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。尽管蛋白编码突变与顺式调控突变对适应性性状的贡献已得到充分阐释，但其他变异来源——例如从单个基因生成可变RNA转录本（即同工型isoform）——的研究仍较为匮乏。本研究聚焦于已知可表达多种可变转录本的色素相关基因Agouti，以探讨转录本同工型使用在鹿鼠属（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，发现两种此前在小家鼠（Mus）中未被鉴定的新型同工型。随后我们证实，栖息于内布拉斯加沙丘的本地适应性浅色棕鹿鼠（Peromyscus maniculatus，简称P. maniculatus）种群，相较于其祖先深色同种个体，上调了名为1C的单一Agouti同工型的表达水平。通过体外实验，我们发现这种对1C同工型的偏好可能由翻译过程中的同工型特异性差异所驱动。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符合强正向选择的特征。最后我们证实，另一物种海滩鹿鼠（Peromyscus polionotus，简称P. polionotus）独立演化出的隐蔽浅色体色，同样由对同一Agouti同工型的偏好所驱动。综上，本研究揭示了可变转录本加工在适应性演化中的作用，并证实了同工型调控层面的分子趋同演化。