Genetic diversity at putatively adaptive but not neutral loci in Primula veris responds to recent habitat change in semi-natural grasslands

Recent habitat change in semi-natural grasslands due to a lack of management has been shown to affect the genetic diversity of grassland plants. However, it is unknown how a change in local environment affects genetic diversity at adaptive loci. We applied RADseq (restriction-site associated DNA sequencing) to extract > 3,000 SNPs across 568 individuals from 32 Estonian populations of Primula veris, a plant species common to semi-natural grasslands. We evaluated the effect of recent grassland overgrowth following management abandonment on the genetic diversity at putatively neutral and adaptive loci, which we distinguished by applying three methods, i.e., linear and categorical environmental association analyses, and an FST outlier test. For validation, we randomised the genotype to sample assignments. Effects of recent habitat change on genetic diversity differed between neutral and adaptive SNP sets. Genetic diversity assessed at putatively neutral loci was similar in open and overgrown habitats but showed a significant difference between these habitat types at putatively adaptive loci: overgrown (i.e. newly established) habitats exhibited higher genetic diversity at putatively adaptive loci than open (i.e. old) habitats, likely due to the exertion of novel selection pressures imposed by new habitat conditions. This increase in genetic diversity at putatively adaptive loci in the new environment points to currently ongoing selection processes where genetic adaptation to the old habitat is potentially lost through altered allele frequencies. Our study suggests that a recent change in local habitat conditions may not be reflected in neutral loci whereas putatively adaptive loci can inform about potential selection processes.