Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest

Abstract

<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>

Holocene chloroplast genetic variation of shrubs (Alnus alnobetula, Betula nana, Salix sp.) at the siberian tundra‐taiga ecotone inferred from modern chloroplast genome assembly and sedimentary ancient DNA analyses

“…Only the conserved chloroplast regions between L. gmelinii and Alnus , Betula, and Salix were captured since the hybridization capture baits were specifically designed for targeting L. gmelinii (Schulte et al., 2020; Zimmermann et al., 2019). The percentage of pairwise identity between the chloroplast genomes of L. gmelinii and A. alnobetula , B. nana, and Salix sp.…”

“…Laboratory work and data processing were performed by Schulte et al. (2020). Core samples were collected at the following depths/ages: 121.5 cm/~6,700 cal yr BP, 87.5 cm/~5,400 cal yr BP, 46.5 cm/~1900 cal yr BP, and 2.5 cm/~60 cal yr BP.…”

“…Ancient DNA damages were estimated using mapDamage (v. 2.0.8; Jónsson et al., 2013) by Schulte et al. (2020), in order to prove the authenticity of the obtained data.…”

“…Schulte et al. (2020) show that shotgun sequencing can result in low sequencing coverage of specific taxa of interest due to the extremely high presence of unknown DNA sequences in sedaDNA. To address this problem, they used a hybridization capture approach specifically designed for the Larix chloroplast genome.…”

“…To address this problem, they used a hybridization capture approach specifically designed for the Larix chloroplast genome. This method successfully enriched targeted sequences and improved accurate detection of genetic variants in sedaDNA (Schulte et al., 2020). However, conserved chloroplast DNA (cpDNA) regions from nontargeted taxa were also captured through the cp conserved regions.…”