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a 5700 year-old human genome and oral microbiome from chewed birch pitch | nature

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. 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 Pleistocene1,2. 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 chewed3. Freshly produced birch pitch hardens on cooling and it has been suggested that chewing was a means to make it pliable again before using it, e.g. for hafting composite stone tools. Medicinal uses have also been suggested, since one of the main constituents of birch pitch, betulin, has antiseptic properties4. This is supported by a large body of ethnographic evidence, which suggests that birch pitch was used as a natural antiseptic for preventing and treating dental ailments and other medical conditions3. The oldest examples of chewed pitch found in Europe date back to the Mesolithic period and chemical analysis by Gas Chromatography-Mass Spectrometry (GC-MS) has shown that many of them were made from birch (Betula pendula)3. Recent work by Kashuba et al5. has shown that pieces of chewed birch pitch contain ancient human DNA, which can be used to link the material culture and genetics of ancient populations. In the current study, we analyse a further piece of chewed birch pitch, which was discovered at a Late Mesolithic/Early Neolithic site in southern Denmark (Fig. 1a; Supplementary Note 1) and demonstrate that it does not only contain ancient human DNA, but also 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. The DNA is so exceptionally well preserved that we were able to recover a complete ancient human genome from the sample (sequenced to an average depth of coverage of 2.3×), which is particularly significant since, so far, no human remains have been recovered from the site6. 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. https://www.nature.com/articles/s41467-019-13549-9

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