The field of ancient DNA is dominated by studies focusing on terrestrial vertebrates. This taxonomic bias limits our understanding of endogenous DNA preservation for species with different bone physiology, such as teleost fish. Teleost bone is typically brittle, porous, lightweight, and is characterized by a lack of bone remodeling during growth. All of these factors potentially affect DNA preservation. Using high-throughput shotgun sequencing, we here investigate the preservation of DNA in a range of different bone elements from over 200 archaeological Atlantic cod (Gadus morhua) specimens from 38 sites in northern Europe, dating up to 8000 years before present. We observe that the majority of archaeological sites (79%) yield endogenous DNA, with 40% of sites providing samples containing high levels (>20%). Library preparation success and levels of endogenous DNA depend mainly on excavation site and pre-extraction laboratory treatment. The use of pre-extraction treatments lowers the rate of libraries that can be sequenced, although — if successful — the fraction of endogenous DNA can be improved by several orders of magnitude. This trade-off between library preparation success and levels of endogenous DNA allows for alternative extraction strategies depending on the requirements of down-stream analyses and research questions. Finally, we do not find particular bone elements to yield higher levels of endogenous DNA, as is the case for denser bones in mammals. Our results highlight the potential of archaeological fish bone as a source for ancient DNA and suggest a possible role of bone remodeling in the preservation of endogenous DNA.

古代DNA领域主要由针对陆地脊椎动物的研究主导。这种分类学偏见限制了我们对具有不同骨骼生理学的物种（例如硬骨鱼）对内源性DNA保存的理解。硬骨骨通常是脆的，多孔的，轻质的，其特征在于在生长过程中缺乏骨重塑。所有这些因素都可能影响DNA的保存。使用高通量shot弹枪测序，我们在这里研究了200多种大西洋大西洋鳕鱼（Gadus morhua）来自北欧38个地点的标本，距今已有8000年的历史。我们观察到，大多数考古遗址（79％）产生内源性DNA，其中40％的遗址提供的样品中含量高（> 20％）。文库制备成功与否和内源性DNA水平主要取决于挖掘位点和提取前的实验室处理。提取前处理的使用降低了可测序文库的速率，尽管（如果成功的话）内源性DNA的比例可以提高几个数量级。在文库制备成功与内源性DNA水平之间进行权衡，可以根据下游分析和研究问题的要求选择其他提取策略。最后，我们没有发现能够产生更高水平内源性DNA的特定骨骼元素，哺乳动物的骨头比较密。我们的结果突出了考古鱼骨作为古代DNA来源的潜力，并暗示了骨骼重塑在保存内源性DNA中的可能作用。