Data from: Population connectivity and phylogeography of a coastal fish, Atractoscion aequidens (Sciaenidae), across the Benguela Current region: evidence of an ancient vicariant event.

Contemporary patterns of genetic diversity and population connectivity within species can be influenced by both historical and contemporary barriers to gene flow. In the marine environment, present day oceanographic features such as currents, fronts and upwelling systems can influence dispersal of eggs/larvae and/juveniles/adults, shaping population substructuring. The Benguela Current system in the southeastern Atlantic is one of the oldest upwelling systems in the world, and provides a unique opportunity to investigate the relative influence of contemporary and historical mechanisms shaping the evolutionary history of warm-temperate fish species. Using the genetic variation in the mitochondrial DNA Control Region and eight nuclear microsatellite DNA loci, we identified the presence of two highly divergent populations in a vagile and warm-temperate fish species, Atractoscion aequidens, across the Benguela region. The geographical distributions of the two populations, on either side of the perennial upwelling cell, suggest a strong correlation between the oceanographic features of the system and the breakdown of gene flow within this species. Genetic divergence (mtDNA φST = 0.902, microsatellite FST = 0.055: probability of genetic homogeneity for either marker = p<0.001), absence of migrants (less than 1% per generation) between populations and coalescent estimates of time since most recent common ancestor suggest that the establishment of the main oceanographic features of the system (2 million years ago), particularly the strengthening and position of the perennial upwelling cell, is the most likely mechanism behind the observed isolation. Concordance between mitochondrial and nuclear genetic markers indicates that isolation and divergence of the northern and southern Benguela populations of A. aequidens occurred deep in the past and has continued to the present day. These findings suggest that the Benguela Current system may constitute an ancient and impermeable barrier to gene flow for warm-temperate fish species.

物种种内当代遗传多样性格局与种群连通性，可同时受到历史与当代基因流障碍的调控。在海洋环境中，现今的海洋学特征（如海流、锋面与上升流系统）可影响卵、幼体、稚体乃至成体的扩散过程，进而塑造种群亚结构。位于东南大西洋的本格拉洋流系统是全球最古老的上升流系统之一，为探究塑造暖温性鱼类进化历史的当代与历史机制的相对影响提供了独特研究契机。本研究依托线粒体DNA控制区（mitochondrial DNA Control Region）与8个核微卫星DNA位点（nuclear microsatellite DNA loci）的遗传变异，在分布于本格拉海域的广布性暖温性鱼类平直叉尾石首鱼（Atractoscion aequidens）中，鉴定出两个高度分化的种群。两个种群的地理分布分别位于常年上升流区两侧，表明该系统的海洋学特征与该物种种内基因流的阻断存在显著相关性。遗传分化分析显示，线粒体DNAφST=0.902、微卫星FST=0.055，两种标记的遗传同质性检验概率均为p<0.001；种群间每世代迁移率不足1%，几乎无基因交流；结合溯祖理论估算的最近共同祖先时间，结果表明该系统主要海洋学特征的形成（200万年前），尤其是常年上升流区的强化与位置变迁，是导致观测到的种群隔离的最可能机制。线粒体与核遗传标记的结果一致性表明，平直叉尾石首鱼（A. aequidens）本格拉南北种群的隔离与分化始于远古，并持续至今。本研究结果证实，本格拉洋流系统或可成为暖温性鱼类种内基因流的古老且难以逾越的屏障。