Weak response to selection on stigma-anther distance in a primarily selfing population of yellow monkeyflower

Stebbins hypothesized that selfing lineages are evolutionary dead ends because they lack adaptive potential. While selfing populations often harbor limited nucleotide variability compared to closely related outcrossers, reductions in the genetic variability of quantitative characters remain unclear, especially for key traits determining selfing rates. Yellow monkeyflower (Mimulus guttatus) populations generally outcross and maintain extensive quantitative genetic variation in floral traits. Here, we study the Joy Road population (Bodega Bay, California, USA) of M. guttatus, where individuals exhibit stigma-anther distances typical of primarily selfing monkeyflowers. We show that this population is closely related to nearby conspecifics on the Pacific coast with a modest 33% reduction in genome-wide variation compared to a more highly outcrossing population. A five-generation artificial selection experiment challenged the hypothesis that the Joy Road population harbors comparatively low ..., Data come in two forms.

DNA sequence data was generated on an Illumina Novaseq machine. These raw sequences were aligned to a Mimulus guttatus reference, followed by haplotype calling and variant calling in GATK. The resulting sequence files are provided, and their format is described in the README file.
Phenotypes were measured on plants across 7 generations in a greenhouse. The description of the traits found in these data files is available in the README file.
, , # Weak response to selection on stigma-anther distance in a primarily selfing population of yellow monkeyflower

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 esti...