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

Matthew Bowser,Steven Swenson,Stephen Burr,Jason Moan,Elizabeth Graham,Isaac Davis,Garret Dubois

doi:10.3897/rio.5.e48536

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.

Highlights

The introduction and establishment of non-native forest insects is considered to be one of the greatest threats to forest health (Rabaglia et al 2008, Ramsfield et al 2016)
Biomonitoring by metabarcoding has been advocated for arthropods because these methods have the potential to be much faster and less costly than identifications obtained by morphology (Hajibabaei et al 2011, Baird and Hajibabaei 2012, Watts et al 2019)
High Throughput Sequencing consistently yielded a higher diversity of taxa and provided identifications mostly at the species or BIN resolution; in contrast, morphological methods yielded lower diversity, with identifications mostly at the resolution of genera

Summary

Introduction

The introduction and establishment of non-native forest insects is considered to be one of the greatest threats to forest health (Rabaglia et al 2008, Ramsfield et al 2016). A potential solution to this taxonomic bottleneck is the use of recently developed metabarcoding methods. Biomonitoring by metabarcoding has been advocated for arthropods because these methods have the potential to be much faster and less costly than identifications obtained by morphology (Hajibabaei et al 2011, Baird and Hajibabaei 2012, Watts et al 2019). Identifications obtained through metabarcoding should be of better taxonomic resolution in Alaska, where a deliberate effort has been made to construct a reference library of DNA barcode sequences useful for species identifications of terrestrial arthropods (Sikes et al 2017), than in regions where such libraries are lacking (see Watts et al 2019)

Methods

Results

Discussion

Conclusion