Jan Strugnell 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, as below:

The impact of fisheries on genetic diversity and effective population sizes of lobsters (co-supervised with Catarina Silva)

Overexploitation of marine species can result in population decline and have indirect effects on ecological processes such as larval dispersal and recruitment. Lobsters support valuable fisheries around the world but the potential impacts of fisheries exploitation on their genetic diversity are still not well understood. This project will employ high resolution genetic markers (SNPs - single nucleotide polymorphisms) to examine the genetic changes and historical effective population sizes of exploited populations of lobsters. Historical (1967 and 1991) and contemporary samples (2014 and 2015) from three species Jasus paulensis, J. lalandii and J. edwardsii are available for this project. This research will provide crucial information on the impact of fisheries in long term genetic diversity of lobsters, an important body of knowledge to inform management decisions. 

Population genomics of the South African West Coast rock lobster (co-supervised with Catarina Silva)

The South African West Coast rock lobster (Jasus lalandii) supports valuable fisheries but catches have declined markedly since the 1950s. There is evidence that this resource is heavily depleted but knowledge about its population genetic structure is still limited. The availability of high resolution genomic resources has allowed and increase in power to define fisheries stocks and its adaptive characteristics. This project will evaluate genetic structure and connectivity of J. lalandii populations using both neutral and adaptive markers (SNPs - single nucleotide polymorphisms). Understanding neutral and adaptive differences among populations will provide critical information for stock delimitation and management efforts.

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.



  • AQ2002: Aquaculture of Tropical Species (Level 2; TSV)
  • AQ3007: Aquatic Animal Ecophysiology (Level 3; TSV)
  • AQ5007: Aquatic Animal Ecophysiology (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)
  • BS2470: Evolution (Level 2; TSV)
  • BS5470: Evolution (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
Conference Papers

ResearchOnline@JCU stores 69+ 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

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

CRC for Developing Northern Australia Scheme - Projects

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

Indicative Funding
$897,023 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

Department of Industry, Innovation and Science - 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

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
$154,074 over 3 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

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

Fisheries Research & Development Corporation - Annual Competitive Round

Genetic diversity audit of farm held stock of greenlip and blacklip abalone

Indicative Funding
Conduct a genetic audit of farm held stocks of greenlip and blacklip abalone to identify current levels of genetic diversity, effective population sizes, and levels of coancestry/relatedness captured within individual farms and the wider industry.
Jan Strugnell (College of Science & Engineering)
Abalone; Genetics

SeaWorld Research and Rescue Foundation Inc - Research Grant

An investigation of multiple paternity in the endangered narrow sawfish, Anoxypristis cuspidata

Indicative Funding
This genetics-based project will investigate multiple paternity in the endangered narrow sawfish for the first time. Sawfishes are arguably the most vulnerable of all marine fishes. Despite this, most aspects of their ecology and reproductive behaviour are poorly understood. A bycatch event of 25 pregnant females in Princess Charlotte Bay has provided a rare opportunity to explore multiple paternity in this species across a large number of litters. Using neutral molecular markers (microsatellites), this study will fill an important knowledge gap and provide information critical to effective conservation and management of this endangered species.
Jan Strugnell, Claire Gauci and Lynne van Herwerden (College of Science & Engineering)
Anoxypristis cuspidata (Pristidae); narrow sawfish; endangered; multiple paternity; microsatellites; conservation genetics

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)

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