The preservation of ancient DNA in archaeological fish bone

Abstract

The field of ancient DNA is taxonomically dominated by studies focusing on mammals. This taxonomic bias limits our understanding of endogenous DNA preservation for vertebrate taxa with different bone physiology, such as teleost fish. In contrast to most mammalian bone, teleost bone is typically brittle, porous, lightweight and is characterized by a lack of bone remodeling during growth. 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 that contain 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 library success, 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 find that -- in contrast to mammalian bones -- different fish bone elements yield similar levels of endogenous DNA. Our results highlight the overall suitability of archaeological fish bone as a source for ancient DNA and provide novel evidence for a possible role of bone remodeling in the preservation of endogenous DNA across different classes of vertebrates.