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.