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Genomic insights on the extinct Baltic harp seal population
Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies. University of Copenhagen, Denmark .ORCID iD: 0000-0003-1569-7878
Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies.
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

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. 

Keywords [en]
Ancient DNA, Baltic Sea, breeding population, haplotype, hunting, migration
National Category
Archaeology Geology
Research subject
Archaeological Science; Geology
Identifiers
URN: urn:nbn:se:su:diva-189307OAI: oai:DiVA.org:su-189307DiVA, id: diva2:1520010
Funder
EU, Horizon 2020, 676154Available from: 2021-01-19 Created: 2021-01-19 Last updated: 2022-02-25Bibliographically approved
In thesis
1. Ancient genomics of Baltic seals: Insights on the past Baltic grey seal and harp seal populations
Open this publication in new window or tab >>Ancient genomics of Baltic seals: Insights on the past Baltic grey seal and harp seal populations
2021 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis aims to study and describe the ancient populations of grey and harp seals in the Baltic Sea, and to present new methodological approaches for general use in ancient DNA studies.

The dissertation is comprised of five studies: a review of the use of paleogenetics in studying ancient human-marine mammal interactions; a method paper investigating patterns of DNA preservation in ancient pinniped samples; a method paper presenting a genetic sex identification method for ancient pinnipeds; a population genomic study of the Baltic grey seal; and a population genomic study of the now extinct Baltic harp seal.

Guidelines for ancient DNA sample selections were deduced from broad-scale statistical modelling of factors influencing DNA preservation in pinniped bones, the most significant of which included type of bone element, collagen content, and whether the bone derive from a cave context. Modern ringed seal samples with known sex were used to test an alternative pinniped sex identification method using the annotated dog genome as a reference for quantification of the relative representation of X chromosome reads. Reliable sex identification was shown to require a minimum of 5,000 total reads mapped to the reference genome. A total of 69 mitochondrial control regions were generated for Baltic grey seals, which revealed that the Mesolithic data largely represent extinct haplotypes, the main of which continued until the Early Neolithic. A population replacement prior to the early Bronze Age introduced mitochondrial variation resembling that of modern Baltic greys seals. The level of genetic differentiation between the Baltic harp seal population and the three contemporary breeding populations, suggests that the White Sea population is the most likely ancestor of the Baltic harp seal breeding population. An increase in genetic diversity, following a hiatus with no Baltic harp seals, combined with the measures of genetic differentiation from this period, further suggests that a second colonization likely occurred from the White Sea during the early Bronze Age.

Place, publisher, year, edition, pages
Stockholm: Department of Archaeology and Classical Studies, 2021. p. 70
Series
Theses and papers in scientific archaeology, ISSN 1400-7835 ; 19
Keywords
Ancient DNA, Baltic Sea, DNA preservation, extinction, mitogenome, seal hunting, sex identification
National Category
History and Archaeology
Research subject
Scientific Archaeology
Identifiers
urn:nbn:se:su:diva-189293 (URN)978-91-7911-396-4 (ISBN)978-91-7911-397-1 (ISBN)
Public defence
2021-02-25, Nordenskiöldsalen, Geovetenskapens hus, Svante Arrhenius väg 12 and online via Zoom, public link is available at the department website., Stockholm, 13:00 (English)
Opponent
Supervisors
Funder
EU, Horizon 2020, 676154
Available from: 2021-02-02 Created: 2021-01-19 Last updated: 2022-02-25Bibliographically approved
2. Prehistoric human impact on wild mammalian populations in Scandinavia
Open this publication in new window or tab >>Prehistoric human impact on wild mammalian populations in Scandinavia
2021 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis aims to study the interactions of pre-agricultural societies in Scandinavia with wild mammals, for example in terms of hunting and translocation. More specifically, the aim is to investigate the possibility of identifying examples of overexploitation, targeted hunting or translocation of wild mammals in prehistoric Scandinavia, and to discuss the implications this could have had for both the wild animals and the humans. The thesis also studies translocation to evaluate the feasibility of using it as a proxy for prehistoric human mobility, and to understand the motivation for this action. 

Although the focus is on the animals in this thesis, the ultimate purpose is to study humans and their interactions with animals in prehistory. The thesis applies genetic analyses to zooarchaeological material of various mammalian species from different Scandinavian sites, in order to study whether the genetic structures have changed in these species over time, and to assess whether these changes were induced by different human actions. The species studied in this thesis were selected on the basis of the importance they are considered to have had for prehistoric people.

The dissertation comprises five studies. The first study investigates the occurrence of mountain hares on the island of Gotland, and discusses how they got there and where they came from. The second study explores the temporal genetic structure of the grey seal in the Baltic Sea, and discusses whether humans and/or climate were the drivers for the sudden disappearance of grey seals from the island of Stora Karlsö. The third study concerns a shift where moose apparently became less important as prey in northern Sweden at the end of the Neolithic period, and discusses whether humans targeted female moose in hunting. The fourth study analyses and discusses the history of the harp seal in the Baltic Sea. The fifth study is a methodological paper which involves identifying seals according to sex, using the dog genome.

The overall result of the different case studies shows that there were major population fluctuations over time in all the species studied, and that in some cases, humans are likely to have contributed to this, e.g. through overhunting and translocation. The study also shows that the population fluctuations often occurred in connection with certain climatic events, though it was not possible to separate climatic effects from human impact in terms of the cause.

Place, publisher, year, edition, pages
Stockholm: Department of Archaeology and Classical Studies, Stockholm University, 2021. p. 85
Series
Theses and papers in scientific archaeology, ISSN 1400-7835 ; 21
Keywords
hunter-gatherers, Baltic Sea, Mesolithic period, grey seal, harp seal, mountain hare, moose, ancient DNA, hunting, translocation
National Category
Archaeology
Research subject
Scientific Archaeology
Identifiers
urn:nbn:se:su:diva-196043 (URN)978-91-7911-592-0 (ISBN)978-91-7911-593-7 (ISBN)
Public defence
2021-10-15, Nordenskiöldsalen, Geovetenskapens hus, Svante Arrhenius väg 12 and online via Zoom, public link is available at the department website, Stockholm, 10:00 (Swedish)
Opponent
Supervisors
Available from: 2021-09-22 Created: 2021-08-31 Last updated: 2022-02-25Bibliographically approved

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