An international team of scientists has successfully sequenced ancient DNA extracted from a 5,700-year-old piece of chewed birch pitch from southern Denmark. In addition to an ancient human genome and mitochondrial DNA (mtDNA), the researchers recovered plant and animal DNA, as well as microbial DNA from several oral species. Further analysis of the human DNA revealed that the individual whose genome the team recovered was female and that she likely had dark skin, dark brown hair and blue eyes.
Birch pitch is a black-brown substance obtained by heating birch bark. Small lumps of this organic material are commonly found at Scandinavian archaeological sites, and while their use is still debated, they often show tooth imprints, indicating that they were chewed.
The chewed piece of birch pitch analyzed in the current study was recovered from the Late Mesolithic/Early Neolithic site of Syltholm on the island of Lolland, southern Denmark.
“Syltholm is completely unique. Almost everything is sealed in mud, which means that the preservation of organic remains is absolutely phenomenal,” said lead author Dr. Theis Jensen, a postdoctoral researcher in the Globe Institute at the University of Copenhagen and the Department of Archaeology at the University of York.
“It is the biggest Stone Age site in Denmark and the archaeological finds suggest that the people who occupied the site were heavily exploiting wild resources well into the Neolithic, which is the period when farming and domesticated animals were first introduced into southern Scandinavia.”
Dr. Jensen and colleagues analyzed the Syltholm specimen and demonstrated that it does not only contain ancient human genome, but also microbial DNA that reflects the oral microbiome of the individual who chewed the pitch, as well as plant and animal DNA from a person’s recent meal.
“It is amazing to have gotten a complete ancient human genome from anything other than bone,” said senior author Dr. Hannes Schroeder, also from the Globe Institute at the University of Copenhagen.
“What is more, we also retrieved DNA from oral microbes and several important human pathogens, which makes this a very valuable source of ancient DNA, especially for time periods where we have no human remains.”
The scientists found that the Syltholm individual who chewed the pitch was female and that she likely had dark skin, dark brown hair and blue eyes.
They also found that her mtDNA belonged to haplogroup K1e, and that she was genetically more closely related to Western hunter-gatherers from mainland Europe than hunter-gatherers from central Scandinavia.
“This combination of physical traits has been previously noted in other European hunter-gatherers, suggesting that this phenotype was widespread in Mesolithic Europe and that the adaptive spread of light skin pigmentation in European populations only occurred later in prehistory,” the authors said.
“The Syltholm individual does not carry any Neolithic farmer ancestry, suggesting that the genetic impact of Neolithic farming communities in southern Scandinavia might not have been as instant or pervasive as once thought.”
The Syltholm birch pitch contained ancient DNA from Streptococcus pneumoniae, a human pathogen that is responsible for the majority of community-acquired pneumonia; from human oral bacteria such as Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola; and from the Epstein-Barr virus.
“The preservation is incredibly good, and we managed to extract many different bacterial species that are characteristic of an oral microbiome,” Dr. Schroeder noted.
“Our ancestors lived in a different environment and had a different lifestyle and diet, and it is therefore interesting to find out how this is reflected in their microbiome.”
The team also identified several DNA reads that could be assigned to different plant and animal species, including birch (Betula pendula), hazelnut (Corylus avellana), and mallard duck (Anas platyrhynchos).
“While the presence of birch DNA is easily explained as it is the source of the pitch, we propose that the hazelnut and mallard DNA may derive from a recent meal,” the scientists said.
The team’s results were published online December 17, 2019 in the journal Nature Communications.
T.Z.T. Jensen et al. 2019. A 5700 year-old human genome and oral microbiome from chewed birch pitch. Nat Commun 10, 5520; doi: 10.1038/s41467-019-13549-9
Source link: https://www.sci.news/archaeology/syltholm-human-dna-07925.html