To bee, or not to bee? One leg is the question

Abstract

Temporal genomic studies that utilise museum insects are invaluable for understanding changes in ecological processes in which insects are essential, such as wild and agricultural pollination, seed dispersal, nutrient cycling, and food web architecture, to name a few. However, given such analyses come at the cost of physical damage to museum specimens required for such work, there is a natural interest in the development and/or application of methods to minimise the damage incurred. We explored the efficacy of a recently published single stranded library construction protocol, on DNA extracted from single legs taken from eight dry‐preserved historic bee specimens collected 150 years ago. Specifically, the DNA was extracted using a “minimally destructive” method that leaves the samples' exterior intact. Our sequencing data revealed not only that the endogenous DNA recovered from some of the samples was at a relatively high level (up to 58%), but that the complexity of the libraries was sufficient in the best samples to theoretically allow deeper sequencing to a predicted level of 69x genome coverage. As such, these combined protocols offer the possibility to generate sequencing data at levels that are suitable for many common evolutionary genomic analyses, while simultaneously minimising the damage conferred to the valuable dried museum bee samples. Furthermore, we anticipate that these methods may have much wider application on many other invertebrate taxa stored in a similar way. We hope that the results from this research may be able to contribute to the increased willingness of museums to loan much needed dry‐preserved insects for future genomic studies.

Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections

“…DNA extraction protocols for ancient and historic DNA have been optimised to obtain good DNA yields from small amounts of material, for example, as low as two milligrams of dry plant tissue ( Latorre et al 2020 ) or one insect leg (e.g. Cavill et al (2022) ). In terms of less invasive sampling, approaches include sampling the embedding fixative solution of wet collection specimens ( Rayo et al 2022 ), rubbing an eraser over herbarium specimens ( Shepherd 2017 ) and gentle digestion followed by drying of teeth ( Rohland et al 2004 ), whole insect specimens ( Gilbert et al 2007a , Korlević et al 2021 ) or herbarium material ( Sugita et al 2020 ).…”

High-throughput sequencing of insect specimens with sub-optimal DNA preservation using a practical, plate-based Illumina-compatible Tn5 transposase library preparation method

“…>10 years) remain unclear. Importantly, while reextractions of the same biological material may produce viable genomic DNA extracts, the first extraction is often the most effective in terms of DNA yield and endogenous DNA content [20]. Using the entire specimen therefore limits any future DNA applications, reduces the long-term biological value of entomological collections, and fails to incorporate ethical guidelines for the destructive sampling of biological specimens [21].…”

“…Using the entire specimen therefore limits any future DNA applications, reduces the long-term biological value of entomological collections, and fails to incorporate ethical guidelines for the destructive sampling of biological specimens [21]. To most effectively preserve insect specimens, for both future entomological applications and future DNA extractions, a more conservative solution would be to sacrifice a small piece of tissue such as a leg [20]. This approach leaves the majority of the insect untouched, although the low sample volume and consequent low DNA yield may constrain specific downstream molecular applications.…”

A fast and inexpensive plate-based NGS library preparation method for insect genomics

“…> 10 years) remain unclear. Importantly, while re-extractions of the same biological material may produce viable genomic DNA extracts, the first extraction is often the most effective in terms of DNA yield and endogenous DNA content (Cavill et al 2022). Using the entire specimen therefore limits any future DNA applications, reduces the long-term biological value of entomological collections, and fails to incorporate ethical guidelines for the destructive sampling of biological specimens (Pálsdóttir et al 2019).…”

“…Using the entire specimen therefore limits any future DNA applications, reduces the long-term biological value of entomological collections, and fails to incorporate ethical guidelines for the destructive sampling of biological specimens (Pálsdóttir et al 2019). To most effectively preserve insect specimens, for both future entomological applications and future DNA extractions, a more conservative solution would be to sacrifice a small piece of tissue such as a leg (Cavill et al 2022). This approach leaves the majority of the insect untouched, although the low sample volume and consequent low DNA yield may constrain specific downstream molecular applications.…”