A dearth of data: fitting parasitoids into ecological networks.

Studying parasitoids can provide insights into global diversity estimates, climate change impacts, and agroecosystem service provision. However, this potential remains largely untapped due to a lack of data on how parasitoids interact with other organisms. Ecological networks are a useful tool for studying and exploiting the impacts of parasitoids, but their construction is hindered by the magnitude of undescribed parasitoid species, a sparse knowledge of host ranges, and an under-representation of parasitoids within DNA-barcode databases (we estimate <5% have a barcode). Here, we advocate the use of DNA metabarcoding to construct the host-parasitoid component of multilayer networks. While the incorporation of parasitoids into network-based analyses has far ranging applications, we focus on its potential for assessing ecosystem service provision within agroecosystems.

Land-use intensity affects the potential for apparent competition within and between habitats.

Arthropod communities dwelling in adjacent habitats are able to impact one another via shared natural enemies. In agricultural landscapes, drastic differences in resource availability between crop and non-crop habitats cause variation in insect herbivore densities over short distances, potentially driving inter-habitat effects. Moreover, the composition of the landscape in which the habitats are embedded likely affects realised attack rates from natural enemies via impacts on local arthropod community structure. Here, we examine indirect effects between herbivore species within and between habitat types by calculating the potential for apparent competition between multiple populations. Firstly, we aim to determine how disparities in resource availability impact the strength of the potential for apparent competition occurring between habitats, secondly to examine the impact of landscape composition upon these effects, and finally to couch these observations in reality by investigating the link between the potential for apparent competition and realised attack rates. We used DNA metabarcoding to characterise host-parasitoid interactions within two habitat types (with divergent nutrient inputs) at 11 locations with variable landscape composition within an agroecosystem context. We then used these interaction networks to estimate the potential for apparent competition between each host pair and to compare expected versus realised attack rates across the system. Shared natural enemies were found to structure host herbivore communities within and across habitat boundaries. The size of this effect was related to the resource availability of habitats, such that the habitat with high nutrient input exerted a stronger effect. The overall potential for apparent competition declined with increasing land-use intensity in the surrounding landscape and exhibited a discernible impact on realised attack rates upon herbivore species. Thus, our results suggest that increasing the proportion of perennial habitat in agroecosystems could increase the prevalence of indirect effects such as apparent competition among insect herbivore communities, potentially leading to enhanced population regulation via increased attack rates from natural enemies like parasitoid wasps.

The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera.

A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of >3000 bp. These sequences were combined into a single dataset together with all mitochondrial data available at GenBank, in addition to nuclear markers widely used in molecular phylogenetics. The resulting matrix of nearly 16,000 species with two or more loci produced trees (RAxML) showing overall congruence with the Linnaean taxonomy at hierarchical levels from suborders to genera. We tested the role of full-length mitogenomes in stabilizing the tree from GenBank data, as mitogenomes might link terminals with non-overlapping gene representation. However, the mitogenome data were only partly useful in this respect, presumably because of the purely automated approach to assembly and gene delimitation, but improvements in future may be possible by using multiple assemblers and manual curation. In conclusion, the combination of data mining and metagenomic sequencing of bulk samples provided the largest phylogenetic tree of Coleoptera to date, which represents a summary of existing phylogenetic knowledge and a defensible tree of great utility, in particular for studies at the intra-familial level, despite some shortcomings for resolving basal nodes.

Metabarcoding of fungal communities associated with bark beetles.

Many species of fungi are closely allied with bark beetles, including many tree pathogens, but their species richness and patterns of distribution remain largely unknown. We established a protocol for metabarcoding of fungal communities directly from total genomic DNA extracted from individual beetles, showing that the ITS3/4 primer pair selectively amplifies the fungal ITS. Using three specimens of bark beetle from different species, we assess the fungal diversity associated with these specimens and the repeatability of these estimates in PCRs conducted with different primer tags. The combined replicates produced 727 fungal Operational Taxonomic Units (OTUs) for the specimen of Hylastes ater, 435 OTUs for Tomicus piniperda, and 294 OTUs for Trypodendron lineatum, while individual PCR reactions produced on average only 229, 54, and 31 OTUs for the three specimens, respectively. Yet, communities from PCR replicates were very similar in pairwise comparisons, in particular when considering species abundance, but differed greatly among the three beetle specimens. Different primer tags or the inclusion of amplicons in separate libraries did not impact the species composition. The ITS2 sequences were identified with the Lowest Common Ancestor approach and correspond to diverse lineages of fungi, including Ophiostomaceae and Leotiomycetes widely found to be tree pathogens. We conclude that Illumina MiSeq metabarcoding reliably captures fungal diversity associated with bark beetles, although numerous PCR replicates are recommended for an exhaustive sample. Direct PCR from beetle DNA extractions provides a rapid method for future surveys of fungal species diversity and their associations with bark beetles and environmental variables.