Jan Strugnell is the Director of the Centre for Sustainable Tropical Fisheries and Aquaculture.  She investigates the evolution and function of marine organisms using genomic and proteomic techniques. Her research encompasses both applied and blue skies questions.

Jan applies next generation sequencing tools to help solve bottlenecks in fisheries and aquaculture industries.  Supported by the ARC, her laboratory group is investigating population differentiation, recruitment and adaptation in a range of commercially important lobster species and are investigating the genetic basis for resilience and susceptibility to temperature stress in abalone.  Jan also works on marine species that are shifting range in response to climate change and employs eDNA techniques to detect rare and invasive aquatic and marine organisms. A/Prof Strugnell also investigates population and species level molecular evolution in Antarctic and deep-sea taxa in the context of past climatic and geological change.

A/Prof Strugnell completed her BSc (hons) at James Cook University before obtaining her DPhil at Oxford University, UK, funded by a Rhodes Scholarship.  During her DPhill she used molecular and fossil evidence to investigate phylogenetic relationship and divergence times within cephalopods (octopus, squids and cuttlefish).  A/Prof Strugnell then worked as a post doctoral research fellow at Queen's University, Belfast, the British Antarctic Survey and Cambridge University, UK, where she investigated evolutionary relationships within and between Antarctic and deep-sea octopods.

PhD, Masters, honours and minor projects are available in my group and enquiries are welcome. Please submit a short cover (1 page max.) letter detailing your suitability and interest, academic transcript and a CV with contact details for two referees by email.

 Available PhD Projects:

 Population connectivity of Antarctic marine invertebrates

The Southern Ocean is poorly studied in terms of the potential dispersal routes and barriers to connectivity for benthic marine species. A lack of understanding about spatial genetic structure limits our knowledge of connections between proposed ecoregions and also to limits our ability model potential changes in distributions in response to climate change.  This project will use population genomic techniques to identify pathways and barriers to dispersal and will investigate environmental features that affect multiple species. Identifying specific versus general dispersal barriers can be useful to inform spatial resource management.

This project may incorporate some Antarctic fieldwork and will also build upon data already collected from Antarctica.

This PhD project will investigate various aspects of the evolutionary history of Southern Ocean taxa. Broader investigations of Southern Ocean ecology will be shaped by the student’s interests, but may focus on:

• phylogeography and population genomic

s• systematics and phylogenetics

• selection and adaptation

The student will be based in the Department of Marine Biology and Aquaculture at James Cook University, Townsville, Australia, under the supervision of Assoc Prof Jan Strugnell and will be co-supervised by Dr Nerida Wilson (Western Australian Museum).  The student will receive expert training in fieldwork, laboratory and bioinformatics skills.Requirements: The successful applicant will have a First Class Honours (or equivalent) in biological science or a related field and will pick up extra points in the scoring system if they have a first authored paper. Preference will be given to those applicants with previous experience in genetics and/or evidence of strong technical and laboratory skills. Journal publications in these fields are desirable but not essential.  Applicants must apply by August 7.

Applicants will need to apply for a JCU competitive Research Scholarship and should be familiar with the Higher Degree by Research Requirements.

Funding: $28,092 pa for 3.5 years (tax exempt), comprising both an APA stipend (2020 rate) and a $1,500 pa top-up provided. Field and laboratory expenses will be supported by the broader project.

Contact: Interested applicants should send their 1) CV, 2) academic transcript and 3) a short (max. 1 page) letter outlining their suitability and interest in the project to Assoc. Prof. Jan Strugnell (jan.strugnell@jcu.edu.au) and Dr Nerida Wilson (Nerida.Wilson@museum.wa.gov.au)


Understanding population connectivity and demographic expansion of introduced Chital deer

In Australia, introduced deer species present a major threat to agriculture and the environment through competition for forage, as vectors of disease, damage to crops, modification of vegetation structure and composition, dispersal of weeds, and as a road hazard. Given that several Australian deer populations are currently expanding in abundance and geographic range, it is imperative that scientists understand how, when, and why these expansions occur. This ARC funded project proposes to use population genomics to determine current patterns of population connectivity, investigate historical patterns of population expansion, and understand how landscape and environmental variables influence gene flow.

This PhD project will employ the latest genomic and bioinformatics techniques in order to investigate connectivity, demography, and adaptation in Chital deer in North Queensland, Australia. Opportunities for field work will be available.

The student will be based in the College of Science and Engineering at James Cook University, Townsville, Australia (under the supervision of Assoc Prof Jan Strugnell, Dr Ben Hirsch, and Prof Lin Schwarzkopf) and supported by an Australian Research Council Linkage Grant. The student will work closely with stakeholders from the Department of Agriculture and Fisheries (Queensland) and the Department of Primary Industry and Resources (NSW).Requirements: Applicants must be competitive for an Australian Postgraduate Award (APA). Domestic applicants should have a First Class Honours (or equivalent) in biological science or a related field, while international applicants should have a Masters by Research. Preference will be given to those applicants with previous experience in genetics and/or evidence of strong technical and laboratory skills. Journal publications in these fields are desirable but not essential.  Students must apply by July 31, 2020 to commence early 2021.  Please note that an opportunity also exists to commence the PhD project in 2020 for domestic students or international students currently residing in Australia.  In this instance please apply by 30 June, 2020. 

Applicants will need to apply for a JCU competitive Research Scholarship and should be familiar with the Higher Degree by Research Requirements.


Funding: $28,092 p.a. for 3.5 years (tax exempt), comprising an APA stipend (2020 rate). Field and laboratory expenses will be supported by the broader project.

Contact: Interested applicants should send their 1) CV, 2) academic transcript, and 3) a short (~1 page max) letter outlining their suitability and interest in the project to Dr Ben Hirsch (ben.hirsch@jcu.edu.au), Assoc Prof Jan Strugnell (jan.strugnell@jcu.edu.au) and Prof Lin Schwarkzopf (lin.schwarzkopf@jcu.edu.au)


  • AQ2002: Aquaculture of Tropical Species (Level 2; TSV)
  • AQ3007: Aquatic Animal Ecophysiology (Level 3; TSV)
  • AQ3008: Aquaculture: Systems Design (Level 3; TSV)
  • AQ5007: Aquatic Animal Ecophysiology (Level 5; TSV)
  • AQ5008: Aquaculture: Systems Design (Level 5; TSV)
  • AQ5009: Aquaculture of Tropical Species (Level 5; TSV)
  • AQ5807: Aquaculture: Animal Ecophysiology (Level 5; TSV)
  • AQ5809: Aquaculture in the Tropics (Level 5; TSV)
  • BS5470: Evolution (Level 5; TSV)
  • MB2080: Invertebrate Biology (Level 2; TSV)
  • MB5380: Invertebrate Biology (Level 5; TSV)
  • 2010 to 2016 - Lecturer/Senior Lecturer/Assoc. Prof., La Trobe University (Melbourne, Australia)
  • 2008 to 2009 - Lloyd’s Tercentenary fellow, University of Cambridge (Cambridge, UK)
  • 2004 to 2007 - Post doctoral research fellow, British Antarctic Survey, Cambridge/Queen’s University (Cambirdge/Belfast, UK)
  • 2000 to 2004 - Rhodes Scholar, Oxford University (Oxford, UK)
  • 1999 to 2000 - Experimental Research Scientist, Australian Institute of Marine Science (Townsville, Australia)
  • 1998 to 1999 - Bachelor of Science (honours), James Cook University (Townsville, Australia)
  • 1995 to 1997 - Bachelor of Science, James Cook University (Townsville, Australia)
Research Disciplines
Socio-Economic Objectives
  • 2010 - James Cook University Outstanding Alumni Award
  • 2015 to 2017 - Australian Research Council (ARC) Discovery Grant - Lost at sea? Understanding adaptation and dispersal in spiny lobsters (Jan Strugnell, Bridget Green, Nicholas Murphy, James Bell)
  • 2015 to 2017 - FRDC : Patterns of interaction between habitat & oceanographic variables affecting the connectivity and productivity of invertebrate fisheries (D Ierodiaconou, A Miller, E Treml, S Swearer, N Murphy, J Strugnell, H Gorfine, C Sherman, B Green, M Young).
  • 2016 - One of Impact Design Hub’s “40 under 40” recognizing some of the brightest young minds at work designing for social good.
  • 2011 to 2013 - Australian Research Council (ARC) Discovery Grant - Stress transcriptomics: development of tests to reduce the incidence of summer mortality in abalone (Jan Strugnell)
  • 2010 to 2011 - Australia and Pacific Science Foundation grant - Gene flow, adaptation and speciation in Antarctic octopus: consequences of climate change (Jan Strugnell)
  • 2006 to 2009 - Best scientific paper on cephalopod research awarded by the Cephalopod International Advisory Council (CIAC)
  • 2000 to 2004 - Rhodes Scholarship, Oxford University, UK
  • 2008 to 2010 - Lloyd’s Tercentenary Foundation Fellowship. Postdoctoral Research Grant
  • 2005 to 2007 - Antarctic Funding Initiative (NERC). Postdoctoral grant. Did Antarctic octopuses colonise the deep sea?

These are the most recent publications associated with this author. To see a detailed profile of all publications stored at JCU, visit ResearchOnline@JCU. Hover over Altmetrics badges to see social impact.

Journal Articles

ResearchOnline@JCU stores 81+ research outputs authored by A/Prof Jan Strugnell from 2003 onwards.

Current Funding

Current and recent Research Funding to JCU is shown by funding source and project.

Australian Research Council - Linkage - Projects

Understanding population growth time lags in invasive species: Chital deer as a model system

Indicative Funding
$394,015 over 6 years, in partnership with QLD Department of Agriculture and Fisheries ($80,000 over 5 yrs)
Lags in population growth of introduced species are common, but poorly understood. Chital deer (Axis axis) are an invasive species introduced to Australia over 130 years ago, but their numbers have only increased dramatically in the past 30-40 years. We will use data collected from wild animals, landholder surveys, and computer simulation models to clarify causes of sudden population expansion in more detail. Understanding lags will allow us to understand their causes, and better control populations of invasive species. By predicting drivers of rapid population growth, we can better mitigate the associated economic and environmental costs of invasive species.
Ben Hirsch, Lin Schwarzkopf and Jan Strugnell in collaboration with Tony Pople (College of Science & Engineering, Department of Agriculture and Fisheries and Forestry)
chital (Axis axis); Invasive Species; landscape geneticfs; beef production demography; deer

Fisheries Research & Development Corporation - Annual Competitive Round

Application of a machine learning approach for effective stock management of abalone

Indicative Funding
$115,649 over 3 years
Determining the number and size distribution of abalone present at various stages of production is critical information for effective stock management. Currently the Australian abalone aquaculture industry spends in the order of $25,000 per annum, per farm, gathering this information by hand. However, the resulting data is of mediocre quality, is limited in its scope, and collecting the data causes stress to the animals which can compromise growth and survival. Automated counting and measuring of abalone will increase farm efficiency and productivity in the short term and, in the longer term, will provide an advanced platform for further R&D improvements. Artificial intelligence and machine learning has now matured to a point that accurately counting and measuring abalone is possible using this approach. This project would involve the development, training and validation of a machine learning model to identify, segment and measure quantitative abalone traits in production systems, and render the product data to be accessible and applicable for farmers.
Jan Strugnell, Marcus Sheaves, Carlo Mattone, Ickjai Lee, Joanne Lee, Jason Holdsworth and Art (Hemmaphan) Suwanwiwat (College of Science & Engineering)
Abalone (Haliotidae); Machine Learning

Department of Agriculture and Water Resources - Science and Innovation Awards for Young People in Agriculture, Fisheries and Forestry

Implementing artificial intelligence for the quantitative assessment of abalone in production systems

Indicative Funding
$19,481 (administered by Australian Bureau of Agricultural and Resource Economics and Sciences)
This project will aim to develop, train, validate and implement an artificial intelligence model to identify and count abalone and measure quantitative abalone traits in production systems from an image. Currently, stock assessment is conducted manually, with large costs associated for the farms. This solution would reduce the cost of stock assessments and would greatly improve data quantity and quality using a ?hands-off? approach. The model would also provide an advanced platform for further R & D improvements above and beyond basic assessments (e.g. growth monitoring in feeding trials).
Phoebe Arbon and Jan Strugnell (College of Science & Engineering)
Artificial Intelligence; Machine Learning; Aquaculture; Haliotis laevigata (Greenlip Abalone)

Australian Research Council - Discovery - Projects

Dating West Antarctic ice sheet collapse using molecular sequence data

Indicative Funding
$285,000 over 3 years
This project aims to investigate the past stability and configuration of the West Antarctic Ice Sheet by examining genomic signatures in present day bottom-dwelling Antarctic marine animals. By employing this novel biological approach to address a key question for physical scientists, this project will provide an independent test of the hypothesis that the West Antarctic Ice Sheet collapsed during the most recent interglacial and formed a transAntarctic seaway. Expected project outcomes include increased resolution of the most recent collapse of the West Antarctic Ice Sheet. This should provide significant benefits in predicting future collapse and its impact on sea level rise which is a key uncertainty resulting from climate change.
Jan Strugnell in collaboration with Nicholas Golledge, Nerida Wilson and Tim Naish (College of Science & Engineering, Victoria University of Wellington and Western Australian Museum)
Palaeoclimatology; Antarctica; climate change; Sea Level Rise; Population Genomics

Department of Industry - Cooperative Research Centres (CRC) Program

Pearls of wisdom - Breeding for increase tolerance to juvenile pearl oyster mortality syndrome

Indicative Funding
$796,585 over 4 years (administered by Ellies Pearls)
A decade ago pearl farming was one of the major employers and contributors to the social-economic fabric of northern Australia, contributing $189.7 million farm-gate to the national economy. However, in recent years Australian pearl production has been severely impacted by episodic and large-scale mortality events by an as yet unidentified causative factor. These mortality events, termed juvenile pearl oyster mortality syndrome (or JPOMS), have resulted in massive write-downs in production and economic value of the industry. This project will develop the genetic knowledge and lay the foundation for a selective breeding program in pearl oysters that are resistance to JPOMS.
Dean Jerry, Kyall Zenger, Jan Strugnell, Dave Jones, David Jackson and James H Brown (College of Science & Engineering, Ellies Pearls and Cygnet Bay Pearls)
Pinctada maxima; JPOMS; Selective Breeding

Great Barrier Reef Foundation - Reef Trust Partnership

Extending the success of REDMAP Australia to Queensland

Indicative Funding
REDMAP (Range Extension Database & Mapping project) is a citizen science initiative inviting fishers, divers and boaters to submit photographs of unusual fish sightings to an interactive website (www.redmap.org.au). The project seeks to inform, engage and educate fishers, divers and boaters about fish that are shifting southwards in accordance with warming waters. This project will roll out this initiative across Queensland through public talks at fishing and diving clubs in conjunction with the distribution of brochures, dive plans and stickers highlighting the fish species for citizen scientists to keep a look out for while they are on or in the waters.
Jan Strugnell in collaboration with Gretta Pecl and Cecilia Villaneuva (College of Science & Engineering and University of Tasmania)
fiwsh; Climate Change; range extension

CRC for Developing Northern Australia Scheme - Expressions of Interest

Northern Aquaculture Industry Situational Analysis

Indicative Funding
$202,117 over 2 years
This project will identify key challenges and opportunities facing the North Australian aquaculture sector and explore potential solutions and/or identify the most strategic research projects for further investment. This will include and not be limited to: infrastructure, policy, investment, environmental, production, knoweldge, training and human capital gaps and the research or alternative solutions to address them. The project will be delivered through a literature review, development of the 'Northern aquaculture industry vision 2028' in consultation with indigenous and non-indigenous stakholders, desktop study and SWOT analysis, and the situational analysis report.
Dean Jerry, Jennifer Cobcroft, Kyall Zenger, Jan Strugnell, Amy Diedrich, Chaoshu Zeng, Rocky de Nys and Sandra Hughes in collaboration with Matthew Cook, Robert Bell, Jane Lovell, Wayne Hutchinson, Kim Hooper and Jo-Anne Ruscoe (College of Science & Engineering, JCU Singapore, Commonwealth Scientific & Industrial Research Organisation, Blueshift Consulting, Seafood Industry Australia, Fisheries Research and Development Corporation, Australian Prawn Farmers Association and Australian Barramundi Farmers Association)
Northern Australia; Aquaculture

Fisheries Research & Development Corporation - Annual Competitive Round

Testing established methods of early prediction of genetic merit in abalone broodstock

Indicative Funding
$85,422 over 4 years
There is a need in the abalone industry to improve production animals. However, abalone are relatively slow growing animals and take several years to reach harvest size. This means that during the establishment of foundation broodstock populations it may be several years before the relative genetic merit of each of the broodstock can be determined and the first selection decisions made. Researchers at JCU have addressed this time-lag problem of obtaining accurate genetic estimated breeding values (gEBV) in other species. They have shown that broodstock gEBV can be estimated accurately from larvae as early as 18 days through the targeting of growth processes at the cellular level that predict genetic-determined long-term growth. This method is as yet untested in abalone, but if successful, has great potential in helping screen broodstock. This project will test the efficacy of this early prediction method in abalone. The impact of this early detection method would be to save costs by assisting in the selection of superior broodstock individuals which would produce faster growing offspring. Currently new broodstock animals are unevaluated with regard to their genetic merit.
Jan Strugnell, Dean Jerry, Jose Domingos and Catarina Silva (College of Science & Engineering)
Abalone; Genetics

Department of the Environment and Energy - National Environmental Science Programme (NESP) - Northern Australia Environmental Resources Hub

The Northern Australia eDNA Program - Revolutionising Aquatic Monitoring and Field Surveys in Tropical Waters

Indicative Funding
$570,000 over 3 years
All organisms shed DNA into their environment. This is termed environment DNA (eDNA). Capture and analysis of eDNA (in soil or water samples) is a highly efficient and sensitive method to detect the presence of a wide range of species without actually requiring physical capture, or sighting of the organisms themselves. eDNA field sampling can involve as little as collecting water samples and
Damien Burrows, Jan Strugnell, Roger Huerlimann, Richard C Edmunds and Dean Jerry (TropWATER and College of Science & Engineering)
eDNA; Threatened Species; Northern Australia; exotic pest species; aquatic monitoring; Genetics

United States Navy - Detection of scalloped hammerhead sharks in Apra Harbor and adjacent nearshore waters, Guam using environmental DNA

Detection of scalloped hammerhead sharks in Apra Harbor and adjacent waters, Guam using Environmental DNA

Indicative Funding
$273,586 over 4 years (administered by University of Guam)
Scalloped hammerhead sharks (Sphyrna lewini) are anecdotally reported in Apra Harbor, Guam, but their spatial and temporal patterns of occurrence are not well understood. Lack of knowledge of population abundance, distribution, and habitat use also extends across the geographic range of the Indo-West Pacific subpopulation. All S. lewini are nationally protected under the Endangered Species Act, and their occurrence within Apra Harbor is of concern to management and conservation strategies and mission-essential operations of the U.S. Department of Navy. This project will determine the temporal and spatial distribution and habitat use of the scalloped hammerhead shark within Apra Harbor and Orote Peninsula nearshore waters.
Tom Schils, Jan Strugnell, Agnes Le Port and Roger Huerlimann in collaboration with Madalyn Cooper (University of Guam and College of Science & Engineering)
eDNA; Guam; Sphyrna lewini (Sphyrnidae); scalloped hammerhead shark

Department of Industry - Cooperative Research Centres (CRC) Program

Rapid iteration selective breeding: Australia's fish to feed the world

Indicative Funding
$1,090,000 over 3 years (administered by Mainstream Aquaculture Pty Ltd)
Barramundi - Australia?s favourite fish ? is gaining popularity worldwide as a farmed solution for supply of white fish. The world needs a sustainable source of white fish, as current supply comes from declining wild catch fisheries. Industrial scale farming offers a solution. Success relies on improved seed stock and the Australian Barramundi industry in conjunction with the CRC-P program is tackling this challenge by applying advanced modern genetics to Australia?s barramundi breeding stocks.
Paul Harrison, Dean Jerry, Kyall Zenger, Jan Strugnell and Nick Robinson (Mainstream Aquaculture Pty Ltd, College of Science & Engineering and The University of Melbourne)
Barramundi; Lates calcarifer; Aquaculture; Selective Breeding; Genetics

Australian Academy of Science - Thomas Davies Research Grant for Marine, Soil and Plant Biology

Dating the collapse of the West Antarctic ice sheet using next generation sequencing of marine invertebrates

Indicative Funding
$24,432 over 3 years
This proposal applies a novel biological approach to address a key question for physical scientists. There is great uncertainty in predictions of future sea level rise and recent modelling suggests that forced displacement of over 180 million people this century is conceivable. Predicting the fate of the West Antarctic Ice Sheet is central for accurate sea level predictions The complete collapse of the West Antarctic ice sheet would lead to the existence of a trans-Antarctic seaway linking the present day Ross, Weddell and Amundsen Seas. Such a seaway would allow marine animal migration across newly opened straights, and a persistent genetic signature of historical connectivity of such events will remain in bottom dwelling animals.
Jan Strugnell (College of Science & Engineering)
Antarctica; Sea Level Rise

Advisory Accreditation: I can be on your Advisory Panel as a Primary or Secondary Advisor.

These Higher Degree Research projects are either current or by students who have completed their studies within the past 5 years at JCU. Linked titles show theses available within ResearchOnline@JCU.

  • Genome wide detection and evolutionary analysis of antimicrobial peptide repertoires in corals (PhD , Secondary Advisor/AM)
  • Quantifying Life History Energetics of an Oviparous Elasmobranch subject to future Warming Waters (PhD , Secondary Advisor/AM)
  • Broodstock Conditioning of the Tropical Blacklip Rock Oyster (Saccostrea Echinata) (Masters , Primary Advisor/AM/Adv)
  • Venom evolution in the blue-ringed octopus (Hapalochlaena) species complex (PhD , Primary Advisor)
  • Genome-wide assessments of thermal plasticity and theshold performance in corals across the Great Barrier Reef (PhD , Advisor Mentor)
  • Were Sub-Antactic Islands Glacial Refugia for Marine Taxa (PhD , Primary Advisor/AM/Adv)

The map shows research collaborations by institution from the past 7 years.
Note: Map points are indicative of the countries or states that institutions are associated with.

  • 5+ collaborations
  • 4 collaborations
  • 3 collaborations
  • 2 collaborations
  • 1 collaboration
  • Indicates the Tropics (Torrid Zone)

Connect with me
Share my profile
Share my profile:

Advisory Accreditation
Advisor Mentor
Find me on…
Icon for Twitter profile page Icon for Google Scholar profile Icon for Wikipedia article Icon for TheConversation author profile Icon for ORCID profile Icon for ResearchGate profile Icon for external homepage Icon for Scopus Author page Icon for ResearcherID page

Similar to me

  1. Prof Dean Jerry
    College of Science & Engineering
  2. Prof Paul Dirks
    College of Science & Engineering
  3. Prof Kyall Zenger
    College of Science & Engineering
  4. Dr Gregory Maes
    College of Science & Engineering
  5. Dr Ira Cooke
    College of Public Health, Medical & Vet Sciences