Purifying selection after episodes of recurrent adaptive diversification in fungal pathogens

Tests of selective neutrality based on comparative and population genetic data target different time scales of selection. Investigating both time scales on the same genes has rarely been done and yet can provide insights into histories of selection. In pathogens, such a comparison can elucidate whether the same genes experience recurrent positive selection across specialization events onto novel hosts and selection in the short term, e.g. by coevolution with a current host. Here, we investigated whether the genes showing signs of positive selection (based on dN/dS ratios) between pathogens specialized on different hosts also exhibited footprints of recent positive selection. We sequenced 58 DNA fragments in the model fungal plant pathogen Microbotryum lychnidis-dioicae infecting Silene latifolia. Eleven focal genes were chosen because they showed a significant signal of positive selection in a previous study and putative functions likely involved in host-parasite interactions. In addition, 47 control genes were randomly chosen among genes showing no evidence of positive selection. We used a population genetics approach to search for signatures of recent selection, controlling for population structure and demographic history. We found footprints of purifying selection in all focal genes and of recent positive selection in two of them. Signs of purifying selection were also found at the same eleven genes in a closely related species, Microbotryum silenes-dioicae, infecting Silene dioica. These results suggest that genes experiencing episodes of adaptive diversification during host shifts may subsequently be under strong functional constraint, although some can remain under positive selection in the short term.