Elucidating the past using ancient genomes and metagenomes

The recognition that DNA from long dead organisms can be extracted and sequenced from a multitude of substrates has revolutionised the field of bioarchaeology. Apart from yielding profound discoveries into the biology, migrations, and admixture of past populations based on the host DNA, some artefacts are now recognised as repositories for dietary and host- associated microbial DNA and thus hold vital clues to the health status and lifestyle of the individual. This thesis is composed of three studies on three quite distinct substrates – historic hide, fluid-preserved museum specimens, and an ancient birch “chewing gum” – where I applied population genomic and metagenomic analyses to infer the population history and microbiome compositions of past organisms. After briefly introducing the broad themes of this dissertation in Chapter 1, Chapter 2 of this dissertation explores the population history of the Honshū wolves, a poorly-understood grey wolf subspecies that was endemic to the Japanese archipelago and went extinct at the beginning of the 20th century. The nuclear genome from the museum hide of one specimen was ge at an average depth of coverage of 3.8×, and I discovered that Honshū wolves were likely the relict of a Pleistocene Siberian wolf population that was up to now believed to have gone extinct about 10,000 years ago. Chapter 3 and Chapter 4 discuss the metagenomic potential of two novel substrates. In Chapter 3 we sequenced gut samples of six historic fluid-preserved birds with the aim of capturing the host-associated microbial profile. While I was able to characterise the gut microbiome of one specimen, further research is necessary to improve the feasibility of performing metagenomic analyses on fluid-preserved samples. Finally, in Chapter 4 I analysed the DNA extracted from a 5,700 year old chewed birch bark pitch. We obtained a complete human genome at an average depth of coverage of 2.3× and found that the female who chewed the birch pitch genetically closely resembles Western hunter-gatherers. The birch “chewing gum” also proved to be a rich source of microbial and non-human eukaryotic DNA, and I was able to recover the genomes of bacterial taxa that are closely associated with the oral microbiome as well as DNA from mallard, hazelnut, and birch that are likely derived from a recent meal and the birch pitch material itself. In conclusion, this dissertation sheds light on wolf and human evolution as well as introduces two novel substrates with potential for future metagenomic analyses. These projects demonstrate that researchers must continue exploring whether unusual archaeological and historic substrates contain genetic material that can be used to resolve long standing questions, thereby unlocking new opportunities to understand the history of our world.