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

Research output: Contribution to journalJournal articlepeer-review

Standard

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; Jordan, Peter; Lidén, Kerstin; Olsen, Morten Tange.

In: Molecular Ecology Resources, Vol. 21, No. 4, 2021, p. 1149-1166.

Research output: Contribution to journalJournal articlepeer-review

Harvard

Keighley, X, Bro-Jørgensen, MH, Ahlgren, H, Szpak, P, Ciucani, MM, Sánchez Barreiro, F, Howse, L, Gotfredsen, AB, Glykou, A, Jordan, P, Lidén, K & Olsen, MT 2021, 'Predicting sample success for large-scale ancient DNA studies on marine mammals', Molecular Ecology Resources, vol. 21, no. 4, pp. 1149-1166. https://doi.org/10.1111/1755-0998.13331

APA

Keighley, X., Bro-Jørgensen, M. H., Ahlgren, H., Szpak, P., Ciucani, M. M., Sánchez Barreiro, F., Howse, L., Gotfredsen, A. B., Glykou, A., Jordan, P., Lidén, K., & Olsen, M. T. (2021). Predicting sample success for large-scale ancient DNA studies on marine mammals. Molecular Ecology Resources, 21(4), 1149-1166. https://doi.org/10.1111/1755-0998.13331

Vancouver

Keighley X, Bro-Jørgensen MH, Ahlgren H, Szpak P, Ciucani MM, Sánchez Barreiro F et al. Predicting sample success for large-scale ancient DNA studies on marine mammals. Molecular Ecology Resources. 2021;21(4):1149-1166. https://doi.org/10.1111/1755-0998.13331

Author

Keighley, Xénia ; Bro-Jørgensen, Maiken Hemme ; Ahlgren, Hans ; Szpak, Paul ; Ciucani, Marta Maria ; Sánchez Barreiro, Fátima ; Howse, Lesley ; Gotfredsen, Anne Birgitte ; Glykou, Aikaterini ; Jordan, Peter ; Lidén, Kerstin ; Olsen, Morten Tange. / Predicting sample success for large-scale ancient DNA studies on marine mammals. In: Molecular Ecology Resources. 2021 ; Vol. 21, No. 4. pp. 1149-1166.

Bibtex

@article{193590cfe09e48bab00e04a7bfa46b27,
title = "Predicting sample success for large-scale ancient DNA studies on marine mammals",
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 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.",
keywords = "aDNA, DNA damage, endogenous content, pinnipeds, sample age, seal, walrus, zooarchaeology",
author = "X{\'e}nia Keighley and Bro-J{\o}rgensen, {Maiken Hemme} and Hans Ahlgren and Paul Szpak and Ciucani, {Marta Maria} and {S{\'a}nchez Barreiro}, F{\'a}tima and Lesley Howse and Gotfredsen, {Anne Birgitte} and Aikaterini Glykou and Peter Jordan and Kerstin Lid{\'e}n and Olsen, {Morten Tange}",
year = "2021",
doi = "10.1111/1755-0998.13331",
language = "English",
volume = "21",
pages = "1149--1166",
journal = "Molecular Ecology",
issn = "0962-1083",
publisher = "Wiley-Blackwell",
number = "4",

}

RIS

TY - JOUR

T1 - Predicting sample success for large-scale ancient DNA studies on marine mammals

AU - Keighley, Xénia

AU - Bro-Jørgensen, Maiken Hemme

AU - Ahlgren, Hans

AU - Szpak, Paul

AU - Ciucani, Marta Maria

AU - Sánchez Barreiro, Fátima

AU - Howse, Lesley

AU - Gotfredsen, Anne Birgitte

AU - Glykou, Aikaterini

AU - Jordan, Peter

AU - Lidén, Kerstin

AU - Olsen, Morten Tange

PY - 2021

Y1 - 2021

N2 - 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.

AB - 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.

KW - aDNA

KW - DNA damage

KW - endogenous content

KW - pinnipeds

KW - sample age

KW - seal

KW - walrus

KW - zooarchaeology

U2 - 10.1111/1755-0998.13331

DO - 10.1111/1755-0998.13331

M3 - Journal article

C2 - 33463014

AN - SCOPUS:85101655206

VL - 21

SP - 1149

EP - 1166

JO - Molecular Ecology

JF - Molecular Ecology

SN - 0962-1083

IS - 4

ER -

ID: 260687497