Marine and Freshwater Research Marine and Freshwater Research Society
Advances in the aquatic sciences

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How does marker choice affect your diet analysis? Comparing genetic markers and digestion levels for diet metabarcoding of tropical reef piscivores

Floriaan Devloo-Delva , Roger Huerlimann , Gladys Chua , Jordan Matley , Michelle Heupel , Colin Simpfendorfer , Gregory Maes


Tropical reefs are highly diverse ecosystems, and reliable biomonitoring, through diet metabarcoding, is needed to understand present and future trophic relationships in this changing habitat. Several studies have assessed the reliability and effectiveness of single molecular markers; however, a cross-marker validation has rarely been performed. The present study identified crucial properties for 12S rDNA, 16S rDNA and COI metabarcoding in tropical reef piscivores (Plectropomus spp.). In addition, three new versatile primer sets for 16S were designed in silico for metabarcoding of reef fish. Results showed COI was overall better at recovering true diversity due a well-supported database. Secondly, optimal 16S amplicon sizes range between 160 and 440 bp for full diversity recovery, with increased species detection for the 270 bp region Finally, blocking of predator-specific COI sequences was not equally effective in all host species, potentially introducing bias when diet compositions are directly compared. In conclusion, this novel study shows that marker success for prey identification is highly dependent on reference database, taxonomic scope, DNA quality, amplicon length and sequencing platform. Results suggest COI, complemented with 16S, yields the best outcome for diet metabarcoding in reef piscivores. Findings in this paper are relevant to other piscivores and other metabarcoding applications.

MF17209  Accepted 15 January 2018

© CSIRO 2018