DOI: 10.5061/dryad.qjq2bvqpr
title: Weak response to selection on stigma-anther distance in a primarily selfing population of yellow monkeyflower

description: 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 evolutionary potential in the stigma-anther distance, a
 critical determinant of selfing rate in Mimulus. Artificial
 selection generated a weak phenotypic response, with low realized
 heritabilities (0.020-0.028) falling 84% below those measured for floral
 characters in more highly outcrossing M. guttatus. These results
 demonstrate substantial declines in evolutionary potential with a
 transition toward selfing. Whether these findings explain infrequent
 reversals to outcrossing or general limits on adaptation in selfers
 requires further investigation.
description: Data come in two forms. DNA
 sequence data was generated on an Illumina Novaseq machine. These raw
 sequences were aligned to a <em>Mimulus guttatus</em>
 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.
description: # 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 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.