Tracing early pastoralism in Central Europe using sedimentary ancient DNA

Central European forests have been shaped by complex human interactions throughout the Holocene, with significant changes following the introduction of domesticated animals in the Neolithic (∼7.5–6.0 ka before present [BP]). However, understanding early pastoral practices and their impact on forests is limited by methods for detecting animal movement across past landscapes. Here, we examine ancient sedimentary DNA (sedaDNA) preserved at the Velký Mamuťák rock shelter in northern Bohemia (Czech Republic), which has been a forested enclave since the early Holocene. We find that domesticated animals, their associated microbiomes, and plants potentially gathered for fodder have clear representation by the Late Neolithic, around 6.0 ka BP, and persist throughout the Bronze Age into recent times. We identify a change in dominant grazing species from sheep to pigs in the Bronze Age (∼4.1–3.0 ka BP) and interpret the impact this had in the mid-Holocene retrogressions that still define the structure of Central European forests today. This study highlights the ability of ancient metagenomics to bridge archaeological and paleoecological methods and provide an enhanced perspective on the roots of the “Anthropocene.” •We analyze metagenomic data from a rock shelter using sedimentary ancient DNA•Ancient DNA reveals domesticated animals and their associated microbiomes•Phylogenetic analyses detect mitochondrial haplogroups in domestic sheep and cattle•sedaDNA can help improve the understanding of our herding practices and forest management Sedimentary ancient DNA buried underneath a rock shelter reveals shifts in the presence of domesticated animals, associated microbiomes, and plants gathered for fodder from the Late Neolithic to the Bronze Age. Zampirolo et al. highlight the potential of using ancient DNA from rock shelter deposits to infer past human-environment interactions.