Coloration has been associated with multiple biologically relevant traits that drive adaptation and diversification in many taxa. However, despite the great diversity of colour patterns present in amphibians the underlying molecular basis is largely unknown. Here, we use insight from a highly colour-variable lineage of the European fire salamander (Salamandra salamandra bernardezi) to identify functional associations with striking variation in colour morph and pattern. The three focal colour morphs-ancestral black-yellow striped, fully yellow and fully brown-differed in pattern, visible coloration and cellular composition. From population genomic analyses of up to 4,702 loci, we found no correlations of neutral population genetic structure with colour morph. However, we identified 21 loci with genotype-phenotype associations, several of which relate to known colour genes. Furthermore, we inferred response to selection at up to 142 loci between the colour morphs, again including several that relate to coloration genes. By transcriptomic analysis across all different combinations, we found 196 differentially expressed genes between yellow, brown and black skin, 63 of which are candidate genes involved in animal coloration. The concordance across different statistical approaches and 'omic data sets provide several lines of evidence for loci linked to functional differences between colour morphs, including TYR, CAMK1 and PMEL. We found little association between colour morph and the metabolomic profile of its toxic compounds from the skin secretions. Our research suggests that current ecological and evolutionary hypotheses for the origins and maintenance of these striking colour morphs may need to be revisited.

中文翻译：

---

功能性颜色基因和颜色多态sal中的选择信号。

着色与许多生物学相关的性状有关，这些性状在许多生物分类中驱动适应性和多样化。然而，尽管两栖动物中存在多种颜色模式，但基本的分子基础仍是未知的。在这里，我们从欧洲火sal（Salamandra salamandra bernardezi）的高度多变的谱系中获得洞察力，以识别出颜色形态和图案有明显变化的功能关联。这三种焦点颜色形态分别为祖先的黑黄色条纹，全黄色和全棕色的图案，可见色和细胞组成。通过对多达4,702个基因座的种群基因组分析，我们发现中性种群遗传结构与颜色形态没有相关性。但是，我们确定了21个具有基因型与表型关联的基因座，其中一些与已知的颜色基因有关。此外，我们推断出对颜色变体之间最多142个基因座的选择反应，同样包括与着色基因有关的几个基因座。通过跨所有不同组合的转录组分析，我们发现了196种在黄色，棕色和黑色皮肤之间差异表达的基因，其中63个是涉及动物着色的候选基因。不同统计方法和“全基因组数据集”之间的一致性为基因座与颜色形态（包括TYR，CAMK1和PMEL）之间的功能差异相关联提供了多条证据。我们发现颜色形态与其皮肤分泌物中有毒化合物的代谢组学特征之间几乎没有关联。