Data for "Introgression despite minimal hybridization: mating system modulates phenotypic associations with introgression in Clarkia"

· The ecological factors and phenotypes that modulate the tremendous variability in the extent of introgression are unclear. Mating system transitions are particularly common and involve a suite of phenotypic changes that often contribute to reproductive isolation. However, the extent to which these phenotypic changes influence the extent of gene flow during speciation is unknown.· Using 410 nuclear and 360 chloroplast genomes, we quantified introgression between selfing-outcrossing sister Clarkia taxa. We used common garden and geospatial data to test for associations between individual admixture proportions and phenotypic and spatial variation within contact zones.· We found substantial admixture in the outcrossing taxon across contact zones in both nuclear and chloroplast genomes, but no early generation hybrids. Introgression was asymmetric, primarily from the selfing to outcrossing taxon. Remarkably, we found complete chloroplast capture by the outcrosser in the most northern population. Although the extent of admixture varied among contact zones of both taxa, only the selfer displayed spatially structured and phenotypic associations with the extent of introgression within contact zones.· Despite recent divergence and evidence of historical introgression, premating isolating mechanisms prevent hybridization. Mating system modulates the direction of introgression and influences fine scale patterns of individual admixture.