Abstract
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.
Highlights
Driven by revolutionary advances in laboratory methods, sequencing technologies and computational analyses, an increasing number of terrestrial vertebrate species have been investigated using ancient DNA
We present the largest study on DNA preservation in ancient fish bones to date, assessing the effects of bone element, archaeological site, DNA extraction and sequencing library preparation protocols on library success and levels of endogenous DNA
Our findings imply that most fish bone elements may be suitable for high-throughput shotgun ancient DNA (aDNA) analyses and further archaeological inference
Summary
Driven by revolutionary advances in laboratory methods, sequencing technologies and computational analyses, an increasing number of terrestrial vertebrate species have been investigated using ancient DNA (aDNA). Knowing how to select the right elements helps minimize the destruction of unique archaeological materials that represent a finite resource (Palsdottir et al, 2019) Such knowledge may further aid archaeologists in making informed choices when collecting and pre serving zooarchaeological material in the field, maximizing the research potential for a variety of studies. High-throughput sequencing (HTS) approaches have yielded high levels (15–50%) of endogenous DNA from a limited number of sites up to one thousand years old (Boessenkool et al, 2017; Star et al, 2017) These studies range from species identification (e.g., Yang et al, 2004; Ludwig et al, 2009), to more complex reconstructions of past population di versity and demographic events (e.g., Olafsdottir et al, 2014; Johnson et al, 2018). We interpret our results in light of down-stream analytical requirements and provide practical recommendations in order to maximize throughput and archaeological inference of whole genome sequencing (WGS) data from ancient fish bone
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
