TY  - JOUR
A1  - Schulte, Luise
A1  - Bernhardt, Nadine
A1  - Stoof-Leichsenring, Kathleen Rosemarie
A1  - Zimmermann, Heike Hildegard
A1  - Pestryakova, Luidmila Agafyevna
A1  - Epp, Laura S.
A1  - Herzschuh, Ulrike
T1  - Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest
JF  - Molecular ecology resources
N2  - 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.
KW  - chloroplast genome
KW  - hybridization capture
KW  - Larix
KW  - sediment core
KW  - sedimentary ancient DNA
KW  - target enrichment
Y1  - 2020
U6  - https://doi.org/10.1111/1755-0998.13311
SN  - 1755-098X
SN  - 1755-0998
VL  - 21
IS  - 3
SP  - 801
EP  - 815
PB  - Wiley
CY  - Hoboken
ER  -