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

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 has 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. 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. Our approach shows that museum entomological specimens are comprised of short DNA fragments with mean lengths below 100 base pairs (BP), suggesting a rapid and large-scale post-mortem reduction in DNA fragment size. After this initial decline, however, we find a relatively consistent rate of DNA decay in our dataset, and estimate a mean reduction in fragment length of 1.9bp per decade. The proportion of quality filtered reads mapping our assembled reference genome was around 50 %, and decreased by 1.1 % per decade. We demonstrate that historical insects have significant potential to act as sources of DNA to create valuable genetic baselines. The relatively consistent rate of DNA degradation, both across collections and through time, mean that population level analyses - for example for conservation or evolutionary studies - are entirely feasible, as long as the degraded nature of DNA is accounted for.Funding provided by: NERCCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100000270Award Number: NE/P012574/1Funding provided by: NERCCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100000270Award Number: NE/P012914/1Funding provided by: Irish Research CouncilCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100002081Award Number: GOIPD/2020/605Funding provided by: Natural History MuseumCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100000831Award Number: Earth Sciences Departmental Infrastructure FundFunding provided by: Biotechnology and Biological Sciences Research CouncilCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100000268Award Number: BB/CCG1720/1Funding provided by: Biotechnology and Biological Sciences Research CouncilCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100000268Award Number: BBS/E/T/000PR9816Funding provided by: Biotechnology and Biological Sciences Research CouncilCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100000268Award Number: BB/CSP1720/1This study used an individual leg per specimen for 113 pinned B. lapidarius drones collected from 1891 to 2004. All samples were treated as degraded DNA and processed through an aDNA pipeline. Data sequenced on a NextSeq 500 and data aligned and prcoessed through bwa, samtools and picard. Linear Regression models in R