Data from: Phylogeography of amphi-boreal fish: tracing the history of the Pacific herring Clupea pallasii in North-East European seas

Background: The relationships between North Atlantic and North Pacific faunas through times have been controlled by the variation of hydrographic circumstances in the intervening Arctic Ocean and Bering Strait. We address the history of trans-Arctic connections in a clade of amphi-boreal pelagic fishes using genealogical information from mitochondrial DNA sequence data. The Pacific and Atlantic herrings (Clupea pallasii and C. harengus) have basically vicarious distributions in the two oceans since pre-Pleistocene times. However, remote populations of C. pallasii are also present in the border waters of the North-East Atlantic in Europe. These populations show considerable regional and life history differentiation and have been recognized in subspecies classification. The chronology of the inter-oceanic invasions and genetic basis of the phenotypic structuring however remain unclear. Results: The Atlantic and Pacific herrings both feature high mtDNA diversities (large long-term population sizes) in their native basins, but an ocean-wide homogeneity of C. harengus is contrasted by deep east-west Pacific subdivision within Pacific C. pallasii. The outpost populations of C. pallasii in NE Europe are identified as members of the western Pacific C. pallasii clade, with some retained inter-oceanic haplotype sharing. They have lost diversity in colonization bottlenecks, but have also thereafter accumulated abundant new variation. The data delineate three phylogeographic groups within the European C. pallasii: herring from the inner White Sea; herring from the Mezen and Chesha Bays; and a strongly bottlenecked peripheral population in Balsfjord of the Norwegian Sea. Conclusions: The NE European outposts of C. pallasii are judged to be early post-glacial colonists from the NW Pacific. A strong regional substructure has evolved since that time, in contrast to the apparent broad-scale uniformity maintained by herrings in their native basins. The structure only partly matches the previous biological concepts based on seasonal breeding stocks or geographical subspecies designations. The trans-Arctic herring phylogeography is notably similar to those of the amphi-boreal mollusk taxa Macoma and Mytilus, suggesting similar histories of inter-oceanic connections. We also considered the time dependency of molecular rates, critical for interpreting timing of relatively recent biogeographical events, by comparing the estimates from coding and non-coding mitochondrial regions of presumably different mutation dynamics.

研究背景：长期以来，北大西洋与北太平洋生物群之间的演化联系，受隔阻其间的北冰洋与白令海峡的水文环境变化所调控。
本研究依托线粒体DNA（mitochondrial DNA, mtDNA）序列数据构建的谱系信息，解析了一支跨北寒带远洋鱼类支系的跨北冰洋连通演化历史。太平洋鲱（Clupea pallasii）与大西洋鲱（C. harengus）自更新世之前便在两大洋呈现典型的替代分布格局。然而，在欧洲东北大西洋的边缘海域也存在太平洋鲱的异地种群。此类种群展现出显著的区域与生活史分化，已被纳入亚种分类体系。但跨洋入侵的时间序列以及表型结构的遗传基础仍未明确。

研究结果：大西洋鲱与太平洋鲱在其原生海域均表现出较高的线粒体DNA多样性（对应长期种群规模较大）；但大西洋鲱在全大洋范围内具有遗传均质性，而太平洋鲱在东-西太平洋间则存在显著的遗传分化。欧洲东北大西洋的太平洋鲱拓殖种群，被归入西太平洋太平洋鲱支系，且保留了部分跨洋单倍型（haplotype）共享现象。此类种群在拓殖奠基瓶颈过程中丢失了部分遗传多样性，但后续又积累了大量新的遗传变异。本研究数据将欧洲太平洋鲱划分为三个系统生物地理学类群：白海内部的鲱鱼种群、梅津湾与切沙湾的鲱鱼种群，以及挪威海巴尔斯峡湾中经历了严重奠基瓶颈的边缘种群。

研究结论：欧洲东北大西洋的太平洋鲱拓殖种群，被判定为源自西北太平洋的冰期后早期拓殖类群。自拓殖以来，此类种群演化出了显著的区域亚结构，而与其原生海域内鲱鱼种群所维持的大范围遗传均质性形成鲜明对比。该区域亚结构仅部分契合此前基于季节性繁殖种群或地理亚种划分所提出的生物学认知。跨北冰洋鲱鱼的系统生物地理学格局，与双北寒带软体动物类群白樱蛤属（Macoma）和贻贝属（Mytilus）的格局显著相似，暗示二者具有相似的跨洋连通演化历史。本研究还通过对比线粒体编码区与非编码区（推测二者突变动态存在差异）的分子钟估计值，探讨了分子速率的时间依赖性——这对于解读较新近生物地理事件的发生时间至关重要。