Data and code from: Global change affects large herbivore forage biomass through gradual successional shifts and abrupt disturbances
Data files
Jul 21, 2025 version files 12.64 GB
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Biomass_Plot_Data.zip
184.07 KB
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code.zip
41.44 KB
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README.md
4.56 KB
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Spatial_Data.zip
12.64 GB
Abstract
Forage availability is a key factor regulating large herbivore populations. Global changes in land use and climate may affect the spatiotemporal distribution of forage across the ranges of large herbivores, especially in mountain ecosystems. We test two synergistic hypotheses for how landscape and climate changes from 2001 to 2023 have affected forb and graminoid biomass at the peak of the growing season within and across ecoregions of the eastern slopes of the Rocky Mountains in Alberta, Canada. The successional change hypothesis posits that the encroachment of woody vegetation into previously herbaceous communities has reduced forage biomass. The disturbance hypothesis proposes that abrupt community shifts caused by fire and timber harvesting have increased forage biomass. We used remote sensing to quantify temporal changes in land cover and disturbances, NDVI greenness and phenology indices, and spring climate. We then used in-situ vegetation data to parameterize generalized linear and gradient boosted regression tree models of forb and graminoid biomass to predict annual peak forb and graminoid biomass. We found that herbaceous land cover declined while shrub and forest area increased, and the percent of annual biomass within herbaceous areas declined from woody encroachment. Disturbance effects varied, with rising forage biomass in conjunction with increased area of logged forests in the foothills ecoregion, while burned areas declined and had a reduced contribution to the percent of annual biomass. We found that spring became warmer across the study area and ended earlier in the alpine, suggesting the effects of long-term climatic shifts may be strongest at higher ecoregions. Disturbance frequency, succession, and climate together shaped forage biomass in space and time. Increased prescribed fire and other ecological restoration actions may be needed to ensure that shifts in forage biomass do not threaten large herbivore persistence in the face of global change.
Dataset DOI: 10.5061/dryad.mw6m9066p
Description of the data and file structure
This repository contains R code and data files for "Global change affects large herbivore forage biomass through gradual successional shifts and abrupt disturbances". An overview of the data collection & analysis is available in the main manuscript.
Files and variables
File: Biomass_Plot_Data.zip
Description: Raw data from the forage biomass plots in .csv form
File: code.zip
Description: R code for all analysis:
- integrating_fire_and_cutblocks_to_landcover_mar162024.RMD is the file that merges our fire polygons from Parks Canada and Alberta into our time-varying landcover raster based on burn year and type of landcover inside the burn.
- spatial_covariate_extraction_jan132025.RMD extracts all spatial variables from our rasters at vegetation point locations for the year of sampling
- prepping_spatial_covars_forpredictions_jan142025.RMD this scales, centers, and aligns rasters as needed to generate spatial model predictions for each year of our study period
- preping_data_for_modelling_jan132025.RMD scales and centers covariates, and uses AIC to test among correlated covariates.
- regression_modelling_jan142025.RMD is analytical code for conducting GLM model fitting and selection, and generating summary figures and tables.
- GBM regression jan142025.RMD is analytical code for gradient boosting machine learning analysis and generation of summary tables and figures.
- model_validation_jan142025.RMD is code for conducting model validation based on withheld training data and YHT long term data
- spatial_model_predictions_2001to2023_jan142025.RMD generates spatial model predictions based on the top models from both methods and from script 4.
- changes_in_landcover_NDVI_and_climate_Jan192025.RMD quantifies changes in the time-varying landcover map, NDVI vegetation indices and climate patterns
- changes_in_foragebiomass_jan192025.RMD quantifies changes in forage (based on predicted values) over time
File: Spatial_Data.zip
Description: Spatial data needed to conduct analyses. Includes time-varying landcover, phenology indices, and topographic covariates. Can be downloaded and opened in R using the terra() package.
Code/software
R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
RStudio version 2024.4.2.764 -- "Chocolate Cosmos"
Access information
Data was derived from the following sources:
- Time-varying landcover for our study area was derived from:
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Hermosilla, T., Wulder, M. A., White, J. C., & Coops, N. C. (2022). Land cover classification in an era of big and open data: Optimizing localized implementation and training data selection to improve mapping outcomes. Remote Sensing of Environment, 268, 112780. https://doi.org/10.1016/j.rse.2021.112780
Hermosilla, T., Wulder, M. A., White, J. C., Coops, N. C., & Hobart, G. W. (2018). Disturbance-informed annual land cover classification maps of Canada’s forested ecosystems for a 29-year Landsat time series. Canadian Journal of Remote Sensing, *44 *(1), 67–87. https://doi.org/10.1080/07038992.2018.1437719
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- NDVI phenology metrics were derived from MODIS MOD13Q1 - MODIS/Terra Vegetation Indices 16-Day L3 Global 250m SIN Grid following methods used in the following papers:
- Merkle, J. A., Monteith, K. L., Aikens, E. O., Hayes, M. M., Hersey, K. R., Middleton, A. D., Oates, B. A., Sawyer, H., Scurlock, B. M., & Kauffman, M. J. (2016). Large herbivores surf waves of green-up during spring. Proceedings of the Royal Society B: Biological Sciences, 283( 1833), 20160456. https://doi.org/10.1098/rspb.2016.0456
- Beck, P. S. A., Atzberger, C., Høgda, K. A., Johansen, B., & Skidmore, A. K. (2006). Improved monitoring of vegetation dynamics at very high latitudes: A new method using MODIS NDVI. Remote Sensing of Environment, 100(3), 321–3
- Bischof, R., Loe, L. E., Meisingset, E. L., Zimmermann, B., Van Moorter, B., & Mysterud, A. (2012). A migratory northern ungulate in the pursuit of spring: Jumping or surfing the green wave? The American Naturalist, 180(4), 407–424. https://doi.org/10.1086/667590