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Data from: Plant DNA metabarcoding of lake sediments: how does it represent the contemporary vegetation

Data from: Plant DNA metabarcoding of lake sediments: how does it represent the contemporary vegetation
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 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.,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.ngsfilterPost 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 reads.140704_SND104_B_L001_GZO-13_R1-1.fastq.gzForward reads (part 2)Compressed FASTQ file containing the second half of the forward reads.140704_SND104_B_L001_GZO-13_R1-2.fastq.gzReverse reads (part 1)Compressed FASTQ file containing the first half of the reverse reads.140704_SND104_B_L001_GZO-13_R2-1.fastq.gzReverse reads (part 2)Compressed FASTQ file containing the second half of the reverse reads.140704_SND104_B_L001_GZO-13_R2-2.fastq.gz,
DRYAD
Alsos, Inger Greve
88244b90-b66f-4271-9064-db0544dec568
Lammers, Youri
c71f60ba-9ac1-4a58-900d-0679c5ba0eea
Yoccoz, Nigel Giles
ad6b4fb5-dc6a-4bc6-b1dc-54a5538e632d
Jørgensen, Tina
281e51ae-f3fb-4d2d-a5cf-584a9019aa05
Sjögren, Per
90bd3dc5-55b4-4e1a-801b-884110b7311d
Gielly, Ludovic
0a5c6314-0ee8-4df7-8af0-7bf31b9b15fe
Edwards, Mary E.
4b6a3389-f3a4-4933-b8fd-acdfef72200e
Alsos, Inger Greve
88244b90-b66f-4271-9064-db0544dec568
Lammers, Youri
c71f60ba-9ac1-4a58-900d-0679c5ba0eea
Yoccoz, Nigel Giles
ad6b4fb5-dc6a-4bc6-b1dc-54a5538e632d
Jørgensen, Tina
281e51ae-f3fb-4d2d-a5cf-584a9019aa05
Sjögren, Per
90bd3dc5-55b4-4e1a-801b-884110b7311d
Gielly, Ludovic
0a5c6314-0ee8-4df7-8af0-7bf31b9b15fe
Edwards, Mary E.
4b6a3389-f3a4-4933-b8fd-acdfef72200e

Alsos, Inger Greve, Lammers, Youri, Yoccoz, Nigel Giles, Jørgensen, Tina, Sjögren, Per and Gielly, Ludovic (2019) Data from: Plant DNA metabarcoding of lake sediments: how does it represent the contemporary vegetation. DRYAD doi:10.5061/dryad.g72v731 [Dataset]

Record type: Dataset

Abstract

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.,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.ngsfilterPost 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 reads.140704_SND104_B_L001_GZO-13_R1-1.fastq.gzForward reads (part 2)Compressed FASTQ file containing the second half of the forward reads.140704_SND104_B_L001_GZO-13_R1-2.fastq.gzReverse reads (part 1)Compressed FASTQ file containing the first half of the reverse reads.140704_SND104_B_L001_GZO-13_R2-1.fastq.gzReverse reads (part 2)Compressed FASTQ file containing the second half of the reverse reads.140704_SND104_B_L001_GZO-13_R2-2.fastq.gz,

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More information

Published date: 1 January 2019

Identifiers

Local EPrints ID: 449015
URI: http://eprints.soton.ac.uk/id/eprint/449015
PURE UUID: be20e604-15e5-4a0b-9ea7-0dfba3826a0f
ORCID for Mary E. Edwards: ORCID iD orcid.org/0000-0002-3490-6682

Catalogue record

Date deposited: 13 May 2021 16:39
Last modified: 14 May 2021 01:39

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Contributors

Creator: Inger Greve Alsos
Creator: Youri Lammers
Creator: Nigel Giles Yoccoz
Creator: Tina Jørgensen
Creator: Per Sjögren
Creator: Ludovic Gielly
Contributor: Mary E. Edwards ORCID iD

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