Selective histories of poplar protease inhibitors: elevated polymorphism, purifying selection, and positive selection driving divergence of recent duplicates

Summary•  To further our understanding of plant defense evolution and the consistency of selection at the nucleotide level we analysed polymorphism data from five protease inhibitor (PI) genes in Populus balsamifera . •  We compared diversity at the five PI genes to diversity at nondefense loci in both range‐wide samples as well as in two subpopulations, one from the northern edge of the species range and one from the southern edge of the range. We also compared our data with previously reported diversity in Populus tremula , a European species with similar ecology to North American P. balsamifera . •  The PIs show diverse histories, including repeated bouts of positive selection and excess diversity. These genes also exhibit diverse histories in P. tremula but the signatures of selection acting at the specific loci differed between the species. One locus, KTI3 , segregates several recent duplicates that show evidence of either positive selection or relaxed selective constraints. •  The patterns of diversity at the PIs varied within P. balsamifera and between two closely related species. The lack of consistent patterns suggests that evolution of host defense genes, including adaptations to enemy‐imposed selection, may often be lineage‐ and gene‐specific.