This record provides an overview of the NESP Marine and Coastal Hub Research Plan 2023 project "Delineation and estimation of the Maugean skate population in Macquarie Harbour, Tasmania". No public data outputs are planned for this project. -------------------- The Maugean skate (Zearaja maugeana) is now only found in Macquarie Harbour on Tasmania’s west coast, which has a long history of environmental degradation. The species is listed as Endangered under Commonwealth and Tasmanian legislation, and its restricted distribution, small population size, and exposure to degraded environmental conditions make population monitoring a high conservation priority. Recent research suggests that the Macquarie Harbour population may be declining. However, existing abundance estimation methods are inadequate because the species is cryptic, capture-based methods pose risks to skate health, and conventional optical surveys are limited by the harbour’s shallow, stratified, and highly turbid conditions. This project developed and tested new approaches to estimate and monitor the Maugean skate population using next-generation genetic sequencing and novel imaging technologies. Non-invasive acoustic methods (adaptive resolution imaging sonar (ARIS), synthetic aperture sonar, performed better than optical approaches (LiDAR, conventional video), under Macquarie Harbour conditions. ARIS was identified as the most suitable image-based monitoring tool for future population surveys. The genetic component generated the first reference-quality whole and mitochondrial genomes for the species and sequenced samples from 162 individuals. Genome-wide single nucleotide polymorphism (SNP) analyses showed that the Macquarie Harbour population has very low genetic diversity, which may influence how genetic risks are interpreted in recovery planning. The project produced new monitoring methodologies, genomic reference resources, and population genetic datasets to support future monitoring of Maugean skate abundance, population structure, and genetic health. The findings will inform conservation planning and evaluation of recovery strategies including captive breeding, translocation, and long-term genetic monitoring under changing environmental conditions. Outputs • Tissue sampling results and genome-wide population genetic structure [dataset] • Final project report [written]

The Maugean Skate Zearaja maugeana is a micro-endemic species known from only two isolated estuaries, Bathurst and Macquarie Harbours in southwestern/western Tasmania. This constitutes one of the most limited distributions of any known extant elasmobranch. As a result, the species is listed as ‘Endangered’ under the Threatened Species Protection Act (Tasmania) and the Environmental Protection and Biodiversity Conservation Act (Commonwealth). Even though it was first discovered in Bathurst Harbour, most of what is known about the species comes from the Macquarie Harbour population. Only four individuals have ever been reported in Bathurst Harbour, with the last known sighting occurring in 1992. This study used environmental DNA (eDNA) to determine the presence/absence of the Maugean skate in Bathurst Harbour on the southwest coast of Tasmania. Water samples were collected from the seafloor in Bathurst Harbour in November 2021 and February 2022, and in Macquarie Harbour (control samples) in December 2021. Samples were filtered using a self-preserving eDNA sampling system. Following each survey DNA from the samples was extracted and analysed through qPCR amplification. Mitochondrial primer pairs from two gene regions were used to detect the presence of Maugean skate DNA in the samples. Where possible, positive detections were sequenced, and their identity verified.