forest stands.
Individual trees were semi-automatically segmented from the co-registered TLS point clouds.

 Background
Accurate estimates of individual tree volume or biomass within forest inventories are essential for calibration and validation of biomass mapping products based on Earth observation data.
Terrestrial laser scanning (TLS) enables detailed and non-destructive volume estimation of individual trees, with existing approaches ranging from simple geometrical features to virtual 3D reconstruction of entire trees. Validating such approaches with weight measurements is a key step before the integration of TLS or other close-range technologies into operational applications such as forest inventories.
In this study, we firstly evaluate individual tree volume estimation approaches based on 3D reconstruction through quantitative structure models (QSM) against destructive reference data of 60 trees and compare them to operational allometric scaling models (ASM).
Secondly, we determine the explanatory power of TLS-derived geometric parameters regarding total tree, stem, coarse wood and fine branch volume.

biomass

display_name: biomass

forest-inventory

display_name: forest-inventory

lidar

display_name: lidar

single-tree

display_name: single-tree

terrestiral-laserscanning

display_name: terrestiral-laserscanning

tree-volume

display_name: tree-volume

en: Individual tree TLS point clouds for tree volume estimation


maintainer: Franziska Gerber

en: static-data cosmo-wrf wrf topography landuse cryowrf

en:
Example GEOGRID.TBL to use with the 1s static data;
Note about naming:
* 121 -> 1-2-1 topography smoothing applied to dataset
* 1 -> one smoothing cycle applied to the data (needs to be changed depending on the chosen resolution to avoid too steep slope angles)

en: Static data for WRF - Landuse

en: Example namelist.wps to use with the 1s static data

en: Documentation

en: Documentation of the dataset

en: Static data for WRF - Soiltype bottom

en: Static data for WRF - Soiltype top

en: Static data for WRF - Topography

en: Static input data (topography, landuse and soiltype) for the WRF preprocessing system WPS is provided for Switzerland and its neighboring countries between 45-49 N and 4-12 E. The data is provided at a resolution of 1 s. Topography is based on the Aster dataset, while landuse is extracted from the Corine landuse dataset. Soil type is set to silty clay loam for the entire domain. This static input data is valid for WRF and CRYOWRF.

cosmo-wrf

display_name: cosmo-wrf

cryowrf

display_name: cryowrf

landuse

display_name: landuse

static-data

display_name: static-data

topography

display_name: topography

wrf

display_name: wrf

educ

en: Education, culture and sport

envidat

en: EnviDat: the Environmental Data Portal

en: High resolution static data for WRF over Switzerland


en: land-use switzerland land-use-change urbanization statistical-model modeling landscape-services

en: Data for Assessing potential landscape service trade-offs driven by urbanization in Switzerland

en:
The provided folder structure follows the set up of the scripts.
Data is only provided when it has been fully produced by us, otherwise dummies are given.
For data that will be produced by one of the scripts, no dummies are given.
The folders may contain sub-folders, which would be filled if the scripts were all run

 00_Analysis_Data
Data produced throughout the process of the calibration and projection that is later needed for analysis

 01_Raw_Data
Primary data from external sources that were used to compile the rasters and numbers used during the calibration and projection of landscape transitions as well as service calculation

 02_Prepared_Data
Data that will be prepared for further use by scripts are put in here
Additionally it contains the parameter sheets for the transition predictors that we compiled

 03_Model_Data
 Model outputs
Folder were the projection models statistics will be saved
 Models
Folder into which the actual transition models will be saved
 Residuals
Folder into which data on models residuals will be saved for future use

 04_Projected_Data
The output of the projections will be saved into this folder

 05_Service_Data
Any service calculations will be saved in here

 06_Results_Analysis
Any Analysis plots and tables as well as intermediate data will be saved here in the respective sub-folder

en: Scripts for Assessing potential landscape service trade-offs driven by urbanization in Switzerland

en:
Scripts ordered by their main purpose within sequential folders in this ReadMe marked with

Within the folders the capital letters refer to the parallel or sequential use of the scripts; scripts here in ReadMe are marked with

 00_Function Scripts
 Functions.r
Script containing several functions for analyzing statistical models: cohen.kappa, meva.table, D2, max-Tss, plot-TSS

 Service_functions.R
Script containing functions for calculating all services and returning sums (and median for bd and rec) as well as rasters

 01_Data Preparation
 A_AS_raster_preparation.R
Preparation of the land use rasters for the years 1985, 1997, and 2009 based on the original Arealstatistik (AS/ASCH); Assigning our categories and assining new values to all "construction sites" for calibrating the models
For model projection starting point (2009) and for service calculations (all ASCH years) the "other" categories were assigned to the land use categories based on dominant neighbor, so that there were no empty cells
Creation of water & mountainous area raster that stayed stable throughout the projections
Creation of MFH raster (2009), to have as base for all new projection years, as this category never becames any other

 B_Factors_preparation.R
Preparation of the factor rasters that were used to calculate service values per cell (see Table 2): LWfactor, Transportation, Vol, Rivers, Lakes, slope, TWW, Hazard_risk

 B_Predictors_preparation.R
Preparation of the raster of the predictors used for calibrating (ASCH years) and projecting (stable) the transition models that do not depend on the land use categories: Temperature (ASCH years), solar radiation (stable), Public transportation access (stable), Elevation (stable), Workers density (ASCH years), Population change (ASCH transitions)

 B_Regions_preparation.R
Preparation of bioregions as raster to be used to mask asxxxx later to calculated services and land use area just for one region

 C_Pred_proj.R
Projecting the dynamic predictors into the future for projecting the land use transitions with the model: Linear extrapolations for workers densities and population; more detailed extrapolation of temperature (based on data for all stations that matched between the temp table we used for the calibration period and the projections from CS2M, and then making a spatial interpolation for all years based on the interpolation of temperature for all years per station)

 02_Model calibration
 A_Bioreg_pred_corr.R
Calculating correlation between the predictors for each bioregion and land use category, Output are those with too high correlation so that one predictor can be removed from transitions were both predictors occur

 A_trans_numbers_bioreg.R
Calculate transition numbers for each bioregion to decide which transitions to primarily consider

 B_Bioreg_ext_eval.R
Calculating TSS based on the external evaluation for the bioregion transitions that happened often enough to try to model them (calibration data: 85-97, evaluation data: 97-09)

 B_Bioreg_int_eval.R
Calculating TSS based on the internal evaluation for the bioregion transitions that happened often enough to try to model them (calibration data: 70%, evaluation data: 30%)

 C_Bioreg_TSS_analysis.R
Extracting TSS numbers from internal and external evaluation, calculating mean and median for each transition for each region for each evaluation method and saving as csv per region to be able to select only the transitions with high enough model performance

 D_Bioreg_Models_for_prediction.R
Calibration of the models that were then used to project land use transitions into the future; calibrated separately for each bioregion

 E_Residuals_trans_models.R
Calculation of Moran's I statistics to analyze the residuals of the land use transition models

 03_Projections
 A_Bioreg_Projections_run.R
Master script for: Extrapolaitng into the future with the regional models and then assembling for each time step to calculate new AS predictors; Several Outputs: txt file to test for NAs in Predictors, txt file with random seed number for sampling, txt file with times for calculation steps (check progress of script while running), csv sheet with projected transition frequencies, tif-rasters for every region and time step, pdf with raster plot for every region and time step

 04_Service calculation
 A_Bioreg_as_services.R
Calculate services per bioregion for years 1985, 1997, 2009

 A_Service_calculation_bioregions.R
Extracting service numbers(sums) per bioregions for all projection runs and storing them in a list of matrixes to be available for further plotting; can be run for swiss wide projections or regional ones

 05_Analysis
 A_Bioreg_ASCH_development.R
Extracting the occurrence of each category per region for all runs (first part), then for ASCH years, and then plotting them nicely; only works for regional projections

 A_Bioreg_Predictors_importanceD2.R
Calculating D2 for each transition and each considered predictor from bivariate models to get value of importance

 B_Bioreg_Pred_imp_analysis.R
Using calculated D2 to sort Predictors according to their importance for each transition

 A_Bioreg_Spatial_results_analysis.R
Plotting randomly sampled runs for ASCH and services to analyses their spatial development

 A_Bioreg_Transition_numbers_check_v1.R
Analyzing the frequency for all transitions for all regions and producing the point plots for each transition separately

 A_Bioreg_Transition_numbers_check_v2.R
Analyzing percentage and numbers of all transitions but plotting them per region and originating ASCH category

 B_Transition_Analysis.R
Further Analysis of transition numbers

 A_Service_analysis.R
Plotting of the service development for bioregions in several ways for analyzing

en:
Data and scripts of publication:

Madleina Gerecke, Oskar Hagen, Janine Bolliger, Anna M. Hersperger, Felix Kienast, Bronwyn Price, Loïc Pellissier (2019) Assessing potential landscape service trade-offs driven by urbanization in Switzerland. Palgrave communications.

Contains land use projections for Switzerland and scripts and data for these projections as well as the calculation of landscape services.

Data Folder:
Contains sub-folder with the data necessary for this study (provided were no copyright issues, otherwise placeholders with descriptions), and folders where produced data may be stored

Scripts Folder:
Contains scripts organized into subfolders depending on their purpose

Note: Some abbreviations within the scripts and data are derived from German words and not English.

land-use

display_name: land-use

land-use-change

display_name: land-use-change

landscape-services

display_name: landscape-services

modeling

display_name: modeling

statistical-model

display_name: statistical-model

switzerland

display_name: switzerland

urbanization

display_name: urbanization

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: Land use projections and services for Switzerland


maintainer: Giulia Francesca Azzurra Donati

en: ecological-corridors integrated-modelling biodiversity human-dominated-landscapes circuit-theory urban-spatial-planning

en: Amphibian monitoring data

en: Processed amphibian occurrence data (2017-2019) in the cantons of Aargau and Zürich. The dataset includes information for the following species: _Alytes obstetricans_,_Bombina variegata_, _Bufo bufo_, _Hyla arborea_, _Ichtyosaura alpestris_, _Lissotriton helveticus_, _Lissotriton vulgaris_, _Rana temporaria_, _Salamandra salamandra_, and _Triturus cristatus_.

en: Binarized "green" and "grey" landcover data (Cantons of Aargau and Zürich)

en: "Green" landcover refers to lawns and vegetated urban surfaces such as, for example private gardens, public parks, cemeteries, green stripes along roadsides, etc. While "grey" landcover refers to impervious grounds such as roads, troittoirs, other impervious. Binarized maps, 30x30m resolution.

en: Amphibian breeding sites of national importance - cantons of Aargau and Zürich

en: Amphibian breeding sites of national importance (focal nodes) in the cantons of Aargau and Zürich, 30x30 m resolution, binarised ascii format.

en: Amphibian species specific landscape resistance maps.

en: For each amphibian species we used the weighted average Ensemble model suitability map and converted it to a resistance map using an exponential decay function following (Duflot et al., 2018) using the species-specific mpa threshold previously computed (Preau et al., 2020). The function assigns a resistance value of 1,000 when habitat suitability equals zero, and a value of one when habitat suitability is greater than or equal to the binarization threshold. The exponential shape strengthens the barrier effect of less favorable areas.

en: Amphibian whole life cycle predictors - 10m resolution

en:
Amphibian whole life cycle predictors include 6 variable types:
(1)	Topographic – slope [°]: derived from the Swiss Topographical Landscape model (swissTLM 3D 2015) at 2 m resolution (elevation uncertainty ± 0.5m) and, subsequently, aggregated to a median value;
(2)	Hydrologic: two predictors including nearest distance to water [m] (all water-related objects and rasterized lotic, lentic and reedbeds from the regional cadastral maps – AV: Daten der Amtliche Vermessung) and runoff coefficient [C] (between 0 and 1 relating amount of runoff to amount of precipitation, mapped AV: Daten der Amtliche Vermessung data against literature values for different land covers);
(3)	Edaphic – soil moisture variability (not available): can gathered from the spatial modelling of Ecological Indicator Values in Switzerland (Descombes et al., 2020) and resampled from 100m to 10m;
(4)	Vegetation: we calculated the median and standard deviation of the Normalized Difference Vegetation Index (NDVI) from all available cloud free Sentinel-2 pixels available between April and October for the years 2016 to 2019 (Drusch et al., 2012) and the median vegetation height [m] (not available) can gathered from Ginzler and Hobi (2015);
(5)	Land-use derived: includes three predictors, grassland density [grassland/cell] (not available) - can be gathered from Pazur et al. (2021), total grasslands area evaluated using a spatial weight matrix and a 250m neighborhood radius around each cell; urbanization [buildings/cell] – average building density for a 250m neighborhood around each cell based on the AV: Daten der Amtliche Vermessung ; and traffic intensity [vehicles/day] – average daily vehicle count (Nationales Personenverkehrsmodells);
(6)	Movement-ecology related: includes three predictors of proximity – nearest forest distance [m]; nearest rock-gravel and sandy area (RGS) distance [m] and nearest road distance [m] (considering any road type) – all calculated based on the AV: Daten der Amtliche Vermessung maps.

en: The data includes (1) amphibian occurrence data (2017-2019) for ten species across the cantons of Aargau and Zürich gathered from the Coordination Center for the Protection of Amphibians and Reptiles of Switzerland (http://www.karch.ch), (2) amphibian whole-life cycle environmental predictors (i.e. topographic, hydrologic, edaphic, vegetation, land-use derived, movement-ecology related), and (3) local urban "green" and "grey" landcover data which can be used to identify opportunities for Blue-Green Infrastructure (through green or grey transitions) in support of regional landscape connectivity.

biodiversity

display_name: biodiversity

circuit-theory

display_name: circuit-theory

ecological-corridors

display_name: ecological-corridors

human-dominated-landscapes

display_name: human-dominated-landscapes

integrated-modelling

display_name: integrated-modelling

urban-spatial-planning

display_name: urban-spatial-planning

en: Amphibian and urban-rural landscape data Swiss Lowlands


maintainer: Martin Schneebeli

en: depth-hoar rounded-snow weak-layer 3d-model snow 3d-print snow-cast new-snow

en: Description of snowtypes, filenames and other metadata

en: This file contains information about the stl-files of the different snow models. Snowtype (Schneeart), International Snow Classification, preview picture, notes about the origin of the snow, filename of the stl-data, and physical size of the model are given.

en: Snow models in STL-format

en: The zipped file contains all data described in the file 3d_snow_models_metadata. The stl-files should be ready for additive manufacturing.

en: The dataset contains several snow models in the Standard Tesselated Geometry File Format (stl) for 3D visualization, printing and additive manufacturing. Different snow types are available (new snow, rounded snow, depth hoar, buried surface hoar, graupel).

depth-hoar

display_name: depth-hoar

new-snow

display_name: new-snow

rounded-snow

display_name: rounded-snow

snow

display_name: snow

snow-cast

display_name: snow-cast

weak-layer

display_name: weak-layer

educ

en: Education, culture and sport

envidat

en: EnviDat: the Environmental Data Portal


maintainer: Frank Techel

en: avalanche-accident-statistics long-term-trends avalanche-accident avalanche-statistics avalanche-fatalities

en: Data avalanche fatalities 1969/1970 - 2014/2015

en: The data comprises avalanche fatality data from the Alpine regions in the seven countries Austria, France, Germany, Italy, Liechtenstein, Slovenia, and Switzerland.

en:
During the last 45 years, about 100 people lost their lives in avalanches in the European Alps each year. Avalanche fatalities in settlements and on transportation corridors have considerably decreased since the 1970s. In contrast, the number of avalanche fatalities during recreational activities away from avalanche-secured terrain doubled between the 1960s and 1980s and has remained relatively stable since, despite a continuing strong increase in winter backcountry recreational activities.

Data complementing Figure 2 in:
_"Avalanche fatalities in the European Alps: long-term trends and statistics"_, by Techel, F., Jarry, F., Kronthaler, G., Mitterer, S., Nairz, P., Pavšek, M., Valt, M., and Darms, G.

Data description:
please refer to section 2 (Data and Methods) in the mentioned publication

avalanche-accident

display_name: avalanche-accident

avalanche-accident-statistics

display_name: avalanche-accident-statistics

avalanche-fatalities

display_name: avalanche-fatalities

avalanche-statistics

display_name: avalanche-statistics

long-term-trends

display_name: long-term-trends

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: Avalanche fatalities in the European Alps (1969/1970 - 2014/2015)


maintainer: Daniela Brito Melo

en: drifting-snow mixed-grain-transport snow-cohesion saltation large-eddy-simulations

en: Data in Figures

en: Simulation results presented in Figures 1 to 11 of the research article "Modeling snow saltattion: the effect of grain size and interparticle cohesion" in csv format.

en: LES-LSM code

en: Source code used to perform the analysis presented at the research article "Modeling snow saltation: the effect of grain size and interparticle cohesion". The source code is also available at the WSL/SLF GitLab Repository (https://gitlabext.wsl.ch/atmospheric-models/les-lsm).

en:
This dataset includes the parallel application and the main results supporting the research article "Modeling snow saltation: the effect of grain size and interparticle cohesion" published at the Journal of Geophysical Research: Atmospheres.
The code is a flow solver based on the Large Eddy Simulation (LES) technique coupled with a Lagrangian Stochastic Model (LSM). The interaction of snow particles with the bed is modeled with statistical and physically-based models for aerodynamic entrainment, rebound and splash, following the works of Groot Zwaaftink et al. (2014), Comola and Lehning (2017) and Sharma et al. (2018). This algorithm was also used by Sigmund et al. (2021) to model snow sublimation.

drifting-snow

display_name: drifting-snow

large-eddy-simulations

display_name: large-eddy-simulations

mixed-grain-transport

display_name: mixed-grain-transport

saltation

display_name: saltation

snow-cohesion

display_name: snow-cohesion


maintainer: Ionuț Iosifescu Enescu

en: map 0.5GB

en: Bulk Data Access

en: Link to the S3 bucket where all the data resources can be downloaded in bulk

en: map 0.2GB

en: huge map 100GB

en: map 1GB

en: map preview 0.5MB

mimetype: image/jpeg

en: large map 10GB

en: map 2GB

en:
The attached data are some large GIS raster files (GeoTIFFs) made with Natural Earth data. Natural Earth is a free vector and raster map data @ naturalearthdata.com. The data used for creating these large files was the "Cross Blended Hypso with Shaded Relief and Water". Data was concatenated to achieve larger and larger files. Internal pyramids were created, in order that the files can be opened easily in a GIS software such as QGIS or by a (future) GIS data visualisation module integrated in EnviDat.

Made with Natural Earth. Free vector and raster map data @ naturalearthdata.com

gis

display_name: gis

large-files

display_name: large-files

natural-earth

display_name: natural-earth

qgis

display_name: qgis

en: Large GIS raster data derived from Natural Earth Data (Cross Blended Hypso with Shaded Relief and Water)


weather-station-klosters

maintainer: Maxime Hervo

title_for_slug: weather-station-klosters

en: weather raclets wind klosters temperature precipitation

en: Weather Station Klosters

en: All in one weather station measuring temperature (°C), humidity (%), wind (m s‾ ¹) and precipitation type. The time format is: number of days from January 0, 0000, UTC.

en: A weather station (Lufft WS600) measured meteorological parameters at Klosters (LON: 9.880413, LAT: 46.869019). Detailed information on the specifications can be found [here](https://www.lufft.com/products/compact-weather-sensors-293/ws600-umb-smart-weather-sensor-1832/productAction/outputAsPdf/).

klosters

display_name: klosters

precipitation

display_name: precipitation

raclets

display_name: raclets

temperature

display_name: temperature

weather

display_name: weather

wind

display_name: wind

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.


maintainer: EnviDat Support

en: wind-speed precipitation par swiss-forest-lab climate-change meteorology meteo long-term relative-humidity temperature

en: Data plot of the forest station (LEB)

en: Data overview for air temperature, relative humidity, precipitation, PAR, wind speed.

en: Forest station data (LEB)

en: Data file.

en: Site photo of the forest station (LEB)

en: Site photo of the forest station from below (viewing upwards the slope)

en: High quality meteorological data are needed for long-term forest ecosystem research, particularly in the light of global change. The long-term data series published here comprises almost 20 years of measurements for one meteorological station in Lens in Switzerland which is located within a natural coniferous forest with Scots pine (_Pinus sylvestris_; 150-170 yrs)) as dominant tree species. The meteorological time series are presented in hourly time resolution of air temperature, relative humidity, precipitation, photosynthetically active radiation (PAR) and wind speed. Lens is part of the Long-term Forest Ecosystem Research Programme (LWF) established and maintained by the Swiss Federal Research Institute WSL.

climate-change

display_name: climate-change

long-term

display_name: long-term

meteo

display_name: meteo

meteorology

display_name: meteorology

par

display_name: par

relative-humidity

display_name: relative-humidity

swiss-forest-lab

display_name: swiss-forest-lab

wind-speed

display_name: wind-speed

en: Lens, Switzerland: Long-term forest meteorological data from the Long-term Forest Ecosystem Research Programme (LWF), from 1997 onwards


maintainer: Jürg Schweizer

en: avalanche-size avalanche-activity avalanche-forcasting danger-level snow-avalanche

en: Readme

en: The Readme file contains the description of the two data files.

en: Snow avalanche data

en: This data file includes data on the avalanches mapped in the region of Davos.

en: Avalanche activity data

en: This data file includes data on the avalanche activity per day aggregated from the avalanche data.

en:
These data include all avalanches that were mapped in the region of Davos, Switzerland during the winters 1998-1999 to 2018-2019 (21 years), in total 13,918 avalanches, and the corresponding forecast danger level valid on the day of avalanche occurrence, 3533 days and danger ratings in total.

This avalanche activity data set was analysed and results published by Schweizer et al. (2020). They found that the
number of avalanches per day strongly increased with increasing danger level, but avalanche size was poorly related to avalanche danger level.

The data are provided in two files: the first includes the avalanche data (13,918 records); the second includes the avalanche activity per day (3533 records).
Please refer to the Read-me file for further details on the data.

These data are the basis of the following publication:
Schweizer, J., Mitterer, C., Techel, F., Stoffel, A. and Reuter, B., 2020. On the relation between avalanche occurrence and avalanche danger level. The Cryosphere, 14, 737-750, https://doi.org/10.5194/tc-14-737-2020.

avalanche-activity

display_name: avalanche-activity

avalanche-forcasting

display_name: avalanche-forcasting

avalanche-size

display_name: avalanche-size

danger-level

display_name: danger-level

snow-avalanche

display_name: snow-avalanche

en: Snow avalanche data Davos, Switzerland, 1999-2019