From bones to sediments: Ancient human DNA from open-air archaeological sites

Abstract

Most ancient human bones degrade and eventually disappear over time, especially in regions with acidic soils, making it challenging to obtain genetic information from past populations. As a consequence, there is currently an overrepresentation of ancient human data for certain regions of the world in contrast to others. To explore alternative sources, we analyzed ancient DNA from sediment samples collected from a burial site and a settlement site in Japan, both dating to around 1000 years ago. We found that ancient human mitochondrial DNA can be obtained from sediments surrounding bones, particularly close to rib bones, while human DNA was rarely detected in the settlement site sediments. Furthermore, the mitochondrial haplogroups identified in the sediments were identical to those from human bones, confirming the reliability of this approach. Our findings suggest that genetic information about past human populations can be directly obtained from archaeological sediments in open-air sites. This method also provides a non-destructive alternative to bones and teeth, expanding possibilities for ancient DNA research in regions where skeletal remains are poorly preserved.