Approaches to integrating genetic data into ecological networks

Abstract

As molecular tools for assessing trophic interactions become common, research is increasingly focused on the construction of interaction networks. Here, we demonstrate three key methods for incorporating DNA data into network ecology and discuss analytical considerations using a model consisting of plants, insects, bats and their parasites from the Costa Rica dry forest. The simplest method involves the use of Sanger sequencing to acquire long sequences to validate or refine field identifications, for example of bats and their parasites, where one specimen yields one sequence and one identification. This method can be fully quantified and resolved and these data resemble traditional ecological networks. For more complex taxonomic identifications, we target multiple DNA loci, for example from a seed or fruit pulp sample in faeces. These networks are also well resolved but gene targets vary in resolution and quantification is difficult. Finally, for mixed templates such as faecal contents of insectivorous bats, we use DNA metabarcoding targeting two sequence lengths (157 and 407 bp) of one gene region and a MOTU, BLAST and BIN association approach to resolve nodes. This network type is complex to generate and analyse, and we discuss the implications of this type of resolution on network analysis. Using these data, we construct the first molecular‐based network of networks containing 3,304 interactions between 762 nodes of eight trophic functions and involving parasitic, mutualistic and predatory interactions. We provide a comparison of the relative strengths and weaknesses of these data types in network ecology.

Molecular diet analysis finds an insectivorous desert bat community dominated by resource sharing despite diverse echolocation and foraging strategies

“…In our analysis, only C. townsendii and Myotis thysanodes fell into the behaviorally flexible guild but both had very high taxonomic richness of their prey (ranking 4th and 1st respectively) and, while the SIMPER analysis suggests they differ most in their use of orders from the diet of clutter‐tolerant species, the NMDS suggests that the other guilds are characterized as consuming a subset of the prey of these two species. This suggests that the behaviorally flexible guild consumes the most diverse diet which has substantial bearing on their resilience to unstable environments (Clare et al, ). One limitation to our collection is the longitudinal nature of the samples.…”

Introduction: Special issue on species interactions, ecological networks and community dynamics – Untangling the entangled bank using molecular techniques

“…The findings regarding particular interactions range from insight into emergent features such as levels of specialization in ecological interaction networks (Clare et al, ; Doña, Proctor, et al, ; Doña, Serrano, et al, ; Koskinen et al, ; Sepp et al, ) to the role of individual seed dispersers in seed dispersal networks. As a case in point, González‐Varo, Arroyo, and Jordano () are able to show how much of an ecological function (seed dispersal) is concentrated to particular species at particular points in time.…”

“…Schröter et al () deal with root‐associated mycobiomes encompassing a total of 5,955 different operational taxonomic units across spatial scales of over 1,000 km in more than 100 temperate forest plots. Clare et al () tabulate 3,304 interactions between 762 nodes of 8 trophic functions, thus encompassing parasitic, mutualistic and predatory interactions. And the list goes on.…”

“…Clare et al () point to particularly fascinating perspectives—and to particularly strong challenges ahead. What this paper proposes is this: Given that we can now delimit both nodes and links by molecular data, may we not base our full description of communities and interaction networks on such data, thus curtailing the reliance on traditional approaches?…”

“…Individual papers reveal how molecular tools are being fruitfully applied to many types of nodes and links, and the many types of networks formed from such elements. As an arguably thought‐provoking perspective, they also show molecular techniques can be applied to describe full communities rather than their parts simultaneously—that is, to resolve multiple types of links among multiple kingdoms of taxa (Clare et al, ), thus opening new vistas on “networks of networks.” Out of necessity, such initiatives so far have had to be built from multiple data sources (Pocock, Evans, & Memmott, ; Wirta et al, ).…”