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Data from: Phenotypic and genomic signatures of adaptation in urban populations of the wild radish (Raphanus raphanistrum)

Chan, Yuan Fu1; Cozzolino, Salvatore1; Scopece, Giovanni1; Pellegrini, Laura1; Cafasso, Donata1; Guzzetti, Lorenzo2; Labra, Massimo2

Research facility: University of Naples Federico II
Published Mar 18, 2026 on Dryad. https://doi.org/10.5061/dryad.sxksn03g5

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Mar 18, 2026 version files 1.77 MB

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Abstract

By modifying biotic and abiotic environments, urbanisation can influence the evolutionary adaptation of organisms, especially when their distribution is fragmented. However, the effects of urbanisation on evolutionary adaptation remain poorly understood within a metapopulation framework, where high gene flow and recurrent extinction/colonisations may counteract local adaptation. To bridge this gap, we integrated phenotypic and genomic data and explored how urbanisation shaped the evolutionary processes in the wild radish Raphanus raphanistrum, a widely distributed ruderal species. We conducted field surveys and a common garden experiment to compare phenotypic differences between urban and natural populations in a Mediterranean area. Additionally, population genetic analysis and a genome-wide association study (GWAS) were performed to uncover the genetic basis of urban adaptation and population structure. Our findings indicate that urban populations of the wild radish exhibit significantly smaller flowers and earlier flowering times compared to natural populations. Their correlations with fitness suggest that earlier flowering and longer petal length have higher adaptive values. However, a trade-off between these traits indicates that earlier flowering is advantageous in urban environments, whereas larger flowers are favoured in natural habitats. Genomic analyses reveal low genetic differentiation and frequent gene flow among urban and natural populations. The GWAS identified 46 single-nucleotide polymorphisms (SNPs) significantly associated with urbanisation, 32 of which are located within gene regions. Notably, one of these genes, AT3g27390, is associated with the shift to the reproductive phase. Overall, our results demonstrate how natural selection in an urban context promotes rapid phenotypic divergence in R. raphanistrum despite ongoing gene flow.