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.

An accurate assignment test for extremely low‐coverage whole‐genome sequence data

“…Second, recent strategies targeting organelle (mitochondrial or chloroplast) reference databases increasingly use genome skimming sequencing approaches (Bohmann et al, 2020). Finally, DNA preservation in subfossil, archaeological, historical, or degraded biological material remains variable and is often context‐specific (Ferrari et al, 2021; Keighley et al, 2021; Tin et al, 2014). In order to account for such unpredictability, ancient DNA sequencing studies typically screen many specimens, from which a subset with the best DNA preservation is selected for deeper sequencing (e.g., Martínez‐García et al, 2021; Star et al, 2018; van der Valk et al, 2021).…”

Ancient DNA sequence quality is independent of fish bone weight

“…Research is further hampered by the inherently destructive nature of DNA extraction, meaning archaeological remains are destroyed or damaged for successful recovery of sequences. Successful DNA recovery is often unpredictable (Ferrari et al, 2021;Tin and Economo, 2014;Keighley et al, 2021), therefore workflows often involve screening large numbers of specimens from which only a small subset ultimately yields useable DNA for analysis (e.g. Star et al, 2018;Valk et al, 2021).…”

An accurate assignment test for extremely low-coverage whole-genome sequence data

“…Despite advances in methodologies that allow for the recovery of higher yields of endogenous ancient DNA (aDNA) (e.g., Boessenkool et al, 2017;Carpenter et al, 2013;Gamba et al, 2014;Pinhasi et al, 2015), DNA preservation in sub-fossil, archaeological, historical, or degraded biological material remains variable and is often context specific (Ferrari et al, 2021;Keighley et al, 2021;Tin et al, 2014). In order to account for such unpredictability, aDNA sequencing projects typically screen many specimens from which a subset with the best DNA preservation is selected for deeper sequencing (e.g.…”