  Mimulus guttatus and M. nasutus are an evolutionary and ecological model
sister species pair differentiated by ecology, mating system, and partial
reproductive isolation. Despite extensive research on this system, the history
of divergence and differentiation in this sister pair is unclear. We present
and analyze a novel population genomic data set which shows that M. nasutus
"budded" off of a central Californian M. guttatus population within the last
200 to 500 thousand years. In this time, the M. nasutus genome has accrued
numerous genomic signatures of the transition to predominant selfing. Despite
clear biological differentiation, we document ongoing, bidirectional
introgression. We observe a negative relationship between the recombination
rate and divergence between M. nasutus and sympatric M. guttatus samples,
suggesting that selection acts against M. nasutus ancestry in M. guttatus.
