Data from: Spatio-temporal genetic structure and the effects of long-term fishing in two partially sympatric offshore demersal fishes

Environmental gradients have been shown to disrupt gene flow in marine species, yet their influence in structuring populations at depth remains poorly understood. The Cape hakes (Merluccius paradoxus and M. capensis) are demersal species co-occurring in the Benguela Current system, where decades of intense fishing resulted in severely depleted stocks in the past. Previous studies identified conflicting mtDNA genetic sub-structuring patterns, and thus contrasting evolutionary trajectories for both species. Using ten microsatellite loci, the control region of mtDNA, and employing a seascape genetics approach, we investigated genetic connectivity and the impact of prolonged exploitation in the two species, which are characterized by different patterns of fishing pressure. Three consecutive years were sampled covering the entire distribution (N = 2100 fishes). Despite large estimated population sizes, both species exhibited low levels of contemporary genetic diversity (0.581 < HE < 0.692), implying that fishing has had a significant impact on their genetic composition and evolutionary trajectories. Further, for M. paradoxus, significant temporal, but not spatial, divergence points to the presence of genetic chaotic patchiness. In contrast, M. capensis exhibited a clear latitudinal cline in genetic differentiation between Namibia and South Africa (FST = 0.063, P < 0.05), with low (0.2% per generation) estimates of contemporary gene flow. Seascape analyses reveal an association with bathymetry and upwelling events, suggesting that adaptation to local environmental conditions may drive genetic differentiation in M. capensis. Importantly, our results highlight the need for temporal sampling in disentangling the complex factors that impact population divergence in marine fishes.

环境梯度已被证实会干扰海洋物种的基因流，但其对深水种群结构的影响仍有待深入阐明。开普鳕（Cape hakes，学名Merluccius paradoxus与M. capensis）是栖息于本格拉洋流系统（Benguela Current system）的底栖（demersal）物种，该海域历经数十年高强度捕捞后，其种群资源曾一度严重枯竭。既往研究针对这两个物种得到了相互矛盾的线粒体DNA（mtDNA）遗传亚结构模式，进而得出了截然不同的演化轨迹推论。本研究采用10个微卫星（microsatellite）位点、线粒体DNA控制区序列，并结合海景遗传学（seascape genetics）研究方法，对这两种受捕捞压力模式各异的物种开展了遗传连通性及长期捕捞影响的探究。研究连续三年采样，覆盖了两个物种的完整分布范围，总计获取2100尾实验个体。尽管估算的种群规模庞大，但两个物种的当代遗传多样性水平均较低（0.581 < HE < 0.692），这表明捕捞活动已对其遗传组成与演化轨迹造成了显著影响。进一步分析显示，歧异银无须鳕（Merluccius paradoxus）存在显著的时间分化，但未检测到空间分化，提示其存在遗传混沌斑块现象。相较而言，南非无须鳕（Merluccius capensis）在纳米比亚与南非海域间呈现出清晰的遗传分化纬度梯度（FST = 0.063, P < 0.05），当代基因流估算值较低（每世代0.2%）。海景遗传学分析揭示，其遗传分化与水深地形（bathymetry）及上升流事件存在显著关联，表明对局部环境条件的适应可能推动了南非无须鳕的遗传分化。尤为重要的是，本研究结果凸显了开展时序采样的必要性，以厘清影响海洋鱼类种群分化的各类复杂因素。