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.