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. 2021 May;21(4):1149-1166.
doi: 10.1111/1755-0998.13331. Epub 2021 Feb 26.

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

Xénia Keighley  1   2 , Maiken Hemme Bro-Jørgensen  1   3 , Hans Ahlgren  3 , Paul Szpak  4 , Marta Maria Ciucani  1 , Fátima Sánchez Barreiro  1 , Lesley Howse  5 , Anne Birgitte Gotfredsen  6 , Aikaterini Glykou  3 , Peter Jordan  7 , Kerstin Lidén  3 , Morten Tange Olsen  1
Affiliations

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

Xénia Keighley et al. Mol Ecol Resour. 2021 May.

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: DNA damage; aDNA; endogenous content; pinnipeds; sample age; seal; walrus; zooarchaeology.

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Figures

FIGURE 1
FIGURE 1
Map of the distribution of the 285 successfully sequenced pinniped samples analysed. Symbol colour corresponds to species (dark blue for walrus, green for grey seal and light blue for harp seal). Sizes of symbols reflect the number of samples, clustered within sample size bins. Please note that symbols are placed at each site included in this study, but samples may have been taken from several different contexts within a single site. The exact details of this are included in the supplementary raw data
FIGURE 2
FIGURE 2
Effect of the samples’ geographic origin on endogenous DNA content (top row) and DNA damage rate (bottom row) represented as box‐plots for each of the three study species. Geographic origin was summarised as one of seven regions: North West Greenland (NWG), Foxe Basin (FB), West Greenland (WG), East Greenland (EG), Iceland (IC), Neustadt (NEU), Varanger Fjord (WS) and Baltic Sea (BS). Sample points and boxes have been colour‐coded to indicate the age of the sample (years BP) within one of five categories. Note that some geographic regions are represented by a single or limited number of samples
FIGURE 3
FIGURE 3
Effect of sample age (years BP) on endogenous content (top row) and damage rate (bottom row). Plots have been separated and points coloured according to species. Smoothed trend lines with Standard Error (shaded area) are shown for each plot. Three walrus samples older than 5000 years BP have been excluded (see Figure S1 for the full version)
FIGURE 4
FIGURE 4
Effect of skeletal element on endogenous DNA content (top row) and DNA damage rate (bottom row) represented as box‐plots. Plots have been separated according to species, and skeletal elements grouped together into simple categories. Sample points and boxes have been colour‐coded to indicate the age of the sample (years BP) within one of five categories. Element categories for which there were fewer than two time periods containing at least two samples were excluded
FIGURE 5
FIGURE 5
Relationships between walrus and harp seal sample endogenous content, damage rate and mitochondrial:nuclear ratio. Dots have been colour‐coded to indicate the age of the sample (years BP) within one of five categories. A smoothed trend line with a shaded area either side represents standard error. Three walrus samples older than 5000 years BP were excluded
FIGURE 6
FIGURE 6
Effect of walrus sample collection date on endogenous content (left) and damage rate (right). The points are colour‐coded based on sample age separated into time periods
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