Data from: The role of vicariance and dispersal on New Zealand's estuarine biodiversity: the case of Paracorophium (Crustacea: Amphipoda)

To investigate the role of vicariance and dispersal on New Zealand’s estuarine biodiversity, we examined variability in mitochondrial cytochrome c oxidase I (COI) gene sequences for the amphipod genus Paracorophium. Individuals from the two nominate endemic species (P. excavatum and P. lucasi) were collected from sites throughout the North and South Islands. Sequence divergences of 12.8% were detected among the species. However, divergences of up to 11.7% were also observed between well supported clades, suggesting the possibility of cryptic species. Nested clade analyses identified four distinct lineages from within both P. excavatum and P. lucasi, with boundaries between clades corresponding to topographical features (e.g. Cook Straight, North and East Cape). Sequence divergences of 3.7 - 4.9% were also observed within geographic regions (e.g. east and west coasts of the upper North Island). Genetic structure in Paracorophium appears to represent prolonged isolation and allopatric evolutionary processes dating back to the Upper Miocene and continuing through the Pliocene and early Pleistocene. Based on molecular clock estimates from sequence divergences and reconstructions of New Zealand’s geological past, we suggest that sea level and landmass changes during the early Pleistocene (2 Mya) resulted in the isolation of previously contiguous populations leading to the present-day patterns. COI genetic structure was largely congruent with previously observed allozyme patterns and highlights the utility of COI as an appropriate marker for phylogeographic studies of the New Zealand estuarine fauna.为探究隔离分化与扩散在新西兰河口生物多样性中的作用，我们针对端足类属副钩虾属（Paracorophium）的线粒体细胞色素c氧化酶亚基I（COI）基因序列变异展开了分析。研究样本采自新西兰北岛与南岛全境的多个采样点，涵盖该属的两种指名特有种（P. excavatum与P. lucasi）。该两个物种间的序列分歧度达12.8%；但在高支持率的进化支之间，亦观测到最高达11.7%的序列分歧，这暗示存在隐存种的可能性。嵌套进化支分析从P. excavatum和P. lucasi类群中分别鉴定出4个独立谱系，进化支间的分界与库克海峡、北角及东角等地形特征高度吻合。在部分地理区域（如北岛上部东西两岸）内，同样观测到3.7%~4.9%的序列分歧。副钩虾属的遗传结构似乎反映了可追溯至中新世晚期、并延续至上新世与更新世早期的长期隔离与异域进化过程。基于序列分歧的分子钟估算结果，结合新西兰地质历史重建成果，我们认为更新世早期（200万年前）的海平面与陆块变化，使得原本连续分布的种群发生隔离，进而形成了现今的遗传格局。COI的遗传结构与此前观测到的等位酶图谱整体一致，这凸显了COI作为新西兰河口动物群系统地理学研究合适分子标记的应用价值。