Towards holistic insect monitoring: species discovery, description, identification and traits for all insects

Abstract

Holistic insect monitoring needs scalable techniques to overcome taxon biases, determine species abundances, and gather functional traits for all species. This requires that we address taxonomic impediments and the paucity of data on abundance, biomass and functional traits. We here outline how these data deficiencies could be addressed at scale. The workflow starts with large-scale barcoding (megabarcoding) of all specimens from mass samples obtained at biomonitoring sites. The barcodes are then used to group the specimens into molecular operational taxonomic units that are subsequently tested/validated as species with a second data source (e.g. morphology). New species are described using barcodes, images and short diagnoses, and abundance data are collected for both new and described species. The specimen images used for species discovery then become the raw material for training artificial intelligence identification algorithms and collecting trait data such as body size, biomass and feeding modes. Additional trait data can be obtained from vouchers by using genomic tools developed by molecular ecologists. Applying this pipeline to a few samples per site will lead to greatly improved insect monitoring regardless of whether the species composition of a sample is determined with images, metabarcoding or megabarcoding. This article is part of the theme issue ‘Towards a toolkit for global insect biodiversity monitoring’.

Sharing insect data through GBIF: novel monitoring methods, opportunities and standards

“…However, integrated approaches are needed to properly describe and understand [ 34 ] the many new species that will be revealed by an increased global coverage of insect diversity. For example, a combination of citizen science, computer vision and AI identification could be used to increase knowledge of insect diversity [ 35 ] in protected areas designated mostly on data on vertebrate and plant diversity [ 36 ]. Moving intensive insect monitoring to poorly known areas with many undescribed species will require interpretation and quantification of species hypotheses (provisional taxa and global operational taxonomic units), such as Barcode Index Numbers (BINs) in the case of eDNA [ 37 ].…”

Towards a toolkit for global insect biodiversity monitoring

“…[ 23 ], who proposed that short pieces of standardized marker genes could serve as reliable keys to species identification. The rapid advance of sequencing techniques has revolutionized this field: sequencing platforms have become more efficient and more affordable, allowing not only the screening of large samples [ 28 , 29 ] but also efficient species discovery [ 30 ]. As a particularly exciting development, DNA barcodes can not only identify the species identity of insects themselves, but also reveal more of their Eltonian niches [ 31 ], including the plant species the pollen they carry belongs to [ 32 ], and their microbiomes, as shown by Łukasik & Kolasa [ 33 ].…”

“…In an exciting outlook, Meier et al . [ 30 ] outline the path to efficient training of image recognition algorithms by drawing on DNA-sequenced specimens, thus combining two techniques outlined in this theme issue. Such integrated approaches can provide the route to high-throughput biodiversity discovery and monitoring.…”

“…[ 37 – 39 ]). In parallel, imaging devices for laboratory studies of insect specimens are being developed that can efficiently capture rich information from bulk samples and single specimens [ 30 , 40 , 41 ]. Designing and assembling such custom-made systems made from cameras, mini-computers, a power source and additional memory, requires mechanical and electrical engineering skills [ 37 , 38 ], making the application of computer vision to insects an inherently interdisciplinary endeavour.…”

“…For molecular methods, some steps can be automated, e.g. using automatic bottle changers for Malaise traps [ 68 ] and parts of the laboratory protocols [ 30 ], but human labour will probably continue to be needed for parts of field and laboratory work.…”