Mr Milad Khosravi1, Dr Michelle T. Guzik1, Mr Jake Thornhill1, Prof Steven J.B. Cooper1,2
1School of Biological Sciences, Adelaide University, Adelaide, Australia, 2South Australian Museum, Adelaide, Australia
Biography:
Animals (freshwater fishes in particular), ecology and evolution are my main interest in life. I'm currently a PhD researcher focusing on developing eDNA methods to detect rare threatened species of blind Cave Gudgeons (Milyeringa spp.) and their populations within groundwater systems of Northwestern Australia.
Abstract:
Environmental DNA is increasingly being effective to study biodiversity, yet its application to population genetics remains limited, particularly for rare and geographically restricted groundwater fauna. Recovering intraspecific genetic diversity directly from environmental samples could transform conservation-focused monitoring programs by providing non-invasive insights into population structure and conservation units. However, robust workflows to achieve this are lacking. We developed a targeted eDNA metabarcoding framework to estimate genetic diversity in two threatened subterranean cavefishes, Milyeringa veritas and Milyeringa justitia, endemic to groundwater aquifers of Cape Range Peninsula and Barrow Island in north-western Australia. Following validation of two species-specific eDNA assays targeting mitochondrial D-loop hypervariable region 1 (HVR1) using tissue-derived DNA sequences, we applied these assays to groundwater eDNA samples collected across known distributions of the target species. A stringent bioinformatic workflow was developed to infer true haplotypes from eDNA metabarcoding data, enabling reconstruction of genetic diversity from environmental samples. Recovered haplotypes were compared with tissue-derived reference datasets to assess concordance and evaluate eDNA's capacity to detect population-level genetic structure. Results demonstrate that targeted eDNA assays can recover multiple mitochondrial haplotypes from groundwater samples, including geographically structured variations consistent with tissue-derived reference datasets. Additionally, we showed that eDNA techniques have potential to identify previously undocumented haplotypes. This study extends eDNA applications beyond species detection in groundwater systems, demonstrating its value as a non-invasive tool for population monitoring of threatened subterranean fauna. The approach supports conservation and management of groundwater-dependent ecosystems where conventional sampling is logistically challenging, time-consuming or invasive.