Bycatch in a bottle: what taxa are recoverable from metabarcoding DNA in historical invertebrate collection preservative fluid?

Abstract

Natural history museum collections are invaluable repositories of biodiversity, offering insights into life on Earth. Genomic approaches provide powerful tools to characterize biodiversity in these collections. However using these collections for genomics without damaging specimens is a challenge. Here, we develop and test non-destructive DNA metabarcoding methods to capture biodiversity from the preservative fluids of archived insect collections ('Bycatch'). We optimized workflows for extracting and amplifying the partial CO1 locus (CO1) and fungal ITS1 locus from ethanol-based preservative fluids, validating ethanol preparation methods, comparing DNA extraction kits, and refining PCR protocols. Our results demonstrate that from museum collections with low DNA yields, CO1 and fungal ITS1 loci can often be recovered from preservative fluids, and we present detailed methodology and workflows. We test metabarcoding success to recover taxa in several museum collections ranging in age and storage condition. This is to support the State of California's effort to catalog and sequence all insects and fungi, building baselines of California biodiversity with help from museum collections. Lastly, we investigate the complementarity of metabarcoding water versus ethanol and morphological identifications aimed to capture benthic macroinvertebrate biodiversity in streams. Our findings highlight that DNA metabarcoding of the preservative fluid is a non-destructive tool for capturing biodiversity in historical specimens, but there are limitations on the overlaps between DNA results and physical contents, where morphological identification still reigns in taxon counts, but metabarcoding sometimes provides more taxonomic resolution, and can be used to track DNA from other organisms such as fungi beyond the directly surveyed specimens.