Performance of DNA metabarcoding, standard barcoding, and morphological approach in the identification of host–parasitoid interactions

Abstract

Understanding interactions between herbivores and parasitoids is essential for successful biodiversity protection and monitoring and for biological pest control. Morphological identifications employ insect rearing and are complicated by insects’ high diversity and crypsis. DNA barcoding has been successfully used in studies of host–parasitoid interactions as it can substantially increase the recovered real host–parasitoid diversity distorted by overlooked species complexes, or by species with slight morphological differences. However, this approach does not allow the simultaneous detection and identification of host(s) and parasitoid(s). Recently, high-throughput sequencing has shown high potential for surveying ecological communities and trophic interactions. Using mock samples comprising insect larvae and their parasitoids, we tested the potential of DNA metabarcoding for identifying individuals involved in host–parasitoid interactions to different taxonomic levels, and compared it to standard DNA barcoding and morphological approaches. For DNA metabarcoding, we targeted the standard barcoding marker cytochrome oxidase subunit I using highly degenerate primers, 2*300 bp sequencing on a MiSeq platform, and RTAX classification using paired-end reads. Additionally, using a large host–parasitoid dataset from a Central European floodplain forest, we assess the completeness and usability of a local reference library by confronting the number of Barcoding Index Numbers obtained by standard barcoding with the number of morphotypes. Overall, metabarcoding recovery was high, identifying 92.8% of the taxa present in mock samples, and identification success within individual taxonomic levels did not significantly differ among metabarcoding, standard barcoding, and morphology. Based on the current local reference library, 39.4% parasitoid and 90.7% host taxa were identified to the species level. DNA barcoding estimated higher parasitoid diversity than morphotyping, especially in groups with high level of crypsis. This study suggests the potential of metabarcoding for effectively recovering host–parasitoid diversity, together with more accurate identifications obtained from building reliable and comprehensive reference libraries, especially for parasitoids.

A modified DNA barcode approach to define trophic interactions between native and exotic pentatomids and their parasitoids

“…The public availability of DNA barcodes will facilitate future forensic studies on host‐parasitoid associations and serves as the foundation upon which additional species can be added to improve the utility of this tool for analysis of trophic interactions between native and exotic species in this system. Future studies employing next‐generation DNA sequencing (NGS) or metabarcoding could make use of these sequence data to characterize all possible trophic interactions simultaneously, as has been shown in aphid‐parasitoid associations (Lefort, Wratten, Cusumano, Varennes, & Boyer, ) and in host‐parasitoid associations in forest dwelling Lepidoptera and Hymenoptera (Šigut et al., ).…”

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

“…To date, no studies have demonstrated the utility of these approaches for detecting species interactions, although see Lefort, Wratten, Cusumano, Varennes, and Boyer () and Šigut et al. () for examples of parasitism using more conventional sample tracking methods.…”

Elevational contrast in predation and parasitism risk to caterpillars in a tropical rainforest

“…On the other hand, this method has also several problems, such as a lack of direct evidence of the cause of death, prey mobility, or requirement for mass rearing of the prey (Kneib & Scheele, ; Molleman et al, ). For evidence of parasitism of the exposed host, the host must be kept until the adult stage, dissected for the presence of parasitoid larvae, or screened by molecular detection methods (Franck et al, ; Šigut et al, ).…”