After the last ice age, species migrated into a newly deglaciated Scandinavia. Brown bear recolonization is thought to have occurred from two directions—from the south and the northeast—resulting in a nonoverlapping distribution of two distinct mitochondrial clades. A contact zone in central Sweden separates populations with mitochondrial clade 1a in the south from those with clade 3a in the north. However, a paucity of brown bear subfossils in Scandinavia has limited testing of this prevailing model using ancient DNA. Here, we present a high-coverage brown bear mitogenome (231×) and nuclear genome-wide data (0.05×) extracted from lake sediment dated to 9.6 cal. ka BP from northern Sweden, representing the oldest known record of brown bear in the region. At this point in the Early Holocene, the Fennoscandian Ice Sheet was in its final stages of recession. Surprisingly, our analyses suggest that this environmental genome represents one male individual carrying clade 1a and with southern brown bear nuclear ancestry, despite being found far north of the contact zone. This suggests the individual was a migratory bear and had dispersed northward from its birthplace. Our finding adds to the scarce genomic record of Early Holocene brown bears and highlights the use of sedimentary ancient DNA as a powerful source of genomic information.

As the Fennoscandian ice-sheet retreated, plants and animals began to recolonise the Scandinavian peninsula. Current knowledge about the recolonisation patterns in Sweden during the Holocene is based mostly on fossil plant remains and preserved osteological remains, of which the latter record is sparse. Even less is known about the ecosystem composition before the Last Glacial Maximum (LGM), since the last ice-sheet eroded and reworked most deposits. Previous limitations due to gaps in the fossil record can now be addressed, as sedimentary ancient DNA (sedaDNA) is established as a powerful tool for reconstructing past ecosystems.

This thesis investigates how ancient environmental genomics based on shotgun sequencing of lake sediments can be used to reveal which species were present at certain points in time during the Holocene in central and northern Sweden. It also includes a glimpse into the Pleistocene pre-LGM ecosystem, as a comparison to the Holocene environment. 

In Paper I, we present an ancient environmental genome from a male brown bear extracted from lake sediment from northern Sweden dated to 9.6 cal. ka BP. With a mitochondrial coverage of 231x and a nuclear genome coverage of 0.05x, we could investigate the genome using population genomic methods. The paper highlights the potential of sedaDNA and non-destructive methods for generating high-quality genomic data. 

For metagenomic processing of sedaDNA data, an open-access ready-to-use bioinformatic pipeline was compiled from existing tools. The pipeline, called metaJAM, is presented in Paper II. It includes a pre-processing step of adapter trimming and removal of low complexity regions and microbial filtering, followed by competitive mapping against reference databases. Lastly, a module of filtering and authentication finalises the output.

From a sediment sequence from lake Orsasjön in central Sweden (Paper III), we reconstructed the local plant composition between ca. 8.1–0.1 cal. ka BP using sedaDNA. The results show a constant presence of woody taxa throughout the sediment sequence, with little turnover in the sedaDNA record. We demonstrate the expansion of spruce (Picea) in the region, with modelled ages overlapping with previous studies. The arrival of maple (Acer) to central Sweden, previously unreported, is also shown. Additionally, we present authenticated sedaDNA from vertebrates, including humans, fish, beaver and water vole.

There are some pre-LGM sediment deposits in Sweden left intact. In Paper IV, we investigated samples from Vålbacken outside Östersund, northern Sweden. The sediments are dated to 55–35 ka BP, i.e. within marine isotope stage 3 (MIS 3). We present indications of a mammoth steppe-like plant composition, and the presence of woolly mammoth (Mammuthus primigenius) in the sedaDNA. Our findings add to the sparse knowledge of pre-LGM ecosystems in Sweden.

A literature review is also included (Paper V). It outlines and summarises the setting for the project, and introduces many relevant concepts for readers not familiar with the field.

In conclusion, this thesis expands the knowledge of how the landscape in Scandinavia was developed before and after the LGM, based on shotgun sequenced sedaDNA. It provides an example of how lake sediments can yield genomic data from a single individual of comparable quality to osteological aDNA, reveals the arrival of maple to central Sweden, and confirms the presence of a mammoth steppe ecosystem in Sweden during MIS 3.

Biostratigraphy is a fundamental tool for age-calibrating marine sediments and enabling palaeoceanographic reconstructions. However, establishing age control in marine sediments of the Arctic Ocean is challenging, due to low micro- and nannofossil abundances, discontinuous occurrences across glacial and interglacial periods, as well as spatial and temporal variations in carbonate preservation. Gephyrocapsa huxleyi is a globally distributed coccolithophore whose first occurrence at ca 290 ka is widely used to date Quaternary marine sediments. Yet, its initial appearance and stratigraphic range in the Arctic Ocean are debated. Here, we present the first combined sedaDNA-nannofossil approach to trace the occurrence of G. huxleyi throughout three sediment cores from the Lomonosov Ridge recovered during the Arctic Ocean 2016 expedition on icebreaker Oden. SedaDNA was extracted from 87 samples spanning key lithological boundaries. Following shotgun sequencing, the presence of G. huxleyi was assessed using three independent bioinformatic tools Kraken2, BWA and BLAST. These results were integrated with lithological data and Gephyrocapsa nannofossil assemblages to evaluate the potential of palaeogenomics as a biostratigraphic tool in the Arctic that could potentially overcome the limitations of conventional nannofossil-based approaches. Although we found broadly overlapping sedaDNA and nannofossil results, key discrepancies and methodological limitations do not allow us to confidently identify the first occurrence of G. huxleyi in the studied sequences. We discuss both the potential and the challenges of sedaDNA as a complementary biostratigraphic tool to improve age control of Arctic marine sediments.

The Swedish Time Scale (STS), based on annual sediment sequences (varves), is a unique tool for detailing Scandinavian deglaciation and climate history. Over a century in development, the STS comprises ∼13,300 varve-years, yet its connections to calendar years are insecure, and it cannot yet be considered a true absolute time scale. Consequently, it has not been possible to reliably investigate leads and lags of paleoclimate and environmental changes recorded in the STS in relation to other climate archives in NW Europe and the North Atlantic region. Here, we radiocarbon dated a series of early Holocene ice-dammed lake drainage events that deposited recognizable varves downstream. In particular, we identified the lake drainage responsible for depositing the so-called “zero varve” of the STS and dated it to 10,008 ± 87 calibrated years before present, A.D. 1950 (cal. yr B.P.). Using a hydrological model, we demonstrate that drainage duration was subseasonal and that drainage marker beds are, in chronological terms, true annual varves. By doing so, we anchor the STS in absolute time, provide revised ages of key deglacial and climatic events of the last glacial-interglacial transition, and present a tightly chronologically constrained reconstruction of early Holocene ice-sheet retreat in central Scandinavia.

Ancient environmental DNA is increasingly vital for reconstructing past ecosystems, particularly when paleontological and archaeological tissue remains are absent. Detecting ancient plant and animal DNA in environmental samples relies on using extensive eukaryotic reference genome databases for profiling metagenomics data. However, many eukaryotic genomes contain regions with high sequence similarity to microbial DNA, which can lead to the misclassification of bacterial and archaeal reads as eukaryotic. This issue is especially problematic in ancient eDNA datasets, where plant and animal DNA is typically present at very low abundance. In this study, we present a method for identifying bacterial- and archaeal-like sequences in eukaryotic genomes and apply it to nearly 3,000 reference genomes from NCBI RefSeq and GenBank (vertebrates, invertebrates, plants) as well as the 1,323 PhyloNorway plant genome assemblies from herbarium material from northern high-latitude regions. We find that microbial-like regions are widespread across eukaryotic genomes and provide a comprehensive resource of their genomic coordinates and taxonomic annotations. This resource enables the masking of microbial-like regions during profiling analyses, thereby improving the reliability of ancient environmental metagenomic datasets for downstream analyses.

The postglacial recolonization of Fennoscandian flora and fauna was initiated when the land became accessible as the last ice sheet retreated. In northern Sweden, plants are represented in pollen and macrofossil records, but there is no genetic evidence from the first plants, animals or humans in the region, mainly owing to an absence of osteological finds. The questions of who the first postglacial peoples, or pioneers, were and where they came from therefore remain unanswered. Previous palaeogenomic analyses from remains from adjacent regions have suggested that two main routes into Sweden could have been taken by the pioneers, one from the SW through modern-day Denmark and Norway, and one from the east via Finland. However, no direct genetic evidence from the pioneers of northern Sweden exists. Modern technology has provided the ancient DNA field with an updated toolbox that could allow for novel approaches for revealing the origin and genetic profiles of the first Scandinavians, of which sedimentary ancient DNA (sedaDNA) is well placed. Lake sediments are now a routine source of sedaDNA that have been used to record environmental changes and detect species that lived in the surrounding lake catchment. This review will provide context and background, a summary of the ground-breaking studies within the field of lacustrine sedaDNA, and relevant methodology to address the scientific questions at hand. We conclude that the field is mature enough to provide insight into the origins and arrival times of the first postglacial humans that migrated into northern Sweden.