Data from: Responses of population structure and genomic diversity to climate change and fishing pressure in a pelagic fish

The responses of marine species to environmental changes and anthropogenic pressures (e.g. fishing) interact with ecological and evolutionary processes that are not well understood. Knowledge of changes in the distribution range and genetic diversity of species and their populations into the future is essential for the conservation and sustainable management of resources. Almaco jack (Seriola rivoliana) is a pelagic fish with high importance to fisheries and aquaculture in the Pacific Ocean. In this study, we assessed contemporary genomic diversity and structure in loci that are putatively under selection (outlier loci) and determined their potential functions. Utilizing a combination of genotype-environment association, spatial distribution models, and demogenetic simulations, we modeled the effects of climate change (under three different RCP scenarios) and fishing pressure on the species' geographic distribution and genomic diversity and structure to 2050 and 2100. Our results show that most of the outlier loci identified were related to biological and metabolic processes that may be associated with temperature and salinity. Contemporary genomic structure showed three populations—two in the Eastern Pacific (Cabo San Lucas and Eastern Pacific) and one in the Central Pacific (Hawaii). Future projections suggest a loss of suitable habitat and potential range contractions for most scenarios, while fishing pressure decreased population connectivity. Our results suggest that future climate change scenarios and fishing pressure will affect the genomic structure and genotypic composition of S. rivoliana and lead to loss of genomic diversity in populations distributed in the eastern-central Pacific Ocean, which could have profound effects in fisheries that depend on this resource.

海洋物种对环境变化及人为压力（例如捕捞活动）的响应，与当前尚未被充分阐明的生态及演化过程相互作用。掌握物种及其种群的分布范围与遗传多样性的未来变化情况，对资源保护与可持续管理而言至关重要。高体鰤（Almaco jack，Seriola rivoliana）是一种远洋鱼类，在太平洋的渔业与水产养殖业中具有重要经济价值。本研究评估了疑似受选择的位点（异常位点，outlier loci）的当代基因组多样性与种群结构，并确定了这些位点的潜在功能。研究结合基因型-环境关联分析（genotype-environment association）、空间分布模型与种群遗传模拟，针对三种不同典型浓度路径（RCP）情景下的气候变化与捕捞压力，模拟了该物种至2050年与2100年的地理分布、基因组多样性与种群结构变化。研究结果显示，绝大多数已识别的异常位点均与可能关联温度与盐度的生物学及代谢过程相关。当代种群基因组结构显示该物种存在三个种群——东太平洋的两个种群（卡波圣卢卡斯种群与东太平洋种群）以及中太平洋的一个种群（夏威夷种群）。未来预测结果显示，在多数情景下，适宜栖息地将出现流失，种群分布范围可能收缩，而捕捞压力会降低种群间的连通性。本研究结果表明，未来气候变化情景与捕捞压力将影响高体鰤的基因组结构与基因型组成，并导致东-中太平洋海域种群的基因组多样性丧失，这可能对依赖该资源的渔业产生深远影响。