Supplemental Files from: Environment-specific selection alters flowering-time plasticity and results in pervasive pleiotropic responses in maize

Article title: Environment-specific selection alters flowering-time plasticity and results in pervasive pleiotropic responses in maize Authors: Nicole E. Choquette, James B. Holland, Teclemariam Weldekidan, Justine Drouault, Natalia de Leon, Sherry Flint-Garcia, Nick Lauter, Seth C. Murray, Wenwei Xu, Randall J. Wisser The following Supporting Files are available for this article. A separate README is also available for each data file. ---- Data files psge_combined_full.csv : Full dataset including design information and all trait measurements from 2014 to 2015. PSGE_Sel_emergence.csv : Planting dates and emergence dates for the selection environments. PSGE_Eval_emergence.csv : Planting dates and emergence dates for the evaluation environments. PSGE_transition.csv : Information for the estimated day of year for flowering time transition for each environment. PSGE_year_by_location_means.csv : Year-by-location means for all accessions/populations (flowering time). Crow_Flies_distances.csv : Geographical “as the crow flies” distances for all locations. PSGE_weather_windows.csv : Summary of weather variables over the three growth periods. ---- R scripts Step0_Weather_Summary.Rmd : Contains the analysis for summarizing the environmental variables over the three periods. Includes adding GDD to psge_combined.csv. Step1_Build_Model_Eq1.Rmd : Runs equation 1, estimates the 8x8 selection responses for flowering time traits, main effects for selection and evaluation locations, runs Wald tests, and saves as R objects. Step2_Sel_Eval_Effects.Rmd : Evaluates the previous R objects and runs the comparisons of the control populations. Step3_Responses_ForwardSel_Env.Rmd : Creates the individual generation by evaluation environment selection responses, runs forward selection, selects the final model, runs env PCA, and selection and evaluation correlations. Uses the summarized environmental files created in Step0_Weather_Summary.Rmd. Step4_Local_Adaptaiton_Distances.Rmd : Tests for local adaptation from the 8 x 8 interactions, isolates the interaction effects for the individual generation selection responses runs the forward selection on variable distances. Uses the summarized environmental files created in Step0_Weather_Summary.Rmd. Step5_Maladaptation_Syndrome.Rmd : Gets the G0 means for all traits, selection responses, and correlates the trait responses to GDD to silking selection responses. Step6_Piecewise_Regression.Rmd : Performs analysis of reaction norms.