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, 10 (1), 5520

A 5700 Year-Old Human Genome and Oral Microbiome From Chewed Birch Pitch

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A 5700 Year-Old Human Genome and Oral Microbiome From Chewed Birch Pitch

Theis Z T Jensen et al. Nat Commun.

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.

Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
A chewed piece of birch pitch from southern Denmark. (a) Photograph of the Syltholm birch pitch and its find location at the site of Syltholm on the island of Lolland, Denmark (map created using data from Astrup). (b) Calibrated date for the Syltholm birch pitch (5,858–5,661 cal. BP; 5,007 ± 7). (c) GC-MS chromatogram of the Syltholm pitch showing the presence of a series of dicarboxylic acids (Cxx diacid) and saturated fatty acids (Cxx:0) and methyl 16-Hydroxyhexadecanoate (C16OH) together with the triterpenes betulin and lupeol, which are characteristic of birch pitch.
Fig. 2
Fig. 2
Genetic affinities of the Syltholm individual. a Principal component analysis of modern Eurasian individuals (in grey) and a selection of over 100 previously published ancient genomes, including the Syltholm genome. The ancient individuals were projected on the modern variation (see Methods). b Allele-sharing estimates between the Syltholm individual, other Mesolithic and Neolithic individuals, and WHGs versus EHGs and Neolithic farmers, respectively, as measured by the statistic f4(Yoruba, X; EHG/Barcın, WHG). c Ancestry proportions based on qpAdm, specifying WHG, EHG, and Neolithic farmers (Barcın) as potential ancestral source populations. PWC Pitted Ware Culture, LBK Linearbandkeramik, GAC Globular Amphora Culture, LP Late Paleolithic, M Mesolithic, EN Early Neolithic, MN Middle Neolithic, LN Late Neolithic. Data are shown in Supplementary Tables 4–6.
Fig. 3
Fig. 3
Metagenomic profile of the Syltholm birch pitch. a PCoA with Bray-Curtis at genera level with 689 microbiomes from HMP and the Syltholm sample (see Methods). b Order-level microbial composition of the Syltholm sample compared to a control sample (soil) and metagenome profiles of healthy human subjects at five major body sites from the HMP, visualised using MEGAN6.
Fig. 4
Fig. 4
Streptococcus pneumoniae consensus genome reconstructed from metagenomic sequences recovered from the ancient pitch. From outer to inner ring: S. pneumoniae virulence genes (black, shared genes are shown in bold); S. pneumoniae coding regions on the positive (blue) and negative (red) strand; mappability (grey); sequence depth for the Syltholm pitch (orange), HOMP sample SRS014468 (light brown), SRS019120 (light blue), SRS013942 (turquoise), SRS015055 (blue), and SRS014692 (dark blue). Sequence depths were calculated by aligning to the S. pneumoniae TIGR4 reference genome and visualised in 100 bp windows using Circos.

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