Microstratigraphic preservation of ancient faunal and hominin DNA in Pleistocene cave sediments

Ancient DNA recovered from Pleistocene sediments represents a rich resource for the study of past hominin and environmental diversity. However, little is known about how DNA is preserved in sediments and the extent to which it may be translocated between archaeological strata. Here, we investigate DNA preservation in 47 blocks of resin-impregnated archaeological sediment collected over the last four decades for micromorphological analyses at 13 prehistoric sites in Europe, Asia, Africa, and North America and show that such blocks can preserve DNA of hominins and other mammals. Extensive microsampling of sediment blocks from Denisova Cave in the Altai Mountains reveals that the taxonomic composition of mammalian DNA differs drastically at the millimeter-scale and that DNA is concentrated in small particles, especially in fragments of bone and feces (coprolites), suggesting that these are substantial sources of DNA in sediments. Three microsamples taken in close proximity in one of the blocks yielded Neanderthal DNA from at least two male individuals closely related to Denisova 5, a Neanderthal toe bone previously recovered from the same layer. Our work indicates that DNA can remain stably localized in sediments over time and provides a means of linking genetic information to the archaeological and ecological records on a microstratigraphic scale.

Automated summary

DNA preserved in ancient sediments can provide valuable genetic information about past hominin and environmental diversity. This study demonstrates that resin-impregnated archaeological sediment blocks can effectively preserve DNA from hominins and other mammals. Microsampling analysis of sediment blocks from Denisova Cave reveals significant variation in the taxonomic composition of mammalian DNA at a millimeter-scale, with DNA concentrated in small particles such as bone and feces fragments. The study also successfully extracts Neanderthal DNA from a sediment block, closely related to a previously recovered Neanderthal toe bone.