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

Mullin, Victoria E., Stephen, William, Arce, Andres N., Nash, Will, Raine, Calum, Notton, David G., Whiffin, Ashleigh, Blagderov, Vladimir, Gharbi, Karim, Hogan, James, Hunter, Tony, Irish, Naomi, Jackson, Simon, Judd, Steve, Watkins, Chris, Haerty, Wilfried ORCID: https://orcid.org/0000-0003-0111-191X, Ollerton, Jeff, Brace, Selina, Gill, Richard J. and Barnes, Ian (2022) First large-scale quantification study of DNA preservation in insects from natural history collections using genome-wide sequencing. Methods in Ecology and Evolution. ISSN 2041-210X

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Abstract

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. 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 1.9 bp per decade. The proportion of quality filtered reads mapping to 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.

Item Type: Article
Additional Information: Funding Information: The work was funded by NERC grants NE/P012574/1 and NE/P012914/1 awarded to I.B and R.J.G. respectively, which supported A.N.A., S.B., V.E.M. and J.O. V.E.M. was additionally supported by The Government of Ireland Postdoctoral Fellowship GOIPD/2020/605. W.S. was supported by the NHM Earth Sciences Departmental Infrastructure Fund. Genome analysis was supported by the Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation, through the Core Capability Grant BB/CCG1720/1 at the Earlham Institute including the National Capability BBS/E/T/000PR9816. W.H. and W.N. are supported by the BBSRC Core Strategic Programme Grant (Genomes to Food Security) BB/CSP1720/1 and its constituent work package BBS/E/T/000PR9818. Publisher Copyright: © 2022 The Authors. Methods in Ecology and Evolution published by John Wiley & Sons Ltd on behalf of British Ecological Society.
Uncontrolled Keywords: adna,bombus,collection genomics,dna degradation,entomological collections,historical dna,museum specimen,pollinators,ecology, evolution, behavior and systematics,ecological modelling ,/dk/atira/pure/subjectarea/asjc/1100/1105
Faculty \ School: Faculty of Science > School of Biological Sciences
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Depositing User: LivePure Connector
Date Deposited: 21 Sep 2022 16:30
Last Modified: 27 Sep 2022 08:32
URI: https://ueaeprints.uea.ac.uk/id/eprint/88561
DOI: 10.1111/2041-210X.13945

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