Whole-genome sequences from archaeological herring remains. 1300 years of Atlantic herring population structure and demography revealed through ancient DNA and mixed-stock analysis

Atlantic herring populations have been the target of highly profitable coastal and pelagic fisheries in northern Europe for well over a thousand years. Their complex and intermingled population dynamics have sparked extensive debate over the impacts of historical overfishing and have complicated their sustainable management today. Recently developed tools – including diagnostic SNP panels for mixed-stock analysis – aim to improve population assignment for fisheries management, however, the biological relevance of such tools over long periods of time remains unknown. Here, we demonstrate the millennium-long applicability of diagnostic SNP panels and identify population perturbations associated with increasing exploitation pressure and climate change by analyzing whole genome data from modern and ancient herring specimens. We find that herring demographic cycles were likely within healthy ecosystem boundaries until the dramatic disruption of these cycles in the 20th century. We find only autumn-spawning herring in our archaeological remains spanning 900 years from 8 sites across Europe, supporting observations that the numerical dominance of specific spawning populations can demographically outcompete other herring types. We also obtain pre-archival aDNA evidence for the famous, cyclical “Bohuslän periods,” during which mass quantities of North Sea autumn-spawning herring congregated in the Skagerrak. Finally, the long-term applicability of diagnostic SNP panels underscores their highly cost-effective application for the genetic monitoring of herring stocks. Our results highlight the utility of ancient DNA and genomic analysis to obtain historical and natural insights in herring ecology and population dynamics with relevance for sustainable fisheries management.

大西洋鲱（Atlantic herring）种群作为北欧地区获利颇丰的沿岸与中上层渔业的捕捞目标已有逾千年历史。其复杂且相互交织的种群动态，长期引发学界围绕历史过度捕捞影响的广泛争论，也为当前的可持续渔业管理带来了诸多难题。
近期开发的一系列工具——包括用于混合种群分析（mixed-stock analysis）的诊断性SNP分型面板（SNP panels）——旨在提升渔业管理中的种群归属鉴定精度，但这类工具在长期时间尺度上的生物学相关性仍未明确。
本研究通过分析现代与古代鲱鱼标本的全基因组数据，证实了诊断性SNP分型面板的千年适用性，并揭示了与捕捞压力加剧及气候变化相关的种群扰动现象。
研究发现，在20世纪鲱鱼种群周期被剧烈打断之前，其种群动态周期始终处于健康的生态系统边界范围内。我们对横跨欧洲8处遗址、跨越900年的考古遗存展开分析，仅检出秋季产卵鲱鱼，这一结果佐证了“特定产卵种群的数量优势可在种群动态层面压制其他鲱鱼类群”的观测结论。
本研究还获取了著名的周期性“博胡斯兰周期（Bohuslän periods）”的档案记录前古代DNA（aDNA）证据：该时期大量北海秋季产卵鲱鱼会聚集于斯卡格拉克海峡（Skagerrak）。
最后，诊断性SNP分型面板的长期适用性凸显了其在鲱鱼资源群遗传监测中的高成本效益。本研究结果彰显了古代DNA与基因组分析在获取鲱鱼生态学与种群动态的历史与自然视角方面的应用价值，其结论可为渔业可持续管理提供重要参考。