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Research data keyboard_double_arrow_right Dataset 2024Publisher:PANGAEA Anhaus, Philipp; Schiller, Martin; Planat, Noémie; Katlein, Christian; Nicolaus, Marcel;Transmitted solar radiance was measured using an ARC (Advanced-Radiance-Collector) RAMSES hyper-spectral radiometer (TriOS) mounted on the ROV during the ARTofMELT2023 expedition in May and June 2023 and normalized by the incident solar irradiance as measured using an ACC (Advanced-Cosine-Collector) RAMSES hyper-spectral radiometer (TriOS) installed on-board the ship. All times are given in Universal Coordinated Time (UTC).
PANGAEA - Data Publi... arrow_drop_down PANGAEA - Data Publisher for Earth and Environmental ScienceDataset . 2024License: CC BYData sources: DatacitePANGAEA - Data Publisher for Earth and Environmental ScienceDataset . 2024License: CC BYData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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more_vert PANGAEA - Data Publi... arrow_drop_down PANGAEA - Data Publisher for Earth and Environmental ScienceDataset . 2024License: CC BYData sources: DatacitePANGAEA - Data Publisher for Earth and Environmental ScienceDataset . 2024License: CC BYData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Dataset 2024Embargo end date: 17 Jun 2024Publisher:Dryad Robinson, John; Naughtin, Sarah; Castilla, Antonio; Smith, Adam; Strand, Allan; Dawson, Andria; Hoban, Sean; Abhainn, Everett; Romero-Severson, Jeanne;# Integrating genomic data and simulations to evaluate alternative species distribution models and improve predictions of glacial refugia and future responses to climate change [https://doi.org/10.5061/dryad.s7h44j1fx](https://doi.org/10.5061/dryad.s7h44j1fx) This repository contains analysis scripts and input data files associated with the integrated distributional, demographic, and coalescent (iDDC; He et al. 2013) modeling analysis conducted to compare alternative species distribution models (SDMs) for green ash (*Fraxinus pennslvanica*) in Naugthin et al. (2024) *Ecography*. ## Description of the data and file structure Simulations for the project were conducted using the R script `hSC_Ash_with_enms.R`. This script uses the R package holoSimCell (available from [https://github.com/stranda/holoSimCell](https://github.com/stranda/holoSimCell) to simulate post-glacial expansion of green ash in eastern North America. We also include the singularity (now apptainer, [https://apptainer.org](https://apptainer.org)) container used for these simulations (`holosim.simg`) in the repository. The most recent version of the `holosim` container can also be pulled from [https://hub.docker.com/r/astrand/holosim](https://hub.docker.com/r/astrand/holosim). Outputs of the simulations under 24 different SDMs are saved in the reference table: `ENMcomparison_RT_50k_subset.csv`, which is provided in zipped format in `ENMcomparison_RT_50k_subset.zip`. This file contains simulation parameters, measures of biotic velocity (see Castilla et al. 2024, [https://doi.org/10.1111/jbi.14754](https://doi.org/10.1111/jbi.14754)) and a total of 473 summary statistics retained for each simulation replicate. Each of the 24 SDMs were simulated 50,000 times for ABC analyses. We also include a .csv file with observed values for these same summary statistics: `Ash_obs_subset_2Oct20.csv`. The observed summary statistic file is shared with Castilla et al. 2024, but the reference table has been expanded considerably for this project. Descriptions of columns in `ENMcomparison_RT_50k_subset.csv` and `Ash_obs_subset_2Oct20.csv` can be found below. Scripts to perform ABC model selection and cross validation analyses presented in our manuscript are included in `ABC.zip` (see Code/Software below for descriptions). ABC analyses can be repeated using these scripts and the two .csv files described above. This repository also contains R scripts used to define the study region for our analysis (in `study_region.zip`), fit correlative species distribution (or ecological niche) models, and predict habitat suitability in 2080 under each of the models considered in this project (both in the `code/` subdirectory in `enms.zip`). Hindcasted and forecasted SDMs are also provided in raster format in the `predictions/ `and `predictions_future/` subdirectories in `enms.zip` (see Code/Software below for more information). Columns of `ENMcomparison_RT_50k_subset.csv` The first 220 columns of the reference table provide parameter values used in each simulation and measures of biotic velocity recorded during the associated forward demographic simulation. 1. `date` - the date and time the simulation was completed, unused in ABC analyses 2. `node` - an index used in filenames produced during simulations. Prevents overwriting of output files produced by separate jobs on a computing cluster, unused in ABC analyses. 3. `rep` - an index for the replicate number of each simulation on each node, unused in ABC analyses. 4. `xdim` - the number of cells in a row of the simulation landscape, the x dimension of the simulation, fixed across simulation replicates and unused in ABC analyses. 5. `ydim` - the number of cells in a column of the simulation landscape, the y dimension of the simulation, fixed across simulation replicates and unused in ABC analyses. 6. `maxtime` - the maximum number of generations that the forward simulation is allowed to run, fixed across simulation replicates and unused in ABC analyses. 7. `K` - the maximum per-cell carrying capacity (in individuals) used in the forward simulation, identical to Ne described below. 8. `xsz` - the size of a cell in the simulated landscape in the x-dimension (longitude), measured in meters. 9. `ysz` - the size of a cell in the simulated landscape in the y-dimension (latitude), measured in meters. 10. `samptime` - variable that allows the same habitat suitability layer to be applied to multiple generations during the forward simulation. Habitat suitability layers are changed every `samptime` generations, fixed across simulation replicates and unused in ABC analyses. 11. `pois.var` - a binary (0/1) indicator specifying whether population size in each cell and time step was drawn from a Poisson distribution to incorporate demographic stochasticity, fixed across simulations and unused in ABC analyses. 12. `shortscale` - the scale parameter for the distribution of short-distance dispersal events (k parameter of Weibull distribution), fixed across simulations and unused in ABC analyses. 13. `shortshape` - the shape parameter for the distribution of short-distance dispersal events (lambda parameter of Weibull distribution), fixed across simulations and unused in ABC analyses. 14. `sz` - DEPRECATED, the size of a square cell in the simulated landscape, replaced with `xsz` and `ysz` to allow rectangular cells. 15. `nloci` - the number of genetic marker loci included in the observed dataset, fixed across simulations and unused in ABC analyses. 16. `seq_length` - the sequence length of the marker in base pairs, used along with `mu` below in the fastsimcoal DNA model, fixed across simulations and unused in ABC analyses. 17. `mu` - the mutation rate (per base pair, per generation) of the simulated locus, used with `seq_length` above in the fastsimcoal DNA model, fixed across simulations and unused in ABC analyses. 18. `G` - the generation time of the species in years, fixed across simulations and unused in ABC analyses. 19. `longmean` - the average distance of long-distance dispersal events in units of cell widths, fixed across simulations and unused in ABC analyses. 20. `lambda` - the rate of population growth within cells (discrete rate of increase), fixed across simulations and unused in ABC analyses. 21. `mix` - the mixture parameter for the distribution of dispersal distances, the proportion of dispersal events that are long-distance. Randomly drawn from a prior distribution for each simulation replicate. 22. `Ne` - the maximum effective population size of a cell in the landscape. Randomly drawn from a prior distribution for each simulation replicate. 23. `preLGM_t` - the time at which refugial populations diverged from one another (e.g., the last interglacial). Randomly drawn from a prior distribution for each simulation replicate. 24. `preLGM_Ne` - the effective population size of the species prior to refuge divergence. Randomly drawn from a prior distribution for each simulation replicate. 25. `found_Ne` - the effective population size of newly colonized populations (used in coalescent simulations only). Randomly drawn from a prior distribution for each simulation replicate. 26. `ref_Ne` - the effective population size of cells included in refugia (scaled by cell-specific habitat suitability in the first time step). Randomly drawn from a prior distribution for each simulation replicate. 27. `refs` - the species distribution model (ENM_1 through ENM_24) used to define habitat suitability across the landscape in each simulation. Each model is represented 50,000 times in the reference table. 28. `BVprev_ybp` - the proportion of habitable (non-NA) cells with abundance >0 in the `DATE` time step relative to all habitable cells. Unitless. 29. `BVmean_ybp` - mean abundance in `DATE` time step. In the same units as the values of the cells (individuals). 30. `BVtotal_ybp` - total abundance across all cells in the simulated landscape at the `DATE` time step. In the same units as the values of the cells (individuals). 31. `BVshared1k_toybp` - abundance-weighted centroid biotic velocity between the `DATE1` and `DATE2` time steps in the simulation, calculated using only cells that are not NA in either of the two time points (to control for changes in available land due to sea level rise). Velocities are given in meters per year and are always positive (direction does not affect velocity). 32. `BVNQshared1k_toybp` - velocity of the 0.95th quantile weight in the north-south direction between the `DATE1` and `DATE2` time steps in the simulation, calculated using only cells that are not NA in either of the two time points (to control for changes in available land due to sea level rise). Velocities are given in meters per year and are positive for northward movement and negative for southward movement. 33. `BVSQshared1k_toybp` - velocity of the 0.05th quantile weight in the north-south direction between the `DATE1` and `DATE2` time steps in the simulation, calculated using only cells that are not NA in either of the two time points (to control for changes in available land due to sea level rise). Velocities are given in meters per year and are positive for northward movement and negative for southward movement. 34. `BVall1k_toybp` - abundance-weighted centroid biotic velocity between the `DATE1` and `DATE2` time steps in the simulation, calculated using all cells. Velocities are given in meters per year and are always positive (direction does not affect velocity). 35. `BVNQall1k_toybp` - velocity of the 0.95th quantile weight in the north-south direction between the `DATE1` and `DATE2` time steps in the simulation, calculated using all cells. Velocities are given in meters per year and are positive for northward movement and negative for southward movement. 36. `BVSQall1k_toybp` - velocity of the 0.05th quantile weight in the north-south direction between the `DATE1` and `DATE2` time steps in the simulation, calculated using all cells. Velocities are given in meters per year and are positive for northward movement and negative for southward movement. 37. `BV_21kyr` - abundance-weighted centroid biotic velocity over the entire 21kyr simulation history, calculated using only cells that are not NA in either of the two time points (to control for changes in available land due to sea level rise). Velocities are given in meters per year and are always positive (direction does not affect velocity). 38. `BVNQ_21kyr` - velocity of the 0.95th quantile weight in the north-south direction over the entire 21kyr simulation history. Quantiles are cumulated starting from the south (0.05th quantile). Velocities are given in meters per year and are positive for northward movement and negative for southward movement. 39. `BVSQ_21kyr` - velocity of the 0.05th quantile weight in the north-south direction over the entire 21kyr simulation history. Quantiles are cumulated starting from the south (0.05th quantile). Velocities are given in meters per year and are positive for northward movement and negative for southward movement. 40. `tot_SNPs` - the total number of single nucleotide polymorphisms in the population genetic dataset output from fastsimcoal. Not used as a summary statistic for ABC analyses, but included to verify that all simulations produce the expected (`nloci`) number of polymorphic markers. The remaining 473 columns in the reference table file contain summary statistics calculated from population genetic datasets produced by the coalescent simulation. The 473 columns in `Ash_obs_subset_2Oct20.csv` are shared with the remainder of the reference table, but were calculated from empirical data for green ash (*Fraxinus pennsylvanica*). 1. `Fst_.` - Pairwise Fst (=1-Hs/Ht) between populations (Wright 1949, 1950). Unitless, ranging from 0 to 1. 210 total statistics. 2. `helat.*` - Summaries of a polynomial model (intercept, first, and second coefficients) relating expected heterozygosity to latitude. 3 total statistics. 3. `helong.*` - Summaries of a polynomial model (intercept, first, and second coefficients) relating expected heterozygosity to longitude. 3 total statistics 4. `HRi_` - Harpending's raggedness index calculated from the Geographic Spectrum of Shared Alleles (Alvarado-Serrano & Hickerson 2018) for each population. 21 total statistics. 5. `Spca.Dmean_` - The mean inter-individual distance in PCA space among individuals within a population (Alvarado-Serrano & Hickerson 2016), calculated from a spatial PCA analysis. 21 total statistics. 6. `Moran.Beta` - Estimate of Moran's I (Moran 1950) measuring spatial autocorrelation in genetic data. 1 total statistic. 7. `Var.*` - Summaries of the variogram (Goovaerts 1998) measuring spatial autocorrelation in the genetic data - beta, sill, nugget, and range of the variogram. 4 total statistics. 8. `Psi_.` - Peter & Slatkin's (2013) directionality index between a pair of populations. 210 total statistics. ## Sharing/Access information Code to define the study region and construct correlative species distribution models is shared with that used in Castilla et al. (2024) and also available from [https://github.com/TIMBERhub](https://github.com/TIMBERhub). Observed data, simulation scripts, and the holoSimCell R package are available from [https://github.com/stranda/holoSimCell](https://github.com/stranda/holoSimCell). A docker image containing the holoSimCell package, all dependencies, and fastsimcoal v. 2.6 is available from [https://hub.docker.com/r/astrand/holosim](https://hub.docker.com/r/astrand/holosim). ## Code/Software We include the R script for **delineating the study region**, plus the raster masks defining the region. These files are included in the `study_region/` directory in `study_region.zip`. 1. `study_region/defining_study_region.r` - R script for defining the study region based on watershed basins, distribution of *Fraxinus pennsylvanica* records, pollen cores, and genetic samples. 2. `study_region/study_region_daltonIceMask_lakesMasked_linearIceSheetInterpolation.tif` - Multi-layer raster in GeoTIFF format with a mask of the area of interest (generally, eastern portion of North America) from 1 Kybp to 0 bp (1950 CE). The “last” or “lowest” layer represents available land (uncovered by sea and ice) 21 Kybp, and the “top” or “first layer” the present, with one layer per 30 years across this period. Values are 1 (available) and NA (unavailable). 3. `study_region/study_region_resampled_to_genetic_demographic_simulation_resolution.tif` - Raster in GeoTIFF format with all cells equal to 1 and in the equal-area spatial resolution used in the genetic/demographic simulations. This is a single layer raster. We also include R scripts used for calibrating the **species distribution models** and creating projections of past and future habitat suitability and the outputs of these projections in raster format. These files are included in the `enms/` directory in `enms.zip`. 1. `enms/code/enms_for_fraxinus_pennsylvanica.r` - Collates specimen data and environmental rasters, constructs data partitions, calibrates and evaluates SDMs, projects models to past, interpolation of rasters to finer timescales, and calculation of biotic velocity. 2. `enms/code/enms_for_fraxinus_pennsylvanica_projected_to_future.r `- Takes models from first script and projects them to future climate scenarios. 3. `enms/predictions/` folder - Contains rasters in GeoTIFF format with predictions to the past. Each file is a “stack” of layers with predictions, from 21 Kybp (“lowest” or “last” layer) to the “present” (1950, “top” or “first” layer). Original values were in the range [0, 1], but they have been rescaled and rounded to {0, 1, 2, 3, … , 100}. File names are as: `_kmExtent_.tif`. For example: `ecbilt_80kmExtent_brt.tif`. 4. `enms/predictions_future/` folder - Contains rasters in GeoTIFF format with predictions to the future. Original values were in the range [0, 1], but they have been rescaled and rounded to {0, 1, 2, 3, … , 100}. File names are as: `__kmExtent_rcp__.tif`. For example: `brt_ecbilt_320kmExtent_rcp45_2050_GFDL-CM3.tif`. The apptainer container (`holosim.simg`) in the repository was used for all simulations in this study and includes the necessary R packages (including holoSimCell) and the coalescent simulation software fastsimcoal v. 2.6. Coupled demographic-genetic simulations can be run using the `hSC_Ash_with_enms.R` script. This containerized version of R and the installed packages can also be used to recreate the SDMs tested. We include several R scripts used for **ABC analysis**. The following scripts are saved in the `ABC/` directory in `ABC.zip`. These scripts use the reference table (`ENMcomparison_RT_50k_subset.csv`) and observed summary statistics (`Ash_obs_subset_2Oct20.csv`) files described above. 1. `ABC/CheckECDF.R` - calculates the location of observed summary statistics within the distribution of statistic values from 50,000 simulations under each SDM. 2. `ABC/AshENM_modsela_subset_mnlog.R` - performs ABC model selection with multinomial logistic regression 3. `ABC/AshENM_modsela_subset_nnet.R` - performs ABC model selection with neural networks 4. `ABC/ENMcomparison_RF_pred_subset.R` - performs ABC model selection with random forests 5. `ABC/ENMcomparison_CV4MS.R` - performs cross validations for model selection using either multinomial logistic regression or neural networks 6. `ABC/ENMcomparison_numreps_modsel_nnet.R` - performs model selection with subsets of the reference table to evaluate changes in model posterior probabilities as the total number of replicates declines from 50,000 to 5000 ## References Alvarado-Serrano, D. F. and Hickerson, M. J. 2016. Spatially explicit summary statistics for historical population genetic inference. – Methods Ecol. Evol. 7: 418–427. Alvarado-Serrano, D. F. and Hickerson, M. J. 2018. Detecting spatial dynamics of range expansions with geo-referenced genomewide SNP data and the geographic spectrum of shared alleles. – bioRxiv 457556. Goovaerts, P. 1998. Geostatistical tools for characterizing the spatial variability of microbiological and physico-chemical soil properties. – Biol. Fertil. Soils 27: 315–334. He, Q., Edwards, D. L. and Knowles, L. L. 2013. Integrative testing of how environments from the past to the present shape genetic structure across landscapes. – Evolution 67: 3386–3402. Moran, P. 1950. Notes on continuous stochastic phenomena. – Biometrika 37: 17–23. Peter, B.M. and Slatkin, M. 2013. Detecting range expansions from genetic data. – Evolution 67: 3274−3289. Wright, S. 1949. The genetical structure of populations. – Ann. Eugen. 15: 323−354. Wright, S. 1950. The genetical structure of populations. – Nature 166: 247-249. Climate change poses a threat to biodiversity, and it is unclear whether species can adapt to or tolerate new conditions, or migrate to areas with suitable habitats. Reconstructions of range shifts that occurred in response to environmental changes since the last glacial maximum from species distribution models (SDMs) can provide useful data to inform conservation efforts. However, different SDM algorithms and climate reconstructions often produce contrasting patterns, and validation methods typically focus on accuracy in recreating current distributions, limiting their relevance for assessing predictions to the past or future. We modeled historically suitable habitat for the threatened North American tree green ash (Fraxinus pennsylvanica) using 24 SDMs built using two climate models, three calibration regions, and four modeling algorithms. We evaluated the SDMs using contemporary data with spatial block cross-validation and compared the relative support for alternative models using a novel integrative method based on coupled demographic-genetic simulations. We simulated genomic datasets using habitat suitability of each of the 24 SDMs in a spatially-explicit model. Approximate Bayesian Computation (ABC) was then used to evaluate the support for alternative SDMs through comparisons to an empirical population genomic dataset. Models had very similar performance when assessed with contemporary occurrences using spatial cross-validation, but ABC model selection analyses consistently supported SDMs based on the CCSM climate model, an intermediate calibration extent, and the generalized linear modeling algorithm. Finally, we projected the future range of green ash under four climate change scenarios. Future projections using the SDMs selected via ABC suggest only minor shifts in suitable habitat for this species, while some of those that were rejected predicted dramatic changes. Our results highlight the different inferences that may result from the application of alternative distribution modeling algorithms and provide a novel approach for selecting among a set of competing SDMs with independent data.
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For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Dataset 2023Publisher:Observatoire Global du Saint-Laurent Chaillou, Gwenaelle; Tanhua, Toste; Hérard, Olivier; Nesbitt, William; Wallace, Douglas;Le projet TReX (Tracer Release eXperiment) est un projet de recherche intersectoriel qui vise à développer et à démontrer la capacité du Canada à prédire la dispersion de contaminants et à répondre à leurs déversements accidentels dans les environnements marins côtiers. Le present jeu de données CTD provient de la première mission de la phase TReX-deep qui vise l’étude des processus de transport et dispersion dans les eaux de fond du Chenal Laurentien, de l'estuaire maritime au Détroit de Cabot. Cette expérience unique, qui combine les expertises de chercheurs du Québec, de la Nouvelle Écosse et de l'Allemagne, est utilisée non seulement pour prévoir la dispersion et l'advection de certains contaminants mais aussi pour comprendre les processus biogéochimiques liés au climat qui contrôlent les conditions d’hypoxie et d’acidification à la tête du Chenal Laurentien. Ce jeu de données CTD issu de la première mission en octobre 2021 présente des profils verticaux de salinité, température, oxygène dissous, densité, et fluorescence de 4 à 360 m pour une trentaine de stations entre Rimouski et le Détroit de Cabot. Bien que les sondes soient calibrées par le fabricant au cours de l'année, des échantillons discrets de salinité ont été prélevés dans toute la colonne d'eau et analysés sur un salinomètre Guildline Autosal 8400 calibré avec l'eau de mer standard de l'IAPSO (International Association for the Physical Sciences of the Oceans) et les profils CTD retraités après la mission. De même, les concentrations d'oxygène dissous ont été déterminées par titrage chimique Winkler (Grasshoff et al., 1999) sur une quarantaine d'échantillons d'eau discrets collectés directement dans les bouteilles Niskin. L'écart-type relatif, basé sur des analyses répétées d'échantillons prélevés dans la même bouteille Niskin, était inférieur à 1 %. Ces mesures ont également servi à étalonner la sonde à oxygène SBE-43 montée sur la rosette. Il a été acquis conjointement par les équipes de Douglas Wallace (U. Dalhousie), Gwénaëlle Chaillou (ISMER-UQAR) et Toste Tanhua (GEOMAR). The TReX (Tracer ReleaseEXperiment) project is an interdisciplinary research project that aims to develop and demonstrate Canada's ability to predict the spread of contaminants and respond to their accidental discharges in coastal marine environments. The present CTD dataset comes from the first mission of the Trex-Deep phase, which aims to study transport and dispersal processes in the bottom waters of the Laurentian Channel, from the maritime estuary to Cabot Strait. This unique experiment, which combines the expertise of researchers from Quebec, Nova Scotia, and Germany, is used to predict the dispersal and advection of certain contaminants and understand the climate-related biogeochemical processes that control hypoxia and acidification conditions at the head of the Laurentian Channel. This CTD dataset from the first mission in October 2021 presents vertical profiles of salinity, temperature, dissolved oxygen, density, and fluorescence from 4 to 360 m for about thirty stations between Rimouski and Cabot Strait. Although the probes were calibrated by the manufacturer during the year, discrete salinity samples were taken throughout the water column and analyzed on a Guildline Autosal 8400 salinometer calibrated with standard IAPSO (International Association for the Physical Sciences of the Oceans) seawater and CTD profiles reprocessed after the mission. Similarly, dissolved oxygen concentrations were determined by Winkler chemical titration (Grasshoff et al., 1999) on about forty discrete water samples collected directly from Niskin bottles. The relative standard deviation, based on repeated analyses of samples taken from the same Niskin bottle, was less than 1%. These measurements were also used to calibrate the SBE-43 oxygen probe mounted on the rosette. It was acquired jointly by the teams of Douglas Wallace (U. Dalhousie), Gwénaëlle Chaillou (ISMER-UQAR) and Toste Tanhua (GEOMAR).
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For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Dataset 2024Embargo end date: 30 Apr 2024Publisher:NERC EDS Environmental Information Data Centre Dusenge, M.E.; González-Caro, S.; Restrepo, Z.; Meir, P.; Hartley, I.P.; Sitch, S; Sanchez, A; Mercado, M.L.;Data collection protocol: in January – March 2022, Aci curves (i.e., CO2 response curves of net photosynthesis) were done at a pre-determined saturating light intensity of 1800 PAR (Qin in the database). Aci curves were done at different leaf temperature targets between 15 and 40 degree Celcius, with 5 degree celcius steps. Before starting any ACi curve, the leaf was allowed to acclimate at each temperature for at least 10 min and the ACi was initiated once both Anet and stomatal conductance were stable for at least 2 min. Throughout each Aci, the stability time at each CO2 reference concentration (410, 50, 100, 150, 250, 410, 800, 1200, 1600, and 2000 in this order) was set to 45 - 180 seconds, the automatic match was programmed before recording any data at each CO2 reference concentration. Measurements were taken with an LI6800 Portable Photosynthesis System under field conditions. LI6800 indicates whether there is a leak, but measurements were always done after ensuring there was no leak in the system, therefore, no subsequent leak correction was necessary. At the beginning of each measurement day, automatic warm-up test was run to detect any problem within the instrument, and only measurements were initiated when all errors have been fixed as suggested by the instrument system. The leaf temperature was derived from the thermocouple of the instrument. This dataset contains information about temperature response curves of ACi (i.e., CO2 response curves of net photosynthesis) that were collected on Colombian Andean forests tree species that were planted in three, common-garden tree plantations along a 2000m altitudinal gradient. Specifically, individuals of cold- and warm-affiliated species were planted under common soil and water conditions, exposing them to the hot and cold extremes of their thermal niches, respectively. This work was supported by the UK Natural Environment Research Council (NE/R001928/1)
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For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Dataset 2023Embargo end date: 28 Apr 2023Publisher:Dryad Luo, Binyu; Huang, Mei; Wang, Wenyin; Niu, Jiahuan; Shrestha, Mani; Zeng, Haijun; Ma, Lin; Degen, Allan; Liao, Jingkang; Zhang, Tao; Bai, Yanfu; Zhao, Jingxue; Fraser, Lauchlan; Shang, Zhanhuan;Warming can decrease feeding activity of soil organisms and affect biogeochemical cycles in alpine ecosystems. Ants (Formica manchu) are active on their nest surface, and prefer a hot and dry environment. Therefore, warming may provide a favorable environment for their activity. We hypothesized that ants might benefit from warming and increase the robustness of ecosystem functions to warming. To test this hypothesis, we examined the effects of ant nests (ant nest absence vs. ant nest presence) and warming (ambient temperature, + 1.3°C and + 2.3°C) on litter decomposition, soil properties and the plant community in an alpine grassland ecosystem. Decomposition stations with two mesh sizes were used to differentiate effects of microorganisms (0.05mm) and macroinvertebrate (1cm) to litter decomposition. Ant nests increased litter decomposition with and without macroinvertebrates accessing the decomposition station when compared to plots without ant nests. Only the litter decomposition in ant nests with macroinvertebrates accessing the decomposition station was not negatively affected by warming. Plots with ant nests had greater soil organic carbon, nutrient contents and plant growth than plots without ant nests, regardless of warming. Consequently, ant nests can mitigate the negative effects of warming on litter decomposition and improve ecosystem functions under warming.
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For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Dataset 2024Publisher:PANGAEA Anhaus, Philipp; Schiller, Martin; Planat, Noémie; Katlein, Christian; Nicolaus, Marcel;Incident solar irradiance was measured using an ACC (Advanced-Cosine-Collector) RAMSES hyper-spectral radiometer (TriOS) installed on-board the ship during the ARTofMELT2023 expedition in May and June 2023. All times are given in Universal Coordinated Time (UTC).
PANGAEA - Data Publi... arrow_drop_down PANGAEA - Data Publisher for Earth and Environmental ScienceDataset . 2024License: CC BYData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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more_vert PANGAEA - Data Publi... arrow_drop_down PANGAEA - Data Publisher for Earth and Environmental ScienceDataset . 2024License: CC BYData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Dataset 2024Publisher:PANGAEA Anhaus, Philipp; Schiller, Martin; Planat, Noémie; Katlein, Christian; Nicolaus, Marcel;Transmitted solar radiance was measured using an ARC (Advanced-Radiance-Collector) RAMSES hyper-spectral radiometer (TriOS) mounted on the ROV during the ARTofMELT2023 expedition in May and June 2023 and normalized by the incident solar irradiance as measured using an ACC (Advanced-Cosine-Collector) RAMSES hyper-spectral radiometer (TriOS) installed on-board the ship. All times are given in Universal Coordinated Time (UTC).
PANGAEA - Data Publi... arrow_drop_down PANGAEA - Data Publisher for Earth and Environmental ScienceDataset . 2024License: CC BYData sources: DatacitePANGAEA - Data Publisher for Earth and Environmental ScienceDataset . 2024License: CC BYData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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more_vert PANGAEA - Data Publi... arrow_drop_down PANGAEA - Data Publisher for Earth and Environmental ScienceDataset . 2024License: CC BYData sources: DatacitePANGAEA - Data Publisher for Earth and Environmental ScienceDataset . 2024License: CC BYData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Dataset 2023Embargo end date: 01 Dec 2023Publisher:Harvard Dataverse Authors: Barchyn, Thomas;doi: 10.7910/dvn/qjutzo
Surface methane concentration data measured to produce a better understanding of surface methane emissions across the landfill.
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For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Dataset 2021Publisher:ICPSR - Interuniversity Consortium for Political and Social Research Authors: Rud, Juan Pablo; Aragon, Fernando; Oteiza, Francisco;This paper examines how subsistence farmers respond to extreme heat. Using micro-data from Peruvian households, we find that high temperatures reduce agricultural productivity, increase area planted, and change crop mix. These findings are consistent with farmers using input adjustments as a short-term mechanism to attenuate the effect of extreme heat on output. This response seems to complement other coping strategies, such as selling livestock, but exacerbates the drop in yields, a standard measure of agricultural productivity. Using our estimates, we show that accounting for land adjustments is important to quantify damages associated with climate change.
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For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Collection 2022Publisher:PANGAEA Oehri, Jacqueline; Schaepman-Strub, Gabriela; Kim, Jin-Soo; Grysko, Raleigh; Kropp, Heather; Grünberg, Inge; Zemlianskii, Vitalii; Sonnentag, Oliver; Euskirchen, Eugénie S; Reji Chacko, Merin; Muscari, Giovanni; Blanken, Peter D; Dean, Joshua F; di Sarra, Alcide; Harding, Richard J; Sobota, Ireneusz; Kutzbach, Lars; Plekhanova, Elena; Riihelä, Aku; Boike, Julia; Miller, Nathaniel B; Beringer, Jason; López-Blanco, Efrén; Stoy, Paul C; Sullivan, Ryan C; Kejna, Marek; Parmentier, Frans-Jan W; Gamon, John A; Mastepanov, Mikhail; Wille, Christian; Jackowicz-Korczynski, Marcin; Karger, Dirk N; Quinton, William L; Putkonen, Jaakko; van As, Dirk; Christensen, Torben R; Hakuba, Maria Z; Stone, Robert S; Metzger, Stefan; Vandecrux, Baptiste; Frost, Gerald V; Wild, Martin; Hansen, Birger Ulf; Meloni, Daniela; Domine, Florent; te Beest, Mariska; Sachs, Torsten; Kalhori, Aram; Rocha, Adrian V; Williamson, Scott N; Morris, Sara; Atchley, Adam L; Essery, Richard; Runkle, Benjamin R K; Holl, David; Riihimaki, Laura; Iwata, Hiroki; Schuur, Edward A G; Cox, Christopher J; Grachev, Andrey A; McFadden, Joseph P; Fausto, Robert S; Göckede, Mathias; Ueyama, Masahito; Pirk, Norbert; de Boer, Gijs; Bret-Harte, M Syndonia; Leppäranta, Matti; Steffen, Konrad; Friborg, Thomas; Ohmura, Atsumu; Edgar, Colin W; Olofsson, Johan; Chambers, Scott D;Despite the importance of surface energy budgets (SEBs) for land-climate interactions in the Arctic, uncertainties in their prediction persist. In-situ observational data of SEB components - useful for research and model validation - are collected at relatively few sites across the terrestrial Arctic, and not all available datasets are readily interoperable. Furthermore, the terrestrial Arctic consists of a diversity of vegetation types, which are generally not well represented in land surface schemes of current Earth system models. Therefore, we here provide four datasets comprising:1. Harmonized, standardized and aggregated in situ observations of SEB components at 64 vegetated and glaciated sites north of 60° latitude, in the time period 1994-20212. A description of all study sites and associated environmental conditions, including the vegetation types, which correspond to the classification of the Circumpolar Arctic Vegetation Map (CAVM, Raynolds et al. 2019).3. Data generated in a literature synthesis from 358 study sites on vegetation or glacier (>=60°N latitude) covered by 148 publications.4. Metadata, including data contributor information and measurement heights of variables associated with Oehri et al. 2022. Code underlying the dataset and publication is available in a Github repository and can be accessed at: https://github.com/oehrij/ArcticSEBSynthesis
PANGAEA - Data Publi... arrow_drop_down PANGAEA - Data Publisher for Earth and Environmental ScienceCollection . 2022License: CC BYData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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more_vert PANGAEA - Data Publi... arrow_drop_down PANGAEA - Data Publisher for Earth and Environmental ScienceCollection . 2022License: CC BYData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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Research data keyboard_double_arrow_right Dataset 2024Publisher:PANGAEA Anhaus, Philipp; Schiller, Martin; Planat, Noémie; Katlein, Christian; Nicolaus, Marcel;Transmitted solar radiance was measured using an ARC (Advanced-Radiance-Collector) RAMSES hyper-spectral radiometer (TriOS) mounted on the ROV during the ARTofMELT2023 expedition in May and June 2023 and normalized by the incident solar irradiance as measured using an ACC (Advanced-Cosine-Collector) RAMSES hyper-spectral radiometer (TriOS) installed on-board the ship. All times are given in Universal Coordinated Time (UTC).
PANGAEA - Data Publi... arrow_drop_down PANGAEA - Data Publisher for Earth and Environmental ScienceDataset . 2024License: CC BYData sources: DatacitePANGAEA - Data Publisher for Earth and Environmental ScienceDataset . 2024License: CC BYData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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more_vert PANGAEA - Data Publi... arrow_drop_down PANGAEA - Data Publisher for Earth and Environmental ScienceDataset . 2024License: CC BYData sources: DatacitePANGAEA - Data Publisher for Earth and Environmental ScienceDataset . 2024License: CC BYData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Dataset 2024Embargo end date: 17 Jun 2024Publisher:Dryad Robinson, John; Naughtin, Sarah; Castilla, Antonio; Smith, Adam; Strand, Allan; Dawson, Andria; Hoban, Sean; Abhainn, Everett; Romero-Severson, Jeanne;# Integrating genomic data and simulations to evaluate alternative species distribution models and improve predictions of glacial refugia and future responses to climate change [https://doi.org/10.5061/dryad.s7h44j1fx](https://doi.org/10.5061/dryad.s7h44j1fx) This repository contains analysis scripts and input data files associated with the integrated distributional, demographic, and coalescent (iDDC; He et al. 2013) modeling analysis conducted to compare alternative species distribution models (SDMs) for green ash (*Fraxinus pennslvanica*) in Naugthin et al. (2024) *Ecography*. ## Description of the data and file structure Simulations for the project were conducted using the R script `hSC_Ash_with_enms.R`. This script uses the R package holoSimCell (available from [https://github.com/stranda/holoSimCell](https://github.com/stranda/holoSimCell) to simulate post-glacial expansion of green ash in eastern North America. We also include the singularity (now apptainer, [https://apptainer.org](https://apptainer.org)) container used for these simulations (`holosim.simg`) in the repository. The most recent version of the `holosim` container can also be pulled from [https://hub.docker.com/r/astrand/holosim](https://hub.docker.com/r/astrand/holosim). Outputs of the simulations under 24 different SDMs are saved in the reference table: `ENMcomparison_RT_50k_subset.csv`, which is provided in zipped format in `ENMcomparison_RT_50k_subset.zip`. This file contains simulation parameters, measures of biotic velocity (see Castilla et al. 2024, [https://doi.org/10.1111/jbi.14754](https://doi.org/10.1111/jbi.14754)) and a total of 473 summary statistics retained for each simulation replicate. Each of the 24 SDMs were simulated 50,000 times for ABC analyses. We also include a .csv file with observed values for these same summary statistics: `Ash_obs_subset_2Oct20.csv`. The observed summary statistic file is shared with Castilla et al. 2024, but the reference table has been expanded considerably for this project. Descriptions of columns in `ENMcomparison_RT_50k_subset.csv` and `Ash_obs_subset_2Oct20.csv` can be found below. Scripts to perform ABC model selection and cross validation analyses presented in our manuscript are included in `ABC.zip` (see Code/Software below for descriptions). ABC analyses can be repeated using these scripts and the two .csv files described above. This repository also contains R scripts used to define the study region for our analysis (in `study_region.zip`), fit correlative species distribution (or ecological niche) models, and predict habitat suitability in 2080 under each of the models considered in this project (both in the `code/` subdirectory in `enms.zip`). Hindcasted and forecasted SDMs are also provided in raster format in the `predictions/ `and `predictions_future/` subdirectories in `enms.zip` (see Code/Software below for more information). Columns of `ENMcomparison_RT_50k_subset.csv` The first 220 columns of the reference table provide parameter values used in each simulation and measures of biotic velocity recorded during the associated forward demographic simulation. 1. `date` - the date and time the simulation was completed, unused in ABC analyses 2. `node` - an index used in filenames produced during simulations. Prevents overwriting of output files produced by separate jobs on a computing cluster, unused in ABC analyses. 3. `rep` - an index for the replicate number of each simulation on each node, unused in ABC analyses. 4. `xdim` - the number of cells in a row of the simulation landscape, the x dimension of the simulation, fixed across simulation replicates and unused in ABC analyses. 5. `ydim` - the number of cells in a column of the simulation landscape, the y dimension of the simulation, fixed across simulation replicates and unused in ABC analyses. 6. `maxtime` - the maximum number of generations that the forward simulation is allowed to run, fixed across simulation replicates and unused in ABC analyses. 7. `K` - the maximum per-cell carrying capacity (in individuals) used in the forward simulation, identical to Ne described below. 8. `xsz` - the size of a cell in the simulated landscape in the x-dimension (longitude), measured in meters. 9. `ysz` - the size of a cell in the simulated landscape in the y-dimension (latitude), measured in meters. 10. `samptime` - variable that allows the same habitat suitability layer to be applied to multiple generations during the forward simulation. Habitat suitability layers are changed every `samptime` generations, fixed across simulation replicates and unused in ABC analyses. 11. `pois.var` - a binary (0/1) indicator specifying whether population size in each cell and time step was drawn from a Poisson distribution to incorporate demographic stochasticity, fixed across simulations and unused in ABC analyses. 12. `shortscale` - the scale parameter for the distribution of short-distance dispersal events (k parameter of Weibull distribution), fixed across simulations and unused in ABC analyses. 13. `shortshape` - the shape parameter for the distribution of short-distance dispersal events (lambda parameter of Weibull distribution), fixed across simulations and unused in ABC analyses. 14. `sz` - DEPRECATED, the size of a square cell in the simulated landscape, replaced with `xsz` and `ysz` to allow rectangular cells. 15. `nloci` - the number of genetic marker loci included in the observed dataset, fixed across simulations and unused in ABC analyses. 16. `seq_length` - the sequence length of the marker in base pairs, used along with `mu` below in the fastsimcoal DNA model, fixed across simulations and unused in ABC analyses. 17. `mu` - the mutation rate (per base pair, per generation) of the simulated locus, used with `seq_length` above in the fastsimcoal DNA model, fixed across simulations and unused in ABC analyses. 18. `G` - the generation time of the species in years, fixed across simulations and unused in ABC analyses. 19. `longmean` - the average distance of long-distance dispersal events in units of cell widths, fixed across simulations and unused in ABC analyses. 20. `lambda` - the rate of population growth within cells (discrete rate of increase), fixed across simulations and unused in ABC analyses. 21. `mix` - the mixture parameter for the distribution of dispersal distances, the proportion of dispersal events that are long-distance. Randomly drawn from a prior distribution for each simulation replicate. 22. `Ne` - the maximum effective population size of a cell in the landscape. Randomly drawn from a prior distribution for each simulation replicate. 23. `preLGM_t` - the time at which refugial populations diverged from one another (e.g., the last interglacial). Randomly drawn from a prior distribution for each simulation replicate. 24. `preLGM_Ne` - the effective population size of the species prior to refuge divergence. Randomly drawn from a prior distribution for each simulation replicate. 25. `found_Ne` - the effective population size of newly colonized populations (used in coalescent simulations only). Randomly drawn from a prior distribution for each simulation replicate. 26. `ref_Ne` - the effective population size of cells included in refugia (scaled by cell-specific habitat suitability in the first time step). Randomly drawn from a prior distribution for each simulation replicate. 27. `refs` - the species distribution model (ENM_1 through ENM_24) used to define habitat suitability across the landscape in each simulation. Each model is represented 50,000 times in the reference table. 28. `BVprev_ybp` - the proportion of habitable (non-NA) cells with abundance >0 in the `DATE` time step relative to all habitable cells. Unitless. 29. `BVmean_ybp` - mean abundance in `DATE` time step. In the same units as the values of the cells (individuals). 30. `BVtotal_ybp` - total abundance across all cells in the simulated landscape at the `DATE` time step. In the same units as the values of the cells (individuals). 31. `BVshared1k_toybp` - abundance-weighted centroid biotic velocity between the `DATE1` and `DATE2` time steps in the simulation, calculated using only cells that are not NA in either of the two time points (to control for changes in available land due to sea level rise). Velocities are given in meters per year and are always positive (direction does not affect velocity). 32. `BVNQshared1k_toybp` - velocity of the 0.95th quantile weight in the north-south direction between the `DATE1` and `DATE2` time steps in the simulation, calculated using only cells that are not NA in either of the two time points (to control for changes in available land due to sea level rise). Velocities are given in meters per year and are positive for northward movement and negative for southward movement. 33. `BVSQshared1k_toybp` - velocity of the 0.05th quantile weight in the north-south direction between the `DATE1` and `DATE2` time steps in the simulation, calculated using only cells that are not NA in either of the two time points (to control for changes in available land due to sea level rise). Velocities are given in meters per year and are positive for northward movement and negative for southward movement. 34. `BVall1k_toybp` - abundance-weighted centroid biotic velocity between the `DATE1` and `DATE2` time steps in the simulation, calculated using all cells. Velocities are given in meters per year and are always positive (direction does not affect velocity). 35. `BVNQall1k_toybp` - velocity of the 0.95th quantile weight in the north-south direction between the `DATE1` and `DATE2` time steps in the simulation, calculated using all cells. Velocities are given in meters per year and are positive for northward movement and negative for southward movement. 36. `BVSQall1k_toybp` - velocity of the 0.05th quantile weight in the north-south direction between the `DATE1` and `DATE2` time steps in the simulation, calculated using all cells. Velocities are given in meters per year and are positive for northward movement and negative for southward movement. 37. `BV_21kyr` - abundance-weighted centroid biotic velocity over the entire 21kyr simulation history, calculated using only cells that are not NA in either of the two time points (to control for changes in available land due to sea level rise). Velocities are given in meters per year and are always positive (direction does not affect velocity). 38. `BVNQ_21kyr` - velocity of the 0.95th quantile weight in the north-south direction over the entire 21kyr simulation history. Quantiles are cumulated starting from the south (0.05th quantile). Velocities are given in meters per year and are positive for northward movement and negative for southward movement. 39. `BVSQ_21kyr` - velocity of the 0.05th quantile weight in the north-south direction over the entire 21kyr simulation history. Quantiles are cumulated starting from the south (0.05th quantile). Velocities are given in meters per year and are positive for northward movement and negative for southward movement. 40. `tot_SNPs` - the total number of single nucleotide polymorphisms in the population genetic dataset output from fastsimcoal. Not used as a summary statistic for ABC analyses, but included to verify that all simulations produce the expected (`nloci`) number of polymorphic markers. The remaining 473 columns in the reference table file contain summary statistics calculated from population genetic datasets produced by the coalescent simulation. The 473 columns in `Ash_obs_subset_2Oct20.csv` are shared with the remainder of the reference table, but were calculated from empirical data for green ash (*Fraxinus pennsylvanica*). 1. `Fst_.` - Pairwise Fst (=1-Hs/Ht) between populations (Wright 1949, 1950). Unitless, ranging from 0 to 1. 210 total statistics. 2. `helat.*` - Summaries of a polynomial model (intercept, first, and second coefficients) relating expected heterozygosity to latitude. 3 total statistics. 3. `helong.*` - Summaries of a polynomial model (intercept, first, and second coefficients) relating expected heterozygosity to longitude. 3 total statistics 4. `HRi_` - Harpending's raggedness index calculated from the Geographic Spectrum of Shared Alleles (Alvarado-Serrano & Hickerson 2018) for each population. 21 total statistics. 5. `Spca.Dmean_` - The mean inter-individual distance in PCA space among individuals within a population (Alvarado-Serrano & Hickerson 2016), calculated from a spatial PCA analysis. 21 total statistics. 6. `Moran.Beta` - Estimate of Moran's I (Moran 1950) measuring spatial autocorrelation in genetic data. 1 total statistic. 7. `Var.*` - Summaries of the variogram (Goovaerts 1998) measuring spatial autocorrelation in the genetic data - beta, sill, nugget, and range of the variogram. 4 total statistics. 8. `Psi_.` - Peter & Slatkin's (2013) directionality index between a pair of populations. 210 total statistics. ## Sharing/Access information Code to define the study region and construct correlative species distribution models is shared with that used in Castilla et al. (2024) and also available from [https://github.com/TIMBERhub](https://github.com/TIMBERhub). Observed data, simulation scripts, and the holoSimCell R package are available from [https://github.com/stranda/holoSimCell](https://github.com/stranda/holoSimCell). A docker image containing the holoSimCell package, all dependencies, and fastsimcoal v. 2.6 is available from [https://hub.docker.com/r/astrand/holosim](https://hub.docker.com/r/astrand/holosim). ## Code/Software We include the R script for **delineating the study region**, plus the raster masks defining the region. These files are included in the `study_region/` directory in `study_region.zip`. 1. `study_region/defining_study_region.r` - R script for defining the study region based on watershed basins, distribution of *Fraxinus pennsylvanica* records, pollen cores, and genetic samples. 2. `study_region/study_region_daltonIceMask_lakesMasked_linearIceSheetInterpolation.tif` - Multi-layer raster in GeoTIFF format with a mask of the area of interest (generally, eastern portion of North America) from 1 Kybp to 0 bp (1950 CE). The “last” or “lowest” layer represents available land (uncovered by sea and ice) 21 Kybp, and the “top” or “first layer” the present, with one layer per 30 years across this period. Values are 1 (available) and NA (unavailable). 3. `study_region/study_region_resampled_to_genetic_demographic_simulation_resolution.tif` - Raster in GeoTIFF format with all cells equal to 1 and in the equal-area spatial resolution used in the genetic/demographic simulations. This is a single layer raster. We also include R scripts used for calibrating the **species distribution models** and creating projections of past and future habitat suitability and the outputs of these projections in raster format. These files are included in the `enms/` directory in `enms.zip`. 1. `enms/code/enms_for_fraxinus_pennsylvanica.r` - Collates specimen data and environmental rasters, constructs data partitions, calibrates and evaluates SDMs, projects models to past, interpolation of rasters to finer timescales, and calculation of biotic velocity. 2. `enms/code/enms_for_fraxinus_pennsylvanica_projected_to_future.r `- Takes models from first script and projects them to future climate scenarios. 3. `enms/predictions/` folder - Contains rasters in GeoTIFF format with predictions to the past. Each file is a “stack” of layers with predictions, from 21 Kybp (“lowest” or “last” layer) to the “present” (1950, “top” or “first” layer). Original values were in the range [0, 1], but they have been rescaled and rounded to {0, 1, 2, 3, … , 100}. File names are as: `_kmExtent_.tif`. For example: `ecbilt_80kmExtent_brt.tif`. 4. `enms/predictions_future/` folder - Contains rasters in GeoTIFF format with predictions to the future. Original values were in the range [0, 1], but they have been rescaled and rounded to {0, 1, 2, 3, … , 100}. File names are as: `__kmExtent_rcp__.tif`. For example: `brt_ecbilt_320kmExtent_rcp45_2050_GFDL-CM3.tif`. The apptainer container (`holosim.simg`) in the repository was used for all simulations in this study and includes the necessary R packages (including holoSimCell) and the coalescent simulation software fastsimcoal v. 2.6. Coupled demographic-genetic simulations can be run using the `hSC_Ash_with_enms.R` script. This containerized version of R and the installed packages can also be used to recreate the SDMs tested. We include several R scripts used for **ABC analysis**. The following scripts are saved in the `ABC/` directory in `ABC.zip`. These scripts use the reference table (`ENMcomparison_RT_50k_subset.csv`) and observed summary statistics (`Ash_obs_subset_2Oct20.csv`) files described above. 1. `ABC/CheckECDF.R` - calculates the location of observed summary statistics within the distribution of statistic values from 50,000 simulations under each SDM. 2. `ABC/AshENM_modsela_subset_mnlog.R` - performs ABC model selection with multinomial logistic regression 3. `ABC/AshENM_modsela_subset_nnet.R` - performs ABC model selection with neural networks 4. `ABC/ENMcomparison_RF_pred_subset.R` - performs ABC model selection with random forests 5. `ABC/ENMcomparison_CV4MS.R` - performs cross validations for model selection using either multinomial logistic regression or neural networks 6. `ABC/ENMcomparison_numreps_modsel_nnet.R` - performs model selection with subsets of the reference table to evaluate changes in model posterior probabilities as the total number of replicates declines from 50,000 to 5000 ## References Alvarado-Serrano, D. F. and Hickerson, M. J. 2016. Spatially explicit summary statistics for historical population genetic inference. – Methods Ecol. Evol. 7: 418–427. Alvarado-Serrano, D. F. and Hickerson, M. J. 2018. Detecting spatial dynamics of range expansions with geo-referenced genomewide SNP data and the geographic spectrum of shared alleles. – bioRxiv 457556. Goovaerts, P. 1998. Geostatistical tools for characterizing the spatial variability of microbiological and physico-chemical soil properties. – Biol. Fertil. Soils 27: 315–334. He, Q., Edwards, D. L. and Knowles, L. L. 2013. Integrative testing of how environments from the past to the present shape genetic structure across landscapes. – Evolution 67: 3386–3402. Moran, P. 1950. Notes on continuous stochastic phenomena. – Biometrika 37: 17–23. Peter, B.M. and Slatkin, M. 2013. Detecting range expansions from genetic data. – Evolution 67: 3274−3289. Wright, S. 1949. The genetical structure of populations. – Ann. Eugen. 15: 323−354. Wright, S. 1950. The genetical structure of populations. – Nature 166: 247-249. Climate change poses a threat to biodiversity, and it is unclear whether species can adapt to or tolerate new conditions, or migrate to areas with suitable habitats. Reconstructions of range shifts that occurred in response to environmental changes since the last glacial maximum from species distribution models (SDMs) can provide useful data to inform conservation efforts. However, different SDM algorithms and climate reconstructions often produce contrasting patterns, and validation methods typically focus on accuracy in recreating current distributions, limiting their relevance for assessing predictions to the past or future. We modeled historically suitable habitat for the threatened North American tree green ash (Fraxinus pennsylvanica) using 24 SDMs built using two climate models, three calibration regions, and four modeling algorithms. We evaluated the SDMs using contemporary data with spatial block cross-validation and compared the relative support for alternative models using a novel integrative method based on coupled demographic-genetic simulations. We simulated genomic datasets using habitat suitability of each of the 24 SDMs in a spatially-explicit model. Approximate Bayesian Computation (ABC) was then used to evaluate the support for alternative SDMs through comparisons to an empirical population genomic dataset. Models had very similar performance when assessed with contemporary occurrences using spatial cross-validation, but ABC model selection analyses consistently supported SDMs based on the CCSM climate model, an intermediate calibration extent, and the generalized linear modeling algorithm. Finally, we projected the future range of green ash under four climate change scenarios. Future projections using the SDMs selected via ABC suggest only minor shifts in suitable habitat for this species, while some of those that were rejected predicted dramatic changes. Our results highlight the different inferences that may result from the application of alternative distribution modeling algorithms and provide a novel approach for selecting among a set of competing SDMs with independent data.
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For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Dataset 2023Publisher:Observatoire Global du Saint-Laurent Chaillou, Gwenaelle; Tanhua, Toste; Hérard, Olivier; Nesbitt, William; Wallace, Douglas;Le projet TReX (Tracer Release eXperiment) est un projet de recherche intersectoriel qui vise à développer et à démontrer la capacité du Canada à prédire la dispersion de contaminants et à répondre à leurs déversements accidentels dans les environnements marins côtiers. Le present jeu de données CTD provient de la première mission de la phase TReX-deep qui vise l’étude des processus de transport et dispersion dans les eaux de fond du Chenal Laurentien, de l'estuaire maritime au Détroit de Cabot. Cette expérience unique, qui combine les expertises de chercheurs du Québec, de la Nouvelle Écosse et de l'Allemagne, est utilisée non seulement pour prévoir la dispersion et l'advection de certains contaminants mais aussi pour comprendre les processus biogéochimiques liés au climat qui contrôlent les conditions d’hypoxie et d’acidification à la tête du Chenal Laurentien. Ce jeu de données CTD issu de la première mission en octobre 2021 présente des profils verticaux de salinité, température, oxygène dissous, densité, et fluorescence de 4 à 360 m pour une trentaine de stations entre Rimouski et le Détroit de Cabot. Bien que les sondes soient calibrées par le fabricant au cours de l'année, des échantillons discrets de salinité ont été prélevés dans toute la colonne d'eau et analysés sur un salinomètre Guildline Autosal 8400 calibré avec l'eau de mer standard de l'IAPSO (International Association for the Physical Sciences of the Oceans) et les profils CTD retraités après la mission. De même, les concentrations d'oxygène dissous ont été déterminées par titrage chimique Winkler (Grasshoff et al., 1999) sur une quarantaine d'échantillons d'eau discrets collectés directement dans les bouteilles Niskin. L'écart-type relatif, basé sur des analyses répétées d'échantillons prélevés dans la même bouteille Niskin, était inférieur à 1 %. Ces mesures ont également servi à étalonner la sonde à oxygène SBE-43 montée sur la rosette. Il a été acquis conjointement par les équipes de Douglas Wallace (U. Dalhousie), Gwénaëlle Chaillou (ISMER-UQAR) et Toste Tanhua (GEOMAR). The TReX (Tracer ReleaseEXperiment) project is an interdisciplinary research project that aims to develop and demonstrate Canada's ability to predict the spread of contaminants and respond to their accidental discharges in coastal marine environments. The present CTD dataset comes from the first mission of the Trex-Deep phase, which aims to study transport and dispersal processes in the bottom waters of the Laurentian Channel, from the maritime estuary to Cabot Strait. This unique experiment, which combines the expertise of researchers from Quebec, Nova Scotia, and Germany, is used to predict the dispersal and advection of certain contaminants and understand the climate-related biogeochemical processes that control hypoxia and acidification conditions at the head of the Laurentian Channel. This CTD dataset from the first mission in October 2021 presents vertical profiles of salinity, temperature, dissolved oxygen, density, and fluorescence from 4 to 360 m for about thirty stations between Rimouski and Cabot Strait. Although the probes were calibrated by the manufacturer during the year, discrete salinity samples were taken throughout the water column and analyzed on a Guildline Autosal 8400 salinometer calibrated with standard IAPSO (International Association for the Physical Sciences of the Oceans) seawater and CTD profiles reprocessed after the mission. Similarly, dissolved oxygen concentrations were determined by Winkler chemical titration (Grasshoff et al., 1999) on about forty discrete water samples collected directly from Niskin bottles. The relative standard deviation, based on repeated analyses of samples taken from the same Niskin bottle, was less than 1%. These measurements were also used to calibrate the SBE-43 oxygen probe mounted on the rosette. It was acquired jointly by the teams of Douglas Wallace (U. Dalhousie), Gwénaëlle Chaillou (ISMER-UQAR) and Toste Tanhua (GEOMAR).
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For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Dataset 2024Embargo end date: 30 Apr 2024Publisher:NERC EDS Environmental Information Data Centre Dusenge, M.E.; González-Caro, S.; Restrepo, Z.; Meir, P.; Hartley, I.P.; Sitch, S; Sanchez, A; Mercado, M.L.;Data collection protocol: in January – March 2022, Aci curves (i.e., CO2 response curves of net photosynthesis) were done at a pre-determined saturating light intensity of 1800 PAR (Qin in the database). Aci curves were done at different leaf temperature targets between 15 and 40 degree Celcius, with 5 degree celcius steps. Before starting any ACi curve, the leaf was allowed to acclimate at each temperature for at least 10 min and the ACi was initiated once both Anet and stomatal conductance were stable for at least 2 min. Throughout each Aci, the stability time at each CO2 reference concentration (410, 50, 100, 150, 250, 410, 800, 1200, 1600, and 2000 in this order) was set to 45 - 180 seconds, the automatic match was programmed before recording any data at each CO2 reference concentration. Measurements were taken with an LI6800 Portable Photosynthesis System under field conditions. LI6800 indicates whether there is a leak, but measurements were always done after ensuring there was no leak in the system, therefore, no subsequent leak correction was necessary. At the beginning of each measurement day, automatic warm-up test was run to detect any problem within the instrument, and only measurements were initiated when all errors have been fixed as suggested by the instrument system. The leaf temperature was derived from the thermocouple of the instrument. This dataset contains information about temperature response curves of ACi (i.e., CO2 response curves of net photosynthesis) that were collected on Colombian Andean forests tree species that were planted in three, common-garden tree plantations along a 2000m altitudinal gradient. Specifically, individuals of cold- and warm-affiliated species were planted under common soil and water conditions, exposing them to the hot and cold extremes of their thermal niches, respectively. This work was supported by the UK Natural Environment Research Council (NE/R001928/1)
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For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Dataset 2023Embargo end date: 28 Apr 2023Publisher:Dryad Luo, Binyu; Huang, Mei; Wang, Wenyin; Niu, Jiahuan; Shrestha, Mani; Zeng, Haijun; Ma, Lin; Degen, Allan; Liao, Jingkang; Zhang, Tao; Bai, Yanfu; Zhao, Jingxue; Fraser, Lauchlan; Shang, Zhanhuan;Warming can decrease feeding activity of soil organisms and affect biogeochemical cycles in alpine ecosystems. Ants (Formica manchu) are active on their nest surface, and prefer a hot and dry environment. Therefore, warming may provide a favorable environment for their activity. We hypothesized that ants might benefit from warming and increase the robustness of ecosystem functions to warming. To test this hypothesis, we examined the effects of ant nests (ant nest absence vs. ant nest presence) and warming (ambient temperature, + 1.3°C and + 2.3°C) on litter decomposition, soil properties and the plant community in an alpine grassland ecosystem. Decomposition stations with two mesh sizes were used to differentiate effects of microorganisms (0.05mm) and macroinvertebrate (1cm) to litter decomposition. Ant nests increased litter decomposition with and without macroinvertebrates accessing the decomposition station when compared to plots without ant nests. Only the litter decomposition in ant nests with macroinvertebrates accessing the decomposition station was not negatively affected by warming. Plots with ant nests had greater soil organic carbon, nutrient contents and plant growth than plots without ant nests, regardless of warming. Consequently, ant nests can mitigate the negative effects of warming on litter decomposition and improve ecosystem functions under warming.
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For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Dataset 2024Publisher:PANGAEA Anhaus, Philipp; Schiller, Martin; Planat, Noémie; Katlein, Christian; Nicolaus, Marcel;Incident solar irradiance was measured using an ACC (Advanced-Cosine-Collector) RAMSES hyper-spectral radiometer (TriOS) installed on-board the ship during the ARTofMELT2023 expedition in May and June 2023. All times are given in Universal Coordinated Time (UTC).
PANGAEA - Data Publi... arrow_drop_down PANGAEA - Data Publisher for Earth and Environmental ScienceDataset . 2024License: CC BYData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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more_vert PANGAEA - Data Publi... arrow_drop_down PANGAEA - Data Publisher for Earth and Environmental ScienceDataset . 2024License: CC BYData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Dataset 2024Publisher:PANGAEA Anhaus, Philipp; Schiller, Martin; Planat, Noémie; Katlein, Christian; Nicolaus, Marcel;Transmitted solar radiance was measured using an ARC (Advanced-Radiance-Collector) RAMSES hyper-spectral radiometer (TriOS) mounted on the ROV during the ARTofMELT2023 expedition in May and June 2023 and normalized by the incident solar irradiance as measured using an ACC (Advanced-Cosine-Collector) RAMSES hyper-spectral radiometer (TriOS) installed on-board the ship. All times are given in Universal Coordinated Time (UTC).
PANGAEA - Data Publi... arrow_drop_down PANGAEA - Data Publisher for Earth and Environmental ScienceDataset . 2024License: CC BYData sources: DatacitePANGAEA - Data Publisher for Earth and Environmental ScienceDataset . 2024License: CC BYData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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more_vert PANGAEA - Data Publi... arrow_drop_down PANGAEA - Data Publisher for Earth and Environmental ScienceDataset . 2024License: CC BYData sources: DatacitePANGAEA - Data Publisher for Earth and Environmental ScienceDataset . 2024License: CC BYData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Dataset 2023Embargo end date: 01 Dec 2023Publisher:Harvard Dataverse Authors: Barchyn, Thomas;doi: 10.7910/dvn/qjutzo
Surface methane concentration data measured to produce a better understanding of surface methane emissions across the landfill.
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more_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Dataset 2021Publisher:ICPSR - Interuniversity Consortium for Political and Social Research Authors: Rud, Juan Pablo; Aragon, Fernando; Oteiza, Francisco;This paper examines how subsistence farmers respond to extreme heat. Using micro-data from Peruvian households, we find that high temperatures reduce agricultural productivity, increase area planted, and change crop mix. These findings are consistent with farmers using input adjustments as a short-term mechanism to attenuate the effect of extreme heat on output. This response seems to complement other coping strategies, such as selling livestock, but exacerbates the drop in yields, a standard measure of agricultural productivity. Using our estimates, we show that accounting for land adjustments is important to quantify damages associated with climate change.
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For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Collection 2022Publisher:PANGAEA Oehri, Jacqueline; Schaepman-Strub, Gabriela; Kim, Jin-Soo; Grysko, Raleigh; Kropp, Heather; Grünberg, Inge; Zemlianskii, Vitalii; Sonnentag, Oliver; Euskirchen, Eugénie S; Reji Chacko, Merin; Muscari, Giovanni; Blanken, Peter D; Dean, Joshua F; di Sarra, Alcide; Harding, Richard J; Sobota, Ireneusz; Kutzbach, Lars; Plekhanova, Elena; Riihelä, Aku; Boike, Julia; Miller, Nathaniel B; Beringer, Jason; López-Blanco, Efrén; Stoy, Paul C; Sullivan, Ryan C; Kejna, Marek; Parmentier, Frans-Jan W; Gamon, John A; Mastepanov, Mikhail; Wille, Christian; Jackowicz-Korczynski, Marcin; Karger, Dirk N; Quinton, William L; Putkonen, Jaakko; van As, Dirk; Christensen, Torben R; Hakuba, Maria Z; Stone, Robert S; Metzger, Stefan; Vandecrux, Baptiste; Frost, Gerald V; Wild, Martin; Hansen, Birger Ulf; Meloni, Daniela; Domine, Florent; te Beest, Mariska; Sachs, Torsten; Kalhori, Aram; Rocha, Adrian V; Williamson, Scott N; Morris, Sara; Atchley, Adam L; Essery, Richard; Runkle, Benjamin R K; Holl, David; Riihimaki, Laura; Iwata, Hiroki; Schuur, Edward A G; Cox, Christopher J; Grachev, Andrey A; McFadden, Joseph P; Fausto, Robert S; Göckede, Mathias; Ueyama, Masahito; Pirk, Norbert; de Boer, Gijs; Bret-Harte, M Syndonia; Leppäranta, Matti; Steffen, Konrad; Friborg, Thomas; Ohmura, Atsumu; Edgar, Colin W; Olofsson, Johan; Chambers, Scott D;Despite the importance of surface energy budgets (SEBs) for land-climate interactions in the Arctic, uncertainties in their prediction persist. In-situ observational data of SEB components - useful for research and model validation - are collected at relatively few sites across the terrestrial Arctic, and not all available datasets are readily interoperable. Furthermore, the terrestrial Arctic consists of a diversity of vegetation types, which are generally not well represented in land surface schemes of current Earth system models. Therefore, we here provide four datasets comprising:1. Harmonized, standardized and aggregated in situ observations of SEB components at 64 vegetated and glaciated sites north of 60° latitude, in the time period 1994-20212. A description of all study sites and associated environmental conditions, including the vegetation types, which correspond to the classification of the Circumpolar Arctic Vegetation Map (CAVM, Raynolds et al. 2019).3. Data generated in a literature synthesis from 358 study sites on vegetation or glacier (>=60°N latitude) covered by 148 publications.4. Metadata, including data contributor information and measurement heights of variables associated with Oehri et al. 2022. Code underlying the dataset and publication is available in a Github repository and can be accessed at: https://github.com/oehrij/ArcticSEBSynthesis
PANGAEA - Data Publi... arrow_drop_down PANGAEA - Data Publisher for Earth and Environmental ScienceCollection . 2022License: CC BYData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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more_vert PANGAEA - Data Publi... arrow_drop_down PANGAEA - Data Publisher for Earth and Environmental ScienceCollection . 2022License: CC BYData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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