Mr Benjamin Heyward1, Dr Nicole White1, Dr Joshua Newton1, Dr Mahsa Mousaviderazmahalleh1, Prof. Morten Allentoft1,2
1Trace and Environmental DNA Laboratory, Curtin University, Perth, Australia, 2Section for GeoGenetics – Globe Institute, University of Copenhagen, Copenhagen, Denmark
Biography:
Ben is a PhD student in the TrEnD Laboratory at Curtin University, Western Australia. His PhD project focuses on the Pilbara olive python, and its genomics and improved biomonitoring.
Abstract:
Environmental DNA (eDNA) detection of terrestrial reptiles remains challenging, due potentially to low DNA shedding rates and uncertainty over substrate selection and molecular approaches. To explore these knowledge gaps, we evaluated six substrates and three molecular approaches for detecting two snake species, the olive python (Liasis olivaceus) and Burmese python (Python bivittatus), in enclosures at Perth Zoo and Caversham Wildlife Park, Western Australia. Water, soil, air, rock and tree surfaces, and spiderwebs were assessed using species-specific qPCR for targeted detection, metabarcoding for community-level assessment, and shotgun sequencing to evaluate recovery of genome-wide DNA. Detection performance was compared among substrates and molecular approaches within and between enclosures. Rock and tree surface swabs and spiderwebs generally produced the strongest and most stable target species signals across molecular approaches, whereas soil and water performed more variably. Additionally, detection patterns were broadly consistent across methods. Through our shotgun sequencing reference genome panel, we were able to assess recovery and mapping confidence of target and non-target DNA, offering insights into DNA deposition patterns within the enclosures. This targeted, competitive-mapping approach is a novel step toward using shotgun sequencing to assess DNA 'beyond the barcode'. Our results provide guidance for substrate selection and molecular method choice in terrestrial snake eDNA monitoring, and demonstrate the value of shotgun sequencing as an emerging method capable of retrieving information beyond simple detection.