Integrative genomic phylogeography reveals signs of mitonuclear incompatibility in a natural hybrid goby population

Hybridization between divergent lineages generates new allelic combinations. One mechanism that can hinder the formation of hybrid populations is mitonuclear incompatibility, i.e. dysfunctional interactions between proteins encoded on the nuclear and mitochondrial genomes (mitogenomes) of diverged lineages. Theoretically, selective pressure due to mitonuclear incompatibility can affect genotypes in a hybrid population in which nuclear genomes and mitogenomes from divergent lineages admix. To directly and thoroughly observe this key process, we de novo sequenced the 747 Mb genome of the coastal goby, Chaenogobius annularis, and investigated its integrative genomic phylogeographics using RNA‐sequencing, RAD‐sequencing, genome re‐sequencing, whole mitogenome sequencing, amplicon‐sequencing, and small RNA‐sequencing. Chaenogobius annularis populations have been geographically separated into Pacific Ocean (PO) and Sea of Japan (SJ) lineages by past isolation events around the Japanese archip...分化支系间的杂交可产生全新的等位基因组合。阻碍杂交种群形成的一种核心机制为核质不相容性（mitonuclear incompatibility），即分化支系的核基因组与线粒体基因组（mitogenome）所编码的蛋白质间出现功能失调的互作。理论上，核质不相容性带来的选择压力，可对携带来自不同支系的核基因组与线粒体基因组的混合杂交种群的基因型产生影响。为直接且全面地观测这一关键过程，我们对沿海虾虎鱼（Chaenogobius annularis）的747 Mb基因组进行了从头测序，并结合RNA测序、RAD测序、基因组重测序、全线粒体基因组测序、扩增子测序与小RNA测序技术，对其整合基因组系统地理学展开了研究。该物种的种群曾因日本列岛周边的历史隔离事件，被地理划分为太平洋支系（PO）与日本海支系（SJ）……