Early Pastoralism in Central European Forests: Insights from Ancient Environmental Genomics

Abstract

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 kyr 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 kyr 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 kyr BP) and interpret the impact this had in the mid-Holocene retrogressions that still define the structure of Central 1 bioRxiv preprint doi: https://doi.org/10.1101/2023.12.01.569562; this version posted December 3, 2023. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license. 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. Main text The emergence of agriculture marks a radical juncture in the entanglement of humans and Earth systems. In Central Europe, the first agricultural sites are associated with the Linearbandkeramik (LBK) peoples, who rapidly occupied fertile lowlands after 7.5 kyr BP, introducing a suite of domesticated plants and animals from the Near East (1, 2). Initially, domesticated animals were kept in proximity to agricultural settlements, typically located on loess soils conducive to cultivation. However, the Late Neolithic (sometimes referred to as Eneolithic ~6.4 – 4.2 kyr BP) witnessed the advent of forest grazing, facilitating a full expansion of pastoralism across varied Central European environments (3–7). By the Bronze Age (~4.1 kyr BP), rich and diverse broadleaf mosaics transitioned into the comparatively species-poor structure that continues to define many Central European forests today (8–10). Human influence likely played a significant role in this profound transformation as pastoral activities can impact forest succession (11). However, detecting domesticated animal movements across past landscapes is challenging, and the coevolution of forest structure and human agency remains poorly understood. In this context, the analysis of ancient environmental DNA from sediments offers an opportunity to refine insights into paleoecological changes through time (12, 13) by complementing traditional fossil evidence (14–16). Prior attempts to extract ancient DNA from archaeological deposits have utilised target capture techniques to detect hominin and mammal DNA in cave sediments (17–19) and rock shelters (20, 21). However, the potential for shotgun sequencing of bulk ancient environmental DNA in a broader range of archaeological settings, such as semi-open to open-air sites, has not yet been fully realised. With this in mind, we identified the Velký Mamuťák (VM) rock shelter as an ideal site for investigation. VM is situated in the Český Ráj region of northern Bohemia, which is a forested area enclosed by sandstone outcrops that create dramatic relief (Fig. 1a). VM is remarkable for its exceptional organic preservation, and deep occupation layers spanning all significant periods from the Mesolithic to the present (Fig 1. b-c). Furthermore, VM benefits from a comprehensive multiproxy account of environmental practices, derived from prior archaeological and paleoecological examinations (22, 23). At VM, we collected a sequence of sediment samples from stratigraphic layers to examine metagenomic changes spanning the early Holocene to recent times. We identified shifts in domesticated animal DNA at the site from the onset of the Late Neolithic (∼6.0 kyr BP) through the Bronze Age (∼3.0 kyr BP) and show, using phylogenetic placement, that key taxa are ancestral lineages to modern species. In addition, microbial source analysis (24, 25) confirms the presence of bovine species, sheep, and pigs within the same sediment layers, demonstrating the stratigraphic integrity of DNA within the site. We even find evidence of human-associated microbes in a Bronze Age (∼3.0 kyr BP) layer. Furthermore, we 2 bioRxiv preprint doi: https://doi.org/10.1101/2023.12.01.569562; this version posted December 3, 2023. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license. track changes in plant DNA which likely corresponds with both grazing practices and wider understandings of environmental retrogressions in this period. Our results at VM support the understanding that the full expansion of herding to forested ecoregions did not take place until the Late Neolithic, with initial management practices focused on sheep (Ovis). Importantly, we identify a gradual change in dominant species from sheep to pigs (Sus) by the Late Bronze Age. This correlates with the mid-Holocene transformation of forest structure and can potentially be the consequence of this shift in forest succession patterns, nutrient depletion, and habitat connectivity. Overall, our results demonstrate the possibilities for sedaDNA to explore past human-environment systems and emphasise the value of archaeological deposits as genetic archives for historical ecology.