Data from: The role of isoforms in the evolution of cryptic coloration in Peromyscus mice

A central goal of evolutionary biology is to understand the molecular mechanisms underlying phenotypic adaptation. While the contribution of protein-coding and cis-regulatory mutations to adaptive traits has been well documented, additional sources of variation – such as the production of alternative RNA transcripts from a single gene, or isoforms – have been understudied. Here, we focus on the pigmentation gene Agouti, known to express multiple alternative transcripts, to investigate the role of isoform usage in the evolution of cryptic colour phenotypes in deer mice (genus Peromyscus). We first characterize the Agouti isoforms expressed in the Peromyscus skin and find two novel isoforms not previously identified in Mus. Next, we show that a locally adapted light-coloured population of P. maniculatus living on the Nebraska Sand Hills shows an upregulation of a single Agouti isoform, termed 1C, compared with their ancestral dark-coloured conspecifics. Using in vitro assays, we show that this preference for isoform 1C may be driven by isoform-specific differences in translation. In addition, using an admixed population of wild-caught mice, we find that variation in overall Agouti expression maps to a region near exon 1C, which also has patterns of nucleotide variation consistent with strong positive selection. Finally, we show that the independent evolution of cryptic light pigmentation in a different species, P. polionotus, has been driven by a preference for the same Agouti isoform. Together, these findings present an example of the role of alternative transcript processing in adaptation and demonstrate molecular convergence at the level of isoform regulation.进化生物学的核心目标之一，是解析表型适应性背后的分子机制。尽管编码蛋白突变与顺式调控突变对适应性性状的贡献已得到充分证实，但其他变异来源——例如单基因产生的可变RNA转录本（转录本异构体isoform）——却尚未得到充分研究。本研究以已知可表达多种可变转录本的色素基因Agouti为研究对象，旨在探究转录本异构体使用在鹿鼠属（Peromyscus）隐蔽色表型演化中的作用。我们首先对鹿鼠皮肤中表达的Agouti转录本异构体进行了系统鉴定，发现了两种此前在小家鼠属（Mus）中未被报道的新型异构体。其次，我们发现栖息于内布拉斯加沙丘的适应性浅色草原鹿鼠（P. maniculatus）种群，相较于其祖先深色同种种群，单一被命名为1C的Agouti转录本异构体出现了表达上调。通过体外实验，我们证实这种对1C异构体的偏好性，可能源于不同异构体间翻译效率的特异性差异。此外，利用野生捕获的混合种群小鼠，我们发现Agouti总表达量的变异定位至外显子1C附近的区域，该区域的核苷酸变异模式也与强正向选择的特征相符。最后，我们证实另一个物种——波氏鹿鼠（P. polionotus）——独立演化出的隐蔽浅色毛色表型，同样由对该Agouti异构体的偏好性所驱动。综上，本研究的发现为可变转录本加工在适应性演化中的作用提供了典型例证，并证实了转录本异构体调控层面的分子趋同演化现象。