Shifts in salamander body size associated with 60 years of climate change
Data files
Sep 17, 2025 version files 105.65 MB
-
data.zip
105.62 MB
-
README.md
9.09 KB
-
scripts.zip
19.34 KB
Abstract
Climate change impacts body size, a fundamental trait central to energetics and reproductive success. Most studies on body size shifts in response to climate change have focused on temperature, with smaller sizes expected under warming. However, precipitation has received less attention even though water and heat balance interact to impact body size. Precipitation changes may be particularly important for wet-skinned amphibians. We examined body size shifts in 10 plethodontid salamander species in the Balsam Mountains, Virginia, USA. Using historical data (1957-1959) as a baseline, we resurveyed salamanders (2021 and 2023) to assess how temperature and precipitation shifts have influenced body size. We hypothesized warmer, wetter conditions would reduce body sizes across species. Over 60 years, temperatures warmed across elevation, while precipitation increased more at higher compared to lower elevations. After accounting for phylogeny, warming generally reduced body size, with temperature effects amplified by increased precipitation at high elevations. However, the direction and magnitude of body size shifts were species-specific indicating that size shifts are a complex interplay of environmental factors and species traits. Our findings highlight the importance of considering interacting climate variables when assessing responses to environmental change, particularly in montane ecosystems.
Dataset DOI: 10.5061/dryad.vt4b8gv3w
Description of the data and file structure
Files and variables
File: data.zip
Description: Contains the below file and folders
Folder: microclimate_data
Description: contains the following files
- File: Contemporary_for_micro_extractions.csv
- Description: Raw data file containing information on all the salamanders collected during the contemporary time period. This file is used in R script '1_ProcB_Microclimate_Extraction_job_array.R' to produce the microclimate data for contemporary salamanders included in ‘Extracted_Microclimate_Data_Historical_and_Contemporary.csv'.
- Variables:
- Field_Number2: unique numeric identifier for each sample (used in downstream analysis)
- Field_Number: unique identifier, as recorded in field notebooks (not used in downstream analysis)
- Species: includes the scientific name of each salamander
- Sex: the sex (male/female/unknown) of each salamander
- LifeStage: adult versus juvenile
- SVL: snout-vent length (mm)
- TL: total length (mm)
- Elevation: the elevation that the salamander was found at (meters)
- TimOfDay: the time of day the salamander was found
- Date: the date the salamander was found (m/dd/yy)
- Month: taken from the 'Date' column to ease downstream analysis
- Day: taken from the 'Date' column to ease downstream analysis
- Year: taken from the 'Date' column to ease downstream analysis
- Transect: the general location of each salamander, as recorded in field notebooks
- Transect_2: a standardized set of locations produced from the 'Transect' column, grouping similar location names into one name to ease downstream analysis.
- Slope & Mountain: two columns that are empty, but add to ease the merging of data files in downstream analysis
- County: indicated which county the salamander was found in
- Latitude: the latitude the salamander was found at (decimal degrees)
- Longitude: the longitude the salamander was found at (decimal degrees)
- Era: What time period the salamander record is from "historical" (1950s) or "contemporary" (2020s).
- File: Extracted_Microclimate_Data_Historical_and_Contemporary.csv
- Description: This datafile is used to run the Bayesian Regression models.
- Variables:
- average annual rainfall: the average total annual rainfall (mm) over five year (starting five years prior to the date the salamander was collected) at the location the salamander was collected.
- mean annual avg humidity: the average annual humidity (%) over five year (starting five years prior to the date the salamander was collected) at the location the salamander was collected.
- mean annual avg temp: the average annual temperature (C) over five year (starting five years prior to the date the salamander was collected) at the location the salamander was collected.
- mean annual avg vpd: the average annual vapor pressure (kPa) deficit over five year (starting five years prior to the date the salamander was collected) at the location the salamander was collected.
- mean annual avg soil wet: the average annual soil surface wetness (%) over five year (starting five years prior to the date the salamander was collected) at the location the salamander was collected.
- DEM_Slope: the slope of the surface where the salamander was collected, pulled from a digital elevation model (DEM)
- DEM_Aspect: the aspect of the surface where the salamander was collected, pulled from a digital elevation model (DEM)
- Species: includes the scientific name of each salamander
- SVL: snout-vent length (mm)
- TL: total length (mm)
- Elevation_recorded: the elevation that the salamander was found at, recorded in the field using a GPS (m)
- Elevation_dem: the elevation that the salamander was found, pulled from a digital elevation model using the gps coordinates record in the field. (m)
- Transect: the general location of each salamander, as recorded in field notebooks
- Latitude: the latitude the salamander was found at (decimal degrees)
- Longitude: the longitude the salamander was found at (decimal degrees)
- Field_Number: unique numeric identifier
- Date: date the salamander was found
- GEOLocate uncertainty value: geographic coordinates for historical salamander records were georeference using GEOLocate software. Depending on the known locality data, there is a level of uncertainty about the actual location. This column gives the uncertainty value in meters.
- Sex: the sex (male/female/unknown) of each salamander
- LifeStage: adult versus juvenile
- Era: What time period the salamander record is from "historical" (1950s) or "contemporary" (2020s).
- Folder: era5_files
- Descriptions: Includes 8 climate raster files, each with 1-years worth of macroclimate data for the project’s study site from 2016-2023 downloaded from the ERA5 Reanalysis Dataset. These macroclimate data are used to interpolate microclimates using the R package mcera5 in '1_ProcB_Microclimate_Extraction_job_array.R'. Here is a link we used to download the .nc files: https://cds.climate.copernicus.eu/cdsapp#!/dataset/reanalysis-era5-single-levels?tab=overview)
Folder: phylo
Description: contains the following files and folders
- File: pruned_tree (this is functionally a .nex file - see Usage Notes below)
- Description: Final phylogenetic tree pruned for the focal taxa in this study. This file is a ‘phylo’ object in R and is loaded into R using the script “3_ProcB_SEM_brm.R”
Folder: macroclimate_data
Description: Contains four climate raster files of temperature or precipitation data for the 1950s and 2010s in the Southern Appalachian Mountains downloaded from the ERA5 Reanalysis dataset. These data are loaded into R in ‘6_ProcB_Macro_temp_precip_change_1950_2020.R” to visualize broadscale climate shifts over time in the Southern Appalachian region.
- File: era5-t2m_contemp.nc
- Description: contains data for the average temperature of the study site from 2010-2019
- File: era5-t2m_hist.nc
- Description: contains data for the total annual precipitation of the study site from 2010-2019
- File: era5-tp_contemp.nc
- Description: contains data for the average temperature of the study site from 1950-1959
- File: era5-tp_contemp.nc
- Description: contains data for the total annual precipitation of the study site from 1950-1959
Folder: sem_outputs
Description: Contains four fitted model objects for structural equation models (SEM) that assess the effects of elevation and climate on body size. Details of the naming conventions for these files are below: models labeled “full” use the complete salamander dataset spanning the entire elevation range, whereas those labeled “subset” include only high-elevation salamanders. Additionally, models marked “sex” incorporate sex as a variable, while those labeled “no_sex” exclude it. These files can be viewed in R using the script ‘4_ProcB_SEM_Outputs.R’.
Usage Notes
This repository contains the following data types:
- .csv: Comma-separated values files. Can be opened in Excel or loaded in R with
read.csv(). - .nc: NetCDF climate rasters. Can be read in R with the
rasterorncdf4packages. - .rds: R objects (e.g., model outputs). Can be loaded in R with
readRDS(). - .nex: Nexus phylogenetic files. Can be read in R with the
apepackage (read.nexus()). The 'pruned_tree' file in the 'phylo' folder is a .nex file.
All files are used within the included R scripts.
Code/software
File: scripts.zip
Description: Contains the below R scripts
All analysis were performed in R version 4.4.1. The R scripts are numerically ordered to indicate the order which they should be run.
File: 1_ProcB_Microclimate_Extraction_job.array.R
Description: Script for Extracting climate data for contemporary salamander data
File: 2_ProcB_Species_specific_models.R
Description: Script for testing for shifts in body size across elevation for each species individually
File: 3_ProcB_SEM_brm.R
Description: Script to run Structural Equation Models using brms
File: 4_ProcB_SEM_Outputs.R
Description: Script for comparing Structural Equation models
File: 5_ProcB_MS_Figures.R
Description: Script for creating main text figures
File: 6_ProcB_Macro_temp_precip_change_1950_2020.R
Description: Script for creating maps of macroclimate data on changes over time in the Southern Apps
File: 7_ProcB_Temp_Precip_Change_Across_Elev.R
Description: Script for calculating the rate of change in temperature and precipiation across elevation
File: 8_ProcB_Supporting_Information_Figures_.R
Description: Script for creating all figures included in the Supplementary Material
