The genomic scale of fluctuating selection in a natural plant population

Abstract This study characterizes evolution at ≈1.86 million Single Nucleotide Polymorphisms (SNPs) within a natural population of yellow monkeyflower (Mimulus guttatus). Most SNPs exhibit minimal change over a span of 23 generations (less than 1% per year), consistent with neutral evolution in a large population. However, several thousand SNPs display strong fluctuations in frequency. Multiple lines of evidence indicate that these ‘Fluctuating SNPs’ are driven by temporally varying selection. Unlinked loci exhibit synchronous changes with the same allele increasing consistently in certain time intervals but declining in others. This synchrony is sufficiently pronounced that we can roughly classify intervals into two categories, “green” and “yellow,” corresponding to conflicting selection regimes. Alleles increasing in green intervals are associated with early life investment in vegetative tissue and delayed flowering. The alternative alleles that increase in yellow intervals are associated with rapid progression to flowering. Selection on the Fluctuating SNPs produces a strong ripple effect on variation across the genome. Accounting for estimation error, we estimate the distribution of allele frequency change per generation in this population. While change is minimal for most SNPs, diffuse hitchhiking effects generated by selected loci may be driving neutral SNPs to a much greater extent than classic genetic drift.