Conclusions

Siberian larch forest covers vast areas of northern Asia withLarix as the only tree-forming species. Lake sediments containing ancient DNA constitute an archive to answer the question of how larch forests respond to changing climate, but the low amount of target DNA in combination with a high degree of sequence divergence make them challenging material to study the population dynamics of a specific species. Here we have shown the success of hybridization capture of near-complete chloroplast genomes from 6700-year old lake sediments originating from northern Siberia. Shotgun sequencing of sed aDNA prior to enrichment showed that, depending on the cautiousness of the bioinformatic approach, only very low rates of reads can be securely assigned to taxa even at the domain level. By using PCR-generated baits covering the whole chloroplast of Larix for hybridization capture we could achieve increases by several orders of magnitude of assignable reads. The enrichment of Larix reads was most distinct,but plant DNA in general was also enriched. With ancient DNA from lake sediments, hybridization capture thus offers the potential of not only analysing the target species in depth, but also of studying the taxonomic diversity of the sample in a similar way to traditional molecular barcoding approaches. The method is more costly than the metabarcoding approach but has several advantages: no restriction to specific fragment length or by primer binding sites, avoidance of PCR introduced bias and the possibility of authentication of ancient DNA. Future studies focusing on plant biodiversity changes could focus on conserved coding regions of a set of diverged species to capture a more complete picture of the past vegetation. The analysed Larix reads confirm a general larch forest decline over the last 6700 years. Low rates of L. sibirica variants in proportion to L. gmeliniivariants in the chloroplast could point to an invasion of L. gmelinii into L. sibirica populations before 6700 years ago. This study represents the first demonstration of hybridization capture from ancient DNA derived from lake sediments. Our results open the way for large scale palaeogenomic analyses of ancient population dynamics using lake sediment cores.