Assessing morphological and DNA‐based diet analysis techniques in a generalist predator, the arrow squid <i>Nototodarus gouldi</i>

Braley, Michelle; Goldsworthy, Simon; Page, Brad; Steer, M. A.; Austin, Jeremy J.

doi:10.1111/j.1755-0998.2009.02767.x

Cited by 65 publications

(84 citation statements)

References 45 publications

(73 reference statements)

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“…However, this problem can be solved by using DNA-based methods on this highly digested matter (Dunshea 2009;Valentini et al 2009). The best results are likely to be obtained using a combination of morphological investigation and DNA-based methods (Casper et al 2007;Braley et al 2010) because the combination increases the number of samples yielding dietary information and the amount of information gained from each sample.…”

Section: Discussionmentioning

confidence: 99%

The diet of polar bears (Ursus maritimus) from Svalbard, Norway, inferred from scat analysis

et al. 2013

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Section: Discussionmentioning

confidence: 99%

The diet of polar bears (Ursus maritimus) from Svalbard, Norway, inferred from scat analysis

et al. 2013

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“…Therefore, we used part of the mtDNA 16S rRNA gene as a barcoding marker. Primers have been designed to amplify short regions of mtDNA 16S DNA from diverse metazoan taxa (Dunshea 2009), the amplified region is variable enough to allow species or genus level identification (Vences et al 2005) and mtDNA 16S sequences are available in GenBank for many southern Australian fish species due to submissions from two previous dietary studies (Deagle et al 2009;Braley et al 2010). In the current study, all DNA samples were PCR amplified using a primer set targeting a short mtDNA 16S fragment (*100 bp) from chordates (16S SHORT).…”

Section: Dna Extraction and Pcr Amplificationmentioning

confidence: 99%

Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out?

et al. 2010

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DNA barcoding of faeces or stomach contents is an emerging approach for dietary analysis. We pyrosequenced mtDNA 16S markers amplified from faeces of captive little penguins (Eudyptula minor) to examine if recovered sequences reflect the proportions of species consumed. We also analysed wild little penguin faeces collected from 100 nests in southeast Australia. In the captive study, pilchards were the primary fish fed to the penguins and DNA sequences from pilchard were the most common sequences recovered. Sequences of three other fish fed in constant mass proportions (45:35:20) were all detected, but proportions of sequences (60:6:34) were considerably different than mass proportions in the diet. Correction factors based on relative mtDNA density in the fish did not improve diet estimates. Consistency between replicate samples suggests that the observed bias resulted from differences in prey digestibility. Detection of DNA from fish consumed before the penguins were brought into captivity indicates that a DNA signal in faeces can persist for at least 4 days after ingestion. In the wild-collected faeces, 24 distinct fish and 1 squid were identified; anchovy, barracouta and pilchard accounted for over 80% of these sequences. Our results highlight that DNA sequences recovered in dietary barcoding studies can provide semi-quantitative information on diet composition, but these data should be given wide confidence intervals.

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“…DNA-based approaches have also yielded breakthrough dietary analyses in complex freshwater systems (e.g., Corse et al 2010;Carreon-Martinez et al 2011;Bartley et al 2015). Most of the studies to date attest to the effectiveness of DNA-based analysis, especially when combined with morphological analysis (e.g., Casper et al 2007;Braley et al 2010;Alonso et al 2014), and they offer new insights in trophic ecology.…”

Section: Clarifying the Links Of Aquatic Food Websmentioning

confidence: 99%

The use of DNA barcodes in food web construction—terrestrial and aquatic ecologists unite!

Roslin

Majaneva

2016

Genome

104

103

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By depicting who eats whom, food webs offer descriptions of how groupings in nature (typically species or populations) are linked to each other. For asking questions on how food webs are built and work, we need descriptions of food webs at different levels of resolution. DNA techniques provide opportunities for highly resolved webs. In this paper, we offer an exposé of how DNA-based techniques, and DNA barcodes in particular, have recently been used to construct food web structure in both terrestrial and aquatic systems. We highlight how such techniques can be applied to simultaneously improve the taxonomic resolution of the nodes of the web (i.e., the species), and the links between them (i.e., who eats whom). We end by proposing how DNA barcodes and DNA information may allow new approaches to the construction of larger interaction webs, and overcome some hurdles to achieving adequate sample size. Most importantly, we propose that the joint adoption and development of these techniques may serve to unite approaches to food web studies in aquatic and terrestrial systems-revealing the extent to which food webs in these environments are structured similarly to or differently from each other, and how they are linked by dispersal.Key words: DNA barcodes, food webs, species delimitation, species identification, trophic links, ecological networks.Résumé : En brossant le tableau de qui mange qui, les réseaux trophiques livrent une description des liens qui unissent des groupes d'espèces ou de populations. Afin de déterminer comment ces réseaux sont constitués et comment ils fonctionnent, il nous faut une description de ces réseaux à différents niveaux de résolution. Les techniques de l'ADN permettent de produire des réseaux trophiques de grande résolution. Dans ce travail, les auteurs décrivent comment les techniques fondées sur l'ADN, en particulier les codes à barres de l'ADN, ont récemment été employées pour étudier la structure des réseaux trophiques chez des systèmes tant terrestres qu'aquatiques. Les auteurs soulignent comment ces techniques peuvent servir à simultanément améliorer la résolution taxonomique des noeuds d'un réseau (i.e. les espèces) ainsi que les relations entre eux (qui mange qui). Les auteurs terminent en proposant des moyens via lesquels les codes à barres et l'information tirée de l'ADN rendent possible de nouvelles approches en vue de la construction de plus grands réseaux d'interaction et permettent de surmonter des difficultés rencontrées dans l'acquisition d'échantillons de taille suffisante. Surtout, les auteurs proposent que l'adoption et le développement conjoints de ces techniques peut contribuer à unifier les approches employées dans l'étude des réseaux trophiques au sein des systèmes aquatiques et terrestres. Cela permettra de révéler l'étendue de la similarité ou de la dissimilarité dans la façon dont sont structurés les réseaux dans ces différents environnements et comment ils sont liés par la dispersion. [Traduit par la Rédaction]

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Assessing morphological and DNA‐based diet analysis techniques in a generalist predator, the arrow squid Nototodarus gouldi

Cited by 65 publications

References 45 publications

The diet of polar bears (Ursus maritimus) from Svalbard, Norway, inferred from scat analysis

The diet of polar bears (Ursus maritimus) from Svalbard, Norway, inferred from scat analysis

Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out?

The use of DNA barcodes in food web construction—terrestrial and aquatic ecologists unite!

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