Data and scripts for the colour analysis from: Gene flow throughout the evolutionary history of a colour polymorphic and generalist clownfish

Even seemingly homogeneous on the surface, the oceans display high environmental heterogeneity across space and time. Indeed, different soft barriers structure the marine environment, which offers an appealing opportunity to study various evolutionary processes such as population differentiation and speciation. Here, we focus on Amphiprion clarkii (Actinopterygii; Perciformes), the most widespread of clownfishes that exhibits the highest colour polymorphism. Clownfishes can only disperse during a short pelagic larval phase before their sedentary adult lifestyle, which might limit connectivity among populations, thus facilitating speciation events. Consequently, the taxonomic status of A. clarkii has been under debate. We used whole-genome resequencing data of 67 A. clarkii specimens spread across the Indian and Pacific Oceans to characterise the species' population structure, demographic history, and colour polymorphism. We found that A. clarkii spread from the Indo-Pacific Ocean to the..., , , # Colour data and scripts for *Amphiprion clarkii*

[https://doi.org/10.5061/dryad.xwdbrv1nd](https://doi.org/10.5061/dryad.xwdbrv1nd)

The datasets contains the scripts and data for the colour analysis of the related manuscript, as well as the final VCF files used for all the analysis. 

## Description of the data and file structure

### VCF file - aclarkii\_final.vcf.gz 

Final VCF files used for all the analysis. It contains the genomic information of 67 *Amphiprion clarkii* specimens from 8 different populations. The following steps were followed to generate this file: we trimmed the generated reads to remove adapter sequences using Cutadapt V2.3 (Martin, 2011). We removed reads shorter than 40 bp and with a Phred quality score below 40 with Sickle V1.33 (Joshi and Fass, 2011). We assessed read quality before and after processing with FastQC V0.11.7 (Andrews, 2010). We mapped the reads that were kept against the reference genome of *A. percula*(Lehmann et al., 2018) using BWA-MEM V...