New publication: The preservation of ancient DNA in archaeological fish bone

By Giada Ferrari, Angélica Cuevas, Agata T. Gondek-Wyrozemska, Rachel Ballantyne, Oliver Kersten1, Albína H. Pálsdóttir, Inge van der Jagt, Anne Karin Hufthammer, Ingrid Ystgaard, Stephen Wickler, Gerald F. Bigelow, Jennifer Harland, Rebecca Nicholson, David Orton, Benoît Clavel, Sanne Boessenkool, James H. Barrett, and Bastiaan Star in Journal of Archaeological Science. Open Access.

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.


Journal of Archaeological Science
Volume 126, February 2021, 105317
Available online 9 January 2021.
Publication webpage.


Giada Ferrari1, Angélica Cuevas1, Agata T. Gondek-Wyrozemska1, Rachel Ballantyne, Oliver Kersten1, Albína H. Pálsdóttir1, Inge van der Jagt, Anne Karin Hufthammer, Ingrid Ystgaard, Stephen Wickler, Gerald F. Bigelow, Jennifer Harland, Rebecca Nicholson, David Orton, Benoît Clavel, Sanne Boessenkool1, James H. Barrett, and Bastiaan Star1

1 Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Blindernveien 31, NO-0371, Oslo, Norway

See the publication webpage for full author information.

Tags: Journal of Archaeological Science;
Published Feb. 10, 2021 11:04 AM - Last modified Mar. 5, 2021 9:25 AM