Data from: Using spatially-nested hierarchical species distribution models to estimate current and future distributions of a cryptic species at a regional scale
Abstract
Understanding a species’ conservation status requires evaluating its ecological relationships, contemporary distribution, and vulnerability to future environmental change. Species distribution models (SDMs) are widely used for these purposes, but regional-scale applications often suffer from extrapolation and niche truncation, reducing model transferability. Spatially-Nested Hierarchical SDMs (N-SDMs), which integrate data across multiple spatial scales, offer a promising solution but remain underutilized in regional conservation research. Crawfish frogs (Rana areolata) are a cryptic grassland species reliant on crayfish burrows that have experienced declines across their range and are data deficient in Oklahoma. This study combines comprehensive regional field surveys across Oklahoma with large-scale occurrence data from GBIF using an N-SDM framework to characterize the species’ current regional distribution, identify factors influencing habitat suitability, and forecast future range shifts under climate and land-use change. Additionally, we compared the performance of N-SDMs to regional-only and rangewide SDMs, and assessed how niche truncation and extrapolation influence model performance and transferability under future environmental conditions. We documented R. areolata at 303 survey locations and found no evidence of historical county-level extirpations, with our models suggesting large amounts of suitable habitat in eastern Oklahoma. Our rangewide SDM lacked the resolution and regional predictive performance necessary for regional conservation planning. While our regional-only SDM had higher predictive performance, it suffered from substantial extrapolation and niche truncation, leading to predictions of significant habitat loss under future conditions. In contrast, our N-SDMs had the highest regional predictive performance, and mitigated the effects of niche truncation and extrapolation, and projected no change or a slight increase in future habitat suitability. Our findings highlight the advantages of N-SDMs for improving model predictions and informing conservation assessments. Failure to account for niche truncation and extrapolation can lead to poor predictions and misguided conservation decisions. We advocate for the broader adoption of this approach in regional-scale studies to improve predictions of species responses to environmental change, and more effectively assess species status at a regional level.
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Authors
- Kaleb M. Banks
- Owen M. Edwards
- Bo Zhang
- Michael S. Reichert
Contact: kaleb.banks@okstate.edu
Date: 4/7/2026
Paper: Banks, K. M., Edwards, O. M., Zhang, B., & Reichert, M. S. (2026). Using
spatially-nested hierarchical species distribution models to estimate current and future
distributions of a cryptic species at a regional scale. Journal of Animal Ecology, 00,
1–16. https://doi.org/10.1111/1365-2656.70248
Dataset: https://doi.org/10.5061/dryad.zw3r228nh
License: CC0 1.0 — https://creativecommons.org/publicdomain/zero/1.0/
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Description
Species distribution models (SDMs) for Rana areolata under current and future climate
scenarios. Models were built in R using the sabinaNSDM package with three algorithms
(GBM, MARS, MAXNET) and 20 cross-validation replicates, applied across three modelling
approaches (Global, Regional, Covariate) plus a Multiply ensemble model which is the
average of the global and regional model. Full detailed methods are described in the
associated paper and its supplementary files.
All coordinates are in WGS84.
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How To Use
- Download data.zip and Place the unzipped
data/folder in the root of an R project. - Download GBIF data from https://doi.org/10.15468/dl.u77byy. Reformat so the data
frame contains columns labeledXfor longitude andYfor latitude values and name
the filerangewide_gbif_occ.csv. Place indata/occurrences_absences/occ_raw/. - Download soil data from https://www.arcgis.com/home/item.html?id=1bfc47d2a0d544bea70588f81aac8afb.
Resample and mask to match the extent and resolution of the 2.5 arc-minute bioclim
variables. Name the filepercent_clayand place in
data/env_var/scenarios_raw/expl.var.regional/. - All script file paths are relative to the project root — do not change the folder
structure. - Download R scripts from GitHub: https://github.com/kalebbanks/crawfrog_NSDM
- Run scripts in numbered order (01_, 02_, etc.) to recreate the model workflow.
R version: 4.5.1
Relevant R packages:
- sabinaNSDM (1.1.0)
- terra (1.8)
- covsel (1.0)
- biomod2 (4.2)
- PresenceAbsence (1.1.11)
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Environmental Variables
Climatic Variables
We used the 19 bioclim variables from the WorldClim database (version 2.1; Fick &
Hijmans, 2017; https://www.worldclim.org/data/bioclim.html).
- Global model: 10 arc-minute resolution
- Regional models: 2.5 arc-minute resolution
- Future scenarios: 2070 (average of 2061–2080), 2.5 arc-minute resolution,
downloaded from WorldClim
Future climate data used two socioeconomic pathways (SSP2-4.5 and SSP5-8.5) and is the average of three global climate models:
- MIROC6
- MPI-ESM1-2-HR
- CMCC-ESM2
Percent Clay
We used the World Soils 250 m percent clay raster (Esri 2020;
https://www.arcgis.com/home/item.html?id=1bfc47d2a0d544bea70588f81aac8afb), which
quantifies the proportion of clay particles (< 0.002 mm) in the fine earth fraction in
g/100g (%) at −80 cm. This variable was used only at the regional extent and was
resampled to 2.5 arc-minute resolution. The same dataset was used for future scenarios.
Percent Prairie
We used a high-resolution land cover raster from the Oklahoma Biological Survey (OBS)
that categorized 167 habitat types at 10-meter resolution for the year 2015 (Oklahoma
Biological Survey 2015; https://www.wildlifedepartment.com/lands-and-minerals/oklahoma-ecological-system-mapping).
We reclassified these categories to identify areas of undisturbed prairie, defined as
open canopy prairies or rangelands with limited soil horizon disturbance. Low-intensity
agriculture such as cattle ranching was assumed untilled and included as suitable habitat
for R. areolata (see Supplementary Table 2). After reclassification, we calculated the
percentage of undisturbed prairie within each 2.5 arc-minute cell and saved it as a
separate raster.
For future scenarios, we used the USGS land use projections for 2070 (Sohl et al., 2014)
as the OBS dataset is not available for future time periods. Two land use scenarios were
tested:
- A1B: Rapid economic and technological growth, moderate land use change, balanced
energy mix and efficient resource management - A2: High population growth, slower economic development, limited technological
advancement, resulting in intensive land use change due to agricultural expansion and
urban sprawl
The USGS land use datasets were reclassified to match the OBS classifications.
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Occurrence Data
- Global model: Downloaded from GBIF (10/18/2024); 405 occurrences
- Regional model: Field surveys conducted by the authors in 2023 and 2024; 303
occurrences
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Future Scenario Key
| Scenario ID | SSP | Land Use | Year |
|---|---|---|---|
| future_scenario_1 (S1) | SSP2-4.5 | Current land use (OBS) | 2070 |
| future_scenario_2 (S2) | SSP5-8.5 | Current land use (OBS) | 2070 |
| future_scenario_3 (S3) | SSP2-4.5 | Projected land use change (USGS A1B) | 2070 |
| future_scenario_4 (S4) | SSP5-8.5 | Projected land use change (USGS A1B) | 2070 |
| future_scenario_5 (S5) | SSP2-4.5 | Severe land use change (USGS A2) | 2070 |
| future_scenario_6 (S6) | SSP5-8.5 | Severe land use change (USGS A2) | 2070 |
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Folder Structure
- data/extent_shapefiles/ — Shapefiles defining the global and regional model extents. The global extent covers the southern plains and southern USA. The regional extent covers central and eastern Oklahoma counties.
- data/env_var/
- correlation_test/ — Spearman correlation matrix CSV of the 19 bioclim variables and two landscape variables at the regional extent.
- scenarios_raw/ — Raw climate rasters used to create the scenarios.
- scenarios_spatraster/ — Processed SpatRaster stacks used as model inputs.
- data/occurrences_absences/
- occ_raw/ — Raw Rana areolata occurrence records (global and regional).
- occ_thinned/ — Spatially thinned occurrences used for modelling.
- abs_global/ — Randomly generated pseudoabsences for the global model.
- abs_reg/ — Randomly generated pseudoabsences for the regional model.
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Citations
Dataset:
Banks, K., Edwards, O., Zhang, B., & Reichert, M. (2026). Using spatially-nested
hierarchical species distribution models to estimate current and future distributions of
a cryptic species at a regional scale [Dataset]. Dryad.
https://doi.org/10.5061/dryad.zw3r228nh
Paper:
Banks, K. M., Edwards, O. M., Zhang, B., & Reichert, M. S. (2026). Using
spatially-nested hierarchical species distribution models to estimate current and future
distributions of a cryptic species at a regional scale. Journal of Animal Ecology, 00,
1–16. https://doi.org/10.1111/1365-2656.70248
Environmental Variables:
Esri. (2020). World Soils 250m Percent Clay. Retrieved July 17, 2023, from
https://www.arcgis.com/home/item.html?id=1bfc47d2a0d544bea70588f81aac8afb
Fick, S. E., & Hijmans, R. J. (2017). WorldClim 2: New 1-km spatial resolution climate
surfaces for global land areas. International Journal of Climatology, 37(12), 4302–4315.
https://doi.org/10.1002/joc.5086
Oklahoma Biological Survey. (2015). Oklahoma Ecological System Mapping [Raster file].
Retrieved August 22, 2024, from https://www.wildlifedepartment.com/lands-and-minerals/oklahoma-ecological-system-mapping
Sohl, T. L., Sayler, K. L., Bouchard, M. A., Reker, R. R., Friesz, A. M., Bennett, S.
L., Sleeter, B. M., Sleeter, R. R., Wilson, T., Soulard, C., Knuppe, M., & Van Hofwegen,
T. (2014). Spatially explicit modeling of 1992–2100 land cover and forest stand age for
the conterminous United States. Ecological Applications, 24(5), 1015–1036.
https://doi.org/10.1890/13-1245.1
Occurrence Data:
GBIF.org (18 October 2024) GBIF Occurrence Download. https://doi.org/10.15468/dl.u77byy
sabinaNSDM:
Mateo, R. G., Morales-Barbero, J., Zarzo-Arias, A., Lima, H., Gómez-Rubio, V., &
Goicolea, T. (2024). sabinaNSDM: An R package for spatially nested hierarchical species
distribution modelling. Methods in Ecology and Evolution, 15(10), 1796–1803.
https://doi.org/10.1111/2041-210X.14417
