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...
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Frontiers Media S.A.
2019-06-01
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| Series: | Frontiers in Ecology and Evolution |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fevo.2019.00189/full |
| _version_ | 1818201501381689344 |
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| author | Laura Parducci Inger Greve Alsos Per Unneberg Mikkel W. Pedersen Lu Han Lu Han Youri Lammers J. Sakari Salonen Minna M. Väliranta Tanja Slotte Tanja Slotte Barbara Wohlfarth |
| author_facet | Laura Parducci Inger Greve Alsos Per Unneberg Mikkel W. Pedersen Lu Han Lu Han Youri Lammers J. Sakari Salonen Minna M. Väliranta Tanja Slotte Tanja Slotte Barbara Wohlfarth |
| author_sort | Laura Parducci |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-12T02:54:33Z |
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| id | doaj.art-5585f9615e8e4d61988946d1252c45c6 |
| institution | Directory Open Access Journal |
| issn | 2296-701X |
| language | English |
| last_indexed | 2024-12-12T02:54:33Z |
| publishDate | 2019-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Ecology and Evolution |
| spelling | doaj.art-5585f9615e8e4d61988946d1252c45c62022-12-22T00:40:48ZengFrontiers Media S.A.Frontiers in Ecology and Evolution2296-701X2019-06-01710.3389/fevo.2019.00189440956Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern SwedenLaura Parducci0Inger Greve Alsos1Per Unneberg2Mikkel W. Pedersen3Lu Han4Lu Han5Youri Lammers6J. Sakari Salonen7Minna M. Väliranta8Tanja Slotte9Tanja Slotte10Barbara Wohlfarth11Department of Ecology and Genetics, The Evolutionary Biology Centre, Uppsala University, Uppsala, SwedenTromsø Museum, University of Tromsø – The Arctic University of Norway, Tromsø, NorwayScience for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, SwedenDepartment of Zoology, University of Cambridge, Cambridge, United KingdomDepartment of Ecology and Genetics, The Evolutionary Biology Centre, Uppsala University, Uppsala, SwedenAncient DNA Laboratory, College of Life Sciences, Jilin University, Changchun, ChinaTromsø Museum, University of Tromsø – The Arctic University of Norway, Tromsø, NorwayDepartment of Geosciences and Geography, University of Helsinki, Helsinki, FinlandEnvironmental Change Research Unit (ECRU), Ecosystems and Environment Research Programme, University of Helsinki, Helsinki, FinlandDepartment of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, SwedenScience for Life Laboratory, Solna, Sweden0Department of Geological Sciences and Bolin Centre for Climate Research, Stockholm University, Stockholm, SwedenThe 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.https://www.frontiersin.org/article/10.3389/fevo.2019.00189/fullenvironmental DNAancient DNAshotgun sequencing (metagenomics)pollenmacrofossils remainslake sediments |
| spellingShingle | Laura Parducci Inger Greve Alsos Per Unneberg Mikkel W. Pedersen Lu Han Lu Han Youri Lammers J. Sakari Salonen Minna M. Väliranta Tanja Slotte Tanja Slotte Barbara Wohlfarth Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden Frontiers in Ecology and Evolution environmental DNA ancient DNA shotgun sequencing (metagenomics) pollen macrofossils remains lake sediments |
| title | 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_short | 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 |
| topic | environmental DNA ancient DNA shotgun sequencing (metagenomics) pollen macrofossils remains lake sediments |
| url | https://www.frontiersin.org/article/10.3389/fevo.2019.00189/full |
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