Predicting sample success for large-scale ancient DNA studies on marine mammals
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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; Jordan, Peter; Lidén, Kerstin; Olsen, Morten Tange.
In: Molecular Ecology Resources, Vol. 21, No. 4, 2021, p. 1149-1166.Research output: Contribution to journal › Journal article › peer-review
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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