Delineation and estimation of the Maugean Skate population in Macquarie Harbour, Tasmania

Declines in the Maugean skate population have coincided with the degradation of environmental conditions across its sole remaining habitat: Macquarie Harbour on Tasmania’s west coast.

Existing population estimates for the skate are highly uncertain, with no robust means of assessing change over time, particularly for juveniles. The harbour presents challenging environmental conditions and individual skates are difficult to find in a reliable way due to their scarcity, behaviour and mimetism (ability to blend into their environment).

This project evaluated monitoring tools and provided new information on the structure and dynamics of the population to help guide recovery actions for the Maugean skate.

An investigation of novel technologies demonstrated the suitability of acoustic imaging as a tool for population monitoring in Macquarie Harbour and recommended ways to optimise survey approaches and data quality.

Genetic sequencing techniques were used to complete the first reference-quality whole genome and mitochondrial genome for the species. Single nucleotide polymorphism (SNP) genotyping of historical and recent samples was used to investigate the species’ genetic structuring and demographic history.

The population was found to be genetically depauperate and possibly to have persisted in this state for thousands of years. The effects of environmental change documented in the past decade, however, would not yet be apparent in this data. Now may be a critical time to conserve the genetic diversity of the species.

Approach and findings

Population monitoring techniques

Novel acoustic and optical imaging techniques were tested in Macquarie Harbour skate habitats. Overall, adaptive resolution imaging sonar (ARIS) and synthetic-aperture sonar (SAS) reliably captured high-quality footage across the halocline and high turbidity conditions. They outperformed traditional video and light detection and ranging (LiDAR) techniques.

ARIS provided the highest resolution imagery in static and dynamic deployments, and was determined the best potential image-based monitoring tool for further testing. Aquarium-based tests demonstrated the reliable use of acoustic video for species identification and measurement.

Dynamic and static platforms for deploying acoustic video were tested in different habitat types and conditions. Remotely operated vehicles provided the highest stability and image quality.

The project recommended prioritising stratified sampling among depths and habitat types. Additional survey design recommendations covered:

• travel speed for towed deployments,
• the need for ground truthing with concurrent net surveys;
• potential use of static deployments to investigate key habitats or collect behavioural observations; and
• actions to improve image analysis.

ARIS surveys could be complemented by other survey techniques. Examples include molecular metabarcoding to explore community level changes and environmental sensors to explore environmental drivers of occurrence.

Further technical and logistical recommendations addressed the potential development of an acoustic video-based monitoring program.

Population genetics and demographic history

Single nucleotide polyimorphism (SNP) genotyping was conducted from the tissue samples of 162 Maugean skates. Additionally, whole genome sequencing (Pac-Bio hi-fi) data was aligned and annotated to produce the first reference-quality whole genome and mitochondrial genome for the species.

The whole genome and the SNPs both indicated relatively low heterozygosity, confirming that the Macquarie Harbour Maugean skate population is genetically depauperate.

Reconstruction of historical demographic patterns suggested the species has existed as a small population with low genetic diversity for 10–20,000 years. Despite this, it genetically stable, suggesting the natural rarity of the Maugean skate may play a role in limiting its vulnerability to inbreeding.

The low genetic diversity could also mean that the species has restricted adaptive potential and may be particularly vulnerable to disease outbreaks and rapid environmental changes such as the decline in dissolved oxygen observed in Macquarie Harbour in recent decades.

A critical time for conservation

In 2016, the first comprehensive study of the Maugean Skate reported that the environmental health of Macquarie Harbour, in particular levels of dissolved oxygen in the bottom waters, was likely to represent a crucial factor in the future wellbeing of the skate population. This relatively recent degradation is likely to be compounded by historical stressors (such as legacy mining waste) and ongoing issues such as climate change, salmonid aquaculture and altered river flows from hydro-electricity production.

It is not clear how recent and future declines in the population may affect the genetic fitness of the species. Additionally, given the life history of the species (long-lived, late-reproduction, few offspring), any changes to genetic structure or diversity caused by the population decline documented between 2014 and 2022 will potentially take a long time to become evident. We may be at a critical opportunity window for conservation action.

Outcomes

High-quality SNPs produced by this project may be suitable to develop Maugean skate close-kin population models.

The whole genome, mitogenome and SNP information will be of value to a wide range of conservation actions for the species including:

• modelling potential recovery scenarios;
• understanding the effects of management interventions such as remediation of dissolved oxygen levels throughout the harbour;
• understanding how the skate responds to environmental conditions (ecophysiology);
• managing captive breeding conservation efforts; and
• re-introduction strategies.

With fewer than 1% of extant elasmobranch species having a sequenced genome, the results also have broader interest for future investigations of evolutionary biology and conservation genetics.

Project location