A 5700 year-old human genome and oral microbiome from chewed birch pitch

Theis Zetner Trolle Jensen ,Katrine Højholt Iversen,Mikkel Winther Pedersen,Søren A Sørensen,Sofie Holtsmark Nielsen,Simon Rasmussen,Mikkel Holger S Sinding ,Martin R Ellegaard,Åshild J Vågene‬ ,Morten E Allentoft,Martin Sikora,Michael W Dee,Martin Mortensen ,Mads Chr Christensen ,Anna K Fotakis,Alberto J Taurozzi,Matthew J Collins,Liam Thomas Lanigan ,Shyam Gopalakrishnan,Jonas Niemann,M Thomas P Gilbert,Hannes Schroeder

doi:10.1038/s41467-019-13549-9

Abstract

The rise of ancient genomics has revolutionised our understanding of human prehistory but this work depends on the availability of suitable samples. Here we present a complete ancient human genome and oral microbiome sequenced from a 5700 year-old piece of chewed birch pitch from Denmark. We sequence the human genome to an average depth of 2.3× and find that the individual who chewed the pitch was female and that she was genetically more closely related to western hunter-gatherers from mainland Europe than hunter-gatherers from central Scandinavia. We also find that she likely had dark skin, dark brown hair and blue eyes. In addition, we identify DNA fragments from several bacterial and viral taxa, including Epstein-Barr virus, as well as animal and plant DNA, which may have derived from a recent meal. The results highlight the potential of chewed birch pitch as a source of ancient DNA.

Highlights

The rise of ancient genomics has revolutionised our understanding of human prehistory but this work depends on the availability of suitable samples
Note 1) and demonstrate that it does contain ancient human DNA, and microbial DNA that reflects the oral microbiome of the person who chewed the pitch, as well as plant and animal DNA which may have derived from a recent meal
Chemical analysis by Fourier-Transform Infrared (FTIR) spectroscopy produced a spectrum very similar to modern birch pitch (Supplementary Fig. 4) and GC-MS revealed the presence of the triterpenes betulin and lupeol, which are characteristic of birch pitch (Fig. 1c; Supplementary Note 3)[3]

Summary

Introduction

The rise of ancient genomics has revolutionised our understanding of human prehistory but this work depends on the availability of suitable samples. We present a complete ancient human genome and oral microbiome sequenced from a 5700 year-old piece of chewed birch pitch from Denmark. Birch pitch is a black-brown substance obtained by heating birch bark and has been used as an adhesive and hafting agent as far back as the Middle Pleistocene[1,2]. Small lumps of this organic material are commonly found on archaeological sites in Scandinavia and beyond, and while their use is still debated, they often show tooth imprints, indicating that they were chewed[3]. The results highlight the potential of chewed birch pitch as a source of ancient human and non-human DNA, which can be used to shed light on the population history, health status, and even subsistence strategies of ancient populations

Methods

Results

Conclusion