A test of metabarcoding for Early Detection and Rapid Response monitoring for non-native forest pest beetles (Coleoptera)

Abstract

In response to the threat of introductions of non-native forest insects, the Early Detection and Rapid Response (EDRR) program in Alaska monitors for arrivals of non-native insects, an effort that is limited by the time required to process samples using morphological methods. We compared conventional methods of processing EDRR traps with metabarcoding methods for processing the same samples. We deployed Lindgren funnel traps at three points of entry in Alaska using standard EDRR methods and trap samples were later processed using routine sorting and identification based on morphology. Samples were then processed using High Throughput Sequencing (HTS) metabarcoding methods. In three samples bycatch was included and in three samples non-native species were added. Morophological and HTS methods yielded generally similar results for scolytine and cerambycid beetle assemblages, but HTS provided more species-resolution identifications (46 species) than morphological methods (4 species plus the 3 non-native species known a priori). None of the non-native species were detected by HTS. Including bycatch did not appear to hinder identifications of scolytine and cerambycid beetles by HTS. From among the bycatch, two Palearctic species adventive to North America, Placusa incompleta Sjöberg, 1934 and Hydrophoria lancifer (Harris, 1780), are newly reported from Alaska. We do not recommend replacing our current morphological monitoring methods with HTS methods because we believe that we would be more likely to detect known non-native pest species using morphology. However, we would use HTS to increase our sample size without greatly increasing time required to process samples. We would also recommend HTS methods for surveillance monitoring where the set of target taxa is not limited to known pest species.

Computational Evaluation of DNA Metabarcoding for Universal Diagnostics of Invasive Insect Pests

“…High sensitivity across a broad taxonomic scope is a defining feature of DNA metabarcoding assays, facilitating their use as a universal diagnostic assay to rapidly screen mixed samples for a range of target pests or pathogens. Despite several studies applying metabarcoding to certain pest taxa (Batovska et al, 2018(Batovska et al, , 2020Bowser et al, 2019;Young et al, 2021), the diagnostic performance of the required mini-barcodes has not until now been systematically evaluated across the broader diversity of invasive insect species. Using a curated reference database covering 110,676 insect species, including 2,625 species registered on global invasive species lists, we here demonstrate that mini-barcodes can achieve comparable resolution to the full-length COI barcode region already widely accepted within insect diagnostic protocols.…”