Postzygotic barriers persist despite ongoing introgression in hybridizing Mimulus species

The evolution of postzygotic isolation is thought to be a key step in maintaining species boundaries upon secondary contact, yet the dynamics and persistence of hybrid incompatibilities in naturally hybridizing species are not well understood. Here, we explore these issues using genetic mapping in three independent populations of recombinant inbred lines between naturally hybridizing monkeyflowers Mimulus guttatus and M. nasutus from the sympatric Catherine Creek population. We discover that the three M. guttatus founders differ dramatically in admixture history, with nearly a quarter of one founder’s genome introgressed from M. nasutus. Comparative genetic mapping in the three RIL populations reveals three new putative inversions, each one segregating among the M. guttatus founders, two due to admixture. We find strong, genome-wide transmission ratio distortion in all RILs, but patterns are highly variable among the three populations. At least some of this distortion appears to be expl..., , , # Postzygotic barriers persist despite ongoing introgression in hybridizing *Mimulus* species

Using inbred lines of *Mimulus guttatus* and *M. nasutus* derived from the sympatric site Catherine Creek (CAC), we produced three Recombinant Inbred Line (RIL) populations from crosses between a common *M. nasutus* maternal parent CAC9 and the *M. guttatus* paternal parents CAC110, CAC162, and CAC415. Dataset includes genetic and phenotypic (male and female fertility) data for these RIL individuals.

## Description of the data and file structure

Male_Fertility: Raw male fertility data for each RIL individual (Plant) in each RIL population (RIL_pop), including the number of darkly stained (Viable) and unstained (Inviable) pollen grains counted from a haphazardly selected group of ≥100, after staining with lactophenol-aniline blue stain, and the proportion of pollen grains which were viable (PropV). Because each row represents pollen collected from a separate flower, each RIL individual is r...