Signatures of selective sweeps in urban and rural white clover populations

Abstract Urbanization is increasingly recognized as a powerful force of evolutionary change. However, anthropogenic sources of selection can often be similarly strong and multifarious in rural habitats, and whether selection differs in either strength or its targets between habitats is rarely considered. Despite numerous examples of phenotypic differentiation between urban and rural populations, we still lack an understanding of the genes enabling adaptation to these contrasting habitats. In this study, we conducted whole genome sequencing of 120 urban, suburban, and rural white clover plants from Toronto, Canada and used these data to identify urban and rural signatures of positive selection. We found evidence for selection in genomic regions involved in abiotic stress tolerance and growth/development in both urban and rural populations, and clinal change in allele frequencies at SNPs within these regions. Patterns of allele frequency and haplotype differentiation suggest that most sweeps are incomplete and our strongest signals of selective sweeps overlap known large-effect structural variants. These results highlight how both urban and rural habitats are driving ongoing selection in Toronto white clover populations, and motivate future work disentangling the genetic architecture of ecologically important phenotypes underlying adaptation to contemporary anthropogenic habitats.