Learning Ecological Networks from Next-Generation Sequencing Data

Vacher, Corinne; Tamaddoni‐Nezhad, Alireza; Kamenova, Stefaniya; Peyrard, Nathalie; Moalic, Yann; Sabbadin, Régis; Schwaller, Loïc; Chiquet, Julien; Smith, M. Alex; Vallance, Jessica; Fievet, Virgil; Jakuschkin, Boris; Bohan, David

doi:10.1016/bs.aecr.2015.10.004

Cited by 81 publications

(67 citation statements)

References 184 publications

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“…For instance, co-occurrence networks (also called association or correlation or coexisting networks; Vacher et al 2016) are usually built on statistically significant co-presence or co-absence of pairs of taxa. Taking such networks as indicative of ecological interactions is problematic, however, as co-existence patterns, such as presence and absence, are not a direct result of pairwise ecological interactions, such as mutualism and competition, respectively.…”

Section: Inferring the Interaction Networkmentioning

confidence: 99%

Invasions of Host-Associated Microbiome Networks

Murall

Abbate

Touzel

et al. 2017

Networks of Invasion: Empirical Evidence and Case Studies

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International audienceThe study of biological invasions of ecological systems has much to offer research on within–host (WH) systems, particularly for understanding infections and developing therapies using biological agents. Thanks to the ground-work established in other fields, such as community ecology and evolutionary biology, and to modern methods of measurement and quantification, the study of microbiomes has quickly become a field at the forefront of modern systems biology. Investigations of host-associated microbiomes (e.g. for studying human health) are often centred on measuring and explaining the structure, functions and stability of these communities. This momentum promises to rapidly advance our understanding of ecological networks and their stability, resilience and resistance to invasions. However, intrinsic properties of host-associated microbiomes that differ from those of free-living systems present challenges to the development of a WH invasion ecology framework. The elucidation of principles underlying the invasibility of WH networks will ultimately help in the development of medical applications and help shape our understanding of human health and disease

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Section: Inferring the Interaction Networkmentioning

confidence: 99%

Invasions of Host-Associated Microbiome Networks

Murall

Abbate

Touzel

et al. 2017

Networks of Invasion: Empirical Evidence and Case Studies

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“…As already discussed in Section 2.1, carabid predation of weed seeds and carabid predation of slugs may be antagonistic and, by extension, all alternative prey could have such interference effects. There is a need, therefore, to evaluate the interactions and antagonisms between ecological interactions across a framework of a meta-network, and it appears to us that the developing technology of next-generation sequencing offers great promise for the identifi cation of both direct and indirect interactions ( Vacher et al, 2016 ;Kamenova et al, 2013;Bohan et al, 2017).…”

Section: Future Trendsmentioning

confidence: 99%

“…The use of next-generation sequencing approaches, a catch-all name for a number of high-throughput sequencing approaches, also offers the potential for widening the assessment of prey species beyond those already known or suspected to affect plant species ( Traugott et al, 2013 ). The reconstruction of ecological networks from DNA data is a growing topic of research ( Vacher et al, 2016 ;Kamenova et al, 2017 ;Bohan et al, in press). …”

Section: Introductionmentioning

confidence: 99%

The use of insects in integrated weed management

Petit¹,

Bohan²

2017

Integrated Weed Management for Sustainable Agriculture

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Seed predation by insects is a potentially promising approach to the regulation of weeds that could offset herbicide use as part of integrated weed management. Using the example of carabid beetles, as the most intensively studied grouping of insect weed seed predators, this chapter describes the current state of knowledge in this subject area and highlights future research trends. The chapter examines the interaction between weeds and predator communities and assesses how fields and landscapes can be managed to enhance weed seed predation. The chapter looks at the level of weed regulation that can realistically be expected from this approach, and provides a detailed case study from the United Kingdom.

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“…Recent advances in molecular techniques has given rise to the possibilities of rapidly 642 analysing field collections to enable measures of taxonomic diversity and a high-throughput 643 quantification of species abundance (Bohmann et al, 2014;Keller et al, 2015;Richardson et 644 al., 2015), to re-construct with high precision and accuracy the structure of different plant-645 pollinator assemblages (see next section 4.2; Vacher et al, 2015). These molecular 646 approaches will also enhance our ability to robustly monitor pollinator populations (Dicks et 647 al., 2013;Lebuhn et al, 2013), and quantify pollinator community structure under different 648 environmental stresses or contexts.…”

Section: Understanding the Stability Of Insect Pollinator Communitiesmentioning

confidence: 99%

“…captured insect pollinators in a pan trap). The most 701 straightforward and cost efficient approach is 'metabarcoding' that applies the principle of 702 DNA barcoding to a bulk sample by conducting PCR and sequencing on the mixture allowing 703 an indiscriminate field collection to be analysed ( Figure 6; Creer et al, 2010;Gibson et al, 704 2014;Taberlet et al, 2012;Vacher et al, 2015;Yu et al, 2012). Massively parallel NGS 705 technologies produce numerous independent sequence reads, each corresponding to a 706 separate PCR amplicon, which may originate from any species in the mixture.…”

Section: Using Molecular Approaches To Monitor Insect Pollinators 651mentioning

confidence: 99%

Protecting an Ecosystem Service

Gill

Baldock

Brown

et al. 2016

Ecosystem Services: From Biodiversity to Society, Part 2

122

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Contact CEH NORA team at noraceh@ceh.ac.ukThe NERC and CEH trademarks and logos ('the Trademarks') are registered trademarks of NERC in the UK and other countries, and may not be used without the prior written consent of the Trademark owner. considers the importance of conserving pollinator diversity to maintain a suite of functional 79 traits to provide a diverse set of pollinator services. We explore how we can better understand 80 and mitigate the factors that threaten insect pollinator richness, placing our discussion within 81 the context of populations in predominantly agricultural landscapes in addition to urban 82 environments. We highlight a selection of important evidence gaps, with a number of 83 complementary research steps that can be taken to better understand: i) the stability of 84 pollinator communities in different landscapes in order to provide diverse pollinator services; 85 ii) how we can study the drivers of population change to mitigate the effects and support 86 stable sources of pollinator services; and, iii) how we can manage habitats in complex 87 landscapes to support insect pollinators and provide sustainable pollinator services for the 88 future. We advocate a collaborative effort to gain higher quality abundance data to 89 understand the stability of pollinator populations and predict future trends. In addition, for 90 effective mitigation strategies to be adopted, researchers need to conduct rigorous field-91 testing of outcomes under different landscape settings, acknowledge the needs of end-users 92 when developing research proposals and consider effective methods of knowledge transfer to 93 ensure effective uptake of actions. 94 95 96 5 | P a g e | P a g e

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Learning Ecological Networks from Next-Generation Sequencing Data

Cited by 81 publications

References 184 publications

Invasions of Host-Associated Microbiome Networks

Invasions of Host-Associated Microbiome Networks

The use of insects in integrated weed management

Protecting an Ecosystem Service

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