Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden
The lake sediments of Hässeldala Port in south-east Sweden provide an archive of local and regional environmental conditions ~14.5–9.5 ka BP (thousand years before present) and allow testing DNA sequencing techniques to reconstruct past vegetation changes. We combined shotgun sequencing with plant m...
Published in: | Frontiers in Ecology and Evolution |
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ftdoajarticles:oai:doaj.org/article:5585f9615e8e4d61988946d1252c45c6 2023-05-15T18:28:32+02:00 Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden Laura Parducci Inger Greve Alsos Per Unneberg Mikkel W. Pedersen Lu Han Youri Lammers J. Sakari Salonen Minna M. Väliranta Tanja Slotte Barbara Wohlfarth 2019-06-01T00:00:00Z https://doi.org/10.3389/fevo.2019.00189 https://doaj.org/article/5585f9615e8e4d61988946d1252c45c6 EN eng Frontiers Media S.A. https://www.frontiersin.org/article/10.3389/fevo.2019.00189/full https://doaj.org/toc/2296-701X 2296-701X doi:10.3389/fevo.2019.00189 https://doaj.org/article/5585f9615e8e4d61988946d1252c45c6 Frontiers in Ecology and Evolution, Vol 7 (2019) environmental DNA ancient DNA shotgun sequencing (metagenomics) pollen macrofossils remains lake sediments Evolution QH359-425 Ecology QH540-549.5 article 2019 ftdoajarticles https://doi.org/10.3389/fevo.2019.00189 2022-12-31T02:29:50Z The lake sediments of Hässeldala Port in south-east Sweden provide an archive of local and regional environmental conditions ~14.5–9.5 ka BP (thousand years before present) and allow testing DNA sequencing techniques to reconstruct past vegetation changes. We combined shotgun sequencing with plant micro- and macrofossil analyses to investigate sediments dating to the Allerød (14.1–12.7 ka BP), Younger Dryas (12.7–11.7 ka BP), and Preboreal (<11.7 ka BP). Number of reads and taxa were not associated with sample age or organic content. This suggests that, beyond the initial rapid degradation, DNA is still present. The proportion of recovered plant DNA was low, but allowed identifying an important number of plant taxa, thus adding valid information on the composition of the local vegetation. Importantly, DNA provides a stronger signal of plant community changes than plant micro- and plant macrofossil analyses alone, since a larger number of new taxa were recorded in Younger Dryas samples. A comparison between the three proxies highlights differences and similarities and supports earlier findings that plants growing close to or within a lake are recorded by DNA. Plant macrofossil remains moreover show that tree birch was present close to the ancient lake since the Allerød; together with the DNA results, this indicates that boreal to subarctic climatic conditions also prevailed during the cold Younger Dryas interval. Increasing DNA reference libraries and enrichment strategies prior to sequencing are necessary to improve the potential and accuracy of plant identification using the shotgun metagenomic approach. Article in Journal/Newspaper Subarctic Directory of Open Access Journals: DOAJ Articles Frontiers in Ecology and Evolution 7 |
institution |
Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
environmental DNA ancient DNA shotgun sequencing (metagenomics) pollen macrofossils remains lake sediments Evolution QH359-425 Ecology QH540-549.5 |
spellingShingle |
environmental DNA ancient DNA shotgun sequencing (metagenomics) pollen macrofossils remains lake sediments Evolution QH359-425 Ecology QH540-549.5 Laura Parducci Inger Greve Alsos Per Unneberg Mikkel W. Pedersen Lu Han Youri Lammers J. Sakari Salonen Minna M. Väliranta Tanja Slotte Barbara Wohlfarth Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden |
topic_facet |
environmental DNA ancient DNA shotgun sequencing (metagenomics) pollen macrofossils remains lake sediments Evolution QH359-425 Ecology QH540-549.5 |
description |
The lake sediments of Hässeldala Port in south-east Sweden provide an archive of local and regional environmental conditions ~14.5–9.5 ka BP (thousand years before present) and allow testing DNA sequencing techniques to reconstruct past vegetation changes. We combined shotgun sequencing with plant micro- and macrofossil analyses to investigate sediments dating to the Allerød (14.1–12.7 ka BP), Younger Dryas (12.7–11.7 ka BP), and Preboreal (<11.7 ka BP). Number of reads and taxa were not associated with sample age or organic content. This suggests that, beyond the initial rapid degradation, DNA is still present. The proportion of recovered plant DNA was low, but allowed identifying an important number of plant taxa, thus adding valid information on the composition of the local vegetation. Importantly, DNA provides a stronger signal of plant community changes than plant micro- and plant macrofossil analyses alone, since a larger number of new taxa were recorded in Younger Dryas samples. A comparison between the three proxies highlights differences and similarities and supports earlier findings that plants growing close to or within a lake are recorded by DNA. Plant macrofossil remains moreover show that tree birch was present close to the ancient lake since the Allerød; together with the DNA results, this indicates that boreal to subarctic climatic conditions also prevailed during the cold Younger Dryas interval. Increasing DNA reference libraries and enrichment strategies prior to sequencing are necessary to improve the potential and accuracy of plant identification using the shotgun metagenomic approach. |
format |
Article in Journal/Newspaper |
author |
Laura Parducci Inger Greve Alsos Per Unneberg Mikkel W. Pedersen Lu Han Youri Lammers J. Sakari Salonen Minna M. Väliranta Tanja Slotte Barbara Wohlfarth |
author_facet |
Laura Parducci Inger Greve Alsos Per Unneberg Mikkel W. Pedersen Lu Han Youri Lammers J. Sakari Salonen Minna M. Väliranta Tanja Slotte Barbara Wohlfarth |
author_sort |
Laura Parducci |
title |
Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden |
title_short |
Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden |
title_full |
Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden |
title_fullStr |
Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden |
title_full_unstemmed |
Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden |
title_sort |
shotgun environmental dna, pollen, and macrofossil analysis of lateglacial lake sediments from southern sweden |
publisher |
Frontiers Media S.A. |
publishDate |
2019 |
url |
https://doi.org/10.3389/fevo.2019.00189 https://doaj.org/article/5585f9615e8e4d61988946d1252c45c6 |
genre |
Subarctic |
genre_facet |
Subarctic |
op_source |
Frontiers in Ecology and Evolution, Vol 7 (2019) |
op_relation |
https://www.frontiersin.org/article/10.3389/fevo.2019.00189/full https://doaj.org/toc/2296-701X 2296-701X doi:10.3389/fevo.2019.00189 https://doaj.org/article/5585f9615e8e4d61988946d1252c45c6 |
op_doi |
https://doi.org/10.3389/fevo.2019.00189 |
container_title |
Frontiers in Ecology and Evolution |
container_volume |
7 |
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1766211039453511680 |