The preservation of ancient DNA in archaeological fish bone

Giada Ferrari; Angélica Cuevas; Agata T. Gondek-Wyrozemska; Rachel Ballantyne; Oliver Kersten; 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; Bastiaan Star

doi:10.1016/j.jas.2020.105317

The preservation of ancient DNA in archaeological fish bone

Giada Ferrari^*, Angélica Cuevas, Agata T. Gondek-Wyrozemska, Rachel Ballantyne, Oliver Kersten, 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, Bastiaan Star

^*Corresponding author for this work

Archaeology

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	105317
Journal	Journal of archaeological science
Volume	126
Early online date	9 Jan 2021
DOIs	https://doi.org/10.1016/j.jas.2020.105317
Publication status	E-pub ahead of print - 9 Jan 2021

Bibliographical note

© 2021 The Authors. Published by Elsevier Ltd.

Funding Information:
We thank C. Amundsen for providing the Kongshavn and Skonsvika bone samples, M. Skage, S. Kollias and A. Tooming-Klunderud at the Norwegian Sequencing Centre for sequencing and processing of samples, and K. Dean for comments on the statistical analyses. This work was supported by Research Council of Norway Project “Catching the Past: Discovering the legacy of Atlantic cod exploitation using ancient DNA” (262777) and Leverhulme Trust Project “Northern Journeys: Reimagining the Medieval Revolution and its Aftermath” ( MRF-2013-065 ). Analyses were performed on the Abel Cluster at the University of Oslo and the Norwegian metacentre for High Performance Computing (NOTUR), operated by the Department for Research Computing at the University of Oslo IT-department (USIT).

Publisher Copyright:
© 2021 The Authors

Copyright:
Copyright 2021 Elsevier B.V., All rights reserved.

Keywords

Bleach
Bone element
Bone remodeling
Endogenous DNA
Petrous bone

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© 2021 The Authors. Published by Elsevier Ltd.
Final published version, 4.01 MBLicence: CC BY

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Ferrari, G., Cuevas, A., Gondek-Wyrozemska, A. T., Ballantyne, R., Kersten, O., Pálsdóttir, A. H., van der Jagt, I., Hufthammer, A. K., Ystgaard, I., Wickler, S., Bigelow, G. F., Harland, J., Nicholson, R., Orton, D., Clavel, B., Boessenkool, S., Barrett, J. H., & Star, B. (2021). The preservation of ancient DNA in archaeological fish bone. Journal of archaeological science, 126, Article 105317. Advance online publication. https://doi.org/10.1016/j.jas.2020.105317

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title = "The preservation of ancient DNA in archaeological fish bone",

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.",

keywords = "Bleach, Bone element, Bone remodeling, Endogenous DNA, Petrous bone",

author = "Giada Ferrari and Ang{\'e}lica Cuevas and Gondek-Wyrozemska, {Agata T.} and Rachel Ballantyne and Oliver Kersten and P{\'a}lsd{\'o}ttir, {Alb{\'i}na H.} and {van der Jagt}, Inge and Hufthammer, {Anne Karin} and Ingrid Ystgaard and Stephen Wickler and Bigelow, {Gerald F.} and Jennifer Harland and Rebecca Nicholson and David Orton and Beno{\^i}t Clavel and Sanne Boessenkool and Barrett, {James H.} and Bastiaan Star",

note = "{\textcopyright} 2021 The Authors. Published by Elsevier Ltd. Funding Information: We thank C. Amundsen for providing the Kongshavn and Skonsvika bone samples, M. Skage, S. Kollias and A. Tooming-Klunderud at the Norwegian Sequencing Centre for sequencing and processing of samples, and K. Dean for comments on the statistical analyses. This work was supported by Research Council of Norway Project “Catching the Past: Discovering the legacy of Atlantic cod exploitation using ancient DNA” (262777) and Leverhulme Trust Project “Northern Journeys: Reimagining the Medieval Revolution and its Aftermath” ( MRF-2013-065 ). Analyses were performed on the Abel Cluster at the University of Oslo and the Norwegian metacentre for High Performance Computing (NOTUR), operated by the Department for Research Computing at the University of Oslo IT-department (USIT). Publisher Copyright: {\textcopyright} 2021 The Authors Copyright: Copyright 2021 Elsevier B.V., All rights reserved.",

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doi = "10.1016/j.jas.2020.105317",

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Ferrari, G, Cuevas, A, Gondek-Wyrozemska, AT, Ballantyne, R, Kersten, O, Pálsdóttir, AH, van der Jagt, I, Hufthammer, AK, Ystgaard, I, Wickler, S, Bigelow, GF, Harland, J, Nicholson, R, Orton, D, Clavel, B, Boessenkool, S, Barrett, JH & Star, B 2021, 'The preservation of ancient DNA in archaeological fish bone', Journal of archaeological science, vol. 126, 105317. https://doi.org/10.1016/j.jas.2020.105317

TY - JOUR

T1 - The preservation of ancient DNA in archaeological fish bone

AU - Ferrari, Giada

AU - Cuevas, Angélica

AU - Gondek-Wyrozemska, Agata T.

AU - Ballantyne, Rachel

AU - Kersten, Oliver

AU - Pálsdóttir, Albína H.

AU - van der Jagt, Inge

AU - Hufthammer, Anne Karin

AU - Ystgaard, Ingrid

AU - Wickler, Stephen

AU - Bigelow, Gerald F.

AU - Harland, Jennifer

AU - Nicholson, Rebecca

AU - Orton, David

AU - Clavel, Benoît

AU - Boessenkool, Sanne

AU - Barrett, James H.

AU - Star, Bastiaan

N1 - © 2021 The Authors. Published by Elsevier Ltd. Funding Information: We thank C. Amundsen for providing the Kongshavn and Skonsvika bone samples, M. Skage, S. Kollias and A. Tooming-Klunderud at the Norwegian Sequencing Centre for sequencing and processing of samples, and K. Dean for comments on the statistical analyses. This work was supported by Research Council of Norway Project “Catching the Past: Discovering the legacy of Atlantic cod exploitation using ancient DNA” (262777) and Leverhulme Trust Project “Northern Journeys: Reimagining the Medieval Revolution and its Aftermath” ( MRF-2013-065 ). Analyses were performed on the Abel Cluster at the University of Oslo and the Norwegian metacentre for High Performance Computing (NOTUR), operated by the Department for Research Computing at the University of Oslo IT-department (USIT). Publisher Copyright: © 2021 The Authors Copyright: Copyright 2021 Elsevier B.V., All rights reserved.

PY - 2021/1/9

Y1 - 2021/1/9

N2 - 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.

AB - 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.

KW - Bleach

KW - Bone element

KW - Bone remodeling

KW - Endogenous DNA

KW - Petrous bone

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U2 - 10.1016/j.jas.2020.105317

DO - 10.1016/j.jas.2020.105317

M3 - Article

AN - SCOPUS:85099246172

SN - 0305-4403

VL - 126

JO - Journal of archaeological science

JF - Journal of archaeological science

M1 - 105317

ER -

The preservation of ancient DNA in archaeological fish bone

Abstract

Bibliographical note

Keywords

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