To recreate our results, use the following scripts and associated data files. In all data files, missing values are 'NA'.

1. GATK script.txt: This file contains the arguments we used when calling variants in GATK, which generated our variant call file (VCF). We processed the resulting VCF, using the steps outlined in the paper's methods, to generate our clean file of synonymous SNPs: 'platy_syn_snps.csv'.

In this file, the rows are positions in the reference genome, and the columns are: Chromosome, position, reference base pair, alternate base pair, J2 genotype, J33 genotype, J58 genotype, J60 genotype, annotation, and putative impact. Each genotype cell corresponds to reference homozyote (0), heterozygote (1), and alternate homozygote (2). The last two columns are annotations added from SnpEff.

2. 'platy_polymorphism.R' is a script that uses 'platy_syn_snps.csv' to estimate nucleotide diversity and Tajima's D.

3. To make Figure 3, use the files in the 'Fig3' folder. 'G1 platycalyx' contains floral trait data (in mm) measured on individuals from the G1 generation in M. platylcalyx. 'G1 rabbit ck' contains data on the same floral traits measured on individuals from the G1 generation of M. guttatus. 'g1means' are means calculated for each M. platycalyx individual. The script 'compare platy_rabbitck.R' uses data from the above files to compare stigma-anther distances between the Joy Road (M. platycalyx) and Rabbit Creek (M. guttatus) populations.

4. To make Figure 4, use the files in the 'Fig4' folder. All of these files were generated by Treemix analysis on an alignment containing whole-genome sequences of several Mimulus species (13mimulus_4treemix.gz). Columns are formatted as in 'platy_syn_snps.csv'. The file 'make_tree.R' generates Figure 4. The files '13mimulus_input.gz' and 'prepTreemix.R' were used to format files so that treemix would run on our files.

5. To make Figure 5, use the files in the 'Fig5' folder. 'allgens.csv' is a summary of the mean trait value in generations 1-6 (G1-G6). These summaries are taken from the full datafile, 'allparents_parents_marked_g1g2g3g4g5g6.csv', which reports trait means for all individuals. Columns denote: individual (X), population (line), an unused indentifier based on individual (ID), days to flower (d2flower), leaf width in mm (max.leaf.W), and floral traits (corolla length in mm, corolla width in mm, tube length in mm, throat width in mm, stigma height in mm, stamen height in mm, stigma-anther distance in mm), parent (FALSE=no, TRUE=yes), and generation of the experiment. The script 'Make_Fig5.R' generates Figure 5 from the above data files.

6. To make Figure 6, use the files in the 'Fig6' folder. The file 'g7means.csv' contains mean floral traits for all individuals in the G7 populations plus the G1 ancestor raised in a common environment. The columns match those described above in 'allparents_parents_marked_g1g2g3g4g5g6.csv,' with the exception that parents are not marked. The script 'Make_Fig6.R' generates Figure 6 from the raw data file.