Higher Degree by Research Application Portal

The deep sea harbours the majority of Earth’s biosphere yet remains underrepresented in genomics and biodiversity datasets and reference data repositories. Environmental DNA (eDNA) metabarcoding has transformed biodiversity assessment, but its efficacy in the deep sea is constrained by two key limitations: (1) reference DNA sequence databases are sparsely populated for deep-sea taxa and (2) primer sets not optimised for targeting deep-sea taxa. As a result, much of the signal that is recovered using traditional eDNA metabarcoding approaches remains unclassified or ambiguously assigned. 

This PhD project will overcome these limitations through an integrated framework that identifies and fills critical gaps in available reference genomic data, and based on this information, develops and validates deep-sea–specific metabarcoding primers, applying them across multiple oceanic regions. By combining reference data curation, molecular laboratory work, genomics and bioinformatics, with comparative ecological analyses, the project will deliver both new knowledge and enduring resources for deep-sea biodiversity discovery and monitoring. 

The candidate will: 

Map gaps in genomic and barcode sequence data repositories for deep-sea taxa and prioritise underrepresented lineages for targeted sequencing. 

Curate and annotate reference barcodes and genomes for key taxa, contributing to public repositories and strengthening global eDNA reference resources. Design and validate new metabarcoding primers optimised for deep-sea metazoans through in silico, in vitro, and in situ testing. 

Apply primer sets across multiple deep-sea regions to quantify gains in taxonomic resolution relative to existing markers. 

Integrate genomic, environmental, and ecological data to assess how this improved resolution reshapes biodiversity estimates, biogeographic patterns, and ecosystem understanding. 

Develop open-access tools and resources (e.g., primer evaluation workflows or reference datasets) to support future deep-sea eDNA research and monitoring programs. 

Minderoo OceanOmics Centre at UWA

Dr Georgia Nester,  georgia.nester@uwa.edu.au (Minderoo OceanOmics Centre at UWA) 

Dr Shannon Corrigan, shannon.corrigan@uwa.edu.au (Minderoo OceanOmics Centre at UWA) 

Key Research Questions 

Where are the most significant taxonomic and genomic gaps in existing deep-sea reference databases, and which lineages should be prioritised for sequencing and curation?  

Where are primer (or otherwise) biases leading to dropout of deep-sea taxa in existing traditional metabarcoding datasets? 

Can newly designed metabarcoding primers enhance detection breadth and taxonomic resolution for deep-sea taxa compared to existing universal markers? 

How do improved primers influence biodiversity estimates and community composition across different deep-sea regions and depth zones? 

How do environmental gradients and geomorphic features (e.g., depth, substrate, productivity) shape biodiversity patterns revealed through enhanced eDNA resolution? 

How can targeted, comprehensive and curated genomic resources and open analytical pipelines accelerate deep-sea biodiversity discovery and standardise future eDNA monitoring efforts?  

Candidate Requirements 

We seek a motivated candidate with a background in molecular ecology, marine genomics, or marine ecology. Experience in one or more of the following areas is desirable: 

DNA metabarcoding, primer design, or environmental DNA techniques 

Experience with bioinformatics workflows for sequence analysis and database curation, including use of high-performance computing environments 

Statistical or ecological modelling in R or Python. 

A strong interest in deep-sea biodiversity, molecular innovation, and conservation genomics is essential. The project offers opportunities to develop advanced skills in primer optimisation, genome curation, and integrative data analysis using large-scale eDNA datasets. 

The successful candidate will work closely with: 

Professor Alan Jamieson (Minderoo-UWA Deep-Sea Research Centre) 

Dr Georgia Nester (Minderoo OceanOmics Centre at UWA) 

Dr Shannon Corrigan (Minderoo OceanOmics Centre at UWA) 

Dr Jess Kolbusz (Minderoo-UWA Deep-Sea Research Centre) 

Dr Philipp Bayer (Minderoo Foundation) 

Dr Emma de Jong (Minderoo OceanOmics Centre at UWA) 

The Doctor of Philosophy (PhD) is a program of independent, supervised research that is assessed solely on the basis of a thesis, sometimes including a creative work component, that is examined externally. The work presented for a PhD must be a substantial and original contribution to scholarship, demonstrating mastery of the subject of interest as well as an advance in that field of knowledge. 

Visit the course webpage for full details of this course including admission requirements, course rules and the relevant CRICOS code/s.