Barriers to reproduction are often how progress in speciation is measured. Nonetheless, an unresolved question concerns the extent to which reproductive barriers diminish gene flow between incipient species. The Sierra Nevada foothill endemic Mimulus glaucescens and the widespread M. guttatus are considered distinct species based on striking differences in vegetative morphology, but barriers to reproduction have not been previously identified, nor has gene flow between species been characterized. Here, we examined 15 potential reproductive barriers within a Northern California area of broad sympatry. Most barriers, with the exception of ecogeographic isolation, were weak or absent, and total isolation for each species was incomplete. Population genomic analyses of range-wide and broadly sympatric accessions revealed extensive gene flow between these taxa, particularly in sympatry. Despite widespread introgression, Mimulus glaucescens, emerged as monophyletic and largely comprised a single ancestry that was found at intermediate frequency within M. guttatus. This result, along with observed ecological and phenotypic differentiation, suggests that natural selection may contribute to the maintenance of distinct phenotypic forms in the earliest stages of speciation. Integrating estimates of barrier strength with direct estimates of gene flow can strengthen a more nuanced interpretation of the process of speciation in natural communities.

Barriers to reproduction are often how progress in speciation is measured. Nonetheless, a key unresolved question is the extent to which reproductive barriers diminish gene flow in incipient species in nature. The Sierra Nevada foothill endemic Mimulus glaucescens and the widespread M. guttatus are considered to be distinct species based on contrasting vegetative traits, but barriers to reproduction are not readily apparent, although these species are not known to hybridize in nature. To explore boundaries between taxa, we examined 15 potential reproductive barriers between species in a Northern California area of broad sympatry. Most barriers, with the exception of ecogeographic isolation, were weak, and total isolation for each species was estimated to be incomplete. Population genomic analyses of range-wide and broadly sympatric accessions revealed that gene flow between these taxa is common across the range, and rampant within areas of sympatry. Thus, despite fairly strong ecological differentiation - which may be involved in maintenance of vegetative differences ecological isolation is a weak barrier to gene flow in this system. This work underscores the value of combining classical measures of reproductive isolation with estimates of natural gene flow for studies of speciation in natural communities.