Delimiting intraspecific genetic variation in harvested species is crucial to the assessment of population status for natural resource management and conservation purposes. Here, we evaluated genetic population structure in lingcod (Ophiodon elongatus), a commercially and recreationally important fishery species along the west coast of North America. We used 16,749 restriction site‐associated DNA sequencing (RADseq) markers, in 611 individuals collected from across the bulk of the species range from Southeast Alaska to Baja California, Mexico. In contrast to previous population genetic work on this species, we found strong evidence for two distinct genetic clusters. These groups separated latitudinally with a break near Point Reyes off Northern California, and there was a high frequency of admixed individuals in close proximity to the break. F‐statistics corroborate this genetic break between northern and southern sampling sites, although most loci are characterized by low F_ST values, suggesting high gene flow throughout most of the genome. Outlier analyses identified 182 loci putatively under divergent selection, most of which mapped to a single genomic region. When individuals were grouped by cluster assignment (northern, southern, and admixed), 71 loci were fixed between the northern and southern cluster, all of which were identified in the outlier scans. All individuals identified as admixed exhibited near 50:50 assignment to northern and southern clusters and were heterozygous for most fixed loci. Alignments of RADseq loci to a draft lingcod genome assembly and three other teleost genomes with chromosome‐level assemblies suggest that outlier and fixed loci are concentrated on a single chromosome. Similar genomic patterns have been attributed to chromosomal inversions in diverse taxonomic groups. Regardless of the evolutionary mechanism, these results represent novel observations of genetic structure in lingcod and designate clear evolutionary units that could be used to inform fisheries management.

中文翻译：

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lingcod（Ophiodon elongatus）的强烈种群分化是由基因组的一小部分驱动的

界定收获物种的种内遗传变异对于评估自然资源管理和保护目的的种群状况至关重要。在这里，我们评估了灵鳕鱼（ Ophiodon elongatus ）的遗传种群结构，灵鳕鱼是北美西海岸的一种重要的商业和娱乐渔业物种。我们在从阿拉斯加东南部到墨西哥下加利福尼亚州大部分物种范围内收集的 611 个个体中使用了 16,749 个限制性位点相关 DNA 测序 (RADseq) 标记。与之前对该物种的群体遗传工作相比，我们发现了两个不同遗传簇的有力证据。这些群体在纬度上分开，在北加州雷耶斯角附近有一个中断处，并且在中断处附近有很高的混合个体。F统计证实了北部和南部采样点之间的这种遗传断裂，尽管大多数位点的特征是较低的F _ST值，表明大部分基因组中的基因流较高。离群值分析假定在发散选择下确定了 182 个基因座，其中大部分映射到单个基因组区域。当个体按聚类分配（北部、南部和混合）进行分组时，北部和南部聚类之间固定了 71 个基因座，所有这些基因座都在异常值扫描中被识别。所有被鉴定为混合的个体都表现出接近 50:50 的分配到北部和南部簇，并且大多数固定基因座都是杂合的。RADseq 位点与 lingcod 基因组组装草案和其他三个硬骨鱼基因组与染色体级组装的比对表明，离群值和固定位点集中在单个染色体上。相似的基因组模式被归因于不同分类群中的染色体倒位。无论进化机制如何，这些结果代表了对灵鳕鱼遗传结构的新观察，并指定了可用于为渔业管理提供信息的明确进化单位。