Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation
This is the final version of the following article: Alsos, I.G., Lammers, Y., Yoccoz, N.G., Jørgensen, T., Sjögren, P., Gielly, L. & Edwards, M.E. (2018). Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation. PLoS ONE, 13(4). https://doi.org/10.1371/journa...
Published in: | PLOS ONE |
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Main Authors: | , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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Public Library of Science
2018
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Online Access: | https://hdl.handle.net/10037/13448 |
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University of Tromsø: Munin Open Research Archive |
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ftunivtroemsoe |
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English |
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VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480 VDP::Mathematics and natural science: 400::Zoology and botany: 480 Lakes Sediment Polymerase chain reaction Sequence databases DNA filter assay Taxonomy Ancient DNA Pollen |
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VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480 VDP::Mathematics and natural science: 400::Zoology and botany: 480 Lakes Sediment Polymerase chain reaction Sequence databases DNA filter assay Taxonomy Ancient DNA Pollen Alsos, Inger Greve Lammers, Youri Yoccoz, Nigel Gilles Jørgensen, Tina Sjögren, Per Gielly, Ludovic Edwards, Mary E. Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation |
topic_facet |
VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480 VDP::Mathematics and natural science: 400::Zoology and botany: 480 Lakes Sediment Polymerase chain reaction Sequence databases DNA filter assay Taxonomy Ancient DNA Pollen |
description |
This is the final version of the following article: Alsos, I.G., Lammers, Y., Yoccoz, N.G., Jørgensen, T., Sjögren, P., Gielly, L. & Edwards, M.E. (2018). Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation. PLoS ONE, 13(4). https://doi.org/10.1371/journal.pone.0195403, which can be retrieved from https://doi.org/10.1371/journal.pone.0195403 . Licensed CC BY-NC-ND 4.0. Metabarcoding of lake sediments have been shown to reveal current and past biodiversity, but little is known about the degree to which taxa growing in the vegetation are represented in environmental DNA (eDNA) records. We analysed composition of lake and catchment vegetation and vascular plant eDNA at 11 lakes in northern Norway. Out of 489 records of taxa growing within 2 m from the lake shore, 17–49% (mean 31%) of the identifiable taxa recorded were detected with eDNA. Of the 217 eDNA records of 47 plant taxa in the 11 lakes, 73% and 12% matched taxa recorded in vegetation surveys within 2 m and up to about 50 m away from the lakeshore, respectively, whereas 16% were not recorded in the vegetation surveys of the same lake. The latter include taxa likely overlooked in the vegetation surveys or growing outside the survey area. The percentages detected were 61, 47, 25, and 15 for dominant, common, scattered, and rare taxa, respectively. Similar numbers for aquatic plants were 88, 88, 33 and 62%, respectively. Detection rate and taxonomic resolution varied among plant families and functional groups with good detection of e.g. Ericaceae, Roseaceae, deciduous trees, ferns, club mosses and aquatics. The representation of terrestrial taxa in eDNA depends on both their distance from the sampling site and their abundance and is sufficient for recording vegetation types. For aquatic vegetation, eDNA may be comparable with, or even superior to, in-lake vegetation surveys and may therefore be used as an tool for biomonitoring. For reconstruction of terrestrial vegetation, technical improvements and more intensive sampling is needed to detect a higher proportion of rare taxa although DNA of some taxa may never reach the lake sediments due to taphonomical constrains. Nevertheless, eDNA performs similar to conventional methods of pollen and macrofossil analyses and may therefore be an important tool for reconstruction of past vegetation. |
format |
Article in Journal/Newspaper |
author |
Alsos, Inger Greve Lammers, Youri Yoccoz, Nigel Gilles Jørgensen, Tina Sjögren, Per Gielly, Ludovic Edwards, Mary E. |
author_facet |
Alsos, Inger Greve Lammers, Youri Yoccoz, Nigel Gilles Jørgensen, Tina Sjögren, Per Gielly, Ludovic Edwards, Mary E. |
author_sort |
Alsos, Inger Greve |
title |
Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation |
title_short |
Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation |
title_full |
Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation |
title_fullStr |
Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation |
title_full_unstemmed |
Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation |
title_sort |
plant dna metabarcoding of lake sediments: how does it represent the contemporary vegetation |
publisher |
Public Library of Science |
publishDate |
2018 |
url |
https://hdl.handle.net/10037/13448 |
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ENVELOPE(-66.333,-66.333,-68.617,-68.617) ENVELOPE(14.817,14.817,67.517,67.517) |
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Norway Lammers Alsos |
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Norway Lammers Alsos |
genre |
Northern Norway |
genre_facet |
Northern Norway |
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Lammers, Y. (2020). Sedimentary ancient DNA: Exploring methods of ancient DNA analysis for different taxonomic groups. (Doctoral thesis). https://hdl.handle.net/10037/17437. PLoS ONE info:eu-repo/grantAgreement/RCN/FRIMEDBIO/213692/Norway/Ancient DNA of NW Europe reveals responses to climate change// info:eu-repo/grantAgreement/RCN/FRIMEDBIO/250963/Norway/Ecosystem change and species persistence over time: a genome-based approach/ECOGEN/ info:eu-repo/grantAgreement/RCN/KLIMAFORSK/230617/Norway/Ancient DNA of NW Europe reveals responses to climate change// Alsos, I.G., Lammers, Y., Yoccoz, N.G., Jørgensen, T., Sjögren, P., Gielly, L. & Edwards, M.E. (2018). Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation. PLoS ONE, 13(4). https://doi.org/10.1371/journal.pone.0195403 FRIDAID 1583395 1932-6203 Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation https://hdl.handle.net/10037/13448 |
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openAccess |
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PLOS ONE |
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e0195403 |
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ftunivtroemsoe:oai:munin.uit.no:10037/13448 2023-05-15T17:43:42+02:00 Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation Alsos, Inger Greve Lammers, Youri Yoccoz, Nigel Gilles Jørgensen, Tina Sjögren, Per Gielly, Ludovic Edwards, Mary E. 2018-04-17 https://hdl.handle.net/10037/13448 eng eng Public Library of Science Lammers, Y. (2020). Sedimentary ancient DNA: Exploring methods of ancient DNA analysis for different taxonomic groups. (Doctoral thesis). https://hdl.handle.net/10037/17437. PLoS ONE info:eu-repo/grantAgreement/RCN/FRIMEDBIO/213692/Norway/Ancient DNA of NW Europe reveals responses to climate change// info:eu-repo/grantAgreement/RCN/FRIMEDBIO/250963/Norway/Ecosystem change and species persistence over time: a genome-based approach/ECOGEN/ info:eu-repo/grantAgreement/RCN/KLIMAFORSK/230617/Norway/Ancient DNA of NW Europe reveals responses to climate change// Alsos, I.G., Lammers, Y., Yoccoz, N.G., Jørgensen, T., Sjögren, P., Gielly, L. & Edwards, M.E. (2018). Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation. PLoS ONE, 13(4). https://doi.org/10.1371/journal.pone.0195403 FRIDAID 1583395 1932-6203 Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation https://hdl.handle.net/10037/13448 openAccess VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480 VDP::Mathematics and natural science: 400::Zoology and botany: 480 Lakes Sediment Polymerase chain reaction Sequence databases DNA filter assay Taxonomy Ancient DNA Pollen Journal article Tidsskriftartikkel Peer reviewed 2018 ftunivtroemsoe 2021-06-25T17:55:55Z This is the final version of the following article: Alsos, I.G., Lammers, Y., Yoccoz, N.G., Jørgensen, T., Sjögren, P., Gielly, L. & Edwards, M.E. (2018). Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation. PLoS ONE, 13(4). https://doi.org/10.1371/journal.pone.0195403, which can be retrieved from https://doi.org/10.1371/journal.pone.0195403 . Licensed CC BY-NC-ND 4.0. Metabarcoding of lake sediments have been shown to reveal current and past biodiversity, but little is known about the degree to which taxa growing in the vegetation are represented in environmental DNA (eDNA) records. We analysed composition of lake and catchment vegetation and vascular plant eDNA at 11 lakes in northern Norway. Out of 489 records of taxa growing within 2 m from the lake shore, 17–49% (mean 31%) of the identifiable taxa recorded were detected with eDNA. Of the 217 eDNA records of 47 plant taxa in the 11 lakes, 73% and 12% matched taxa recorded in vegetation surveys within 2 m and up to about 50 m away from the lakeshore, respectively, whereas 16% were not recorded in the vegetation surveys of the same lake. The latter include taxa likely overlooked in the vegetation surveys or growing outside the survey area. The percentages detected were 61, 47, 25, and 15 for dominant, common, scattered, and rare taxa, respectively. Similar numbers for aquatic plants were 88, 88, 33 and 62%, respectively. Detection rate and taxonomic resolution varied among plant families and functional groups with good detection of e.g. Ericaceae, Roseaceae, deciduous trees, ferns, club mosses and aquatics. The representation of terrestrial taxa in eDNA depends on both their distance from the sampling site and their abundance and is sufficient for recording vegetation types. For aquatic vegetation, eDNA may be comparable with, or even superior to, in-lake vegetation surveys and may therefore be used as an tool for biomonitoring. For reconstruction of terrestrial vegetation, technical improvements and more intensive sampling is needed to detect a higher proportion of rare taxa although DNA of some taxa may never reach the lake sediments due to taphonomical constrains. Nevertheless, eDNA performs similar to conventional methods of pollen and macrofossil analyses and may therefore be an important tool for reconstruction of past vegetation. Article in Journal/Newspaper Northern Norway University of Tromsø: Munin Open Research Archive Norway Lammers ENVELOPE(-66.333,-66.333,-68.617,-68.617) Alsos ENVELOPE(14.817,14.817,67.517,67.517) PLOS ONE 13 4 e0195403 |