Project Overview

This PhD projects forms part of an ARC Discovery project called: eGenomics - Next generation biomonitoring of threatened species. Reptiles are declining at a global scale with >20% of the worlds’ species threatened by extinction. Efficient biomonitoring methods are crucial and because reptiles (snakes in particular) are often elusive and difficult to observe in the field, an environmental DNA (eDNA) approach could seem like an obvious solution. Unfortunately, the general notion is that eDNA biomonitoring is not suited for reptiles due to their low shedding rate6. However, 40% of Australia’s terrestrial vertebrates are reptiles, many of which are both endemic and endangered, so unless we can overcome this challenge, eDNA has a major limitation as a terrestrial biomonitoring tool on this continent. This calls for an ambitious and thorough proof-of-concept study based on high-end genomic technology. As a representative of a well-known Australian reptile, we will study the western tiger snake (WTS) (Notechis scutatus) in our eGenomics framework. WTS is a highly venomous elapid and common across Southwestern Australia. It prefers wetlands and can be found in disjunct populations in both urban and exurban environments. Although WTS is not currently considered an endangered species, wetlands in Southwestern Australia have disappeared at an alarming rate due to human activity. Thus, WTS can serve as an important model organism for assessing the impacts of anthropogenic pressures on a vertebrate species associated with our wetlands. In this model system we will first and foremost be advancing critically needed eDNA monitoring of reptiles by thoroughly testing different eDNA substrates, DNA extraction methods, and qPCR assays. We will also obtain eDNA and eRNA data from snake enclosures and in situ environments and coanalyse these with dozens of complete N. scutatus genomes, to explore how genome-wide reptile DNA and RNA can be recovered and identified directly in environmental samples. Developing and optimizing cutting-edge eDNA and eRNA tools for improved reptile biomonitoring is of worldwide conservational relevance but importantly, our study will also contribute direct insight into an understudied group of animals occupying a habitat that is under tremendous threat in Australia.

Aims

This project aims to: 
1) Pioneer a new approach for eDNA biomonitoring of reptiles. Using the common western tiger snake (Notechis scutatus) as a reptilian model organism, we will develop a high precision eDNA biomonitoring tool with potential implications for the conservation management of reptiles worldwide. 

2) Develop a genome-scale biomonitoring framework. We will explore the concept of genome scale biomonitoring by sequencing complete genomes of tiger snakes from known populations and then co-analyse these with eDNA and eRNA shotgun sequencing data of environmental samples from the same sites. This comparative setup will reveal if population genomic information and RNA data of great conservational importance can be obtained directly from 
environmental samples.

Objectives

The overriding project objective is to improve eDNA biomonitoring of reptiles

Significance 

The global biodiversity crisis is real and ongoing, and efficient tools to monitor the richness and health of our biodiversity are at the forefront of our fight against this crisis. This project will deliver new, cutting-edge, molecular technology to improve detection of rare and endangered species. This will allow for more efficient conservation management to preserve our unique biodiversity.

This PhD project forms part of an ARC Discovery project starting in December 2024 (DP240100966: eGenomics - Next generation biomonitoring of threatened species). The candidate will work in TrEnD lab which is internationally recognized for its intellectual and technical capacity and has a strong track record of attracting, retaining and mentoring the best minds globally in this field. 

An internship may be available for this project. Prof Allentoft is 20% affiliated with the world renowned Globe Institute (University of Copenehagen) and there will be ample opportunity for a 2-3 month internship here. In fact this is already written into the ARC project proposal. If the candidate prefers an industry internship, we have very tight collaborations with BHPs biodiversity group and social investment Fund (funding our eDGES research programme) and several consultancies engaged with biomonitoring in WA (Biologic, Stantec etc).

• Future Students

• Faculty of Science & Engineering
  • Science courses
  • Engineering courses

• Higher Degree by Research

• Australian Citizen
• Australian Permanent Resident
• New Zealand Citizen
• Permanent Humanitarian Visa

• Merit Based

The annual scholarship package, covering both stipend and tuition fees, amounts to approximately $70,000 per year.

In 2024, the RTP stipend scholarship offers $35,000 per annum for a duration of up to three years. Exceptional progress and adherence to timelines may qualify students for a six-month completion scholarship.

Selection for these scholarships involves a competitive process, with shortlisted applicants notified of outcomes by November 2024.

1

All applicable HDR courses.

We are looking for a highly motivated PhD candidate with excellent organisation, problem-solving and project management skills. The candidate should have a passion for natural history and/or molecular biology, and have hands-on experience with basic wetlab techniques such as DNA extraction, PCR, DNA quantification etc. Ideally the candidate also have computational experience with DNA sequence analyses and some bioinformatics skills.

 

Please send your CV, academic transcripts and brief rationale why you want to join this research project via the HDR expression of interest form to the project lead researcher, listed below. 

You must be enrolled in a Higher Degree by Research Course at Curtin University by March 2025.

Project Lead: Professor Morten Allentoft