Data from: Molecular analysis reveals high compartmentalisation in aphid-primary parasitoid networks and low parasitoid sharing between crop and non-crop habitats.

The ecosystem service of insect pest regulation by natural enemies, such as primary parasitoids, may be enhanced by the presence of uncultivated, semi-natural habitats within agro-ecosystems, although quantifying such host-parasitoid interactions is difficult. Here we use rRNA 16S gene sequencing to assess both the level of parasitism by Aphidiinae primary parasitoids and parasitoid identity on a large sample of aphids collected in cultivated and uncultivated agricultural habitats in Western France. We used this data to construct ecological networks to assess the level of compartmentalisation between aphid–parasitoid food webs of cultivated and uncultivated habitats. We evaluated the extent to which uncultivated margins provided a resource for parasitoids shared between pest and non pest aphids. We compared the observed quantitative ecological network described by our molecular approach to an empirical qualitative network based on aphid–parasitoid interactions from traditional rearing data found in the literature. We found that the molecular network was highly compartmentalised and that parasitoid sharing is relatively rare between aphids, especially between crop and non-crop compartments. Moreover, the few cases of putative shared generalist parasitoids were questionable and could be due to the lack of discrimination of cryptic species or from intra-specific host specialization. Our results suggest that apparent competition mediated by Aphidiinae parasitoids is probably rare in agricultural areas and that the contribution of field margins as a source of these biocontrol agents is much more limited than expected. Further large-scale (spatial and temporal) studies on other crops and non-crop habitats are needed to confirm this.