Aim: The majority of the non-volant mammals now present on the island of Gotland, Sweden, have been introduced in modern times. One exception is the mountain hare (Lepus timidus), which was present on the island more than 9000 years ago. This paper investigates the origins of the Gotland hares and temporal changes in their genetic structure, and considers how they may have reached the island.

Location: The island of Gotland, Sweden (57°30′ N, 18°20′ E).

Methods: Two fragments of the mitochondrial D-loop 130 + 164 base pairs in length from skeletal remains from 40 ancient mountain hares from Gotland, 38 from the Swedish mainland and five from Lithuania were analysed and compared with 90 modern L. timidus haplotypes from different locations in Eurasia and five haplotypes of the Don-hare (Lepus tanaiticus) morphotype.

Results: The Mesolithic hares from Gotland (7304 bc–5989 bc) cluster with modern hares from Russia, Scotland, the Alps and Fennoscandia whereas the Gotland hares from the Neolithic and onwards (2848 bc–1641 ad) cluster with Neolithic hares from the Swedish mainland and modern hares from Fennoscandia. The Neolithic haplotypes from Lithuania and the Don-hare haplotypes were dispersed within the network. The level of differentiation (F_ST) between the Mesolithic and Neolithic hares on Gotland was twice as great as that observed on the mainland.

Main conclusions: The ancient hares on Gotland fall into two haplogroups separated in time, indicating that the mountain hare became extinct at one point, with subsequent re-colonization events. In view of the isolated location of Gotland, it is probable that the hares were brought there by human means of transport.

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.