Dave Jones
- david.jones3@jcu.edu.au
https://orcid.org/0000-0002-5862-6335- Senior Research Fellow - Breeding Program Management
- Marine Biology & Aquaculture
Projects
6
Publications
45
Awards
0
Biography
Dr Dave Jones is a researcher specialising in the application of genomics within advanced breeding programs for aquaculture species.
Dave aims to enhance the productivity and efficiency of aquaculture production systems by applying advanced genomic technologies to address industry-driven research questions. Through co-designing research projects with industry partners, he focuses on delivering actionable insights and translating research outcomes into operational improvements.
His expertise spans the development and application of genetic and genomic tools for aquaculture. He has designed and validated numerous commercial single nucleotide polymorphism (SNP) panels across leading platforms for a wide range of species. These resources have enabled the creation of genomic linkage maps and strengthened understanding of how genetic variation underpins ecologically and commercially important traits.
Dave has contributed substantially to co-funded ARC and CRC-P genomic research projects at JCU within the Centre for Sustainable Tropical Fisheries and Aquaculture (CSTFA). He maintains active collaborations with researchers at the University of Sydney, AGRF, IFREMER in French Polynesia and Montpellier, and Jeju National University in South Korea, as well as commercial aquaculture partners in Western Australia, Queensland and Victoria.
Research
Projects
AEA Ignite - Gold Barramundi
11 Feb 2026 - 30 Jun 2027
ACIAR PCAARRD Shrimp genomics for health
01 Jan 2026 - 30 Apr 2026
Workshop in Advanced Genomics Tools to Enhance Korean Aquaculture
01 Nov 2024 - 31 Oct 2025
AutoFish: Automatic Fish Phenotyping Tool for Sustainable Aquaculture and Smart Fisheries (Old ID 28947)
01 Mar 2023 - 30 Jun 2023
Research Data
Teaching
Research Advisor Accreditation
Advisor Type
Primary
Current JCU Research Students
Building the foundations of a selective breeding program in giant grouper Epinephelus lanceloatus
Doctor of Philosophy (Agriculture, Environmental and Related Studies)
Optimising selective breeding techniques for implementation into Black Tiger Prawn (Penaeus monodon) and Silver Lipped Pearl Oyster (Pinctada maxima) commercial breeding programs
Doctor of Philosophy (Natural and Physical Sciences)
Genetic Architecture and advanced selective Breeding of Health-related Production Traits in the Australian Giant Grouper (Epinephelus lanceolatus)
Doctor of Philosophy (Agriculture, Environmental and Related Studies)
Completed JCU Research Students
Unravelling the genetic architecture of black tiger shrimp (Penaeus monodon) production traits through development and utilisation of novel genomic resources.
Doctor of Philosophy (Natural and Physical Sciences)- 2024
Domestication in aquaculture fishes - Elucidating the genetic consequences in Nile tilapia (Oreochromis niloticus)
Doctor of Philosophy (Natural and Physical Sciences)- 2020
Activities
Employment
Research Fellow, James Cook University
2019 - 2021
Research Fellow, Ifremer Centre du Pacifique
2017 - 2019
Research Fellow, James Cook University
2015 - 2017
Genomics Research Worker, James Cook University
2009 - 2013
Field Research Worker, James Cook University
2009 - 2010
Bachelor of Science, James Cook University
2005 - 2007
Output
Jones, David Byron (2013) Genomic resources and genetic dissection of complex quantitative traits in the silver-lipped pearl oyster, Pinctada maxima. [Thesis]
Rhodes, Emily; Jerry, Dean; Jones, David B.; Goldsbury, Julie; Vu, Nga (2026) 'Swift SNPs: Evaluating Rapid DNA Extraction Methods for Scalable Genotyping in Aquaculture'. Marine Biotechnology, 28 . [DOI]
Kodagoda, Yasara Kavindi; Kim, Gaeun; Liyanage, D.S.; Omeka, W.K.M.; Park, Cheonguk; Kim, Jeongeun; Hanchapola, H.A.C.R.; Dilshan, M A.H.; Rodrigo, D.C.G.; Ganepola, G A.N.P.; Jones, David B.; Massault, Cecile; Jerry, Dean R.; Lee, Jihun; Lee, Jehee (2026) 'Genomic prediction of survival traits for scuticociliatosis resistance in a vaccinated olive flounder cohort: Comprehensive evaluation and optimization of statistical and machine learning models'. Aquaculture Reports, 47 . [DOI]
Liyanage, D.S.; Lee, Sukkyoung; Yang, Hyerim; Lim, Chaehyeon; Omeka, W. K.M.; Sandamalika, W.M.Gayashani; Udayantha, H.M.V.; Kim, Gaeun; Hanchapola, H.A.C.R.; Ganeshalingam, Subothini; Jeong, Taehyug; Oh, Seong Rip; Won, Seung Hwan; Koh, Hyoung Bum; Kim, Mun Kwan; Jones, David B.; Massault, Cecile; Jerry, Dean R.; Lee, Jehee (2025) 'Genomic prediction of survival traits in the response of olive flounder (Paralichthys olivaceus) to viral hemorrhagic septicemia virus: Comparing machine learning models and traditional approaches'. Aquaculture, 595 (Part 2). [DOI]
Journal Publication
ResearchOnline@JCU
Udayantha, H.M.V.; Kim, Jeongeun; Kim, Gaeun; Lee, Jihun; Lee, Sukkyoung; Park, Cheong Uk; Jones, David B.; Massault, Cecile; Jerry, Dean R.; Liyanage, D.S.; Lee, Jehee (2025) 'Genome-wide association and genomic prediction of thermal tolerance in olive flounders (Paralichthys olivaceus): A validation study'. Aquaculture Reports, 45 . [DOI]
Kodagoda, Yasara Kavindi; Kim, Gaeun; Liyanage, D. S.; Omeka, W. K.M.; Park, Cheonguk; Kim, Jeongeun; Lee, Ji Hun; Hanchapola, H. A.C.R.; Dilshan, M. A.H.; Rodrigo, D. C.G.; Jones, David B.; Massault, Cecile; Jerry, Dean R.; Lee, Jehee (2025) 'Genome-wide association mapping of scuticociliatosis resistance in a vaccinated population of olive flounder (Paralichthys olivaceus)'. Fish and Shellfish Immunology, 162 . [DOI]
Journal Publication
ResearchOnline@JCU
Massault, Cecile; Jones, David B.; Lillehammer, Marie; Cate, Holly; Harrison, Paul; Strugnell, Jan M.; Zenger, Kyall R.; Robinson, Nicholas A.; Jerry, Dean R. (2025) 'Accuracies of genomic prediction accounting for genotype by environment remain high when using small sets of selected SNPs in barramundi Lates calcarifer'. Aquaculture, 599 . [DOI]
Journal Publication
ResearchOnline@JCU
Genomic prediction model optimization for growth traits of olive flounder (Paralichthys olivaceus)
2024
Omeka, W.K.M.; Liyanage, D.S.; Lee, Sukkyoung; Udayantha, H.M.V.; Kim, Gaeun; Ganeshalingam, Subothini; Jeong, Taehyug; Jones, David B.; Massault, Cecile; Jerry, Dean R.; Lee, Jehee (2024) 'Genomic prediction model optimization for growth traits of olive flounder (Paralichthys olivaceus)'. Aquaculture Reports, 36 . [DOI]
Moran, Megan N.; Jones, D.B.; Jensen, S.A.; Marcoli, R.; Jerry, D. R. (2024) 'Optimising commercial traits through gene editing in aquaculture: Strategies for accelerating genetic improvement'. Reviews in Aquaculture, 16 (3):1127-1159. [DOI]
Marcoli, Roberta; Jones, Dave B.; Massault, Cecile; Harrison, Paul J.; Cate, Holly; Jerry, Dean R. (2024) 'Barramundi (Lates calcarifer) rare coloration patterns: a multiomics approach to understand the “panda” phenotype'. Journal of Fish Biology, 105 (4):1268-1279. [DOI]
Marcoli, R.; Jones, D.B.; Massault, C.; Moran, M.; Harrison, P.; Cate, H.S.; Jerry, D.R. (2024) 'Revealing the genetic and molecular drivers behind golden and platinum coloration in barramundi (Lates calcarifer)'. Aquaculture, 586 . [DOI]
Bertola, Lorenzo V.; Hoskin, Conrad J.; Jones, David B.; Zenger, Kyall R.; McKnight, Donald T.; Higgie, Megan (2023) 'The first linkage map for Australo-Papuan Treefrogs (family: Pelodryadidae) reveals the sex-determination system of the Green-eyed Treefrog (Litoria serrata)'. Heredity, 131 :263-272. [DOI]
Vu, Nga T.T.; Jerry, Dean R.; Edmunds, Richard C.; Jones, David B.; Zenger, Kyall R. (2023) 'Development of a global SNP resource for diversity, provenance, and parentage analyses on the Indo-Pacific giant black tiger shrimp (Penaeus monodon)'. Aquaculture, 563 (1). [DOI]
Journal Publication
ResearchOnline@JCU
Saleh, Alzayat; Jones, David; Jerry, Dean; Azghadi, Mostafa Rahimi (2023) 'MFLD-net: a lightweight deep learning network for fish morphometry using landmark detection'. Aquatic Ecology, 57 :913-931. [DOI]
Marcoli, R.; Jones, D.B.; Massault, C.; Marc, A.F.; Moran, M.; Harrison, P.J.; Cate, H.S.; Lopata, A.L.; Jerry, D.R. (2023) 'The skin structure in multiple color variants of barramundi (Lates calcarifer): A histological, immunohistochemical and ultrastructural overview'. Aquaculture, 576 . [DOI]
Udayantha, H.M.V.; Lee, Sukkyoung; Liyanage, D.S.; Lim, Chaehyeon; Jeong, Taehyug; Omeka, W.K.M.; Yang, Kyerim; Kim, Gaeun; Lee, Jihun; Nadarajapillai, Kishanthini; Ganeshalingam, Subothini; Park, Cheong-Uk; Lee, Jiwon; Oh, Seong-Rip; Gong, Po; Jang, Yeounghwan; Hyun, Jaemin; Park, Aejen; Koh, Hyoung-Bum; Kim, Mun-Kwan; Jones, David B.; Massault, Cecile; Jerry, Dean R.; Lee, Jeehee (2023) 'Identification of candidate variants and genes associated with temperature tolerance in olive flounders by Genome-Wide Association Study (GWAS)'. Aquaculture, 576 . [DOI]
Journal Publication
ResearchOnline@JCU
Leahy, Susannah M.; Jerry, Dean R.; Wedding, Brett B.C.; Robins, Julie; Wright, Carole L.; Sadekov, Aleksey; David, Stephen B.; Jones, David B.; Williams, Samuel M.; Grauf, Steve; Pavich, Luke; McLennan, Mark; Sellini, Michelle J.; Goldsbury, Julie A.; Saunders, Richard J. (2023) 'Multimethod approach to advance provenance determination of fish in stocked systems'. Canadian Journal of Fisheries and Aquatic Sciences, 80 :1410-1424. [DOI]
Jerry, Dean R.; Jones, David B.; Lillehammer, Marie; Massault, Cecile; Loughnan, Shannon; Cate, Holly S.; Harrison, Paul J.; Strugnell, Jan M.; Zenger, Kyall R.; Robinson, Nicholas A. (2022) 'Predicted strong genetic gains from the application of genomic selection to improve growth related traits in barramundi (Lates calcarifer)'. Aquaculture, 549 . [DOI]
Journal Publication
ResearchOnline@JCU
Whitelaw, Brooke L.; Jones, David B.; Guppy, Jarrod; Morse, Peter; Strugnell, Jan M.; Cooke, Ira R.; Zenger, Kyall (2022) 'High-Density Genetic Linkage Map of the Southern Blue-ringed Octopus (Octopodidae: Hapalochlaena maculosa)'. Diversity, 14 (12). [DOI]
Genome-wide association study (GWAS) of growth traits in olive flounder (Paralichthys olivaceus)
2022
Omeka, W.K.M.; Liyanage, D.S.; Lee, Sukkyoung; Lim, Chaehyeon; Yang, Hyerim; Sandamalika, W.M.Gayashani; Udayantha, H.M.V.; Kim, Gaeun; Ganeshalingam, Subothini; Jeong, Taehyug; Oh, Seong-Rip; Won, Seung-Hwan; Koh, Hyoung-Bum; Kim, Mun-Kwan; Jones, David B.; Massault, Cecile; Jerry, Dean R.; Lee, Jehee (2022) 'Genome-wide association study (GWAS) of growth traits in olive flounder (Paralichthys olivaceus)'. Aquaculture, 555 . [DOI]
Journal Publication
ResearchOnline@JCU
Liyanage, D.S.; Lee, Sukkyoung; Yang, Hyerim; Lim, Chaehyeon; Omeka, W.K.M.; Sandamalika, W.M. Gayashani; Udayantha, H.M.V.; Kim, Gaeun; Ganeshalingam, Subothini; Jeong, Taehyug; Oh, Seong-Rip; Won, Seung-Hwan; Koh, Hyoung-Bum; Kim, Mun-Kwan; Jones, David B.; Massault, Cecile; Jerry, Dean R.; Lee, Jehee (2022) 'Genome-wide association study of VHSV-resistance trait in Paralichthys olivaceus'. Fish and Shellfish Immunology, 124 :391-400. [DOI]
Journal Publication
ResearchOnline@JCU
Massault, Cecile; Jeffrey, Cara; Jones, David B.; Barnard, Roger; Strugnell, Jan M.; Zenger, Kyall R.; Jerry, Dean R. (2022) 'Non-invasive DNA collection for parentage analysis for bivalves: A case study from the silver-lipped pearl oyster (Pinctada maxima)'. Aquaculture, 552 . [DOI]
Journal Publication
ResearchOnline@JCU
Arbon, Phoebe M.; Silva, Catarina N.S.; Jones, David B.; Jaccoud, Damian; Gervis, Mark; Jerry, Dean R.; Strugnell, Jan M. (2021) 'Development and validation of a SNP-based genotyping tool for pedigree establishment in Australian greenlip abalone Haliotis laevigata Donovan, 1808'. Aquaculture Reports, 20 . [DOI]
Massault, C.; Jones, D.B.; Zenger, K.; Strugnell, J.M.; Barnard, R.; Jerry, D.R. (2021) 'A SNP parentage assignment panel for the silver lipped pearl oyster (Pinctada maxima)'. Aquaculture Reports, 20 . [DOI]
Nayfa, Maria G.; Jones, Dave B.; Benzie, John A.H.; Jerry, Dean R.; Zenger, Kyall R. (2020) 'Comparing genomic signatures of selection between the Abbassa Strain and eight wild populations of Nile tilapia (Oreochromis niloticus) in Egypt'. Frontiers in Genetics, 11 . [DOI]
Nayfa, Maria G.; Jones, David B.; Lind, Curtis E.; Benzie, John A.H.; Jerry, Dean R.; Zenger, Kyall R. (2020) 'Pipette and paper: combining molecular and genealogical methods to assess a Nile tilapia (Oreochromis niloticus) breeding program'. Aquaculture, 523 . [DOI]
Journal Publication
ResearchOnline@JCU
Jones, David B.; Nguyen, Huu; Khatkar, Mehar; Simma, David; Jerry, Dean; Raadsma, Herman; Van Der Steen, Hein; Prochaska, Jeffrey; Zenger, Kyall (2020) 'The identification of a major sex QTL in the white-leg shrimp, Litopenaeus vannamei'. Aquaculture, 529 . [DOI]
Journal Publication
ResearchOnline@JCU
Guppy, Jarrod L.; Jones, David B.; Kjeldsen, Shannon R.; Le Port, Agnes; Khatkar, Mehar S.; Wade, Nicholas M.; Sellars, Melony J.; Raadsma, Herman W.; Jerry, Dean R.; Zenger, Kyall R. (2020) 'Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs'. BMC Genomics, 21 . [DOI]
Zenger, Kyall R.; Khatkar, Mehar S.; Jones, David B.; Khalilisamani, Nima; Jerry, Dean R.; Raadsma, Herman W. (2019) 'Genomic selection in aquaculture: application, limitations and opportunities with special reference to marine shrimp and pearl oysters'. Frontiers in Genetics, 9 . [DOI]
Guppy, Jarrod L.; Jones, Dave B.; Jerry, Dean R.; Wade, Nicholas M.; Raadsma, Herman W.; Huerlimann, Roger; Zenger, Kyall R. (2018) 'The state of omics research for farmed penaeids: advances in research and impediments to industry utilization'. Frontiers in Genetics, 9 . [DOI]
Jones, David B.; Jerry, Dean R.; Khatkar, Mehar; Raadsma, Herman W.; van der Steen, Hein; Prochaska, Jeffrey; Fôret, Sylvain; Zenger, Kyall R. (2017) 'A comparative integrated gene-based linkage and locus ordering by linkage disequilibrium map for the Pacific white shrimp, Litopenaeus vannamei'. Scientific Reports, 7 . [DOI]
Goncalves, Priscila; Jones, David B.; Thompson, Emma L.; Parker, Laura M.; Ross, Pauline M.; Raftos, David A. (2017) 'Transcriptomic profiling of adaptive responses to ocean acidification'. Molecular Ecology, 26 (21):5974-5988. [DOI]
Journal Publication
ResearchOnline@JCU
Jones, David B.; Jerry, Dean R.; Khatkar, Mehar S.; Moser, Gerhard; Raadsma, Herman W.; Taylor, Joseph J.; Zenger, Kyall R. (2014) 'Determining genetic contributions to host oyster shell growth: quantitative trait loci and genetic association analysis for the silver-lipped pearl oyster, Pinctada maxima'. Aquaculture, 434 :367-375. [DOI]
Journal Publication
ResearchOnline@JCU
Jones, David B.; Jerry, Dean R.; Khatkar, Mehar S.; Moser, Gerhard; Raadsma, Herman W.; Taylor, Joseph J.; Zenger, Kyall R. (2014) 'Quantitative trait loci and genetic association analysis reveals insights into complex pearl quality traits in donor silver-lipped pearl oysters'. Aquaculture, 434 :476-485. [DOI]
Journal Publication
ResearchOnline@JCU
Jones, David B.; Jerry, Dean R.; Forêt, Sylvain; Konovalov, Dmitry A.; Zenger, Kyall R. (2013) 'Genome-wide SNP validation and mantle tissue transcriptome analysis in the silver-lipped pearl oyster, Pinctada maxima'. Marine Biotechnology, 15 (6):647-658. [DOI]
Journal Publication
ResearchOnline@JCU
Jones, David B.; Jerry, Dean R.; Khatkar, Mehar S.; Raadsma, Herman W.; Zenger, Kyall R. (2013) 'A high-density SNP genetic linkage map for the silver-lipped pearl oyster, Pinctada maxima: a valuable resource for gene localisation and marker-assisted selection'. BMC Genomics, 14 :1-18. [DOI]
McGinty, E.L.; Zenger, K.R.; Jones, D.B.; Jerry, D.R. (2012) 'Transcriptome analysis of biomineralisation-related genes within the pearl sac: host and donor oyster contribution'. Marine Genomics, 5 :27-33. [DOI]
Journal Publication
ResearchOnline@JCU
Jones, D.B.; Zenger, K.R.; Jerry, D.R. (2011) 'In silico whole-genome EST analysis reveals 2322 novel microsatellites for the silver-lipped pearl oyster, Pinctada maxima'. Marine Genomics, 4 (4):287-290. [DOI]
Journal Publication
ResearchOnline@JCU
Jones, D.B.; Jerry, D.R.; McCormick, M.I.; Bay, L.K. (2010) 'The population genetic structure of a common tropical damselfish on the Great Barrier Reef and eastern Papua New Guinea'. Coral Reefs, 29 (2):455-467. [DOI]
Journal Publication
ResearchOnline@JCU
Jones, David; Jerry, Dean; McCormick, Mark; Bay, Line (2008) 'Development of nine microsatellite markers for
Pomacentrus amboinensis'. Molecular Ecology Resources, 8 (6):1332-1334. [DOI]
Journal Publication
ResearchOnline@JCU
Lapico, Adrian; Sankupellay, Mangalam; Cianciullo, Louis; Myers, Trina; Konovalov, Dmitry A.; Jerry, Dean R.; Toole, Preston; Jones, David B.; Zenger, Kyall R. (2019) 2019 Digital Image Computing: Techniques and Applications (DICTA) Using image processing to automatically measure pearl oyster size for selective breeding Perth, WA, Australia, [DOI]
Conference Publication
ResearchOnline@JCU
Khatkar, M.S.; Zenger, K.R.; Jones, D.B.; Prochaska, Jeff; van der Steen, H.A.M.; Jerry, D.R.; Raadsma, H.W. (2017) Proceedings of the Association for the Advancement of Animal Breeding and Genetics Quantitative genomic analyses in the pacific whiteleg shrimp litopenaeus vannamei Townsville, QLD, Australia,
Conference Publication
ResearchOnline@JCU
Jones, D.B.; Zenger, K.R.; Khatkar, M.S.; Raadsma, H.W.; van der Steen, H.A.M.; Prochaska, J.; Fôret, S.; Jerry, D.R. (2017) Proceedings of the Association for the Advancement of Animal Breeding and Genetics Development of a low density commercial genotyping array for
the white legged shrimp, Litopenaeus vannamei Townsville, QLD, Australia,
Conference Publication
ResearchOnline@JCU
Khatkar, M.S.; Jones, D.B.; Toole, P.B.; Raadsma, H.W.; Jerry, D.R.; Zenger, K.R. (2017) Proceedings of the Association for the Advancement of Animal Breeding and Genetics Reconstruction of unknown donor genome from chimeric pearl sac tissue and host genotypes in pinctada maxima Townsville, QLD, Australia,
Conference Publication
ResearchOnline@JCU
Jones, D.B.; Toole, P.B.; Khatkar, M.S.; Raadsma, H.W.; Jerry, D.R.; Zenger, K.R. (2017) Proceedings of the Association for the Advancement of Animal Breeding and Genetics Developing a genomic selection breeding program for complex pearl colour traits within the silver-lipped pearl oyster Townsville, QLD, Australia,
Conference Publication
ResearchOnline@JCU