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 selec..., , # Data from: The genomic basis of adaptive leaf variation in the Galápagos giant daisies

Dataset DOI: [10.5061/dryad.j9kd51cr0](10.5061/dryad.j9kd51cr0)

## Description of the data and file structure

### Files and variables

#### File: ScalesiaCode.sh

**Description:** This file contains bash code that calls external programs used for the analysis. All command-line arguments are included. The program version used can either be found in this file or in the methods section of the manuscript. This file is available in the linked Zenodo publication ([https://doi.org/10.5281/zenodo.18865669)](https://doi.org/10.5281/zenodo.18865669).

**Programs/tools used: **angsd v0.935, angsd v.0.941, Plink v1.9, java 1.8, GATK v3.7-0, bedtools v2.30, PCangsd v0.98, NGSadmix32, bedtools v2.26.0, samtools v. 1.10, GATK v4.2.3, vcftools v0.1.17, picardtools v2.25.5, Dsuite, bcftools v.1.10

#### File: Network_final.cys

**Description:** Cytoscape file used for the transcriptome network analysis...., ,