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...

尽管海洋在表面上看似均一，但在空间与时间尺度上却展现出极高的环境异质性。事实上，各类软质屏障构建了海洋环境，这为研究种群分化、物种形成等多种进化过程提供了极具吸引力的研究契机。

本研究聚焦于克氏海葵鱼（Amphiprion clarkii，辐鳍鱼纲（Actinopterygii）；鲈形目（Perciformes）），它是分布范围最广的海葵鱼，同时展现出最高程度的体色多态性。海葵鱼仅在短暂的浮游幼虫阶段具备扩散能力，随后便会转变为固着的成体生活模式，这一特性可能会限制种群间的连通性，进而促进物种形成过程。正因如此，克氏海葵鱼的分类学地位长期存在争议。

我们利用覆盖印度洋与太平洋的67份克氏海葵鱼样本的全基因组重测序数据，对该物种的种群结构、种群动态历史以及体色多态性进行了解析。研究发现，克氏海葵鱼的分布范围从印度-太平洋海域延伸至……

# 克氏海葵鱼（Amphiprion clarkii）的体色数据与分析脚本

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

本数据集包含对应研究论文的体色分析所需的脚本与数据，以及所有分析所用的最终VCF（Variant Call Format）文件。

## 数据与文件结构说明

### VCF（Variant Call Format）文件：aclarkii_final.vcf.gz
本文件为所有分析所用的最终VCF文件，包含来自8个不同种群的67份克氏海葵鱼样本的基因组信息。该文件的生成遵循以下步骤：我们使用Cutadapt V2.3（Martin, 2011）对生成的测序读段（reads）进行修剪以去除接头序列；使用Sickle V1.33（Joshi and Fass, 2011）移除长度短于40 bp且Phred质量分数低于40的测序读段（reads）；我们通过FastQC V0.11.7（Andrews, 2010）对处理前后的测序读段（reads）质量进行评估；我们使用BWA-MEM V……将保留的测序读段（reads）比对至公子小丑鱼（Amphiprion percula，Lehmann et al., 2018）的参考基因组。