Portal
Suchergebnisse
Results list
Simulated and observed prevalence of dispersal-related traits in tropical reef fish assemblages worldwide
This dataset contains all data and R codes (R Development Core Team, https://www.R-project.org) used in the following publication: Donati GFA, Parravicini V, Leprieur F, Hagen O, Gaboriau T, Heine C, Kulbicki M, Rolland J, Salamin N, Albouy C, Pellissier L. "A process-based model supports an association between dispersal and the prevalence of species traits in tropical reef fish assemblages" accepted by Ecography in August 2019. When using this data and R scripts the above publication should be cited. The interaction of habitat dynamics with species dispersal abilities could generate gradients in species diversity and prevalence of life-history and ecological traits, when the latter are associated with dispersal potential. In this dataset, we use a spatial mechanistic model of speciation, extinction and dispersal, constrained by a dispersal parameter. This model allows to simulate the interplay between reef habitat dynamics over the past 140 million years and dispersal, shaping lineage diversification history and global assemblage composition of over 6000 tropical reef fish species. Global trait distribution data of tropical reef fish are used to evaluate the congruence between simulations and observations.
2013-2020 gas exchange at Pfynwald
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.
Dataset for OGRS 2018 publication
This dataset contains the road and plot data used for the geospatial analysis example showcased in "Fostering Open Science at WSL with the EnviDat Environmental Data Portal", a contribution to the 5th Open Source Geospatial Research and Education Symposium (OGRS), 2018. The example uses Jupyter Notebook to calculate road densities in the neighbourhood of sample plot locations with Python. Road data were extracted from OpenStreetMap, while the point data (sample plots) were generated manually.
Environmental DNA Marine France Evhoe 2019
Environmental DNA complements scientific trawling in surveys of marine fish biodiversity (Dataset 2019) In October 2019 we chose 15 sites from the 2019 EVHOE survey for eDNA sampling. The French international EVHOE bottom trawl survey is carried out annually during autumn in the BoB to monitor demersal fish resources. At each site, we sampled seawater using Niskin bottles deployed with a circular rosette. There were nine bottles on the rosette, each of them able to hold ∼5 l of water. At each site, we first cleaned the circular rosette and bottles with freshwater, then lowered the rosette (with bottles open) to 5 m above the sea bottom, and finally closed the bottles remotely from the boat. The 45 l of sampled water was transferred to four disposable and sterilized plastic bags of 11.25 l each to perform the filtration on-board in a laboratory dedicated to the processing of eDNA samples. To speed up the filtration process, we used two identical filtration devices, each composed of an Athena® peristaltic pump (Proactive Environmental Products LLC, Bradenton, Florida, USA; nominal flow of 1.0 l min–1 ), a VigiDNA 0.20 μm filtration capsule (SPYGEN, le Bourget du Lac, France), and disposable sterile tubing. Each filtration device filtered the water contained in two plastic bags (22.5 l), which represent two replicates per sampling site. We followed a rigorous protocol to avoid contamination during fieldwork, using disposable gloves and single-use filtration equipment and plastic bags to process each water sample. At the end of each filtration, we emptied the water inside the capsule that we replaced by 80 ml of CL1 conservation buffer and stored the samples at room temperature following the specifications of the manufacturer (SPYGEN, Le Bourget du Lac, France). We processed the eDNA capsules at SPYGEN, following the protocol proposed by Polanco-Fernández et al., (2020). We performed library preparation and sequencing at Fasteris (Geneva, Switzerland). Specifically, we prepared four libraries using the MetaFast protocol (a ligation-based method) and sequenced them separately. We carried out paired-end sequencing using a MiSeq sequencer (2 × 125 bp, Illumina, San Diego, CA, USA) on two MiSeq Flow Cell Kits (v3; Illumina), following the manufacturer’s instructions. We analysed the sequence reads using the OBITools package (http://metabarcoding.org/obitools; Boyer et al., 2016), following the protocol described by Valentini et al. (2016). Data content: * rawdata/: contains the raw reads for each individual sample. One archive contains the paired-end reads specified by the _R1 or _R2 suffix as well as individually tagged PCR replicates (if available) together with an archive containing all extraction and PCR blank samples of the library. Reads have been demultiplexed using cutadapt but not trimmed, individual demultiplexing tags and primers remain present in the sequences. * taxadata/: contains the table with all detected taxonomy for each sample after bioinformatic processing (see Polanco et al. 2020 for details; https://doi.org/10.1002/edn3.140) and associated field metadata. * metadata/: contains two metadata files, one related to the data collected in the field for each filter, and the second related to the sequencing process in the lab (including the tag sequence, library name, and marker information for each sample)
Snow Depth Mapping
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
Soil respiration - exclosure experiment
Location of data collection The Swiss National Park (SNP) is located in the southeastern part of Switzerland, and covers an area of 170 km2, 50 km2 of which is forested, 33 km2 is occupied by alpine and 3 km2 by subalpine grasslands. Elevations range from 1350 to 3170 m a.s.l., and mean annual precipitation and temperature are 871 mm and 0.6°C measured at the Park’s weather station in Buffalora (1980 m a.s.l.) between 1960 and 2009 (MeteoSchweiz 2011). Founded in 1914, the SNP received minimal human disturbance for almost 100 years (no hunting, fishing, or camping, visitors are not allowed to leave the trails). Large (> 1 ha) homogeneous patches of short- and tall-grass vegetation characterize the subalpine grasslands. The average vegetation height of short-grass vegetation is 2 to 5 cm. Red fescue (Festuca rubra L.), quaking grass (Briza media L.) and common bent grass (Agrostis tenuis Sipthrob) are the predominating plant species in this vegetation type. Tussocks of evergreen sedge (Carex sempervirens Vill.) and mat grass (Nardus stricta L.) are predominant in the tall-grass vegetation, which averages 20 cm in vegetation height (Schütz and others 2006). Short-grass vegetation developed in areas where cattle and sheep rested (high nutrient input) during agricultural land-use (from 14th century until 1914); tall-grass vegetation developed in areas where cattle and sheep used to graze, but did not rest (Schütz and others 2003, 2006). Herbivores were shown to consume > 60% of the biomass in short-grass compared to < 20% in tall-grass vegetation (Schütz and others 2006). The herbivore community present in the SNP can be divided into four groups based on body size/weight: large [red deer (Cervus elaphus L.) and chamois (Rupricapra rupricapra L.); 30 - 150 kg], medium [marmot (Marmota marmota L.) and snow hare (Lepus timidus L.); 3 – 6 kg], and small vertebrate herbivores (small rodents: e.g. Clethrionomys spp., Microtus spp., Apodemus spp.; 30 – 100 g) as well as invertebrates (e.g. grasshoppers, caterpillars, cicadas, < 5 g). Experimental design We selected 18 subalpine grassland sites (9 short-grass, 9 tall-grass vegetation). The sites were spread across the entire park on dolomite parent material at altitudes of 1975 to 2300 meters. At each site we established an exclosure network (fences) in spring 2009 (early June), immediately after snowmelt. Each exclosure network consisted of a total of five 2 × 3 m sized plots that progressively excluded the different herbivores listed above (further labeled according to the herbivore guilds that had access to the respective plots “All”, “Marmot/Mice/Invertebrates”, “Mice/Invertebrates”, “Invertebrates”, “None”). The “All” treatment was thus accessible to all herbivores, was not fenced and was located at least 5 m away from a 2.1 m tall and 7 × 9 m main fence that enclosed the other four treatments. This fence was constructed of 10 × 10 cm wooden posts and electrical equestrian tape (AGRARO ECO, Landi, Bern, Switzerland; 20 mm width) mounted at 0.7 m, 0.95 m, 1.2 m, 1.5 m and 2.1 m above the ground that were connected to a solar charged battery (AGRARO Sunpower S250, Landi, Bern, Switzerland). We also mounted non-electrically charged equestrian tape at 0.5 m to help exclude deer and chamois, yet allow marmots and hares to enter safely. Within each main fenced area we randomly established four 2 × 3 m plots: (1) The “Marmot/Mice/Invertebrates” plot remained unfenced, thus, with the exception of red deer and chamois, all herbivores were able to access the plot, (2) The “Mice/Invertebrates” plot consisted of a 90 cm high electric sheep fence (AGRARO Weidezaunnetz ECO, Landi, Bern, Switzerland; mesh size 10 × 10 cm) connected to the solar panel and excluded all medium sized mammals (marmots, hares), but provided access for small mammals and invertebrates, (3) The “Invertebrates” plot provided access for invertebrates only and was surrounded by 1 m high metal mesh (Hortima AG, Hausen, Schweiz; mesh size 2 × 2 cm), (4) The “None” plot was surrounded by a 1 m tall mosquito net (Sala Ferramenta AG, Biasca, Switzerland; mesh size 1.5 × 2 mm) to exclude all herbivores. This plot was covered with a roof constructed of a wooden frame lined with mosquito mesh that was mounted on the wooden corner posts. We also treated this plot with a biocompatible insecticide (Clean kill original, Eco Belle GmbH, Waldshut-Tiengen, Germany) when needed to remove insects that might have entered during data collection or that hatched from the soil. !!! The here published data set only contains data for “All”, and “Marmot/Mice/Invertebrates” (= ungulates excluded) plots !!! Data collection In-situ soil CO2 emissions were measured 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) on two randomly selected locations on one subplot within each of the 90 plots. For each measurement the soil chamber (15 cm high; 10 cm diameter) was placed on a permanently installed PVC collar (10 cm diameter) driven five centimeters into the soil at the beginning of the study (June 2009). The measurements were conducted between 0900 and 1700 hours every two weeks from early to early September 2009, 2010, 2011 and 2013. Freshly germinated plants growing within the PVC collars were removed prior to each measurement to avoid measuring plant respiration/photosynthesis. The two measurements collected per plot every two weeks were averaged. Please acknowledge the funding of the study: funded by the Swiss National Science Foundation, SNF grant-no 31003A_122009/1 to Anita C. Risch, Martin Schütz and Flurin Filli
DISCHMEX - High-resolution WRF simulations in complex alpine terrain and station measurements
The data presented here corresponds to the publication "Spatial variability in snow precipitation and accumulation in COSMO-WRF simulations and radar estimations over complex terrain" (Gerber et al., 2018a), which investigates the precipitation variability of snow precipitation in the central northern part of the Grisons (CH) and the publication "The importance of near-surface winter precipitation processes in complex alpine terrain" (Gerber et al., 2018b). The dataset contains: * WRFsimulations: WRF simulation output for simulations with 4x (14x) terrain smoothing with an output timestep of 30 min/5 min and horizontal grid spacings of 1350 m, 450 m, 150 m and 50 m (currently: data available upon request). * StationData: Meteorological station data of 18 meteorological stations in the central northern part of the Grisons with 30 minute resolution for the period 1 January 2016 till 1 May 2016. * ADS80data: Photogrammetrically determined snow depth distribution data over the Dischma valley for the 26 January 2016 and 9 March 2016. Snow heights are corrected for buildings, vegetation (> 1m), outliers, and pixles, which are obivously snow-free on the pictures (Bühler et al., 2015). In addition the snow depth differences (snow depth on 9 March 2016 minus snow depth on 26 January 2016) are provided. For more details about the simulation and observation data, see Gerber et al., 2018 and Gerber and Sharma (2018). Publications: Bühler, Y., Marty, M., Egli, L., Veitinger, J., Jonas, T., Thee, P., and Ginzler, C.: Snow depth mapping in high-alpine catchments using digital photogrammetry. Cryosphere, 9, 229–243, doi:10.5194/tc-9-229-2015, 2015. Gerber, F., Besic, N., Sharma, V., Mott, R., Daniels, M., Gabella, M., Berne, A., Germann, U., and Lehning, M.: Spatial variability in snow precipitation and accumulation in COSMO-WRF simulations and radar estimations over complex terrain, The Cryosphere, 12, 3137–3160, doi:10.5194/tc-12-3137-2018, 2018. Gerber, F., Mott, R. and Lehning, M.: The importance of near-surface winter precipitation processes in complex alpine terrain, Journal of Hydrometeorology, accepted, 2018. Gerber, F., and Sharma, V.: Running COSMO-WRF on very-high resolution over complex terrain. Laboratory of Cryospheric Sciences CRYOS, École Polytechnique Fédérale de Lausanne EPFL, Lausanne, Switzerland. doi:10.16904/envidat.35, 2018.
Elk and bison carcasses in Yellowstone, USA
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.
Dataset for "Sorting and Surging 3D LiDAR and Pulse-Doppler Radar Analysis of a Natural Debris Flow"
LiDAR and PD radar data as well as camera videos of the 30 June 2022 debris flow at the Illgraben (Switzerland).
Spatio-temporal soil and local snow monitoring in a glide-snow avalanche prone slope above Davos Switzerland
This dataset consists of spatio-temporal soil measurements and local snow measurements which were recorded to investigate glide-snow avalanche release in the Seewer Berg slope (Davos, Switzerland) from Nov 2021 to June 2024. Investigations based on this dataset were published in the research article: Fees A., Lombardo M., van Herwijnen A., Lehmann P., Schweizer J. (2025). The source, quantity, and spatial distribution of interfacial water during glide-snow avalanche release: experimental evidence from field monitoring. The Cryosphere The dataset consists of: - Soil measurements (temperature and liquid water content) at soil depths of -5cm, -10cm, and -20cm - Matric potential at depths of -5cm, -10cm, and -20cm - Manual snow profiles (Snow height, temperature, liquid water content, bulk density) - Metadata and manual snow profiles on glide-snow avalanches that released in the Seewer Berg slope - Snow height, air temperature and rain simulated with SNOWPACK.