Species identification using DNA – what is the key to success?

[Read time: 1 min 40 seconds]

Emerging environmental DNA (eDNA) methods are a game changer for surveying and monitoring.

By matching fragments of DNA found in water, soil and air samples, against DNA sequence libraries, we can understand exactly what is living there, even the elusive species which can be hard to see, hear or catch.

But DNA is much like fingerprints – you’re only able to make a match with information you already have on file.

DNA libraries store all the sequence data that is used to identify species – matching it against a DNA fragment from specimens that have been collected, or against environmental DNA (samples collected from a specific area, containing the DNA of species that live there). This is often called DNA barcoding.

So when it comes to DNA barcode libraries, bigger really is better.

The more DNA sequences stored in a DNA barcoding library, the higher likelihood we have of finding a match.

At Biologic, we have sequenced thousands of invertebrate specimens, to assist with identification, species discovery and to contribute to publicly accessible DNA libraries.

We have been building an enviable database since 2020, sequencing over eight thousand specimens of arachnids, insects, crustaceans, worms, reptiles and mammals.

These sequences have been essential for providing high quality survey and monitoring data for our clients, understanding species’ distributions and discovering new species.

We have also contributed to collective knowledge, making almost 30% of our sequences publicly available on GenBank, with data released as projects are completed.

Records are updated on GenBank as identifications are refined and specimens are accessioned in museums. We are also working with the WA Museum to assist in the GenBank accessioning of legacy barcode datasets from their collections.

These barcode sequences have been used in numerous metabarcoding eDNA studies to design assays (the tests that look for DNA matches) or in comparative sequence libraries. The continual release of these data will grow the utility of eDNA to support environmental surveys.

Biologic has also undertaken genome skimming of plant tissue samples to build plastid genomes and nuclear ribosomal DNA datasets. These datasets have been crucial for confirming the identity of threatened species, identifying hybrids, and testing species boundaries in conservation significant taxa.

A crucial part of building DNA barcode libraries is the purification of high-quality DNA from tissues. This starts in the field, and Biologic’s experienced field teams have developed standard operating procedures to maximise the quality and quantity of DNA in specimens.

Our laboratory staff maintain high standards to minimise contamination and maximise the amplification of on-target DNA. For specimens where Biologic has been responsible for the entire field collection to sequencing workflow (n=7.3k specimens), we have a success rate of almost 90%, which includes challenging groups such as microcrustanceans and trogolofauna.