The preservation of ancient DNA in archaeological fish bone

Abstract

40The field of ancient DNA is taxonomically dominated by studies focusing on mammals. This 41 taxonomic bias limits our understanding of endogenous DNA preservation for vertebrate taxa 42 with different bone physiology, such as teleost fish. In contrast to most mammalian bone, teleost 43 bone is typically brittle, porous, lightweight and is characterized by a lack of bone remodeling 44 during growth. Using high-throughput shotgun sequencing, we here investigate the preservation 45 of DNA in a range of different bone elements from over 200 archaeological Atlantic cod (Gadus 46 morhua) specimens from 38 sites in northern Europe, dating up to 8000 years before present. We 47 observe that the majority of archaeological sites (79%) yield endogenous DNA, with 40% of sites 48 providing samples that contain high levels (> 20%). Library preparation success and levels of 49 endogenous DNA depend mainly on excavation site and pre-extraction laboratory treatment. The 50 use of pre-extraction treatments lowers the rate of library success, although -if successful -the 51 fraction of endogenous DNA can be improved by several orders of magnitude. This trade-off 52 between library preparation success and levels of endogenous DNA allows for alternative 53 extraction strategies depending on the requirements of down-stream analyses and research 54 questions. Finally, we find that -in contrast to mammalian bones -different fish bone elements 55 yield similar levels of endogenous DNA. Our results highlight the overall suitability of 56 archaeological fish bone as a source for ancient DNA and provide novel evidence for a possible 57 role of bone remodeling in the preservation of endogenous DNA across different classes of 58 vertebrates. 59 60 Dabney et al., 2013), with the inclusion of a pre-digestion step (DD, Damgaard et al., 2015), or with 129

Ancient DNA evidence for the ecological globalisation of cod fishing in medieval and post-medieval Europe

“…We processed 18 English (London) fish bone samples in the aDNA laboratory at the University of Oslo [36,37] (Table S1). Treatment of samples prior to DNA extraction was according to Ferrari, et al [38] and Martínez-García, et al [39]. In short, fish bones were UV-treated for 10 minutes per side and milled using a stainless-steel mortar [40].…”

An accurate assignment test for extremely low-coverage whole-genome sequence data

“…Modern herring reads were aligned to the Atlantic herring reference genome (GCA_900700415.1) (Pettersson et al, 2019) as above. Ancient herring reads were aligned as described in Ferrari et al (2021), using BWA-backtrack. Genotypes for the reference database were called and filtered as described above.…”

“…Despite advances in methodologies that allow for the recovery of higher yields of endogenous ancient DNA (aDNA) (e.g., Boessenkool et al, 2017;Carpenter et al, 2013;Gamba et al, 2014;Pinhasi et al, 2015), DNA preservation in sub-fossil, archaeological, historical, or degraded biological material remains variable and is often context specific (Ferrari et al, 2021;Keighley et al, 2021;Tin et al, 2014). In order to account for such unpredictability, aDNA sequencing projects typically screen many specimens from which a subset with the best DNA preservation is selected for deeper sequencing (e.g.…”

Pleistocene stickleback genomes reveal the constraints on parallel evolution

“…To the best of our knowledge, these are the oldest fish bones from which genomic data have been obtained (18,19).…”