Reinforcement has the potential to generate strong reproductive isolation through the evolution of barrier traits as a response to selection against maladaptive hybridization, but the genetic changes associated with this process remain largely unexplored. Building upon the increasing evidence for a role of structural variants in adaptation and speciation, we addressed the role of copy-number variation in the reinforcement of sexual isolation evidenced between the two European subspecies of the house mouse. We characterized copy-number divergence between populations of Mus musculus musculus that display assortative mate choice, and those that do not, using whole-genome resequencing data. Updating methods to detect deletions and tandem duplications (collectively: copy-number variants, CNVs) in Pool-Seq data, we developed an analytical pipeline dedicated to identifying genomic regions showing the expected pattern of copy-number displacement under a reinforcement scenario. This strategy allowed us to detect 1824 deletions and seven tandem duplications that showed extreme differences in frequency between behavioural classes across replicate comparisons. A subset of 480 deletions and four tandem duplications were specifically associated with the derived trait of assortative mate choice. These ‘Choosiness-associated’ CNVs occur in hundreds of genes. Consistent with our hypothesis, such genes included olfactory receptors potentially involved in the olfactory-based assortative mate choice in this system as well as one gene, Sp110, that is known to show patterns of differential expression between behavioural classes in an organ used in mate choice—the vomeronasal organ. These results demonstrate that fine-scale structural changes are common and highly variable within species, despite being under-studied, and may be important targets of reinforcing selection in this system and others.

This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.

强化有可能通过屏障性状的进化产生强大的生殖隔离，作为对适应不良杂交选择的反应，但与这一过程相关的遗传变化在很大程度上仍未被探索。基于越来越多的证据表明结构变异在适应和物种形成中的作用，我们研究了拷贝数变异在加强家鼠两个欧洲亚种之间的性隔离中的作用。我们利用全基因组重测序数据，描述了表现出选型择偶选择的小家鼠群体与不表现出选型择偶选择的小家鼠群体之间的拷贝数差异。通过更新检测 Pool-Seq 数据中的删除和串联重复（统称：拷贝数变异，CNV）的方法，我们开发了一个分析管道，专门用于识别在强化场景下显示预期拷贝数位移模式的基因组区域。这一策略使我们能够检测到 1824 个缺失和 7 个串联重复，这些重复表明在重复比较中行为类别之间的频率存在极大差异。480 个缺失和四个串联重复的子集与选型择偶的衍生特征特别相关。这些“选择性相关”CNV 存在于数百个基因中。与我们的假设一致，这些基因包括可能参与该系统中基于嗅觉的选型配偶选择的嗅觉受体，以及一个基因Sp110，已知该基因在用于配偶选择的器官中显示行为类别之间的差异表达模式——犁鼻器。这些结果表明，尽管研究不足，但精细尺度的结构变化在物种内是常见的且高度可变，并且可能是该系统和其他系统中加强选择的重要目标。

本文是“迈向物种形成的完成：超越第一道障碍的生殖隔离的进化”主题的一部分。