Background Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfully track their habitats during this period to eventually flourish and recolonise the holarctic regions. So far, the genomic impacts of these climate fluctuations on ungulates from high latitudes have been little explored. Here, we assemble a de-novo genome for the European moose (Alces alces) and analyse it together with re-sequenced nuclear genomes and ancient and modern mitogenomes from across the moose range in Eurasia and North America. Results We found that moose demographic history was greatly influenced by glacial cycles, with demographic responses to the Pleistocene/Holocene transition similar to other temperate ungulates. Our results further support that modern moose lineages trace their origin back to populations that inhabited distinct glacial refugia during the Last Glacial Maximum (LGM). Finally, we found that present day moose in Europe and North America show low to moderate inbreeding levels resulting from post-glacial bottlenecks and founder effects, but no evidence for recent inbreeding resulting from human-induced population declines. Conclusions Taken together, our results highlight the dynamic recent evolutionary history of the moose and provide an important resource for further genomic studies.

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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.

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.

Determining the male and female representation in zooarchaeological material from hunted animal species is essential, to fully investigate the effects and means of prehistoric hunting practices, and may further provide valuable biological information on past animal life-history, behaviour and demography. However, the fragmented nature of the zooarchaeological record and a lack of clear diagnostic skeletal markers, often prevents such inference. Here, we test the usability of the dog nuclear genome (CanFam3.1) for sex identification of pinnipeds. First, a contemporary sample set (n=72) of ringed seals (Pusa hispida), with known sex was used to test the genetic sex identification method. By quantifying the proportion of X chromosome reads, as the chrX/chr1 ratio, the ratios clustered in two clearly distinguishable sex groups. Of the 72 individuals, 69 were identified to the accurate sex, which proves a high reliability of the genetic method. Second, random down sampling of a subset of the ringed seal samples to different read number, suggests at least 5000 DNA sequence reads mapped to the reference genome as the lower limit for which this method is applicable. Finally, applying this standard, sex identification was successfully carried out on a broad set of ancient pinniped samples, including walruses (Odobenus rosmarus), grey seals (Halichoerus grypus) and harp seals (Pagophilus groenlandicus), which all showed clearly distinct male and female chrX/chr1 ratio groups.