Data from: Candidate gene analysis suggests untapped genetic complexity in melanin-based pigmentation in birds

Studies on melanin-based color variation in a context of natural selection have provided a wealth of information on the link between phenotypic and genetic variation. Here, we evaluated associations between melanic plumage patterns and genetic polymorphism in the Réunion grey white-eye (Zosterops borbonicus), a species in which mutations on MC1R do not seem to play any role in explaining melanic variation. This species exhibits five plumage color variants that can be grouped into three color forms which occupy discrete geographic regions in the lowlands of Réunion and a fourth form which comprises two color morphs (grey and brown), occurs at high elevation, and represents a true color polymorphism. We conducted a comprehensive survey of sequence variation in 96 individuals at a series of seven candidate genes other than MC1R that have been previously shown to influence melanin-based color patterns in vertebrates, including genes that have rarely been studied in a wild bird species before: POMC, Agouti, TYR, TYRP1, DCT, Corin and SLC24A5. Of these seven genes, two (Corin and TYRP1) displayed an interesting shift in allele frequencies between lowland and highland forms and a departure from mutation-drift equilibrium consistent with balancing selection in the polymorphic highland form only. Sequence variation at Agouti, a gene frequently involved in melanin-based pigmentation patterning, was not associated with color forms or morphs. Thus, we suggest that functionally important changes in loci other than those classically studied may beare involved in the color polymorphism exhibited by the Réunion grey white-eye and possibly many other non-model species.

针对自然选择背景下黑色素依赖型颜色变异的相关研究，已为表型变异与遗传变异之间的关联积累了丰富的实证数据。本研究以留尼汪灰绣眼鸟（Zosterops borbonicus）为研究对象，评估了其深色羽色模式与遗传多态性之间的关联——该物种的黑皮质素1受体（MC1R）突变似乎并未参与调控其深色羽色变异。该物种共存在5种羽色变异型，可划分为3种色型，分别占据留尼汪岛低海拔区域的离散分布区；另有1种色型包含灰色与棕色2种色变种，分布于高海拔区域，属于典型的颜色多态类群。我们对96个个体的7个非MC1R候选基因的序列变异开展了全面筛查，这些基因此前已被证实可影响脊椎动物的黑色素依赖型羽色模式，其中包括少数此前极少在野生鸟类中开展研究的基因：POMC、Agouti、TYR、TYRP1、DCT、Corin与SLC24A5。在这7个基因中，仅Corin与TYRP1这2个基因在低海拔与高海拔色型间呈现出显著的等位基因频率偏移，且仅在多态性高海拔色型中表现出偏离突变-漂移平衡的特征，符合平衡选择的作用模式。而在黑色素沉着模式调控中频繁发挥作用的Agouti基因，其序列变异与该物种的色型或色变种均无显著关联。据此我们推测，留尼汪灰绣眼鸟所表现出的颜色多态性，其背后的功能变异可能源自经典研究靶点之外的其他基因座；这一机制或许也适用于诸多其他非模式物种。