Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest
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 extr...
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ftubpotsdam:oai:kobv.de-opus4-uni-potsdam:58146 2023-12-17T10:50:56+01:00 Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest Schulte, Luise (Dr.) Bernhardt, Nadine Stoof-Leichsenring, Kathleen Rosemarie Zimmermann, Heike Hildegard Pestryakova, Luidmila Agafyevna Epp, Laura S. Herzschuh, Ulrike (Prof. Dr.) 2020-12-15 https://publishup.uni-potsdam.de/frontdoor/index/index/docId/58146 https://doi.org/10.1111/1755-0998.13311 eng eng https://publishup.uni-potsdam.de/frontdoor/index/index/docId/58146 https://doi.org/10.1111/1755-0998.13311 https://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/closedAccess ddc:570 Institut für Biochemie und Biologie article doc-type:article 2020 ftubpotsdam https://doi.org/10.1111/1755-0998.13311 2023-11-19T23:35:18Z 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. Article in Journal/Newspaper Taymyr Siberia University of Potsdam: publish.UP Taymyr ENVELOPE(89.987,89.987,68.219,68.219) Molecular Ecology Resources 21 3 801 815 |
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Open Polar |
collection |
University of Potsdam: publish.UP |
op_collection_id |
ftubpotsdam |
language |
English |
topic |
ddc:570 Institut für Biochemie und Biologie |
spellingShingle |
ddc:570 Institut für Biochemie und Biologie Schulte, Luise (Dr.) Bernhardt, Nadine Stoof-Leichsenring, Kathleen Rosemarie Zimmermann, Heike Hildegard Pestryakova, Luidmila Agafyevna Epp, Laura S. Herzschuh, Ulrike (Prof. Dr.) Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest |
topic_facet |
ddc:570 Institut für Biochemie und Biologie |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Schulte, Luise (Dr.) Bernhardt, Nadine Stoof-Leichsenring, Kathleen Rosemarie Zimmermann, Heike Hildegard Pestryakova, Luidmila Agafyevna Epp, Laura S. Herzschuh, Ulrike (Prof. Dr.) |
author_facet |
Schulte, Luise (Dr.) Bernhardt, Nadine Stoof-Leichsenring, Kathleen Rosemarie Zimmermann, Heike Hildegard Pestryakova, Luidmila Agafyevna Epp, Laura S. Herzschuh, Ulrike (Prof. Dr.) |
author_sort |
Schulte, Luise (Dr.) |
title |
Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest |
title_short |
Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest |
title_full |
Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest |
title_fullStr |
Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest |
title_full_unstemmed |
Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest |
title_sort |
hybridization capture of larch (larix mill.) chloroplast genomes from sedimentary ancient dna reveals past changes of siberian forest |
publishDate |
2020 |
url |
https://publishup.uni-potsdam.de/frontdoor/index/index/docId/58146 https://doi.org/10.1111/1755-0998.13311 |
long_lat |
ENVELOPE(89.987,89.987,68.219,68.219) |
geographic |
Taymyr |
geographic_facet |
Taymyr |
genre |
Taymyr Siberia |
genre_facet |
Taymyr Siberia |
op_relation |
https://publishup.uni-potsdam.de/frontdoor/index/index/docId/58146 https://doi.org/10.1111/1755-0998.13311 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/closedAccess |
op_doi |
https://doi.org/10.1111/1755-0998.13311 |
container_title |
Molecular Ecology Resources |
container_volume |
21 |
container_issue |
3 |
container_start_page |
801 |
op_container_end_page |
815 |
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1785576054952296448 |