Cis-regulatory changes in locomotor genes are associated with the evolution of burrowing behavior. Cis-regulatory changes in locomotor genes are associated with the evolution of burrowing behavior

How evolution modifies complex, innate behaviors is largely unknown. Divergence in many morphological traits has been linked, at least in part, to cis-regulatory changes in gene expression, a pattern also observed for some behaviors in recently diverged populations. Given this, we compared the gene expression in the brains of two interfertile sister species of Peromyscus mice, including allele-specific expression (ASE) of their F1 hybrids, that show large and heritable differences in burrowing behavior. Because cis-regulation may contribute to constitutive as well as activity-dependent gene expression, we also captured a molecular signature of burrowing circuit divergence by quantifying gene expression in mice shortly after burrowing. We found that several thousand genes were differentially expressed between the two sister species regardless of behavioral context, with several thousand more showing behavior-dependent differences. Allele-specific expression in F1 hybrids showed a similar pattern, suggesting that much of the differential expression is driven by cis-regulatory divergence. Genes related to locomotor coordination showed the strongest signals of lineage-specific selection on burrowing-induced cis-regulatory changes. By comparing these candidate genes to independent quantitative trait locus (QTL) mapping data, we found that the closest QTL markers to these candidate genes are associated with variation in burrow shape, demonstrating an enrichment for candidate locomotor genes near segregating causal loci. Together, our results provide insight into how cis-regulated gene expression can depend on behavioral context as well as how this dynamic regulatory divergence between species can be integrated with forward genetics to enrich our understanding of the genetic basis of behavioral evolution. Overall design: Whole-brain mRNA profiles of burrowing P. polionotus, P. maniculatus, and their F1 hybrids

演化如何重塑复杂的先天行为，这一问题在很大程度上尚未明确。诸多形态学性状的分化至少在一定程度上与基因表达的顺式调控变化（cis-regulatory changes）相关，这一规律在近期分化种群的部分行为特征中同样得到了验证。
有鉴于此，本研究对两种可杂交的鹿鼠属（Peromyscus）姐妹物种的脑部基因表达情况开展了比较分析，其中还包含二者F1杂交个体的等位基因特异性表达（allele-specific expression, ASE）；这两个物种在掘洞行为上存在显著且可遗传的差异。
由于顺式调控（cis-regulation）既参与组成型基因表达调控，也可调控活动依赖型基因表达，本研究还通过量化掘洞行为后短时间内小鼠的基因表达水平，捕捉到了掘洞神经环路分化的分子特征。
研究发现，无论行为背景如何，两个姐妹物种间均存在数千个差异表达基因；另有数千个基因的表达差异则依赖于行为情境。F1杂交个体的等位基因特异性表达模式与此相似，这表明大部分差异表达由顺式调控分化所驱动。
与运动协调功能相关的基因，在掘洞诱导的顺式调控变化中表现出最强的谱系特异性选择信号。
通过将这些候选基因与独立的数量性状位点（quantitative trait locus, QTL）定位数据进行比对，本研究发现，与这些候选基因距离最近的QTL标记与掘洞形状的变异显著相关，这提示运动相关候选基因在分离的因果位点附近存在富集现象。
综上，本研究结果阐明了顺式调控的基因表达如何依赖行为情境，同时也展示了如何将物种间这种动态的调控分化与正向遗传学（forward genetics）研究相结合，以加深我们对行为演化遗传基础的理解。
实验设计概况：对具有掘洞行为的P. polionotus、P. maniculatus及其F1杂交子代进行全脑mRNA表达谱分析。