Testing the evolutionary theory of inversion polymorphisms in the yellow monkeyflower (Mimulus guttatus)

Chromosomal inversions have been implicated in a remarkable range of natural phenomena, but it remains unclear how much they contribute to standing genetic variation. Here, we evaluate 64 inversions that segregate within a single natural population of the yellow monkeyflower (Mimulus guttatus). Nucleotide diversity patterns confirm low internal variation for the derived orientation (predicted by recent origin), elevated diversity between orientations (predicted by natural selection), and localized fluctuations (predicted by gene flux). Sequence divergence between orientations varies idiosyncratically by position, not following the suspension bridge pattern predicted if the breakpoints are the targets of selection. Genetic variation in gene expression is not inflated close to inversion breakpoints but is clearly partitioned between orientations. Like sequence variation, the pattern of expression variation suggests that the capture of coadapted alleles is more important than the breakpoints for the fitness effects of inversions. This work confirms several evolutionary predictions for inversion polymorphisms, but clarity emerges only by synthesizing estimates across many loci.