Data from: Causations of phylogeographic barrier of some rocky shore species along the Chinese coastline

Background: Substrate, ocean current and freshwater discharge are recognized as important factors that control the larval dispersal and recruitment of intertidal species. Life history traits of individual species will determine the differential responses to these physical factors, and hence resulting in contrasting phylogeography across the same biogeographic barrier. To determine how these factors affect genetic structure of rocky shore species along the China coast, a comparative phylogeographic study of four intertidal and subtidal species was conducted using mitochondrial and nuclear DNA by combining new sequences from Siphonaria japonica with previously published sequences from three species (Cellana toreuma, Sargassum horneri and Atrina pectinata). Results: Analysis of molecular variance and pairwise ΦST revealed significant genetic differences between the Yellow Sea (YS) and the other two marginal seas (East China Sea, ECS and South China Sea, SCS) for rocky-shore species (S. japonica, C. toreuma, S. horneri), but not for muddy-shore species Atrina pectinata. Demographic history analysis proved that the population size of all these four species were persistent though the Last Glacial Maximum (LGM, ~20 ka BP). Migration analysis revealed that gene flow differentiated northward and southward migration for these four species. However, the inferred direction of gene flow using alternatively mitochondrial or nuclear markers was contradictory in S. japonica. Conclusions: It is concluded that there is a phylogeographical break at the Yangtze River estuary for the rocky shore species and the causation of the barrier is mainly due to the unsuitable substratum and freshwater discharge. All four intertidal and subtidal species appear to have persisted through the LGM in China, indicating the lower impact of LGM on intertidal and subtidal species than generally anticipated. The imbalanced gene flow between YS and ESCS groups for these four species could be explained by historical refugia. The discordance between mitochondrial and nuclear markers in the MIGRATE analysis of S. japonica prove the importance of employing multi-locus data in biogeographic study. Climate change, land reclamation and dam construction, which are changing substrate and hydrological conditions around Yangtze River estuary, will consequently affect the biogeographic pattern of intertidal species.

研究背景：底质（substrate）、海流与淡水径流被学界公认为调控潮间带物种幼虫扩散与种群补充的核心因子。不同物种的生活史特征会使其对这些物理因子产生差异化响应，最终在同一生物地理屏障（biogeographic barrier）下形成截然不同的系统生物地理学（phylogeography）格局。为明确上述因子对中国沿海岩岸物种遗传结构的影响机制，本研究结合日本松螺（Siphonaria japonica）的新测序序列，与已发表的托氏笠螺（Cellana toreuma）、角叉菜（Sargassum horneri）及栉江珧（Atrina pectinata）3个物种的序列数据，基于线粒体DNA（mitochondrial DNA）与核DNA（nuclear DNA）对4种潮间带及亚潮间带物种开展了比较系统生物地理学研究。
研究结果：分子方差分析（Analysis of molecular variance）与成对ΦST分析显示，岩岸物种（日本松螺、托氏笠螺、角叉菜）的黄海（Yellow Sea, YS）种群与另外两个边缘海——东海（East China Sea, ECS）及南海（South China Sea, SCS）种群间存在显著遗传分化，但泥岸物种栉江珧并未呈现该分化模式。种群历史动态分析表明，4个物种种群规模在末次盛冰期（Last Glacial Maximum, LGM，约20 ka BP）期间保持稳定。基因流（gene flow）分析显示，4个物种的基因流均存在南北向迁移的分化特征。然而，针对日本松螺的分析中，分别基于线粒体标记与核标记所推断的基因流方向存在矛盾。
研究结论：本研究证实岩岸物种在长江口（Yangtze River estuary）存在系统生物地理学断裂带，该屏障的成因主要为不适宜的底质条件与淡水径流输入。4种潮间带与亚潮间带物种均在末次盛冰期存续于中国海域，表明末次盛冰期对这类物种的影响较此前学界普遍预期更低。黄海与东-南海群组间的不平衡基因流可通过历史冰期避难所（refugia）加以解释。日本松螺的MIGRATE分析中，线粒体标记与核标记结果的不一致性，证实了多位点数据在生物地理学研究中的重要性。当前气候变化、围填海与大坝建设正在改变长江口周边的底质与水文条件，进而会对潮间带物种的生物地理格局产生影响。