Wild and domesticated animal abundance is associated with greater late-Holocene alpine plant diversity

11 pages, 3 figures, 1 table, supplementary information https://doi.org/10.1038/s41467-025-59028-2.-- Data availability: The lookup dataset for all tag and sample combinations generated in this study have been deposited at the Zenodo repository (https://doi.org/10.5281/zenodo.14283341). The full accession codes for projects are PRJEB85748 https://www.ebi.ac.uk/ena/browser/view/PRJEB85748 and PRJEB52290: https://www.ebi.ac.uk/ena/browser/view/PRJEB52290. The raw OBITools output data, both the P6-loop (all reference libraries) and 16S datasets, are available at the Zenodo repository (https://doi.org/10.5281/zenodo.15132382). The Source Data for Figs. 1–3 and Supplementary Figs. 1–11 generated in this study are provided in the Supplementary Data 11. For acces to any raw materials or core sediments from this study, please contact Dr. Inger Greve Alsos.-- Code availability: The R code used for the statistical analyses can be found in Supplementary Code 1. The identified sequences were filtered in R using a custom script (available at https://github.com/Y-Lammers/MergeAndFilter)

In the face of human land use and climate dynamics, it is essential to know the key drivers of plant species diversity in montane regions. However, the relative roles of climate and ungulates in alpine ecosystem change is an open question. Neither observational data nor traditional palaeoecological data have the power to resolve this issue over decadal to centennial timescales, but sedimentary ancient DNA (sedaDNA) does. Here we record 603 plant taxa, as well as 5 wild, and 6 domesticated mammals from 14 lake sediment records over the last 14,000 years in the European Alps. Sheep were the first domesticated animals detected (at 5.8 ka), with cattle appearing at the early Bronze Age (4.2 ka) and goats arriving later (3.5 ka). While sheep had an impact similar to wild ungulates, cattle have been associated with increased plant diversity over the last 2 ka by promoting the diversity of forbs and graminoids. Modelling of the sedaDNA data revealed a significantly larger effect of cattle and wild ungulates than temperature on plant diversity. Our findings highlight the significant alteration of alpine vegetation and the entire ecosystem in the Alps by wild and domesticated herbivores. This study has immediate implications for the maintenance and management of high plant species diversity in the face of ongoing anthropogenic changes in the land use of montane regions

I.G.A. and Y.L. were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 819192) and the ECOGEN project “Ecosystem change and species persistence over time: A genome-based approach,” financed by Research Council of Norway grant 250963/F20, the latter also supported P.D.H., S.G.-P., and S.Z., most fieldwork, and other running costs. Open access funding was provided by UiT The Arctic University of Norway. S.G.-P. was also supported by the Beatriu de Pinós Programme (BP-2021-00131) and a fellowship from “la Caixa” Foundation (ID 100010434, fellowship code LCF/BQ/PI24/12040011). P.D.H. acknowledges support from the Knut and Alice Wallenberg Foundation (KAW 2021.0048 and KAW 2022.0033). Coring and stratigraphic analyses at Lake Sulzkar were funded through an Earth System Sciences grant from the Austrian Academy of Sciences: “Pulling the plug—Restoration of an Alpine lake”. Coring at Lakes Sangiatto, Hopschu, Emines, Bretaye, and Sulsseewli was supported by the Oeschger Centre for Climate Change Research (OCCR) as part of the Graduate School of Climate Sciences at the University of Bern. The PhyloAlps reference database was built thanks to the following projects: the joint ANR-SNF project Origin-Alps (ANR-16-CE93-0004, SNF-310030L_170059), European Research Council under the European Community’s Seventh Framework Programme FP7/2007-2013 grant agreement 281422 (TEEMBIO), and by the SNF grant 31003A_149508. The sequencing for the PhyloAlps reference database was performed within the framework of the PhyloAlps project, funded by France Génomique (ANR-10-INBS-09-08)

With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)

Peer reviewed