Phylogeography infers the demographic history of various species by resolving genetic relationships among populations across a geographic range. Comparison of phylogeographic patterns of multiple species with similar geographic distributions, i.e., comparative phylogeography, allows us to assess the roles of regional historical events and species-specific ecological factors in shaping intraspecific genetic diversity, providing model systems for studying the processes and genetic basis of adaptive evolution and speciation. In addition, these patterns can also be compared among species from different regions to infer the impact of global-scale historical and present events, such as Pleistocene glacial cycles, on current biodiversity. In this review, I summarize and integrate recent findings of phylogeographic studies for two geographic lineages, Pacific Ocean (PO) and Sea of Japan (SJ) lineages, of five coastal gobies distributed around the Japanese Archipelago. Using mitochondrial and nuclear DNA markers, these studies revealed genetic divergences of the PO and SJ lineages in the coastal gobies. However, the two types of markers showed discordant patterns for genetic divergences between the two lineages (mitonuclear discordance), suggesting different coalescent processes between these genetic markers. Ecological features that depend on shallow coastal resources may contribute to restricted gene flow and be responsible for the existence of the two lineages that are predominantly found in the coastal gobies. All coastal gobies shared sharp contrasts in genetic diversity between the two lineages, with the SJ lineages rapidly expanding during Pleistocene interglacial periods. Such rapid population expansions can provide alternative ways to obtain recent calibration points to estimate divergence times of the two lineages. A comparison of the geographic distributions between the two lineages indicated that the centers of their secondary contact zones vary, which may appear to represent the continuous transition process of the two lineage distributions. Compared with results of phylogeographic studies from other oceans, multiple divergence times, sharply contrasting demographic histories, and two independent secondary contact zones are unique characteristics of the divergence between the PO and SJ lineages. These characteristics will allow us to test the continuous processes of genomic divergence during geographical isolation with environmental fluctuations and the consequences of hybridization of divergent lineages in independent secondary contact zones with different environmental settings.

系统地理学通过解决地理范围内种群之间的遗传关系来推断各种物种的人口统计历史。具有相似地理分布的多个物种的系统地理学模式的比较，即比较系统地理学，使我们能够评估区域历史事件和物种特定生态因素在形成种内遗传多样性中的作用，为研究过程和遗传基础提供模型系统。适应性进化和物种形成。此外，还可以比较来自不同地区的物种之间的这些模式，以推断全球范围的历史和当前事件（例如更新世冰川循环）对当前生物多样性的影响。在这篇综述中，我总结并整合了两个地理谱系的系统地理学研究的最新发现，分布在日本群岛周围的五个沿海虾虎鱼的太平洋 (PO) 和日本海 (SJ) 谱系。使用线粒体和核 DNA 标记，这些研究揭示了沿海虾虎鱼中 PO 和 SJ 谱系的遗传差异。然而，这两种类型的标记显示两个谱系之间的遗传差异（线粒体不一致）模式不一致，表明这些遗传标记之间的合并过程不同。依赖浅海沿岸资源的生态特征可能导致基因流动受限，并导致主要在沿海虾虎鱼中发现的两个谱系的存在。所有沿海虾虎鱼在两个谱系之间的遗传多样性上都有鲜明的对比，SJ 谱系在更新世间冰期迅速扩展。这种快速的人口扩张可以提供替代方法来获得最近的校准点来估计两个谱系的分歧时间。两个世系地理分布的比较表明，其次要接触带的中心不同，这似乎代表了两个世系分布的连续过渡过程。与其他海洋的系统地理学研究结果相比，多次分化时间、鲜明对比的人口历史和两个独立的次生接触区是 PO 和 SJ 谱系之间分化的独特特征。