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

Abstract

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]

Assessing the Functional Limitations of Lipids and Fatty Acids for Diet Determination: The Importance of Tissue Type, Quantity, and Quality

“…The field of trophic ecology has seen a substantial increase in the number of available techniques and applications across aquatic and terrestrial taxa within the last half century (Layman et al, 2012(Layman et al, , 2015Christiansen et al, 2015;Nielsen et al, 2015;Young et al, 2015;Roslin and Majaneva, 2016). More recently, there has been a growing number of studies moving from traditional stomach-content analysis, which may provide a potentially limited view due to differences in digestibility among prey species (Hyslop, 1980), to time-integrated biochemical methods (reviewed in Traugott et al, 2013;Pethybridge et al, 2018).…”

Barcoding the food chain: from Sanger to high-throughput sequencing

“…By examining gut contents or faeces with DNA barcoding (sometimes termed molecular scatology), we can examine trophic interactions in a non-invasive way which also has the potential for higher taxonomic resolution . This high-resolution analysis of interactions holds promise for improving our understanding of entire interaction networks (Roslin and Majaneva 2016) and, when applied to vulnerable farmland predators (e.g., aerial insectivores), could provide valuable information on subtle differences in how species use habitats set aside for conservation.…”

“…Programmes and data cleaning steps vary between research groups; the different clustering methods and data cleaning steps can considerably change the estimate of MOTU diversity (Brandon-Mong et al 2015;Clare et al 2016). Analysis of how bioinformatics pipelines affect ecological conclusions will be valuable, but as yet they are rare (although see Clare et al 2016;Roslin and Majaneva 2016).…”

From Barcodes to Biomes: Special Issues from the 6th International Barcode of Life Conference

“…With the addition of DNA barcode data, nodes (species units) and links among nodes (species interactions) become better resolved than when using traditional methods alone for identifying specimens and, especially, their gut contents. Among the multiple case studies that they highlight (see references therein), Roslin and Majaneva (2016) review how a focal ecosystem in Greenland-whose plant and animal species have been comprehensively DNA barcoded-has been shown to be more complex and more densely linked than would be concluded with traditional methods. These interesting findings stress the importance of expanding this line of work; applying the same methods elsewhere would permit exploration of the generality of these patterns among taxa and habitat types and to test for potential large-scale trends, such as latitudinal gradients in food web structure.…”