In recent years, non-human 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 the feasibility of 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 pinnipedsamples collected from across the North Atlantic. Using generalised linear and mixed-effectmodels, 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 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 Arcticgenerally 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 significantrelationship with DNA preservation. Overall, the 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.

The grey seal (Halichoerus grypus) has been part of the Baltic Sea fauna for more than 9000 years and has ever since been subjected to extensive human hunting, particularly during the early phases of its presence in the Baltic Sea, but also in the early 20th century. In order to study their temporal genetic structure and to investigate whether there has been a genetically continuous grey seal population in the Baltic, we generated mitochondrial control region data from skeletal remains from ancient grey seals from the archaeological sites Stora Förvar (Sweden) and Neustadt (Germany) and compared these with modern grey seal data. We found that the majority of the Mesolithic grey seals represent haplotypes that is not found in contemporary grey seals, indicating that the Baltic Sea population went extinct, likely due to human overexploitation and environmental change. We hypothesize that grey seals recolonised the Baltic Sea from the North Sea. during the Bronze Age or Iron Age, and that the contemporary Baltic grey seal population is direct descendants of this recolonisation. Our study highlights the power of biomolecular archaeology to understand the factors that shape contemporary marine diversity. 

The harp seal is a cold adapted seal species, which requires a suitable formation of pack ice during winter and spring to secure successfully breeding. Today harp seals live in sub-Arctic regions and the North Atlantic, but during the middle Holocene Period, a breeding population existed in the Baltic Sea. In order to investigate the genetic affinity and faith of the now extinct Baltic harp seal population we analysed contemporary and ancient mitogenomes from across the species contemporary and ancient range. Ancient mitochondrial genomes were generated for a total of 49 Baltic harp seals ranging from Late Mesolithic to the Iron Age, together with five Neolithic samples from the White Sea and two Neolithic samples from the Northwest Atlantic Ocean. The ancient data was compared to published modern harp seal data assigned to the present breeding populations around Newfoundland, the Greenland Sea and the White Sea. Surprisingly only limited phylogenetic resolution was found among the ancient and modern localities. The statistical measures for genetic differentiation, however, identified significant levels of population genetic differentiation between the Baltic harp seal population and all modern populations, which suggest an independent breeding population in the Baltic Sea. The low level of genetic differentiation to the White Sea population indicate a shared ancestry between the Baltic and White Sea. The generated Skyline plot suggest second wave of colonization after a hiatus in the Baltic Sea. Interestingly, the genetic diversity in the Baltic harp seal population was significantly higher than in any of the modern populations. However, a drastic decrease in genetic diversity is observed from the Bronze Age to the Iron Age, which might be linked to effects of high hunting pressure and climatic changes towards the final extirpation of harp seals in the Baltic.