EUROPEAN JOURNAL OF ENTOMOLOGY

Eur. J. Entomol. 123: 48-60, 2026 | DOI: 10.14411/eje.2026.008

Optimization of DNA extraction for insect museomics substantially increases DNA yieldOriginal article

Marie DJERNÆS¹, Audrey BRAS ORCID...², Thomas Johannes SIMONSEN ORCID...³, Mads Reinholdt JENSEN ORCID...^{1, 4}, Jesper Smærup BECHSGAARD ORCID...¹, Jeppe Bayer PEDERSEN ORCID...¹, Monica Anne MOWERY ORCID...^{5, 6}, Trine BILDE ORCID...¹, Philip Francis THOMSEN ORCID...¹

¹ Department of Biology, Centre for Ecological Genetics, Aarhus University, Aarhus C, Denmark; e-mails: marie_djernaes@hotmail.com, jesper.bechsgaard@bio.au.dk, jeppe.bayer@bio.au.dk, trine.bilde@bio.au.dk, pfthomsen@bio.au.dk

² Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland; e-mail: audrey.bras@helsinki.fi

³ Department of Research and Collections, Natural History Museum Aarhus, Aarhus C, Denmark; e-mail: t.simonsen@nathist.dk

⁴ Norwegian College of Fishery Science, UiT - The Arctic University of Norway, Tromsø, Norway; e-mail: mads.jensen@uit.no

⁵ Department of Biology, York College, The City University of New York, Jamaica, NY, USA

⁶ Graduate Center of the City University of New York, New York, NY, USA; e-mail: mmowery@york.cuny.edu

Historical samples from museum and private collections can serve as a time machine, allowing us to follow changes in genetic composition through time as well as obtaining genomic data on past biodiversity. Thus, genetic data from collections (museomics) are increasingly being utilized in scientific studies. However, although several different DNA extraction techniques have been used successfully in insect museomics, direct comparisons between methods are uncommon. It is therefore unclear to what extent simple adjustments of DNA extraction protocols can increase yields. This is especially important when analysing museum specimens that are decades or even hundreds of years old with low endogenous DNA content. Here, we first compared two recommended protocols which include the widely used QIAamp DNA Micro Kit or the Monarch PCR & DNA Cleanup Kit, respectively. We found that the Monarch kit performed substantially better than the QIAamp kit in terms of yield. We then compared various lysis temperatures, the effect of non-destructive versus destructive lysis, and the relative yield from a second round of extraction using the Monarch kit. We evaluated our results both by measurements of DNA concentration and fragment length and results from low coverage whole genome sequencing. We found that a lysis temperature of 42°C performed better than either 56°C or 37°C, using a lysis time of approximately 20 h. Destructive extraction increased yield in some species, and a second round of non-destructive extraction can substantially increase total yield. Finally, we used our selected Monarch kit protocol to extract DNA from legs of 492 additional butterfly specimens (23-128 years old) and 21 small wasp specimens. We observed virtually no effects of specimen age on the amount of DNA extracted or the endogenous DNA content, while older specimens yielded slightly shorter lengths of sequenced fragments. The DNA extraction procedure worked well for specimens up to 128 years of age and we would expect this to be the case for substantially older specimens, which would enable successful DNA extraction from the vast majority of dried insects in collections.

Keywords: Monarch PCR & DNA Cleanup Kit, Monarch Spin PCR & DNA Cleanup Kit, insect collections, whole genome sequencing, endogenous DNA

Received: June 6, 2025; Revised: February 17, 2026; Accepted: February 17, 2026; Published online: February 26, 2026  Show citation