The preservation of ancient DNA in archaeological fish bone
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 character...
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Online Access: | http://hdl.handle.net/10852/86413 http://urn.nb.no/URN:NBN:no-89049 https://doi.org/10.1016/j.jas.2020.105317 |
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ftoslouniv:oai:www.duo.uio.no:10852/86413 2023-05-15T15:27:42+02:00 The preservation of ancient DNA in archaeological fish bone Ferrari, Giada Cuevas, Angelica Gondek, Agata Ballantyne, Rachel Kersten, Oliver Palsdottir, Albina Hulda van der Jagt, Inge Hufthammer, Anne Karin Ystgaard, Ingrid Wickler, Stephen Bigelow, Gerald F Harland, Jennifer Nicholson, Rebecca Orton, David Clavel, Benoît Boessenkool, Sanne Barrett, James H Star, Bastiaan 2021-01-16T00:08:39Z http://hdl.handle.net/10852/86413 http://urn.nb.no/URN:NBN:no-89049 https://doi.org/10.1016/j.jas.2020.105317 EN eng NFR/262777 NOTUR/NORSTORE/NS9244K NOTUR/NORSTORE/NS9003K http://urn.nb.no/URN:NBN:no-89049 Ferrari, Giada Cuevas, Angelica Gondek, Agata Ballantyne, Rachel Kersten, Oliver Palsdottir, Albina Hulda van der Jagt, Inge Hufthammer, Anne Karin Ystgaard, Ingrid Wickler, Stephen Bigelow, Gerald F Harland, Jennifer Nicholson, Rebecca Orton, David Clavel, Benoît Boessenkool, Sanne Barrett, James H Star, Bastiaan . The preservation of ancient DNA in archaeological fish bone. Journal of Archaeological Science. 2021, 126(105317) http://hdl.handle.net/10852/86413 1872450 info:ofi/fmt:kev:mtx:ctx&ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Journal of Archaeological Science&rft.volume=126&rft.spage=&rft.date=2021 Journal of Archaeological Science 126 https://doi.org/10.1016/j.jas.2020.105317 URN:NBN:no-89049 Fulltext https://www.duo.uio.no/bitstream/handle/10852/86413/1/article95207.pdf Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/ CC-BY 0305-4403 Journal article Tidsskriftartikkel Peer reviewed PublishedVersion 2021 ftoslouniv https://doi.org/10.1016/j.jas.2020.105317 2021-06-23T22:30:56Z 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. Article in Journal/Newspaper atlantic cod Gadus morhua Universitet i Oslo: Digitale utgivelser ved UiO (DUO) Journal of Archaeological Science 126 105317 |
institution |
Open Polar |
collection |
Universitet i Oslo: Digitale utgivelser ved UiO (DUO) |
op_collection_id |
ftoslouniv |
language |
English |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Ferrari, Giada Cuevas, Angelica Gondek, Agata Ballantyne, Rachel Kersten, Oliver Palsdottir, Albina Hulda van der Jagt, Inge Hufthammer, Anne Karin Ystgaard, Ingrid Wickler, Stephen Bigelow, Gerald F Harland, Jennifer Nicholson, Rebecca Orton, David Clavel, Benoît Boessenkool, Sanne Barrett, James H Star, Bastiaan |
spellingShingle |
Ferrari, Giada Cuevas, Angelica Gondek, Agata Ballantyne, Rachel Kersten, Oliver Palsdottir, Albina Hulda van der Jagt, Inge Hufthammer, Anne Karin Ystgaard, Ingrid Wickler, Stephen Bigelow, Gerald F Harland, Jennifer Nicholson, Rebecca Orton, David Clavel, Benoît Boessenkool, Sanne Barrett, James H Star, Bastiaan The preservation of ancient DNA in archaeological fish bone |
author_facet |
Ferrari, Giada Cuevas, Angelica Gondek, Agata Ballantyne, Rachel Kersten, Oliver Palsdottir, Albina Hulda van der Jagt, Inge Hufthammer, Anne Karin Ystgaard, Ingrid Wickler, Stephen Bigelow, Gerald F Harland, Jennifer Nicholson, Rebecca Orton, David Clavel, Benoît Boessenkool, Sanne Barrett, James H Star, Bastiaan |
author_sort |
Ferrari, Giada |
title |
The preservation of ancient DNA in archaeological fish bone |
title_short |
The preservation of ancient DNA in archaeological fish bone |
title_full |
The preservation of ancient DNA in archaeological fish bone |
title_fullStr |
The preservation of ancient DNA in archaeological fish bone |
title_full_unstemmed |
The preservation of ancient DNA in archaeological fish bone |
title_sort |
preservation of ancient dna in archaeological fish bone |
publishDate |
2021 |
url |
http://hdl.handle.net/10852/86413 http://urn.nb.no/URN:NBN:no-89049 https://doi.org/10.1016/j.jas.2020.105317 |
genre |
atlantic cod Gadus morhua |
genre_facet |
atlantic cod Gadus morhua |
op_source |
0305-4403 |
op_relation |
NFR/262777 NOTUR/NORSTORE/NS9244K NOTUR/NORSTORE/NS9003K http://urn.nb.no/URN:NBN:no-89049 Ferrari, Giada Cuevas, Angelica Gondek, Agata Ballantyne, Rachel Kersten, Oliver Palsdottir, Albina Hulda van der Jagt, Inge Hufthammer, Anne Karin Ystgaard, Ingrid Wickler, Stephen Bigelow, Gerald F Harland, Jennifer Nicholson, Rebecca Orton, David Clavel, Benoît Boessenkool, Sanne Barrett, James H Star, Bastiaan . The preservation of ancient DNA in archaeological fish bone. Journal of Archaeological Science. 2021, 126(105317) http://hdl.handle.net/10852/86413 1872450 info:ofi/fmt:kev:mtx:ctx&ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Journal of Archaeological Science&rft.volume=126&rft.spage=&rft.date=2021 Journal of Archaeological Science 126 https://doi.org/10.1016/j.jas.2020.105317 URN:NBN:no-89049 Fulltext https://www.duo.uio.no/bitstream/handle/10852/86413/1/article95207.pdf |
op_rights |
Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/ |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1016/j.jas.2020.105317 |
container_title |
Journal of Archaeological Science |
container_volume |
126 |
container_start_page |
105317 |
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