DOI: 10.5061/dryad.37pvmcvpr
title: Data from: DNA metabarcoding improves the taxonomic resolution of visually determined diet composition of beaked redfish (Sebastes sp.)

description: Beaked redfishes (Sebastes fasciatus and Sebastes mentella) of the
 northwest Atlantic have recently reached record abundance levels in the
 estuary and the northern Gulf of St. Lawrence, dominated
 by Sebastes mentella. Knowledge of their diet composition is
 essential to understand the trophic role that these groundfish play in the
 ecosystem. The objective of the present study was to compare the
 performance of visual examination and DNA metabarcoding of stomach
 contents of the same individual redfish caught in the lower Estuary and
 northern Gulf of St. Lawrence. Using a universal metazoan mitochondrial
 cytochrome c oxidase subunit I (COI) marker, we identified a total of 24
 taxonomic groups, composed of 22 species and two genera in the content of
 185 stomachs with DNA metabarcoding. We compared these results to the 25
 prey types, eight identified at the genus and nine at the species level,
 obtained with visual stomach content analysis (SCA). While both techniques
 revealed a similar diet composition, our results showed that the SCA and
 DNA metabarcoding perform differently for particular prey categories, both
 in terms of detectability and taxonomic resolution, as well as in the
 estimated relative importance of weight and occurrence in the diet. The
 use of DNA metabarcoding along with SCA validates and improves the
 taxonomic resolution of visually determined prey, which supports the
 concept that both techniques provide useful complementary information on
 the diet of these redfish species.
description: Redfish stomachs were thawed for visual analysis at the
 Maurice-Lamontagne Institute (Mont-Joli, Canada) and each prey taxon found in the stomach contents
 was weighed and identified to the lowest taxonomic level
 possible under a
 dissecting microscope using keys and identification guides.
 For metabarcoding, we annotated each unique read of each
 sample to the most similar species of the database if the sequences had at
 least 98% similarity. In cases of ties, referred to as multiple hits, when
 more than one species from the database had the same distance from the
 queried sequence, all the tied annotations were reported. Barque then
 produced a table of prey taxa counts (including the multiple hits) for
 each sample.
description: # Data from: DNA metabarcoding improves the taxonomic resolution of
 visually determined diet composition of beaked redfish (*Sebastes* sp.) ##
 Description of the Data Redfish diet composition data were analysed within
 three defined size classes: small (&lt; 20 cm, n=95), medium (20–30 cm,
 n=53), and large redfish (≥ 30 cm, n=37), for both the visual and
 molecular methods. ### **Excel tab 1 (Sequence Dropout)** Sequencing
 result information: Total reads produced by the MiSeq sequencer and total
 reads after each step of Barque. Two negative controls (Control_blank_1
 and Control_blank_2) were treated and extracted as regular samples and
 sequenced to check for DNA contamination. The first blank control
 corresponds to samples whose boxes are in gray and the second white
 control corresponds to samples whose boxes are not highlighted. ### Excel
 tab 2 (SequenceRead\_before\_processing) Raw metabarcoding results. We
 used Barque
 ([https://github.com/enormandeau/barque](https://github.com/enormandeau/barque) to examine the biodiversity of stomach contents at the species level. All the animal bins (barcode index number) were downloaded from the BOLD database on 2023-09-12 and all the COI fragments corresponding to the used primers were incorporated into the database used by Barque v1.8.5 ([https://boldsystems.org/index.php/Public_BarcodeIndexNumber_Home](https://boldsystems.org/index.php/Public_BarcodeIndexNumber_Home). We annotated each unique read of each sample to the most similar species of the database if the sequences had at least 98% similarity. In cases of ties, referred to as multiple hits, when more than one species from the database had the same distance from the queried sequence, all the tied annotations were reported. Barque then produced a table of prey taxa counts (including the multiple hits) for each sample. Sample Read counts from negative controls have been subtracted from the results of prey taxa for each species. The first blank control corresponds to samples whose boxes are in gray and the second white control corresponds to samples whose boxes are not highlighted. ### Excel tab 3 (SequenceRead\_after\_processing) Reads that had equal similarity scores for more than one species were assigned to a higher taxonomic level since it was impossible to discriminate species with certainty (e.g., *Ammodytes* sp. for the multiple hits referencing *Ammodytes americanus* and *Ammodytes dubius*). Read counts from negative controls have been subtracted from the results of prey taxa for each species. ### Excel tab 4 (SCA\_MassPrey\_Redfish) Mass of prey is in grams. Redfish stomachs were thawed for visual analysis at the Maurice-Lamontagne Institute (Mont-Joli, Canada) and each prey taxon found in the stomach contents was weighed to the nearest grams and identified to the lowest taxonomic level possible under a dissecting microscope using keys and identification guides.