Ancient DNA reconstruction of late holocene ecosystems within the Carpathian basin from paleo-meanders and archaeological deposits

Abstract

The diverse ecology in the Carpathian Basin supported a variety of subsistence strategies throughout the Holocene, ranging from animal husbandry to the management of woodlands, grasslands, and wetlands. The earliest evidence of aquatic resource use in the region dates back to the Early Neolithic (~ 6200−5300 cal BC), with cultural practices extending into recent times. This is reflected in the numerous open-air archaeological sites widely distributed across the landscape and on the Danube meanders. However, the archaeological record, especially organic remains and fossils, may not fully capture the region’s species diversity due to degradation and scarcity, hindering the accurate reconstruction of past human-environment interactions. Recent studies have shown that ancient DNA in sediments (sedaDNA) can survive even in the absence of visible fossils, however, these studies have primarily been limited to cave-, lake- and permanently frozen sedimentary deposits. Here, we investigate two open-air archaeological sites and three paleo meander deposits of the Danube in Serbia (southeastern Europe) using sedaDNA. Our analysis reveals genetic traces from past freshwater and terrestrial ecosystems and local exploitation of the migratory sturgeon species, currently extirpated from the region. We find sedaDNA preserved in sediments from unsheltered archaeological contexts and explore the associated challenges that require further investigation. Supplementary Information The online version contains supplementary material available at 10.1038/s41598-026-35509-2. Subject terms: Ecology, Ecology, Evolution