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。尽管编码蛋白质的突变与顺式调控突变对适应性性状的贡献已得到充分研究与证实，但其他变异来源——例如从单个基因生成的可变RNA转录本（即同工型isoforms）——的相关研究仍较为匮乏。本研究以已知可表达多种可变转录本的色素沉着基因Agouti为研究对象，旨在探讨转录本同工型的使用在鹿鼠属（Peromyscus）隐蔽体色表型进化中的作用。我们首先对鹿鼠皮肤中表达的Agouti同工型进行表征，发现了两种此前在小家鼠属（Mus）中未被鉴定的新型同工型。随后我们发现，栖息于内布拉斯加沙丘的浅色适应性种群——北美鹿鼠（Peromyscus maniculatus，P. maniculatus）——相较于其祖先的深色同种个体，其名为1C的单一Agouti同工型表达量显著上调。通过体外实验，我们证实这种对1C同工型的表达偏好，可能源于不同同工型在翻译过程中的特异性差异。此外，利用野生捕获的混血小鼠种群，我们发现Agouti总表达量的变异定位于外显子1C附近的区域，该区域的核苷酸变异模式也与强烈的正向选择特征相符。最后我们证实，另一物种波氏鹿鼠（Peromyscus polionotus，P. polionotus）独立演化出的隐蔽浅色体色，同样由对同一Agouti同工型的表达偏好所驱动。综上，本研究不仅揭示了可变转录本加工在适应性演化中的作用，还证实了转录本同工型调控层面的分子趋同现象。