Cultivation and naturalization of plants beyond their natural range can bring previously geographically isolated taxa together, thereby increasing the opportunity for hybridization and inter-specific gene flow, the outcomes of which are not predictable. These anthropogenic events therefore allow us to study how hybridization and inter-specific gene flow affect genetic and phenotypic diversity. Here, we explore the phenotypic and genomic effects of increased inter-specific gene flow following the re-introduction of the cultivated Mentha spicata (spearmint) into the ranges of the native mints M. longifolia and M. suaveolens. Using morphological analyses, we show that the cultivated M. spicata has altered trichome characters, which is likely a product of human imposed selection for a more palatable plant or a byproduct of selection on essential oil production. Using whole genome sequencing, we then show that there is extensive genetic admixture between the morphologically defined mint taxa that to some extent is mediated by the cultivated M. spicata. This has, at least partially, resulted in a breakdown of the species barriers. However, despite this breakdown, we find that genetic variants associated with the cultivated trichome morphology continue to segregate in cultivated, naturalized, and wild populations and we identify three genes that may function in the production of the characteristic aromatic oils of mints. Although hybridization can increase species richness by forming new hybrid taxa, we here show that unless reproductive barriers are strong it can also merge species into population/coalescent complexes over evolutionary time.

Geographical isolation facilitates the emergence of distinct phenotypes within a single species, but reproductive barriers or selection is needed to maintain the polymorphism after secondary contact. Here, we explore the processes that maintain intraspecific variation of C4 photosynthesis, a complex trait that results from the combined action of multiple genes. The grass Alloteropsis semialata includes C4 and non-C4 populations, which have co-existed for more than one million years in the miombo woodlands of Africa. Using population genomics, we show that there is genome-wide divergence for the photosynthetic types, but the current distribution is not a result of a simple habitat displacement scenario as the genetic clusters overlap in ecology and geography, being occasionally mixed within a given habitat. We find evidence of introgression between photosynthetic types, but hybrids are rare and no clear hybrid zone is formed. Selection against hybrids likely limits gene flow and differentiation is accentuated in multiple parts of the genome pointing to selection on numerous genes. Coupled with strong isolation by distance within each genetic group, this selection created a geographical mosaic of photosynthetic types, which was further reinforced by recurrent polyploidization. Together, these factors enabled the persistence of divergent physiological traits of ecological importance within a single species despite gene flow and habitat overlap.