DOI: 10.5061/dryad.vt4b8gv3w
title: Shifts in salamander body size associated with 60 years of climate change

description: 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. 
description: # Dryad dataset Dataset DOI:
 [10.5061/dryad.vt4b8gv3w](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](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 `raster` or `ncdf4` packages. * **.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 `ape` package (`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