Temperature variability has limited effects on phenotypic plasticity in ectotherms – a meta-analysis
Year: 2025
Type: article
Abstract: Temperature variability has limited effects on phenotypic plasticity in ectotherms – a meta-analysis This repository contains data and R code for the associated manuscript. Clayton W. Stocker, Stephanie M. Bamford, Miki Jahn, Geoffrey P. F. Mazué, Amanda K. Pettersen, Daniel Ritchie, Alexander Rubin, Daniel W.A. Noble*, Frank Seebacher*. (2025) Temperature variability has limited effects on phenotypic plasticity in ectotherms – a meta-analysis. Ecology Letters. Please email [email protected] or [email protected] for any inquiries. A release is also lodged on Zenodo How to use this repository? Clone or download the repository to your local machine. Open the Plasticity_Fluctuation_Meta.Rproj file which will open RStudio and set your working directory. Ensure you have all the required R packages installed (see Software Dependencies section below). Run through the Analysis_Final.R script to reproduce the analyses and figures from the manuscript. Note that you do not need to re-run the entire analysis if you use the saved model objects in the output/models/directory. But, you need to set rerun = FALSE in the Analysis_Final.R script to use the saved models. There are additional scripts and resources in this repository that are important and are detailed below: Complexity_Final_data.csv: This is the final processed dataset used for the meta-analysis. complexity_tree.nwk: This file contains the phylogenetic tree used in the analysis. func.R: This script contains custom functions used in the analysis. output/figs/: This directory contains all figures generated from the analysis. output/tables/: This directory contains all tables generated from the analysis. output/models/: This directory contains saved model objects from the analysis. Use these so you don't have to re-run the entire analysis. Analyses All code for analyses reproducing the results and figures is found in Analysis_Final.R script. The code also generates supplementary tables and results, which are saved to the output/ directory. Data The data is the Complex_Final_Data.csv file. This file contains the data used in the meta-analysis. The meta-data that describes the columns are as follows. Note that some columns are created during the analysis (e.g., transformed means and SDs, effect sizes). Column Name Description Study_ID Unique identifiers for each paper. Species_ID Identifier for each species that a study investigates. Treatment_ID_T1 Identifier for the studies’ first constant and fluctuating temperature treatment pair (fluctuating mean matching constant temperature). Treatment_ID_T2 Identifier for the studies’ second constant and fluctuating temperature treatment pair (fluctuating mean matching constant temperature). Trait_ID Identifier for each phenotypic trait a study measures. First_Author Initials and surname for the first author of the study. Title Title of the study. Year Year of publication. Journal Name of the journal the study was published in. Journal_Impact_Factor-2021 Journal impact factor as of 2021 (most recent records at time of data collection). Kingdom Kingdom for each species that a study investigates. Phylum Phylum for each species that a study investigates. Class Class for each species that a study investigates. Order Order for each species that a study investigates. Family Family for each species that a study investigates. Scientific_Name Binomial nomenclature for species. Ecosystem Ecosystem the species is naturally observed (Aquatic and Terrestrial). Amphibians considered aquatic. Plasticity_Mechanism Mechanism of plasticity the treatments were exposed to (Acclimation or Developmental Plasticity). Developmental_Exposure_Time_Category Categorisation of Developmental Exposure Time. Developmental_Exposure_Time The period of exposure for treatments imposed during development. Acclimation_Exposure_Time The duration of exposure for acclimation treatments. Exposure_Units Units of Acclimation Exposure Time (Days). T1_constant Temperature of the first constant temperature treatment. T1_fluctuation Mean temperature of the first fluctuating temperature treatment. T2_constant Temperature of the second constant temperature treatment. T2_fluctuation Mean temperature of the second fluctuating temperature treatment. Fluctuation_Magnitude Amplitude of the two fluctuating temperature treatments. Fluctuation_Category Type of fluctuations imposed (Sinusoidal, Alternating, Stepwise, Stochastic). Fluctuation_Period Period of one fluctuation oscillation. Fluctuation_Unit Units of Fluctuation Period (Days). Number_Of_Fluctuations Acclimation Exposure Time/Fluctuation Period for acclimation treatments. Acclimation_Life-History_Stage Life-history stage of organisms for acclimation treatments. Acclimation_Life-History_Stage_Category Categorisation of Acclimation Life-history Stages. Trait_Category Categorisation of Trait Measurements. Measurement Phenotypic traits measured following treatment exposure. Trait_Unit Units for measurements. per_transform Indicator whether means and SDs need to be transformed from proportion scale (“Yes” or “No”). ln_transform Indicator whether means and SDs need to be transformed from log scale (“Yes” or “No”). Sex Sex of the organisms investigated (Both, Female or Male). NA = not specified. Performance_Curve Whether a performance curve was recorded in the study (Yes, No). Complex_Design Whether a comparison between constant and fluctuating treatments was made at multiple temperatures (Yes). Shared_Control_Number Unique identifier for shared control codes across effect sizes. Shared_Animal_Number Unique identifier for shared animal codes across effect sizes. n_T1_C Sample size of the constant treatment (first pair). Mean_T1_C Mean response of the constant treatment (first pair). SD_Final_T1_C Standard deviation of the constant treatment (first pair). n_T1_F Sample size of the fluctuating treatment (first pair). Mean_T1_F Mean response of the fluctuating treatment (first pair). SD_Final_T1_F Standard deviation of the fluctuating treatment (first pair). n_T2_C Sample size of the constant treatment (second pair). Mean_T2_C Mean response of the constant treatment (second pair). SD_Final_T2_C Standard deviation of the constant treatment (second pair). n_T2_F Sample size of the fluctuating treatment (second pair). Mean_T2_F Mean response of the fluctuating treatment (second pair). SD_Final_T2_F Standard deviation of the fluctuating treatment (second pair). obs Unique observation identifier (for random effect). phylo Open Tree of Life identifier used for phylogenetic random effect. vert_invert Whether species is “Invertebrate” or “Vertebrate” (for MLMR models). Mean_T1_C_trans Corrected mean of constant T1 after transformation. Mean_T1_F_trans Corrected mean of fluctuating T1 after transformation. Mean_T2_C_trans Corrected mean of constant T2 after transformation. Mean_T2_F_trans Corrected mean of fluctuating T2 after transformation. SD_Final_T1_C_trans Corrected SD of constant T1 after transformation. SD_Final_T1_F_trans Corrected SD of fluctuating T1 after transformation. SD_Final_T2_C_trans Corrected SD of constant T2 after transformation. SD_Final_T2_F_trans Corrected SD of fluctuating T2 after transformation. PRRD Uncorrected plasticity response ratio difference (PRRD). v_PRRD Sampling variance for PRRD. lnRR1 Log response ratio of high vs low temperature in constant treatment. lnRR2 Log response ratio of high vs low temperature in fluctuating treatment. combined Reaction norm direction (Positive, Negative, Opposite). meaning Whether slope is steeper in constant (C) or fluctuating (F) treatment. PRRD_cor Corrected PRRD with consistent sign across studies. Year_Z Z-transformed year of publication. inv_n_eff Inverse of the effective sample size (publication bias metric). sqrt_inv_n_eff Square root of inverse effective sample size (publication bias metric). Software Dependencies R version 4.5.1 (2025-06-13) Platform: aarch64-apple-darwin20 Running under: macOS Tahoe 26.0.1 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1 locale: [1] C.UTF-8/C.UTF-8/C.UTF-8/C/C.UTF-8/C.UTF-8 time zone: Australia/Sydney tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rphylopic_1.5.0 janitor_2.2.1 gridExtra_2.3[4] ggbeeswarm_0.7.2 ggridges_0.5.6 ggpmisc_0.6.2[7] ggpp_0.5.9 robumeta_2.1 orchaRd_2.0[10] metaAidR_0.0.0.9000 MCMCglmm_2.36 coda_0.19-4.1[13] phytools_2.4-4 maps_3.4.3 flextable_0.9.9[16] brms_2.22.0 Rcpp_1.0.14 metafor_4.8-0[19] numDeriv_2016.8-1.1 metadat_1.4-0 Matrix_1.7-3[22] latex2exp_0.9.6 patchwork_1.3.1 emmeans_1.11.1[25] ape_5.8-1 DescTools_0.99.60 rotl_3.1.0[28] gtsummary_2.3.0 readxl_1.4.5 lubridate_1.9.4[31] forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4[34] purrr_1.0.4 readr_2.1.5 tidyr_1.3.1[37] tibble_3.3.0 ggplot2_3.5.2 tidyverse_2.0.0 loaded via a namespace (and not attached): [1] cubature_2.1.4 splines_4.5.1 cellranger_1.1.0[4] XML_3.99-0.18 lifecycle_1.0.4 doParallel_1.0.17[7] lattice_0.22-7 MASS_7.3-65 backports_1.5.0[10] magrittr_2.0.3 rmarkdown_2.29 grImport2_0.3-3[13] zip_2.3.3 askpass_1.2.1 gld_2.6.7[16] pbapply_1.7-2 RColorBrewer_1.1-3 multcomp_1.4-28[19] abind_1.4-8 expm_1.0-0 quadprog_1.5-8[22] TH.data_1.1-3 tensorA_0.36.2.1 sandwich_3.1-1[25] gdtools_0.4.2 rentrez_1.2.4 MatrixModels_0.5-4[28] bridgesampling_1.1-2 codetools_0.2-20 xml2_1.3.8[31] tidyselect_1.2.1 bayesplot_1.13.0 farver_2.1.2[34] matrixStats_1.5.0 base64enc_0.1-3 mathjaxr_1.8-0[37] jsonlite_2.0.0 e1071_1.7-16 survival_3.8-3[40] iterators_1.0.14 systemfonts_1.2.3 foreach_1.5.2
Language: English
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
Open Access status: green
OpenAlex ID: W7085504193
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