Merging DNA metabarcoding and ecological network analysis to understand and build resilient terrestrial ecosystems

Summary 1. Significant advances in both mathematical and molecular approaches in ecology offer unprecedented opportunities to describe and understand ecosystem functioning. Ecological networks describe interactions between species, the underlying structure of communities and the function and stability of ecosystems. They provide the ability to assess the robustness of complex ecological communities to species loss, as well as a novel way of guiding restoration. However, empirically quantifying the interactions between entire communities remains a significant challenge. 2. Concomitantly, advances in DNA sequencing technologies are resolving previously intractable questions in functional and taxonomic biodiversity and provide enormous potential to determine hitherto difficult to observe species interactions. Combining DNA metabarcoding approaches with ecological network analysis presents important new opportunities for understanding large-scale ecological and evolutionary processes, as well as providing powerful tools for building ecosystems that are resilient to environmental change. 3. We propose a novel ‘nested tagging’ metabarcoding approach for the rapid construction of large, phylogenetically structured species-interaction networks. Taking tree–insect–parasitoid ecological networks as an illustration, we show how measures of network robustness, constructed using DNA metabarcoding, can be used to determine the consequences of tree species loss within forests, and forest habitat loss within wider landscapes. By determining which species and habitats are important to network integrity, we propose new directions for forest management. 4. Merging metabarcoding with ecological network analysis provides a revolutionary opportunity to construct some of the largest, phylogenetically structured species-interaction networks to date, providing new ways to: (i) monitor biodiversity and ecosystem functioning; (ii) assess the robustness of interacting communities to species loss; and (iii) build ecosystems that are more resilient to environmental change

Merging DNA metabarcoding and ecological network analysis to understand and build resilient terrestrial ecosystems

1. Significant advances in both mathematical and molecular approaches in ecology offer unprecedented opportunities to describe and understand ecosystem functioning. Ecological networks describe interactions between species, the underlying structure of communities and the function and stability of ecosystems. They provide the ability to assess the robustness of complex ecological communities to species loss, as well as a novel way of guiding restoration. However, empirically quantifying the interactions between entire communities remains a significant challenge. 2. Concomitantly, advances in DNA sequencing technologies are resolving previously intractable questions in functional and taxonomic biodiversity and provide enormous potential to determine hitherto difficult to observe species interactions. Combining DNA metabarcoding approaches with ecological network analysis presents important new opportunities for understanding large-scale ecological and evolutionary processes, as well as providing powerful tools for building ecosystems that are resilient to environmental change. 3. We propose a novel ‘nested tagging’ metabarcoding approach for the rapid construction of large, phylogenetically structured species-interaction networks. Taking tree–insect–parasitoid ecological networks as an illustration, we show how measures of network robustness, constructed using DNA metabarcoding, can be used to determine the consequences of tree species loss within forests, and forest habitat loss within wider landscapes. By determining which species and habitats are important to network integrity, we propose new directions for forest management. 4. Merging metabarcoding with ecological network analysis provides a revolutionary opportunity to construct some of the largest, phylogenetically structured species-interaction networks to date, providing new ways to: (i) monitor biodiversity and ecosystem functioning; (ii) assess the robustness of interacting communities to species loss; and (iii) build ecosystems that are more resilient to environmental change

Barriers to gene flow in the deepest ocean ecosystems: evidence from global population genomics of a cosmopolitan amphipod

The deepest marine ecosystem, the hadal zone, hosts endemic biodiversity resulting from geographic isolation and environmental selection pressures. However, the pan-ocean distribution of some fauna challenges the concept that the hadal zone is a series of isolated island-like habitats. Whether this remains true at the population genomic level is untested. We investigated phylogeographic patterns of the amphipod, Bathycallisoma schellenbergi, from 12 hadal features across the Pacific, Atlantic, Indian, and Southern oceans and analyzed genome-wide single-nucleotide polymorphism markers and two mitochondrial regions. Despite a cosmopolitan distribution, populations were highly restricted to individual features with only limited gene flow between topographically connected features. This lack of connectivity suggests that populations are on separate evolutionary trajectories, with evidence of potential cryptic speciation at the Atacama Trench. Together, this global study demonstrates that the shallower ocean floor separating hadal features poses strong barriers to dispersal, driving genetic isolation and creating pockets of diversity to conserve

Detecting host-parasitoid interactions in an invasive Lepidopteran using nested tagging DNA metabarcoding

Determining the host-parasitoid interactions and parasitism rates for invasive species entering novel environments is an important first step in assessing potential routes for biocontrol and integrated pest management. Conventional insect rearing techniques followed by taxonomic identification are widely used to obtain such data, but this can be time-consuming and prone to biases. Here, we present a next-generation sequencing approach for use in ecological studies which allows for individual-level metadata tracking of large numbers of invertebrate samples through the use of hierarchically organised molecular identification tags. We demonstrate its utility using a sample data set examining both species identity and levels of parasitism in late larval stages of the oak processionary moth (Thaumetopoea processionea-Linn. 1758), an invasive species recently established in the United Kingdom. Overall, we find that there are two main species exploiting the late larval stages of oak processionary moth in the United Kingdom with the main parasitoid (Carcelia iliaca-Ratzeburg, 1840) parasitising 45.7% of caterpillars, while a rare secondary parasitoid (Compsilura concinnata-Meigen, 1824) was also detected in 0.4% of caterpillars. Using this approach on all life stages of the oak processionary moth may demonstrate additional parasitoid diversity. We discuss the wider potential of nested tagging DNA metabarcoding for constructing large, highly resolved species interaction networks.</p

Network science: applications for sustainable agroecosystems and food security

The global challenge of feeding two billion more people by 2050, using more sustainable agricultural practices whilst dealing with uncertainties associated with environmental change, requires a transformation of food systems. We present a new perspective for how advances in network science can provide novel ways to better understand, harness, and restore multiple ecological processes in agricultural environments. We describe: (i) a network-focused framework for managing agro-ecosystems that accounts for the multiple interactions between biodiversity and associated ecosystem services; (ii) guidance for incorporating socio-economic factors into ecological networks; and (iii) the potential to upscale network methods to inform efforts to build resilience, including global food-supply chains. In doing so we aim to facilitate the application of network science as a systems-based way to tackle the challenges of securing an equitable distribution of food