Written evidence submitted by Dr Claire Carvell (INS0045)

To accompany Oral evidence given by Dr Claire Carvell on Wednesday 7 June 2023

The research teams at UKCEH considered the three panel sessions on 7th June to address a broad range of complex issues that were included within the inquiry and MPs questions relating to insect decline.

One element which received little attention, and which we would like to follow up on, was the application of DNA barcoding technology to tackle some of our knowledge gaps on insects.

Novel technology – how can DNA barcoding, AI or other passive techniques help with studying/ monitoring insect abundance?

As outlined during the oral evidence session and other written evidence, traditional insect monitoring methods (such as repeated observational transects, pan traps or malaise traps) are typically time consuming, require detailed knowledge (e.g. for identifying species) and are subject to certain biases such as variability in detection of species between observers or between methods.

Novel technologies such as DNA barcoding and automated systems that use artificial intelligence (AI) are opening exciting new possibilities for insect monitoring and ecological research, but they cannot be used in isolation and must complement existing long-term surveillance monitoring approaches that continue to use critical taxonomic skills.

For DNA barcoding, new techniques and lowering costs mean DNA approaches are becoming more practical to use at large scale. Its’ important not to set unrealistic expectations of what they can achieve, but we are well-placed in the UK, with the ecological research infrastructure, and volunteer base, to make the most of these with appropriate investment.

The Defra DNA Centre of Excellence (CoE) champions the development and uptake of DNA-based tools for monitoring the environment across the Defra group. In 2021, the CoE set out “An Action Plan for making progress with using DNA to monitor terrestrial invertebrates” (Woodcock et al., 2021). This JNCC report emphasises the main barriers which, aside from funding, included the need to establish consistent operational methods and improve end-user understanding of potential DNA-based methods and metrics. More complete barcode libraries are also key – DNA can potentially identify things to species level but only if the DNA can be linked to a correctly identified specimen.

The need to improve insect barcode libraries was also highlighted through a report led by Natural England (Macadam et al., 2020). This provided a gap analysis to identify which of the 13,690 taxa listed in Natural England’s Pantheon database for invertebrates are represented in the widely used Barcode of Life Database (BOLD), and to assess confidence in these barcodes. The report highlighted a lack of high confidence UK barcodes for the majority of invertebrates, which affects the ability to use DNA methods for invertebrate monitoring (2020 Gap Analysis of the BOLD Database for Key English Invertebrates - NECR324 (naturalengland.org.uk). Ongoing work to improve UK barcode libraries is being co-ordinated through the UK Barcode of Life (UKBoL) project, though this is considering all taxa and not just insects.

The CoE funded a pilot study that explored the value of metabarcoding in bulk the pan-trap samples collected and archived on the UK Pollinator Monitoring Scheme (PoMS) (Liu et al., 2021). This showed that DNA methods could provide information on all the non-target and understudied insects being sampled, but so far only generating a list of the species or ‘Operational Taxonomic Units’ present in each sample rather than giving information on the abundance (number) of each species.

The UK Pollinator Monitoring Scheme, led by UKCEH, is now partnering with the BIOSCAN–UK project (led by the Wellcome Sanger Institute https://www.sanger.ac.uk/collaboration/bioscan/ ) to test and validate their cheaper, high-throughput and non-destructive DNA extraction and sequencing protocol. This works on individually plated insects and would give us data on abundance. BIOSCAN’s high throughput sample processing pipeline allows 10,000 insects to be studied in a single sequencing run (provided the costs of first handling the specimens can be met).

If this is successful, it would move DNA methods closer to operational use for archived and future insect samples that are generated from PoMS or other passive sampling schemes. We are probably only 5-6 years away from being able to implement a pipeline that sees these insect samples transfer from the field to yielding robust DNA-based metrics that could be used to monitor change and the impact of environmental stressors.

Traditional taxonomy currently takes up about 20% of the annual UK PoMS budget (for the identification of bees and hoverflies to species, and counting of other insects to group level). From 2017-21, >335,000 insects were sampled from 95 PoMS sites across the UK, and the intention is for these same sites to receive annual sampling long-term. Combining the traditional taxonomy with high-throughput and non-destructive DNA sequencing could provide a powerful tool for understanding population changes across a vast range of insect groups in the near-future.

New image-based and AI-assisted tools are also being developed alongside traditional methods to widen the scope of standardised insect monitoring. At UKCEH for example we have designed an “AMI-trap” that offers a platform for long-term, autonomous monitoring of moths using high res cameras and computer vision. A priority is to develop this further to harness the combined power of bioacoustics, computer vision and deep learning for standardised monitoring, so its scope could be widened for other insects, bats and birds.

18 July 2023

References

Liu, H., Vogler, A., Riccomagno, S., Read, D., Carvell, C. (2021) Pollinator-plant interactions and insect community dynamics: DNA Centre of Excellence project as part of the UK Pollinator Monitoring and Research Partnership 2019-2020 (unpublished report to Defra BE0159 ECM 55342).

Macadam, C., Robins, J. & Thomson, T. (2020) 2020 Gap Analysis of the BOLD Database for Key English Invertebrates, Natural England Commissioned Report Number 324.

Woodcock, P., Cottrell, J., Heaver, D., Barsoum, N., Leatherland, D., Askew, R., Briscoe, A., Burian, A., Cole, A., Cooke, D., Day, J., Deiner, K., Genney, D., Gurney, M., Harris, M., Hipperson, H., Jones, E., Lawniczak, M., Macadam, C., McSorley, C., Miller, K., Mynott, S., Nisbet, A., Peck, K., Preston, M., Price, B., Read, D., Rees, H., Robinson, A., Stringer, A. & Yu, D. 2021. An Action Plan for making progress with using DNA to monitor terrestrial invertebrates, JNCC Report No. 691. JNCC, Peterborough, ISSN 0963-8091.