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Data from: All is fish that comes to the net: metabarcoding for rapid fisheries catch assessment

Citation

Talarico, Lorenzo et al. (2020), Data from: All is fish that comes to the net: metabarcoding for rapid fisheries catch assessment, Dryad, Dataset, https://doi.org/10.5061/dryad.7m0cfxpsh

Abstract

AbstractMonitoring marine resource exploitation is a key activity in fisheries science and biodiversity conservation. Since research surveys are time-consuming and costly, fishery-dependent data (i.e. derived directly from fishing vessels) are increasingly credited with a key role in expanding the reach of ocean monitoring. Fishing vessels may be seen as widely ranging data-collecting platforms, which could act as a fleet of sentinels for monitoring marine life, in particular exploited stocks. Here, we investigate the possibility of assessing catch composition of single hauls carried out by trawlers by applying DNA metabarcoding to the “slush” collected from fishing nets just after the end of hauling operations. We assess the performance of this approach in portraying β-diversity and examining the quantitative relationship between species abundances in the catch and DNA amount in the slush (reads counts generated by amplicon sequencing). We demonstrate that the assemblages identified using DNA in the slush mirror those returned by visual inspection of net content and detect a strong relationship between read counts and species abundances in the catch. We therefore argue that this approach could be upscaled to serve as a powerful source of information on the structure of demersal assemblages and the impact of fisheries.

Usage Notes

  • COI_R1.fastq and COI_R2.fastq: COI paired-end FastQ files from the Illumina HiSeq 2x250 bp run.

  • COI_tag&primers.txt: COI primers and unique dual-tag combinations (forward and reverse) for 63 COI amplicons (54 slush samples, 2 extraction blanks, 1 PCR negative control, 6 seawater blanks).

  • 12S_R1.fastq and 12S_R2.fastq: 12S paired-end FastQ files from the Illumina MiSeq 2x150 bp run.

  • 12S_tag&primers.txt: 12S primers and unique dual-tag combinations (forward and reverse) for 63 12S amplicons (54 slush samples, 2 extraction blanks, 1 PCR negative control, 6 seawater blanks).

  • metabarcoding_COI_data.xlsx: number of reads per species/replicate/site after data post-processing and cleaning. Data refer to analyzed taxa: teleosts, elasmobranchs, cephalopods and decapods.

  • metabarcoding_12S_data.xlsx: number of reads per species/replicate/site after data post-processing and cleaning. Data refer to analyzed taxa: teleosts and elasmobranchs.

Funding

UK Natural Environment Research Council, Award: NE/N005759/1

Ministero delle Politiche Agricole Alimentari e Forestali, Award: Italian Program for the Data Collection in the Fisheries Sector