Natural selection preserves trans-specific chloroplast diversity in a Mediterranean evergreen oak

Cork oak (Quercus suber) is an ecologically and economically important Western Mediterranean tree species in severe risk of decline due to aggravated tree mortality and lack of natural regeneration. In Q. suber, two distinct chloroplast lineages, one of them of trans-specific origin, occur in sympatry in the western half of its species distribution. We hypothesize that selection may drive the maintenance of the two lineages and investigate this hypothesis by sequencing chloroplast genomes of 259 Q. suber samples across 24 locations. Protein-coding chloroplast genes were scanned for selection signal using different codon-based methods. Selection signal was found at different sites and genes, and polymorphism in selected sites was shown to segregate between the two chloroplast lineages. We postulate that trans-specific chloroplast diversity in Q. suber is preserved by balancing selection, rather than resulting exclusively from ongoing introgression. These results correspond to an unusual case of balancing selection on whole plastid genomes in a long-lived woody plant species and have implications on conservation and management practices for Q. suber, which may benefit from taking into account genetic variation in plastid genomes as a possible source of increased adaptive potential for the species.