Introgression despite minimal hybridization: mating system modulates phenotypic associations with introgression in <i>Clarkia</i>

Secondary contact between incipient species provides the opportunity to understand how trait divergence restricts gene flow. While mating system transitions are particularly common and involve a suite of phenotypic changes, the extent to which these changes influence gene flow during speciation is poorly understood. Using 410 genomes, we quantified introgression between selfing-outcrossing sister Clarkia taxa in four independent contact zones. We used common garden and geospatial data to determine the frequency of early generation hybrids and test for associations between individual admixture proportions and phenotypic and spatial variation within contact zones. We found substantial admixture across contact zones, but no early generation hybrids. Introgression was consistently asymmetric, from the selfer to outcrosser. Patterns of chloroplast capture suggest that F1 hybrids often form on the selfer. Although the extent of admixture varied among contact zones, only the selfer displayed spatially structured and phenotypic associations with introgression. Secondary sexual traits that minimize pollinator visitation in the selfer (e.g. flower color) may reduce admixture and promote asymmetric introgression. Despite recent divergence and evidence of historical introgression, premating isolation minimizes hybridization. Mating system consistently modulates the direction of introgression and phenotypic variation appears to contribute to the dynamics of backcrossing following F1 formation.