Genomic methodologies offer unprecedented opportunities for statistically robust studies of species broadly distributed in environments conducive to high gene flow, providing valuable information for wildlife conservation and management. Here, we sequence restriction site‐associated DNA to characterize genome‐wide single nucleotide polymorphisms (SNPs) in a broadly distributed and highly migratory large pelagic fish, striped marlin (Kajikia audax). Assessment of over 4,000 SNPs resolved spatiotemporal patterns of genetic connectivity throughout the species range in the Pacific and, for the first time, Indian oceans. Individual‐based cluster analyses identified six genetically distinct populations corresponding with the western Indian, eastern Indian, western South Pacific, and eastern central Pacific oceans, as well as two populations in the North Pacific Ocean (F_ST = 0.0137–0.0819). F_ST outlier analyses identified a subset of SNPs (n = 59) putatively under the influence of natural selection and capable of resolving populations separated by comparatively high degrees of genetic differentiation. Temporal collections available for some regions demonstrated the stability of allele frequencies over three to five generations of striped marlin. Relative migration rates reflected lower levels of genetic connectivity between Indian Ocean populations (m_R ≤ 0.37) compared with most populations in the Pacific Ocean (m_R ≥ 0.57) and highlight the importance of the western South Pacific in facilitating gene flow between ocean basins. Collectively, our results provide novel insights into rangewide population structure for striped marlin and highlight substantial inconsistencies between genetically distinct populations and stocks currently recognized for fisheries management. More broadly, we demonstrate that species capable of long‐distance dispersal in environments lacking obvious physical barriers to movement can display substantial population subdivision that persists over multiple generations and that may be facilitated by both neutral and adaptive processes. Importantly, surveys of genome‐wide markers enable inference of population‐level relationships using sample sizes practical for large pelagic fishes of conservation concern.

中文翻译：

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全基因组 SNP 解析了条纹马林鱼 (Kajikia audax) 内的时空连接模式，条纹马林鱼是一种分布广泛且高度洄游的中上层物种

基因组方法为对广泛分布在有利于高基因流动的环境中的物种进行统计上稳健的研究提供了前所未有的机会，为野生动物保护和管理提供了宝贵的信息。在这里，我们对限制性位点相关的 DNA 进行测序，以表征广泛分布且高度洄游的大型中上层鱼类条纹马林鱼 ( Kajikia audax ) 的全基因组单核苷酸多态性 (SNP) 。对 4,000 多个 SNP 的评估解决了太平洋和印度洋整个物种范围内遗传连通性的时空模式。基于个体的聚类分析确定了与印度西部、印度东部、南太平洋西部和太平洋中东部相对应的六个遗传上不同的种群，以及北太平洋的两个种群（F ST = 0.0137-0.0819 _）  。F _ST离群值分析确定了 SNP 的子集 ( n  = 59)，这些 SNP 可能受到自然选择的影响，并且能够解决由相对较高程度的遗传分化分开的群体。某些地区的时间收集证明了三到五代条纹马林鱼等位基因频率的稳定性。相对迁移率反映了与太平洋大多数种群（ m _R  ≥ 0.57）相比，印度洋种群之间的遗传连通性水平较低（ m _R  ≤ 0.37），并凸显了南太平洋西部在促进大洋盆地之间基因流动的重要性。总的来说，我们的研究结果为条纹马林鱼的种群结构提供了新颖的见解，并强调了遗传上不同的种群与目前公认的渔业管理种群之间的实质性不一致。更广泛地说，我们证明，能够在缺乏明显的物理运动障碍的环境中进行长距离扩散的物种可以表现出大量的种群细分，这种细分会持续多代，并且可能通过中性和适应性过程来促进。重要的是，对全基因组标记的调查可以使用对保护关注的大型中上层鱼类实用的样本量来推断种群水平关系。