Abstract
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 6700years 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 6700years 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.
Highlights
Siberian forests are unique as they cover a vast area of about 263.2 million ha (Abaimov, 2010) dominated by a single genus of tree, the deciduous conifer larch (Larix Mill.)
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 complex mixture of sequences makes them challenging material to study the population dynamics of a specific species
We have shown the success of hybridization capture of complete chloroplast genomes from 6700-year-old lake sediments originating from northern Siberia
Summary
Siberian forests are unique as they cover a vast area of about 263.2 million ha (Abaimov, 2010) dominated by a single genus of tree, the deciduous conifer larch (Larix Mill.). Beyond the retrieval of short fragments useful for species identification (as used in metabarcoding), it is not clear how complete the genomic record of plants in sediment cores is This is true for chloroplast DNA, which holds valuable ecological and adaptive information, through the genes for photosynthesis, and is widely used for taxonomic identification and phylogenetic analyses (CBOL Plant Working Group et al, 2009; Jansen et al, 2007; Shaw et al, 2007). We apply shotgun sequencing and a hybridization capture approach targeting the complete Larix gmelinii chloroplast genome to sedaDNA samples from a small lake in the Taymyr region of northeastern Siberia. This study presents the first successful recovery of complete chloroplast genomes from ancient lake sediments
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