10.5061/DRYAD.NM3PQ
Elbrecht, Vasco
University of Duisburg-Essen
Vamos, Ecaterina Edith
University of Duisburg-Essen
Meissner, Kristian
Finnish Environment Institute
Aroviita, Jukka
Finnish Environment Institute
Leese, Florian
University of Duisburg-Essen
Data from: Assessing strengths and weaknesses of DNA metabarcoding based
macroinvertebrate identification for routine stream monitoring
Dryad
dataset
2018
2018-03-29T00:00:00Z
2018-03-29T00:00:00Z
en
https://doi.org/10.1111/2041-210x.12789
1012476067 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
1) DNA metabarcoding holds great promise for the assessment of
macroinvertebrates in stream ecosystems. However, few large-scale studies
have compared the performance of DNA metabarcoding with that of routine
morphological identification. 2) We performed metabarcoding using four
primer sets on macroinvertebrate samples from 18 stream sites across
Finland. The samples were collected in 2013 and identified based on
morphology as part of a Finnish stream monitoring program. Specimens were
morphologically classified, following standardised protocols, to the
lowest taxonomic level for which identification was feasible in the
routine national monitoring. 3) DNA metabarcoding identified more than
twice the number of taxa than the morphology-based protocol, and also
yielded a higher taxonomic resolution. For each sample, we detected more
taxa by metabarcoding than by the morphological method, and all four
primer sets exhibited comparably good performance. Sequence read abundance
and the number of specimens per taxon (a proxy for biomass) were
significantly correlated in each sample, although the adjusted R2 were
low. With a few exceptions, the ecological status assessment metrics
calculated from morphological and DNA metabarcoding datasets were similar.
Given the recent reduction in sequencing costs, metabarcoding is currently
approximately as expensive as morphology-based identification. 4) Using
samples obtained in the field, we demonstrated that DNA metabarcoding can
achieve comparable assessment results to current protocols relying on
morphological identification. Thus, metabarcoding represents a feasible
and reliable method to identify macroinvertebrates in stream
bioassessment, and offers powerful advantage over morphological
identification in providing identification for taxonomic groups that are
unfeasible to identify in routine protocols. To unlock the full potential
of DNA metabarcoding for ecosystem assessment, however, it will be
necessary to address key problems with current laboratory protocols and
reference databases.
Metabarcoding pipeline and scriptsThis folder contains all scripts used to
process the raw sequence data into OTUs. Additionally, all scripts for
data analysis and figure generation were
included.Dryad_Finland_2017.zipDNA extraction and PCR protocolsRaw data on
laboratory protocols. Includes gel pictures, PCR sheets and scans of the
laboratory protocols as well as pictures of the dried samples.laboratory
notes.zipPreprocessed HTS data (144 samples)Sequence data for the 144
sequenced PCR reactions. Files are PE merged, trimmed and quality filtered
as described in the manuscript using the scripts also provided on dryad.
The sequence files are dereplicated ready to be clustered into OTUs. For
OTU sequences and counts see table S4 of the manuscript.6 dereplicate.zip
Finland