My PhD research

Characterising large-scale coastal fish biodiversity in South Africa using eDNA metabarcoding

Molly Czachur PhD research

My research

I am currently working towards my PhD in Zoology at Stellenbosch University, South Africa. I am describing coastal fish biodiversity in the region using an environmental DNA (eDNA) metabarcoding approach.  You can check out my recent cartoon to learn more about these methods by clicking here.

I am researching the biodiversity of fishes across the South African coastline. Interestingly, these fishes (and all organisms) shed DNA into the environment as they move and exist in their habitat, and the DNA that they shed can come from things like their scales, their urine and their faeces. The oceans are therefore a big soup containing loads of amazing creatures, and also the free-floating DNA of these creatures!


Using an increasingly powerful method called environmental DNA metabarcoding, I am capturing the free-DNA (called environmental DNA or eDNA) and matching this DNA to known DNA sequences to identify which fishes are present along different areas of the South African coastline. It involves me travelling to many different shores, from rocky and sandy shores to seagrass meadows and mangrove forests, and collecting seawater. I filter this seawater to capture any DNA that is floating in the water, and bring it back to the lab for DNA extractions, followed by sequencing, and then computer-based processing and analyses (this whole process is known as DNA metabarcoding).

A wide-scale approach

I am lucky to spend time in the field collecting water samples, but the really exciting stuff happens once we get back to the lab and process the data, which contains species lists for all the places that we visited! This method allows us to describe fish biodiversity without ever having to actually see the fishes that we are trying to describe. Most fish biodiversity estimates in the region rely on data from fish that are caught on commercial fishing vessels, which is very selective depending on the type of fishing gear you use and therefore not representative of what fish are actually occurring in those waters. Even using visual surveys (e.g. by SCUBA diving and recording the species that you see) can be biased towards larger species, surveys can often mis-identify cryptic or similar species, and require lots of taxonomic expertise.

We are therefore describing fish biodiversity across South Africa using the DNA metabarcoding approach instead, giving us rapid, cost-effective and more up-to-date information on fishes in the region. This type of data is vital for appropriately managing these important coastal resources.

Join the conversation and see how I’m progressing by visiting my socials @ZoologyMolly