This is a repository for data and code pertaining to the manuscript "The genetic architecture of multiple mutualisms and mating system in Turnera ulmifolia"
Below are a description of each file included in this repository. For ease of interpretation, I have broken code and data files into conceptual sections.
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- "Keystone" data summarizing key information or used in multiple analyses.
a. Trait and seedset data.xlsx: excel file containing phenotype data for all Turnera ulmifolia plants. Second tab includes data from seedset experiment.
b. pheno.txt: text file containing data for all plants. This file is uploaded in the following R codes : GMatrix_Estimation_final.R, Population_Mean_Trait_Variation.R.
c. seedset.txt: text file containing data for the seedest experiment. This file is uploaded in the following R codes : GMatrix_Estimation_Final.R.
d. Pedigree.xlsx: excel file containing pedigree information for all Turnera ulmifolia plants.
e. pedmat.txt: text file containing pedigree information. This file is used in the following R codes : GMatrix_Estimation_final.R, Bayesian_Heritability_final.R, 5pop_ran_G_simulation.R.
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- Fitting G matrices and univariate Bayesian objects
a. GMatrix_Estimation_final.R: (sample) code that fits G matrices and univariate Bayesian objects for all populations of T. ulmifolia. Also includes code for construction of G matrix for seedset experiment, the signigicance testing of diagonal elements, the generation of randomized data sets for each population, and the model fitting average G within populations and D simultaneously.
b. Bayesian_Heritability_final.R: (sample) code that fits univariate Bayesian objects to randomized datasets for each population of T. ulmifolia for the purposes of significance testing.
c. 5pop_ran_G_simulation.R: (sample) code for estimating null G matrices based on randomized phenotypes.
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- Comparison of G matrices
a. Gcomp_final.R: code which assesses differences among our 5 population-specific estimates of G, and uploads summary statistics from comparing randomly-generated G matrices for the purposes of significance testing.
b. final_krzan.txt: text file containing the results of Krzanowski's analysis performed on null G matrices fitted per Morrisey et al., 2019, Evolution. This file is used in the following R codes : Gcomp_final.R
c. final_fourth_order.txt: text file containing the results of the fourth order genetic covariance tensor performed on null G matrices fitted per Morrisey et al., 2019, Evolution. This file is used in the following R codes : Gcomp_final.R
d. final_ranskew.txt: text file containing the results of the random skewer analysis performed on null G matrices fitted per Morrisey et al., 2019, Evolution. This file is used in the following R codes : Gcomp_final.R
e. Gcom_random.R: code to be run on a server, that uploads the randomized G's and then runs comparisons for each set of null results.
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- Miscellaneous
a. Population_Mean_Trait_Variation.R: code that generates Figure 3, which displays variation in mean trait values among populations.
b. Evolutionary_Constraint.T: code that multiplies matrices by selection skewers to assess constraint/facilitation and calculate R values.