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Predicting sample success for large-scale ancient DNA studies on marine mammals

Keighley, Xénia ; Bro-Jørgensen, Maiken Hemme ; Ahlgren, Hans ; Szpak, Paul ; Ciucani, Marta Maria ; Sánchez Barreiro, Fátima ; Howse, Lesley ; Gotfredsen, Anne Birgitte ; Glykou, Aikaterini and Jordan, Peter LU orcid , et al. (2021) In Molecular Ecology Resources 21(4). p.1149-1166
Abstract

In recent years, nonhuman ancient DNA studies have begun to focus on larger sample sizes and whole genomes, offering the potential to reveal exciting and hitherto unknown answers to ongoing biological and archaeological questions. However, one major limitation to such studies is the substantial financial and time investments still required during sample screening, due to uncertainty regarding successful sample selection. This study investigates the effect of a wide range of sample properties including latitude, sample age, skeletal element, collagen preservation, and context on endogenous content and DNA damage profiles for 317 ancient and historic pinniped samples collected from across the North Atlantic and surrounding regions. Using... (More)

In recent years, nonhuman ancient DNA studies have begun to focus on larger sample sizes and whole genomes, offering the potential to reveal exciting and hitherto unknown answers to ongoing biological and archaeological questions. However, one major limitation to such studies is the substantial financial and time investments still required during sample screening, due to uncertainty regarding successful sample selection. This study investigates the effect of a wide range of sample properties including latitude, sample age, skeletal element, collagen preservation, and context on endogenous content and DNA damage profiles for 317 ancient and historic pinniped samples collected from across the North Atlantic and surrounding regions. Using generalised linear and mixed-effect models, we found that a range of factors affected DNA preservation within each of the species under consideration. The most important findings were that endogenous content varied significantly within species according to context, the type of skeletal element, the collagen content and collection year. There also appears to be an effect of the sample's geographic origin, with samples from the Arctic generally showing higher endogenous content and lower damage rates. Both latitude and sample age were found to have significant relationships with damage levels, but only for walrus samples. Sex, ontogenetic age and extraction material preparation were not found to have any significant relationship with DNA preservation. Overall, skeletal element and sample context were found to be the most influential factors and should therefore be considered when selecting samples for large-scale ancient genome studies.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
aDNA, DNA damage, endogenous content, pinnipeds, sample age, seal, walrus, zooarchaeology
in
Molecular Ecology Resources
volume
21
issue
4
pages
1149 - 1166
publisher
Wiley-Blackwell
external identifiers
  • pmid:33463014
  • scopus:85101655206
ISSN
1755-098X
DOI
10.1111/1755-0998.13331
language
English
LU publication?
yes
id
0d60dbaa-b650-46df-80e0-892c0b50020e
date added to LUP
2021-03-16 08:26:44
date last changed
2024-06-13 08:38:42
@article{0d60dbaa-b650-46df-80e0-892c0b50020e,
  abstract     = {{<p>In recent years, nonhuman ancient DNA studies have begun to focus on larger sample sizes and whole genomes, offering the potential to reveal exciting and hitherto unknown answers to ongoing biological and archaeological questions. However, one major limitation to such studies is the substantial financial and time investments still required during sample screening, due to uncertainty regarding successful sample selection. This study investigates the effect of a wide range of sample properties including latitude, sample age, skeletal element, collagen preservation, and context on endogenous content and DNA damage profiles for 317 ancient and historic pinniped samples collected from across the North Atlantic and surrounding regions. Using generalised linear and mixed-effect models, we found that a range of factors affected DNA preservation within each of the species under consideration. The most important findings were that endogenous content varied significantly within species according to context, the type of skeletal element, the collagen content and collection year. There also appears to be an effect of the sample's geographic origin, with samples from the Arctic generally showing higher endogenous content and lower damage rates. Both latitude and sample age were found to have significant relationships with damage levels, but only for walrus samples. Sex, ontogenetic age and extraction material preparation were not found to have any significant relationship with DNA preservation. Overall, skeletal element and sample context were found to be the most influential factors and should therefore be considered when selecting samples for large-scale ancient genome studies.</p>}},
  author       = {{Keighley, Xénia and Bro-Jørgensen, Maiken Hemme and Ahlgren, Hans and Szpak, Paul and Ciucani, Marta Maria and Sánchez Barreiro, Fátima and Howse, Lesley and Gotfredsen, Anne Birgitte and Glykou, Aikaterini and Jordan, Peter and Lidén, Kerstin and Olsen, Morten Tange}},
  issn         = {{1755-098X}},
  keywords     = {{aDNA; DNA damage; endogenous content; pinnipeds; sample age; seal; walrus; zooarchaeology}},
  language     = {{eng}},
  month        = {{02}},
  number       = {{4}},
  pages        = {{1149--1166}},
  publisher    = {{Wiley-Blackwell}},
  series       = {{Molecular Ecology Resources}},
  title        = {{Predicting sample success for large-scale ancient DNA studies on marine mammals}},
  url          = {{http://dx.doi.org/10.1111/1755-0998.13331}},
  doi          = {{10.1111/1755-0998.13331}},
  volume       = {{21}},
  year         = {{2021}},
}