Siberian larch (Larix Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the world. It is important to understand the past dynamics of larches in order to predict their likely response to a changing climate in the future. Sedimentary ancient DNA extracted from lake sediment cores can serve as archives to study past vegetation. However, the traditional method of studying sedimentary ancient DNA—metabarcoding—focuses on small fragments, which cannot resolve Larix to species level nor allow a detailed study of population dynamics. Here, we use shotgun sequencing and hybridization capture with long‐range PCR‐generated baits covering the complete Larix chloroplast genome to study Larix populations from a sediment core reaching back to 6700 years from the Taymyr region in northern Siberia. In comparison with shotgun sequencing, hybridization capture results in an increase in taxonomically classified reads by several orders of magnitude and the recovery of complete chloroplast genomes of Larix. Variation in the chloroplast reads corroborates an invasion of Larix gmelinii into the range of Larix sibirica before 6700 years ago. Since then, both species have been present at the site, although larch populations have decreased with only a few trees remaining in what was once a forested area. This study demonstrates for the first time that hybridization capture applied directly to ancient DNA of plants extracted from lake sediments can provide genome‐scale information and is a viable tool for studying past genomic changes in populations of single species, irrespective of a preservation as macrofossil.

<p>Siberian larch (<em>Larix</em> Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the earth. To be able to predict future responses of these forests to a changing climate, it is important to understand also past dynamics of larch populations. One well-preserved archive to study vegetation changes of the past is sedimentary ancient DNA (sedaDNA) extracted from lake sediment cores. We studied a lake sediment core covering 6700 calibrated years BP, from the Taymyr region in northern Siberia. To enrich the sedaDNA for DNA of our focal species <em>Larix</em>, we combine shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the complete <em>Larix</em> chloroplast genome. In comparison to shotgun sequencing, hybridization capture results in an increase of taxonomically classified reads by several orders of magnitude and the recovery of near-complete chloroplast genomes of <em>Larix</em>. Variation in the chloroplast reads confirm an invasion of <em>Larix gmelinii</em> into the range of <em>Larix sibirica</em> before 6700 years ago. In this time span, both species can be detected at the site, although larch populations have decreased from a forested area to a single-tree tundra at present. This study demonstrates for the first time that hybridization capture applied to ancient DNA from lake sediments can provide genome-scale information and is a viable tool for studying past changes of a specific taxon.</p>

Climate change has a major impact on arctic and boreal terrestrial ecosystems as warming leads to northward treeline shifts, inducing consequences for heterotrophic organisms associated with the plant taxa. To unravel ecological dependencies, we address how long-term climatic changes have shaped the palaeo-ecosystems at selected sites in Siberia. We investigated sedimentary ancient DNA from five lakes spanning the last 47,000 years, using the ITS1 marker for fungi and the chloroplast P6 loop marker for vegetation metabarcoding. After bioinformatic processing with the OBItools pipeline, we obtained 706 unique fungal operational taxonomic units (OTUs) and 243 amplicon sequence variants (ASVs) for the plants. We show higher OTU numbers in dry forest tundra as well as boreal forests compared to wet southern tundra. The most abundant fungal taxa in our dataset are Pseudeurotiaceae, Mortierella, Sordariomyceta, Exophiala, Oidiodendron, Protoventuria, Candida vartiovaarae, Pseudeurotium, Gryganskiella fimbricystis, and Trichosporiella cerebriformis. The overall fungal composition is explained by the plant composition as revealed by redundancy analysis. The fungal functional groups show antagonistic relationships in their climate susceptibility. The advance of woody taxa in response to past warming led to an increase in the abundance of mycorrhizae, lichens, and parasites, while yeast and saprotroph distribution declined. We also show co-occurrences between Salicaceae, Larix, and Alnus and their associated pathogens and detect higher mycorrhizal fungus diversity with the presence of Pinaceae. Under future warming, we can expect feedback between fungus compositional and plant diversity changes which will affect forest advance and stability in arctic regions.