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.