GENERAL INFORMATION -------------------------------------------- 1. Title of Dataset: Data and code for: Plastic responses to warmer climates: a semi-natural experiment on lizard populations, Bestion et al 2023, Evolution doi: 10.1093/evolut/qpad070 2. Author Information A. First Author Contact Information Name: Elvire Bestion Institution: Station d’Ecologie Théorique et Expérimentale, CNRS, UAR 2029 Address: 2 route du CNRS, 09200 Moulis, France Email: elvire.bestion@sete.cnrs.fr B. Last Author Contact Information Name: Julien Cote Institution: Laboratoire Evolution et Diversité Biologique, CNRS, Université Toulouse III Paul Sabatier, UMR 5174 Address: 118 route de Narbonne, 31062 Toulouse, France Email: julien.cote@univ-tlse3.fr 3. Abstract: Facing warming environments, species can exhibit plastic or microevolutionary changes in their thermal physiology to adapt to novel climates. Here, using semi-natural mesocosms, we experimentally investigated over two successive years whether a 2°C-warmer climate produces selective and inter- and intragenerational plastic changes in the thermal traits (preferred temperature and dorsal colouration) of the lizard Zootoca vivipara. In a warmer climate, the dorsal darkness, dorsal contrast and preferred temperature of adults plastically decreased and covariances between these traits were disrupted. While selection gradients were overall weak, selection gradients for darkness were slightly different between climates and in the opposite direction to plastic changes. Contrary to adults, male juveniles were darker in warmer climates either through plasticity or selection and this effect was strengthened by intergenerational plasticity when juveniles’ mothers also experienced warmer climates. While the plastic changes in adult thermal traits alleviate the immediate overheating costs of warming, its opposite direction to selective gradients and to juveniles’ phenotypic responses may slow down evolutionary shifts towards phenotypes that are better adapted to future climates. Our study demonstrates the importance of considering inter- and intragenerational plasticity along with selective processes to better understand adaptation and population dynamics in light of climate change. 4. Keywords: climate change, ectotherm, lizard, phenotypic plasticity, natural selection, intergenerational plasticity, thermal physiology 5. Date of data collection: May 2012 to May 2014 for the main dataset, and May 2013 to May 2015 for the side-experiment on maternal effects 6. Geographic location of data collection: Station of Theoretical and Experimental Ecology, Ariège, France, 43°01' N, 1°05' E 7. Taxon/species from which data was collected: Common lizards (Zootoca vivipara, Jacquin 1787) SHARING/ACCESS INFORMATION --------------------------------------------------- 1. Licenses/restrictions placed on the data: The data is usable under Creative Commons Attribution 4.0 International licence but we would appreciate if we were contacted prior to meaningful use, and this dataset and the matching paper cited if appropriate. 2. Links to publications that cite or use the data: This dataset corresponds to the data used in: Bestion E, San-Jose LM, Di Gesu L, Richard M, Sinervo B, Côte J, Calvez O, Guillaume O, & Cote J. 2023. Plastic responses to warmer climates: a semi-natural experiment on lizard populations. Evolution, doi: 10.1093/evolut/qpad070 3. Links to other publicly accessible locations of the data: The data can be found on zenodo at doi:10.5281/zenodo.7845944 4. Was data derived from another source? NO 5. Recommended citation for this dataset: Bestion et al, 2023. Data and code from: Plastic responses to warmer climates: a semi-natural experiment on lizard populations. Evolution, Zenodo doi: 10.5281/zenodo.7845944 DATA & FILE OVERVIEW ------------------------------------- The data is composed of a zip file containing: * The present README.txt file * Nine R files used to run the analyses: # 0_important_functions.R --> functions used in the main analysis scripts # 1_climate_impact_on_phenotype_at_tp1.R --> the 1st part of the main R script. The script calls to the 0_important_functions.R for functions, uses data in the /data folder, outputs diagnostic plots and info in the /interm folder, outputs means and SEM for figures to the /figure_values folders. This first part of the analysis script tests for the impacts of climate warming on thermal phenotype at t+1 in the juveniles and adults from the main 2012-2013 experiment. # 2_plasticity.R --> The 2nd part of the main script, to be run after #1 script. This part of the analysis tests for plastic effects of climate warming on phenotype in juveniles and adults from the main 2012-2013 experiment. # 3_selection.R --> The 3rd part of the main script, to be run after #2 script. This part of the analysis tests for differential selection in phenotypic traits depending on climate in juveniles and adults from the main 2012-2013 experiment. # 4_heritability.R --> The 4th part of the main script, to be run after #3 script. This part of the analysis tests heritability of phenotypic traits in juveniles from the main 2012-2013 experiment. # 5_SEM.R --> The 5th part of the main script, to be run after #4 script. This part of the analysis tests for the impact of climate warming on thermal syndromes, i.e. covariation between thermal traits in juveniles and adults from the main 2012-2013 experiment. # 6_maternal_effects.R --> The 6th part of the main script, to be run after #5 script. This part of the analysis uses the data from juveniles in 2013 issued from surviving mothers from the 2012 experiment, supplemented with a side experiment in 2014 on the juveniles issued from surviving mothers from the 2013 experiment, to test for the impact of climate warming on intergenerational plasticity of thermal traits. # 7_checking_models_with_deltaAIC_4.R --> The 7th part of the main script, to be run after #6 script. This part checks for the of the analysis tests for the impact of climate warming on thermal syndromes, i.e. covariation between thermal traits in juveniles and adults from the main 2012-2013 experiment. # 8_exporting_tables_to_word.R --> The 8th part of the main script, to be run after all scripts. This part creates the composite figures and outputs them and the tables to the /out folder. * A /data folder with 3 datasets: # data/Bestion_adults.csv --> dataset for adults and yearlings from the main 2012-2013 experiment, to test the impacts of climate warming on phenotype at t+1, selection and plasticity on the traits. # data/Bestion_adults.csv --> dataset for juveniles from the main 2012-2013 experiment, to test the impacts of climate warming on phenotype at t+1, selection and plasticity on the traits, and heritability of the traits. # data/Bestion_juveniles_for_maternal_effects.csv --> dataset including juveniles in 2013 born from the mothers surviving the 2012 experiment, and including juveniles in a side-experiment in 2014 that were born from the mothers surviving the 2013 experiment, to test the impact of intergenerational plasticity. * An /interm folder with : # interm/R_session_info_2023-03-29.txt --> the session information about the R version and R packages used when running the R code # note that while running the R code, other data will be saved to the /interm folder (e.g. heritability models, diagnostic plots about all models, …). Only the files that cannot be reproduced by the R code alone such as the session info were kept in the folder for facility of use. * An empty /figure_values folder. While running the R code, data with the means and SEM of the traits by climates will be saved to the folder, to easily reproduce figures and get summarised data for meta-analyses. * An /out folder with the figures and tables resulting from the analysis and found in the main paper and the supplementary data: # out/Figure_2_traits_adults_tp1.png --> the figure 2 # out/Figure_3_plasticity_selection_adults.png--> the figure 3 # out/Figure_4_maternal_effects_juveniles.png --> the figure 4 # out/Figure_SB1_traits_juveniles_tp1.png --> the figure SB1 # out/Figure_SC1_selection_juveniles.png--> the figure SC1 # out/Figure_SD1_plasticity_juveniles.png--> the figure SD1 # out/Figure_SD2_impacts_of_plasticity_on_survival_adults.png--> the figure SD2 # out/Appendix B - Impact of climatic treatment on phenotype at tp1.docx --> The tables SB1 to SB4 from the appendix B, as well as information about the models from the tables to add to the legends of the tables (e.g. N, R²m and R²c, SD explained by random components, variance inflation factors for the variables in the models). # out/Appendix C - Selective processes.docx --> The tables SC1 to SC3 from the appendix C, as well as information about the models from the tables to add to the legends of the tables. # out/Appendix D - Trait plasticity.docx --> The tables SD1 to SD3 from the appendix D, as well as information about the models from the tables to add to the legends of the tables. # out/Appendix E - Heritability of phenotypic traits.docx -->The table SE1 from the appendix E. # out/Appendix F - Maternal effects.docx --> The table SF1 from the appendix F, as well as information about the models from the table to add to the legend of the table. # out/Appendix G - Robustness of statistical results.docx --> The tables SG1 to SG4 from the appendix G, as well as information about the models from the tables to add to the legends of the tables. METHODOLOGICAL INFORMATION -------------------------------------------------- 1. Description of methods used for collection/generation of data: A detailed explanation of the methods is provided in the related Bestion et al 2023 Evolution article, please refer to it for a full understanding of the methods and results. Briefly: Our aim was to study experimentally whether climate warming affected the thermal phenotype (i.e. preferred temperature, dorsal darkness, dorsal contrast) of a lizard through selection, intra-generational and inter-generational plasticity. Between May 2012 and May 2014, we performed two one-year experiments inside of the Metatron (Legrand et al. 2012, Nature Methods), a system of forty-eight 10 x 10 m semi-natural mesocosms. Over the two years of experiment, we created 16 populations in 16 mesocosms, and simulated present-day and +2°C warmer climatic conditions through the use of automatic shutters. Every year, mid-May, we captured all surviving lizards from the mesocosms. We measured them for body size, a tail tip was taken for paternity analysis, and a dorsal picture was taken to measure dorsal darkness and dorsal contrast. We assessed lizard preferred temperature in a thermal gradient. Female gave birth inside of the terraria, and juveniles were also genotyped for paternity analysis, measured for body size, and their preferred temperature was assessed. In June-July, lizards were released into the mesocosms to form 16 populations released into 3 mesocosms per climate (i.e. 6 mesocosms) in 2012, and 5 mesocosms per climate (i.e. 10 mesocosms) in 2013. . Each mesocosm contained 11 ± 1 two-or-more-year-old (2+yo) females, 6 ± 1 (2+yo) males, 9 ± 2 one-year-olds (1yo) and 37 ± 4 juveniles ( The data from the two years of experiment allowed to test 4 main questions: 1) What is the impact of a warmer climate on lizard thermal phenotype (studying traits at t+1 on survivors) and thermal syndromes between traits, 2) Is the impact due to plasticity (effect of climate on traits at t and t+1), 3) Is the impact due to selection (impacts of traits at t on survival at t+1), 4) Are the traits heritable? Further, the data from the 2013 experiment on juveniles, together with data from a side-experiment in 2014 also on juveniles maintained in the Metatron in the two climate treatments, allowed to test a 5th question: 5) what is the impact of inter- and intra-generational plasticity on thermal traits? 2. Instrument- or software-specific information needed to interpret the data: To reproduce the analyses, the data should be read in R with the provided R scripts. The R version and the version of the packages used to reproduce the data are found in the interm/ R_session_info_2023-03-29.txt file. 3. Environmental/experimental conditions: The experiment was done in 10 x 10 m semi-natural mesocosms, in which lizards were maintained for one year at a time. Two climatic treatments were applied to the mesocosms, a present-day climate and a +2°C warmer climate. 4. People involved with sample collection, processing, analysis and/or submission: Elvire Bestion and Julien Cote designed the study, Elvire Bestion, Lucie Di Gesu, Olivier Calvez, Olivier Guillaume and Julien Cote performed the experiment, Murielle Richard performed the extractions, the polymerase chain reaction and analysed the paternity data. Barry Sinervo, Jessica Côte and Luis M. San Jose provided assistance with the animal models. Elvire Bestion and Julien Cote analysed and interpreted the data. Elvire Bestion and Julien Cote wrote the first draft and Luis M. San Jose, Barry Sinervo, Murielle Richard and Jessica Côte significantly contributed to redrafting. 5. Ethics statement: Experiments followed French ethics regulations and CNRS institutional ethics guidelines. We applied the 3R rule by reducing the number of lizards to the minimum to form enough populations and providing care appropriate to the species. Lizards were captured from the wild according to the capture licence number 2010-189-16 DREAL and transferred to the laboratory (laboratory use of animals: agreement B09583). Experiments were started before the need of obtaining a permit following French law (article R.214-113, ordonnance 2012-10, décret 2013-118, arrêtés 1er février 2013, transposing EU directive 2010/63/UE), however we then obtained a permit for further experiments following the same procedure (permits number APAFIS#15897-2018070615164391 v3 and APAFIS#19523-201902281559649 v3 obtained from the ethics comity n°068). DATA-SPECIFIC INFORMATION ----------------------------------------------- DATA-SPECIFIC INFORMATION FOR: Bestion_adults.csv ----------------------------------------------- 1. Number of variables: 20 2. Number of cases/rows: 380 3. Variable List: Year: year of the experiment (2012 or 2013) Code: code of the individual (identification) Age_t: age of the individual at the time of the start of the experiment, as a class (A: adult: 2+ year-old, Y: yearling: 1 year-old) Sex: sex of the individual, M or F Body_size_t: body size at the start of the experiment, snout-vent length in mm Tpref_t: preferred temperature at the start of the experiment, in °C Dorsal_darkness_t: mean dorsal darkness at the start of the experiment, mean percentage of black pixels between the median part and the flanks Dorsal_contrast_t: dorsal contrast at the start of the experiment, as absoltue darkness difference between the flanks and median parts divided by median darkness Darkness_median_part_t: dorsal darkness in the median part of the lizard body at the start of the experiment, percentage of black pixels in transformed pictures Darkness_flanks_t: dorsal darkness in the flanks of the lizard at the start of the experiment, percentage of black pixels in transformed pictures Climate_Intro: Climatic treatment inside of the mesocosm, either warm or present Mesocosm_Intro: mesocosm number (identification) Population_Intro: composite identification number composed of the mesocosm number and the year (identification) Survival: survival after one year of experiment inside of the mesocosms, 1= survived or 0 = dead Body_size_tp1: body size at the end of the experiment on survivors, snout-vent length in mm Tpref_tp1: preferred temperature at the start of the experiment, in °C Dorsal_darkness_tp1: mean dorsal darkness at the end of the experiment on survivors, mean percentage of black pixels between the median part and the flanks Dorsal_contrast_tp1: dorsal contrast at the end of the experiment on survivors, as absolute darkness difference between the flanks and median parts divided by median darkness Darkness_median_part_tp1: dorsal darkness in the median part of the lizard at the end of the experiment on survivors, percentage of black pixels in transformed pictures Darkness_flanks_tp1: dorsal darkness in the flanks of the lizard at the end of the experiment on survivors, percentage of black pixels in transformed pictures 4. Missing data codes: NA (for traits at t+1 of individuals that did not survive to t+1, and rare missing measurements at t or t+1) DATA-SPECIFIC INFORMATION FOR: Bestion_juveniles.csv ----------------------------------------------- 1. Number of variables: 19 2. Number of cases/rows: 536 3. Variable List: Year: year of the experiment (2012 or 2013) Code: code of the individual (identification) Code_Mother: code of the mother of the individual (identification) Code_Father: code of the father of the individual (identification) Age_t