Data from: The genomic basis of adaptive leaf variation in the Galápagos giant daisies

Scalesia (Asteraceae) is the largest endemic plant genus of the Galápagos archipelago and an example of adaptive radiation. While Scalesia species are highly varied in habit and morphology, most remarkable is their variety of leaf shapes, especially in the differential presence of leaf lobing/serration, a derived trait that evolved multiple times as a likely adaptation to the islands’ hot and dry equatorial climate. Using population-level genomic data from 396 individuals representing all 15 recognized Scalesia species, we characterize this young radiation (around 1 million years ago), and reveal that their substantial morphological divergence and ecological specialization are primarily based on shared genetic variation. To further elucidate the repeated adaptive evolution of leaf lobing in Scalesia, we integrate genomic and leaf morphometric data, with transcriptomes from different developmental stages, and conclude that leaf lobing evolved through diversifying selection. Natural selection occurs independently on different regulators in the pathway controlling the development of adaxial-abaxial leaf polarity, highlighting the importance of the founder populations’ high genetic diversity maintained via allopolyploidy. Finally, our findings have implications for the conservation of Scalesia’s threatened biodiversity, as unexpectedly high intra-specific genetic structure and long-term isolation among populations indicate widespread nascent speciation. This dataset contains files associated with the article. Specifically, it contains code and scripts used to analyse the data, the source data files for the main text and supplementary figures, and the Cytoscape file used for the transcriptomics analysis in the article. It also contains example input and output files to calculate dxy and genome-wide Tajima's D.