Selection on Plant Male Function Genes Identifies Candidates for Reproductive Isolation of Yellow Monkeyflowers
Figure 2
Diversity and selection among pollen tube proteins (PTPs) from a natural population of Mimulus guttatus.
PTP Exomes of 28 wild collected individuals from the Cone Peak population of M. guttatus [81] were captured on a custom Agilent micro-array and Illumina sequenced, after which reads were assembled and mapped to IM62 CDSs. Base calls were made for sites with ≥10 reads, from which measures of nucleotide diversity per site (expected heterozygosity) and Tajima's D [64] were made after excluding sites with missing data and those that violate the infinite sites model [88]. (A) Our SNP calling procedure identified ∼1.3×106 variants (of 3.4×106 total bases called after filtering), with at least one SNP called for 97% of successfully captured CDSs (2,419; File S3) yielding 0.47% of a PTPs coding sequence on average polymorphic. (B) The distribution of Tajima's D values calculated from PTPs harboring SNPs (2,352; File S3) shows no evidence of confounding demographic forces at Cone Peak (mean D = 0.0269), thus the upper and lower tails of the distribution (2.5%) were chosen as constituting a 95% confidence interval beyond which PTPs may be targets of balancing selection or sweeps, respectively.