Unlocking natural history collections to improve eDNA reference databases and biodiversity monitoring
Creators
- 1. ETH Zurich
- 2. University of Bergen
- 3. Swedish Museum of Natural History
- 4. Natural History Museum
- 5. Ludwig-Maximilians-Universität München
- 6. University of Copenhagen
- 7. University of Florence
- 8. Natural History Museum Vienna
- 9. University of Bern
- 10. Senckenberg Research Institute and Natural History Museum Frankfurt/M
- 11. University of Lausanne
- 12. Université Montpellier 2
Description
Biodiversity changes due to human activities highlight the need for efficient biodiversity monitoring approaches. Environmental DNA (eDNA) metabarcoding offers a non-invasive method used for biodiversity monitoring and ecosystem assessment, but its accuracy depends on comprehensive DNA reference databases. Natural history collections often contain rare or difficult-to-obtain samples that can serve as a valuable resource to fill gaps in eDNA reference databases. Here, we discuss the utility of specimens from natural history collections in supporting future eDNA applications. Museomics—the application of -omics techniques to museum specimens—offers a promising avenue for improving eDNA reference databases by increasing species coverage. Furthermore, museomics can provide transferable methodological advancements for extracting genetic material from samples with low and degraded DNA. The integration of natural history collections, museomics, and eDNA approaches has the potential to significantly improve our understanding of global biodiversity, highlighting the continued importance of natural history collections.
Notes
Funding provided by: Swiss National Science Foundation
ROR ID: https://ror.org/00yjd3n13
Award Number: 205556
Funding provided by: Agence Nationale de la Recherche
ROR ID: https://ror.org/00rbzpz17
Award Number: ANR-21-CE02-0032
Funding provided by: European Molecular Biology Organization
ROR ID: https://ror.org/04wfr2810
Award Number: 10549
Methods
Dataset for analyzing the potential of museum specimens to improve the DNA reference database
To examine the cumulative number of species sequenced for a given DNA barcode/mitochondrial genome (also referred to as mitogenome) over the years, we retrieved all data available from NCBI using the R package rentrez v1.2.3 (Winter 2017). We searched the nucleotide database for the rRNA 12S, rRNA 16S, rRNA 18S, cytochrome B (cytB), cytochrome oxidase I (COI) barcodes, as well as for the complete mitogenomes for all fish orders. In addition, we also retrieved all the fish species with available data on the sequence read archive (SRA) using the Entrez Direct (Kans 2024), which provides access to the NCBI databases from a Unix terminal window.
To highlight the potential of museum specimens for increasing the number of species with an available barcode/mitogenome sequence, we first downloaded all available datasets on the Global Biodiversity Information Facility (GBIF) listing fish specimens stored in European natural history museum collections (see table S1). Subsequently, we downloaded a list of all existing fish species using the R package rfishbase v5.0.0 (Boettiger et al. 2012) and extracted their geographic range (field AreaCode). In addition, we retrieved information about the Red List status of all fish species from the International Union for Conservation of Nature and Natural Resources (IUCN) website. All the datasets (barcodes, museum specimens, IUCN status and fish species list, and geographic range) were combined in R v.4.3.0 and subsequently plotted.
Files
scripts.zip
Files
(176.6 MB)
| Name | Size | Download all |
|---|---|---|
|
md5:db7fc41709704720afceec44ea790a8e
|
176.6 MB | Preview Download |
Additional details
Related works
- Is cited by
- 10.1093/biosci/biaf140 (DOI)
- Is source of
- 10.5061/dryad.0zpc8677g (DOI)