How does marker choice affect your diet analysis: comparing genetic markers and digestion levels for diet metabarcoding of tropical-reef piscivores

Devloo‐Delva, Floriaan; Huerlimann, Roger; Chua, Gladys; Matley, Jordan K.; Heupel, Michelle R.; Simpfendorfer, Colin A.; Maes, Grégory E.

doi:10.1071/mf17209

Cited by 34 publications

(28 citation statements)

References 38 publications

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“…Both the confidence and the resolution of taxonomic assignment procedures are highly dependent on the completeness of reference sequence databases (e.g., Gibson et al, ; Porter et al, ; Devloo‐Delva et al, ). In this study, we illustrated that the accuracy of taxonomic assignment of prey depended on the environment of the predators (Figure b).…”

Section: Discussionmentioning

confidence: 99%

One‐locus‐several‐primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies

Corse

Tougard

Archambaud‐Suard

et al. 2019

Ecology and Evolution

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In diet metabarcoding analyses, insufficient taxonomic coverage of PCR primer sets generates false negatives that may dramatically distort biodiversity estimates. In this paper, we investigated the taxonomic coverage and complementarity of three cytochrome c oxidase subunit I gene (COI) primer sets based on in silico analyses and we conducted an in vivo evaluation using fecal and spider web samples from different invertivores, environments, and geographic locations. Our results underline the lack of predictability of both the coverage and complementarity of individual primer sets: (a) sharp discrepancies exist observed between in silico and in vivo analyses (to the detriment of in silico analyses); (b) both coverage and complementarity depend greatly on the predator and on the taxonomic level at which preys are considered; (c) primer sets’ complementarity is the greatest at fine taxonomic levels (molecular operational taxonomic units [MOTUs] and variants). We then formalized the “one‐locus‐several‐primer‐sets” (OLSP) strategy, that is, the use of several primer sets that target the same locus (here the first part of the COI gene) and the same group of taxa (here invertebrates). The proximal aim of the OLSP strategy is to minimize false negatives by increasing total coverage through multiple primer sets. We illustrate that the OLSP strategy is especially relevant from this perspective since distinct variants within the same MOTUs were not equally detected across all primer sets. Furthermore, the OLSP strategy produces largely overlapping and comparable sequences, which cannot be achieved when targeting different loci. This facilitates the use of haplotypic diversity information contained within metabarcoding datasets, for example, for phylogeography and finer analyses of prey–predator interactions.

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Section: Discussionmentioning

confidence: 99%

One‐locus‐several‐primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies

Corse

Tougard

Archambaud‐Suard

et al. 2019

Ecology and Evolution

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“…Therefore, describing an entire marine food web will require the use of several primers in combination (e.g. see Devloo‐Delva et al, ).…”

Section: Discussionmentioning

confidence: 99%

Reconstructing hyperdiverse food webs: Gut content metabarcoding as a tool to disentangle trophic interactions on coral reefs

et al. 2019

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Anthropogenic stressors have strong impacts on ecosystems. To understand their influence, detailed knowledge about trophic relationships among species is critical. However, this requires both exceptional resolution in dietary assessments and sampling breadth within communities, especially for highly diverse, tropical ecosystems. We used gut content metabarcoding across a broad range of coral reef fishes (8 families, 22 species) in Mo'orea, French Polynesia, to test whether this technique has the potential to capture the structure of a hyperdiverse marine food web. Moreover, we explored whether taxonomic groups (families) and traditional, broad‐scale trophic assignments explained fish diet across four different metrics of quantifying predator–prey interactions. Metabarcoding yielded a large number (4,341) of unique operational taxonomic units (i.e. prey) with high‐resolution taxonomic assignments (i.e. often to the level of genus or species). We demonstrate that across multiple metrics, taxonomic group at the family level is a consistently better, albeit still weak, predictor of empirical trophic relationships than frequently used, broad‐scale functional assignments. Our method also reveals a complex trophic network with fine‐scale partitioning among species, further emphasizing the importance of examining fish diets beyond broad trophic categories. We demonstrate the capacity of metabarcoding to reconstruct diverse and complex food webs with exceptional resolution, a significant advancement from traditional food web reconstruction. Furthermore, this method allows us to pinpoint the trophic niche of species with niche‐based modelling, even across hyperdiverse species assemblages such as coral reefs. In conjunction with complementary techniques such as stable isotope analysis, applying metabarcoding to whole communities will provide unparalleled information about energy and nutrient fluxes and inform their susceptibility to disturbances even in the world's most diverse ecosystems.

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“…Devloo‐Delva et al. () established the method's ability for prey diversity recovery in Plectropomus spp., using cytochrome oxidase I primers (mlCOIintF/jgHCO2198; Leray et al., ). Amplicon polymerase chain reactions (PCR) were completed with this primer set in a 20 μl reaction volume with 1 μl of template DNA, 1X MyTaq reaction buffer (Bioline, UK), 0.4 μM tailed forward and reverse primer with 10% untailed primers (to initiate amplification), and 0.05 u/μl MyTaq DNA polymerase (Bioline).…”

Section: Methodsmentioning

confidence: 99%

“…Stomach contents from each individual were homogenized and DNA extracted following the CTAB protocol from Tamari and Hinkley (2016). Devloo-Delva et al (2018) established the method's ability for prey diversity recovery in Plectropomus spp., using cytochrome oxidase I primers (mlCOIintF/jgHCO2198; Leray et al, 2013).…”

Section: Diet Metabarcodingmentioning

confidence: 99%

“…The ability to sequence prey items from degraded stomach contents enhances diet data and has the capacity to reduce inefficiencies caused by unidentifiable samples. Nevertheless, this metabarcoding approach is still limited by the completeness of reference sequence databases and the choice of genetic markers (Devloo‐Delva et al., ); consequently, prior validation is needed for newly studied species/systems. Another method to characterize diet is stable isotope analysis (e.g., δ 15 N and δ 13 C), a biogeochemical indicator of prey assimilation in the tissues of consumers (see Newsome, Clementz, & Koch, for review).…”

Section: Introductionmentioning

confidence: 99%

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Integrating complementary methods to improve diet analysis in fishery‐targeted species

Matley

Maes

Devloo‐Delva

et al. 2018

Ecology and Evolution

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Developing efficient, reliable, cost‐effective ways to identify diet is required to understand trophic ecology in complex ecosystems and improve food web models. A combination of techniques, each varying in their ability to provide robust, spatially and temporally explicit information can be applied to clarify diet data for ecological research. This study applied an integrative analysis of a fishery‐targeted species group—Plectropomus spp. in the central Great Barrier Reef, Australia, by comparing three diet‐identification approaches. Visual stomach content analysis provided poor identification with ~14% of stomachs sampled resulting in identification to family or lower. A molecular approach was successful with prey from ~80% of stomachs identified to genus or species, often with several unique prey in a stomach. Stable isotope mixing models utilizing experimentally derived assimilation data, identified similar prey as the molecular technique but at broader temporal scales, particularly when prior diet information was incorporated. Overall, Caesionidae and Pomacentridae were the most abundant prey families (>50% prey contribution) for all Plectropomus spp., highlighting the importance of planktivorous prey. Less abundant prey categories differed among species/color phases indicating possible niche segregation. This study is one of the first to demonstrate the extent of taxonomic resolution provided by molecular techniques, and, like other studies, illustrates that temporal investigations of dietary patterns are more accessible in combination with stable isotopes. The consumption of mainly planktivorous prey within this species group has important implications within coral reef food webs and provides cautionary information regarding the effects that changing resources could have in reef ecosystems.

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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

Cited by 34 publications

References 38 publications

One‐locus‐several‐primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies

One‐locus‐several‐primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies

Reconstructing hyperdiverse food webs: Gut content metabarcoding as a tool to disentangle trophic interactions on coral reefs

Integrating complementary methods to improve diet analysis in fishery‐targeted species

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