First large‐scale quantification study of DNA preservation in insects from natural history collections using genome‐wide sequencing

Abstract

1. Insect declines are a global issue with significant ecological and economic ramifications. Yet, we have a poor understanding of the genomic impact these losses can have. Genome-wide data from historical specimens have the potential to provide baselines of population genetic measures to study population change, with natural history collections representing large repositories of such specimens. However, an initial challenge in conducting historical DNA data analyses is to understand how molecular preservation varies between specimens.2. Here, we highlight how Next-Generation Sequencing methods developed for studying archaeological samples can be applied to determine DNA preservation from only a single leg taken from entomological museum specimens, some of which are more than a century old. An analysis of genome-wide data from a set of 113 red-tailed bumblebee Bombus lapidarius specimens, from five British museum collections, was used to quantify DNA preservation over time.Additionally, to improve our analysis and further enable future research, we generated a novel assembly of the red-tailed bumblebee genome.3. Our approach shows that museum entomological specimens are comprised of short DNA fragments with mean lengths below 100 base pairs (BP), suggesting

The last days ofAporia crataegi(L.) in Britain: evaluating genomic erosion in an extirpated butterfly

“…Our extraction of historic DNA was contaminant free and we obtained short fragment lengths which decreased in length with specimen age, a degradation pattern consistent with other studies using historical DNA (e.g. Mullin et al ., 2023). We used these historical genomes of A. crataegi to provide a genomic perspective on its extirpation from the British Isles in the early twentieth century and their post-glacial colonization history in Britain.…”

Sampling and curation of rove beetles (Insecta, Coleoptera, Staphylinidae) for comprehensive and DNA-grade collections to enhance biodiversity exploration in Northern Eurasia

“…Another take-home message is that some of the expensive approaches, for example, immediate or long-term liquid nitrogen deep freezing of samples may not be necessary for the main goals of systematic entomology and related disciplines collections for which they are frequently used. As shown by Mullin et al (2022) for traditional museum specimens, the initial post-mortem decline (fragmentation) of DNA is the strongest, after which a rate of DNA decay is low and consistent for decades. Finding a simple method for inhibiting this initial DNA decline is the most important target, which is beyond the scope of our experience and goals of this paper.…”

“…Another issue is that the DNA extraction and sequencing techniques are fast evolving towards their ability to cope with the degraded DNA, i.e. with the suboptimally preserved or simply traditionally pinned specimens that initially were not even intended for molecular work ( Nakahama 2021 ; Lalonde and Marcus 2020 ; Mullin et al 2022 ). According to the above-cited reviews and recent developments with museomics, preservation techniques may vary depending on the kind of the DNA for which data are sought.…”

The genome sequence of the Violet Carpenter Bee, Xylocopa violacea (Linnaeus, 1785): a hymenopteran species undergoing range expansion.

“…High molecular weight (HMW) DNA was extracted from thorax tissue of iyXylViol4 using the Qiagen MagAttract HMW DNA Kit, with modifications as described in Mullin et al (2022). HiFi library preparation and Pacific Biosciences (PacBio) sequencing were carried out following the low-input protocol described in Mullin et al (2022) NovaSeq 6000 instrument set up to sequence 150bp paired end reads.…”