Photosynthetic diversity in sympatry is maintained in a grass species despite gene flow and habitat overlap

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 parts of Africa. Here we show genome-wide divergence among photosynthetic types, despite ecological and geographical overlap. Hybrids are occasionally formed, but do not increase in frequency with geographic proximity. Selection against hybrids, coupled with strong isolation by distance, created a geographical mosaic of genetic lineages associated with distinct photosynthetic types, which was further reinforced by recurrent polyploidization. Together, these factors enabled the long-term persistence of divergent physiological traits of ecological importance within a single species despite gene flow and habitat overlap.