Data from: Comparative phylogeography in marginal seas of the northwestern Pacific

The maturation of marine phylogeography depends on integration of comparative information across different regions globally. The northwestern Pacific, characterized by unique tectonic setting, however, is still underrepresented. This study seeks to highlight its phylogeographical history based on available population data, focusing on three seas: the East China Sea (ECS), the South China Sea (SCS), and the Sea of Japan (SOJ). We first conducted a literature survey to evaluate current research efforts, and then re-analysed the population structure, historical demography and genealogy for two selections of studies (namely ‘the ECS category’ and ‘the multiple-sea category’) to elucidate the evolutionary processes within and across the seas, respectively. For the ECS category, the meta-analyses revealed most studies displayed a shallow phylogeny, indicating a single origin from the sea. Significant population structure was commonplace, particularly in mollusk and crustacean studies, with proportions of 89% and 80%, respectively. Nearly all studies selected showed signals of population expansion: the times estimated were closely linked to a period of ~120-140 Kya rather than the last glacial maximum. For the latter category, divergent intraspecific lineages appeared among seas and overlapped in the adjacent regions, a pattern implying each sea had served as an independent refugium during glaciations. The genetic splits, however, were estimated to arise from separate events dating from late Miocene to middle Pleistocene. As phylogeography is still in its infancy in the region, more effort is needed to test and complement the general rules abstracted here. Finally challenges and prospects were discussed to accelerate further research.

海洋系统发生生物地理学（phylogeography）的成熟发展，有赖于整合全球不同区域的比较研究数据。然而，以独特构造环境为特征的西北太平洋（Northwestern Pacific），其相关研究仍较为匮乏。本研究基于现有种群数据，旨在阐明西北太平洋的系统发生生物地理学历史，研究聚焦于三大海域：东海（East China Sea, ECS）、南海（South China Sea, SCS）以及日本海（Sea of Japan, SOJ）。研究首先通过文献调研评估当前研究进展，随后针对两类研究（即"东海类群"与"多海域类群"）分别重新分析其种群结构、历史种群动态与谱系关系，以阐明各海域内部及跨海域的演化过程。针对东海类群的荟萃分析（meta-analysis）显示，多数研究呈现出浅谱系树特征，表明该海域的类群均起源于单一祖先种群。显著的种群结构普遍存在，尤以软体动物与甲壳动物类研究为甚，两类研究的占比分别为89%与80%。纳入分析的几乎所有研究均检测到种群扩张信号，其估算的扩张时间与距今约12万至14万年的时期高度相关，而非末次冰盛期（last glacial maximum）。对于多海域类群而言，不同海域间存在种内谱系分化，且在相邻海域存在谱系重叠，这一模式表明各海域在冰期均充当了独立的避难所（refugium）。然而，遗传分化的发生时间被估算为中新世晚期至更新世中期的一系列独立事件。鉴于该区域的系统发生生物地理学研究仍处于起步阶段，未来仍需开展更多研究以验证和补充本文归纳的通用规律。最后，本文探讨了该领域面临的挑战与未来发展前景，以期推动该领域的进一步研究。