Data from: Plant DNA metabarcoding of lake sediments: how does it represent the contemporary vegetation ...
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...
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Online Access: | https://dx.doi.org/10.5061/dryad.g72v731 https://datadryad.org/stash/dataset/doi:10.5061/dryad.g72v731 |
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ftdatacite:10.5061/dryad.g72v731 2024-02-04T10:03:16+01:00 Data from: Plant DNA metabarcoding of lake sediments: how does it represent the contemporary vegetation ... Alsos, Inger Greve Lammers, Youri Yoccoz, Nigel Giles Jørgensen, Tina Sjögren, Per Gielly, Ludovic Edwards, Mary E. 2019 https://dx.doi.org/10.5061/dryad.g72v731 https://datadryad.org/stash/dataset/doi:10.5061/dryad.g72v731 en eng Dryad https://dx.doi.org/10.1371/journal.pone.0195403 Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode cc0-1.0 biomonitoring palaeobotany Holocene Dataset dataset 2019 ftdatacite https://doi.org/10.5061/dryad.g72v73110.1371/journal.pone.0195403 2024-01-05T01:14:15Z 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. ... : NGSfilter file.The ngsfilter file containing the sample - PCR tag information necessary for demultiplexing the sequence data in OBITools.140704_SND104_B_L001_GZO-13.ngsfilterPost OBITools analysis scriptThe R script contains the various commands that were used for filtering the metabarcoding data and matching it to the vegetation.FilterDNAandCompareToVegetation.RVegetation dataThe results of the vegetation surveys of the 11 lakes. Abundance assignment in the >2m survey is follows: Dominant taxa are recorded as 4, common taxa as 3, scattered taxa as 2 and rare taxa as 1.Vegetation.csvMetabarcoding resultsThe OBITools output, expanded with the lake name, core number, depth information and and a shorter taxa code used for linking the results to the vegetation data.IdentifiedDNA.tsvSample code informationFile that links the sample codes used in the study to the lake name, core and depth information.SampleToSampleInfo.tsvForward reads (part 1)Compressed FASTQ file containing the first half of the forward ... Dataset Northern Norway DataCite Metadata Store (German National Library of Science and Technology) Norway |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
English |
topic |
biomonitoring palaeobotany Holocene |
spellingShingle |
biomonitoring palaeobotany Holocene Alsos, Inger Greve Lammers, Youri Yoccoz, Nigel Giles Jørgensen, Tina Sjögren, Per Gielly, Ludovic Edwards, Mary E. Data from: Plant DNA metabarcoding of lake sediments: how does it represent the contemporary vegetation ... |
topic_facet |
biomonitoring palaeobotany Holocene |
description |
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. ... : NGSfilter file.The ngsfilter file containing the sample - PCR tag information necessary for demultiplexing the sequence data in OBITools.140704_SND104_B_L001_GZO-13.ngsfilterPost OBITools analysis scriptThe R script contains the various commands that were used for filtering the metabarcoding data and matching it to the vegetation.FilterDNAandCompareToVegetation.RVegetation dataThe results of the vegetation surveys of the 11 lakes. Abundance assignment in the >2m survey is follows: Dominant taxa are recorded as 4, common taxa as 3, scattered taxa as 2 and rare taxa as 1.Vegetation.csvMetabarcoding resultsThe OBITools output, expanded with the lake name, core number, depth information and and a shorter taxa code used for linking the results to the vegetation data.IdentifiedDNA.tsvSample code informationFile that links the sample codes used in the study to the lake name, core and depth information.SampleToSampleInfo.tsvForward reads (part 1)Compressed FASTQ file containing the first half of the forward ... |
format |
Dataset |
author |
Alsos, Inger Greve Lammers, Youri Yoccoz, Nigel Giles Jørgensen, Tina Sjögren, Per Gielly, Ludovic Edwards, Mary E. |
author_facet |
Alsos, Inger Greve Lammers, Youri Yoccoz, Nigel Giles Jørgensen, Tina Sjögren, Per Gielly, Ludovic Edwards, Mary E. |
author_sort |
Alsos, Inger Greve |
title |
Data from: Plant DNA metabarcoding of lake sediments: how does it represent the contemporary vegetation ... |
title_short |
Data from: Plant DNA metabarcoding of lake sediments: how does it represent the contemporary vegetation ... |
title_full |
Data from: Plant DNA metabarcoding of lake sediments: how does it represent the contemporary vegetation ... |
title_fullStr |
Data from: Plant DNA metabarcoding of lake sediments: how does it represent the contemporary vegetation ... |
title_full_unstemmed |
Data from: Plant DNA metabarcoding of lake sediments: how does it represent the contemporary vegetation ... |
title_sort |
data from: plant dna metabarcoding of lake sediments: how does it represent the contemporary vegetation ... |
publisher |
Dryad |
publishDate |
2019 |
url |
https://dx.doi.org/10.5061/dryad.g72v731 https://datadryad.org/stash/dataset/doi:10.5061/dryad.g72v731 |
geographic |
Norway |
geographic_facet |
Norway |
genre |
Northern Norway |
genre_facet |
Northern Norway |
op_relation |
https://dx.doi.org/10.1371/journal.pone.0195403 |
op_rights |
Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode cc0-1.0 |
op_doi |
https://doi.org/10.5061/dryad.g72v73110.1371/journal.pone.0195403 |
_version_ |
1789970559505793024 |