Ancient DNA diffuses from human bones to cave stones

Abstract

Recent studies have demonstrated the potential to recover ancient human mitochondrial DNA and nuclear DNA from cave sediments. However, the source of such sedimentary ancient DNA is still under discussion. Here we report the case of a Bronze Age human skeleton, found in a limestone cave, which was covered with layers of calcite stone deposits. By analyzing samples representing bones and stone deposits from this cave, we were able to: i) reconstruct the full human mitochondrial genome from the bones and the stones (same haplotype); ii) determine the sex of the individual; iii) reconstruct six ancient bacterial and archaeal genomes; and finally iv) demonstrate better ancient DNA preservation in the stones than in the bones. Thereby, we demonstrate the direct diffusion of human DNA from bones into the surrounding environment and show the potential to reconstruct ancient microbial genomes from such cave deposits, which represent an additional paleoarcheological archive resource.

Keywords: Anthropology; Archeology; Biological sciences; Evolutionary biology; Paleobiology; Paleogenetics.

Graphical abstract

Figure 1

Skeleton finding site (A) Location of the Wimsener caves in Baden-Württemberg, Germany. (B) Longitudinal section of the first 200 meters of the Wimsener caves; the scale bar refers to the cave length. (C) Cross section of the “Schatzkammer”; the red star refers to the location of the tibia. (D) Photograph showing the difficult accessibility of the finding site; the red arrow indicates the protruding part of the sampled tibia.

Figure 2

Metagenomic analysis of human and microbial DNA of cave human bone and its surrounding stone deposits (A) On-site sampling of human tibia covered with a layer of calcite deposits. (B) Close-up cross-section of sampled tibia slice, indicating the sampling locations for DNA analysis; the black arrow refers to the direction of gravity. (C) Number of metagenomic reads of each sample mapped to the human autosomal DNA (Ref genome hg19). (D) Mean read lengths of the mapped reads against the human genome (hg19). (E) Heatmap showing the abundance of different metagenome-assembled genomes (MAGs) in different samples (genome copies per million reads). The color intensity indicates row z-scores. (F) Mean read lengths of the mapped reads the MAGs. For the (E and F) the names of MAGs refer to the source of the MAGs (stone or bone) e.g., “Stone_1” means that this genome was assembled from the stone sample.