Article

Saleh, Alzayat, Hasan, Md Mehedi, Raadsma, Herman W., Khatkar, Mehar S., Jerry, Dean, and Rahimi Azghadi, Mostafa (2024) Prawn Morphometrics and Weight Estimation from Images using Deep Learning for Landmark Localization. Aquacultural Engineering, 106. 102391.

Pacoureau, Nathan, Carlson, John K., Kindsvater, Holly K., Rigby, Cassandra L., Winker, Henning, Simpfendorfer, Colin A., Charvet, Patricia, Pollom, Riley A., Barreto, Rodrigo, Samantha Sherman, C., Talwar, Brendan S., Skerritt, Daniel J., Rashid Sumaila, U., Matsushiba, Jay H., VanderWright, Wade J., Yan, Helen F., and Dulvy, Nicholas K. (2023) Conservation successes and challenges for wide-ranging sharks and rays. Proceedings of the National Academy of Sciences of the United States of America, 120 (5). e2216891120.

Lemke, L.R., and Simpfendorfer, C.A. (2023) Gillnet size selectivity of shark and ray species from Queensland, Australia. Fisheries Management and Ecology, 30 (3). pp. 300-309.

Sherman, C. Samantha, Simpfendorfer, Colin A., Pacoureau, Nathan, Matsushiba, Jay H., Yan, Helen F., Walls, Rachel H.L., Rigby, Cassandra L., Vanderwright, Wade J., Jabado, Rima W., Pollom, Riley A., Carlson, John K., Charvet, Patricia, Bin Ali, Ahmad, Fahmi, Cheok, Jessica, Derrick, Danielle H., Herman, Katelyn B., Finucci, Brittany, Eddy, Tyler D., Palomares, Maria Lourdes D., Avalos-Castillo, Christopher G., Kinattumkara, Bineesh, Blanco-Parra, María del Pilar, Dharmadi, Espinoza, Mario, Fernando, Daniel, Haque, Alifa B., Mejía-Falla, Paola A., Navia, Andrés F., Pérez-Jiménez, Juan Carlos, Utzurrum, Jean, Yuneni, Ranny R., and Dulvy, Nicholas K. (2023) Half a century of rising extinction risk of coral reef sharks and rays. Nature Communications, 14. 15.

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., and Saunders, Richard J. (2023) Multimethod approach to advance provenance determination of fish in stocked systems. Canadian Journal of Fisheries and Aquatic Sciences, 80. pp. 1410-1424.

Matley, Jordan K., Klinard, Natalie V., Barbosa Martins, Ana P., Aarestrup, Kim, Aspillaga, Eneko, Cooke, Steven J., Cowley, Paul D., Heupel, Michelle R., Lowe, Christopher G., Lowerre-Barbieri, Susan K., Mitamura, Hiromichi, Moore, Jean Sébastien, Simpfendorfer, Colin A., Stokesbury, Michael J.W., Taylor, Matthew D., Thorstad, Eva B., Vandergoot, Christopher S., and Fisk, Aaron T. (2022) Global trends in aquatic animal tracking with acoustic telemetry. Trends in Ecology & Evolution, 37 (1). pp. 79-94.

Emmons, Sophia M., D'Alberto, Brooke M., Smart, Jonathan J., and Simpfendorfer, Colin A. (2021) Age and growth of tiger shark (Galeocerdo cuvier) from Western Australia. Marine and Freshwater Research, 72 (7). pp. 950-963.

Raoult, Vincent, Grant, Michael I., Barbosa Martins, Ana Paula, Feitosa, Leonardo Manir, Braccini, Matias, Cardeñosa, Diego, Carlson, John, Chin, Andrew, Curtis, Tobey, Carvalho Costa, Luís Fernando, Rodrigues Filho, Luís Fernando, Giarrizzo, Tommaso, Nunes, Jorge Luiz S., Sales, João Bráullio L., Williamson, Jane E., and Simpfendorfer, Colin (2021) Assigning shark fin origin using species distribution models needs a reality check. Biology Letters, 17 (7).

Bartes, Saia, Simpfendorfer, Colin, Walker, Terence I., King, Carissa, Loneragan, Neil, and Braccini, Matías (2021) Conventional tagging of sharks in Western Australia: the main commercial species exhibit contrasting movement patterns. Marine and Freshwater Research, 72 (11).

Pacoureau, Nathan, Rigby, Cassandra L., Kyne, Peter M., Sherley, Richard B., Winker, Henning, Carlson, John K., Fordham, Sonja V., Barreto, Rodrigo, Fernando, Daniel, Francis, Malcolm P., Jabado, Rima W., Herman, Katelyn B., Liu, Kwang-Ming, Marshall, Andrea D., Pollom, Riley A., Romanov, Evgeny V., Simpfendorfer, Colin A., Yin, Jamie S., Kindsvater, Holly K., and Dulvy, Nicholas K. (2021) Half a century of global decline in oceanic sharks and rays. Nature, 589. pp. 567-571.

Campbell, Matthew J., McLennan, Mark F., Courtney, Anthony J., and Simpfendorfer, Colin A. (2021) Life-history characteristics of the eastern shovelnose ray, Aptychotrema rostrata (Shaw, 1794), from southern Queensland, Australia. Marine and Freshwater Research, 72 (9). pp. 1280-1289.

Priyambodo, Bayu, Jones, Clive M., and Sammut, Jesmond (2020) Assessment of the lobster puerulus (Panulirus homarus and Panulirus ornatus, Decapoda: Palinuridae) resource of Indonesia and its potential for sustainable harvest for aquaculture. Aquaculture, 528. 735563.

Martin, Gerardo, Espinoza, Mario, Heupel, Michelle, and Simpfendorfer, Colin A. (2020) Estimating marine protected area network benefits for reef sharks. Journal of Applied Ecology, 57 (10). pp. 1969-1980.

Campbell, Matthew J., Tonks, Mark L., Miller, Margaret, Brewer, David T., Courtney, Anthony J., and Simpfendorfer, Colin A. (2020) Factors affecting elasmobranch escape from turtle excluder devices (TEDs) in a tropical penaeid-trawl fishery. Fisheries Research, 224. 105456.

Dwyer, Ross G., Krueck, Nils C., Udyawer, Vinay, Heupel, Michelle R., Chapman, Demian, Pratt, Harold L., Garla, Ricardo, and Simpfendorfer, Colin A. (2020) Individual and population benefits of marine reserves for reef sharks. Current Biology, 30 (3). e5. pp. 480-489.

Currey-Randall, Leanne M., Cappo, Mike, Simpfendorfer, Colin A., Farabaugh, Naomi F., and Heupel, Michelle R. (2020) Optimal soak times for Baited Remote Underwater Video Station surveys of reef-associated elasmobranchs. PLoS One, 15 (5). e0231688.

White, William T., Baje, Leontine, Appleyard, Sharon A., Chin, Andrew, Smart, Jonathan J., and Simpfendorfer, Colin A. (2020) Shark longline fishery of Papua New Guinea: size and species composition and spatial variation of the catches. Marine and Freshwater Research, 71. pp. 627-640.

Candebat, Caroline L., Booth, Mark, Williamson, Jane E., and Pirozzi, Igor (2020) The critical oxygen threshold of Yellowtail Kingfish (Seriola lalandi). Aquaculture, 516. 734519.

Jones, David B., Nguyen, Huu, Khatkar, Mehar, Simma, David, Jerry, Dean, Raadsma, Herman, Van Der Steen, Hein, Prochaska, Jeffrey, and Zenger, Kyall (2020) The identification of a major sex QTL in the white-leg shrimp, Litopenaeus vannamei. Aquaculture, 529. 735673.

Bradley, Michael, Baker, Ronald, Nagelkerken, Ivan, and Sheaves, Marcus (2019) Context is more important than habitat type in determining use by juvenile fish. Landscape Ecology, 34. pp. 427-442.

Woodings, Laura N., Murphy, Nicholas P., Jeffs, Andrew, Suthers, Iain M., Liggins, Geoffrey, and Strugnell, Jan M. (2019) Distribution of Palinuridae and Scyllaridae phyllosoma larvae within the East Australian Current: a climate change hot spot. Marine and Freshwater Research, 70. pp. 1020-1033.

George, Lachlan W., Martins, Ana P.B., Heupel, Michelle R., and Simpfendorfer, Colin A. (2019) Fine-scale movements of juvenile blacktip reef sharks Carcharhinus melanopterus in a shallow nearshore nursery. Marine Ecology Progress Series, 623. pp. 85-97.

D'Alberto, Brooke M., Carlson, John K., Pardo, Sebastián, and Simpfendorfer, Colin A. (2019) Population productivity of shovelnose rays: inferring the potential for recovery. PLoS ONE, 14 (11). e0225183.

Thorbjørnsen, Susanna Huneide, Moland, Even, Simpfendorfer, Colin, Heupel, Michelle, Knutsen, Halvor, and Olsen, Esben Moland (2019) Potential of a no-take marine reserve to protect home ranges of anadromous brown trout (Salmo trutta). Ecology and Evolution, 9 (1). pp. 417-426.

Martins, A.P.B, Heupel, M. R., Chin, A., and Simpfendorfer, C. A. (2018) Batoid nurseries: definition, use and importance. Marine Ecology - Progress Series, 595. pp. 253-267.

Feitosa, Leonardo Manir, Barbosa Martins, Ana Paula, Giarrizzo, Tommaso, Macedo, Wagner, Monteiro, Iann Leonardo, Gemaque, Romário, Nunes, Jorge Luiz Silva, Gomes, Fernanda, Schneider, Horácio, Sampaio, Iracilda, Souza, Rosália, Sales, João Bráullio, Rodrigues-Filho, Luís Fernando, Tchaicka, Lígia, and Carvalho-Costa, Luís Fernando (2018) DNA-based identification reveals illegal trade of threatened shark species in a global elasmobranch conservation hotspot. Scientific Reports, 8 (1). 3347.

Russ, Garry R., Payne, Cody S., Bergseth, Brock J., Rizzari, Justin R., Abesamis, Rene A., and Alcala, Angel C. (2018) Decadal-scale response of detritivorous surgeonfishes (family Acanthuridae) to no-take marine reserve protection and changes in benthic habitat. Journal of Fish Biology, 93 (5). pp. 887-900.

Goetze, Jordan S., Langlois, Tim J., McCarter, Joe, Simpfendorfer, Colin A., Hughes, Alec, Tingo Leve, Jacob, and Jupiter, Stacy D. (2018) Drivers of reef shark abundance and biomass in the Solomon Islands. PLoS ONE, 13 (7). e0200960.

Taylor, Matthew D., and Creighton, Colin (2018) Estimating the potential fishery benefits from targeted habitat repair: a case study of school prawn (Metapenaeus macleayi) in the lower Clarence River estuary. Wetlands, 38 (6). pp. 1199-1209.

Harry, Alastair (2018) Evidence for systemic age underestimation in shark and ray ageing studies. Fish and Fisheries, 19 (2). pp. 185-200.

Matley, Jordan K., Maes, Gregory E., Devloo-Delva, Floriaan, Huerlimann, Roger, Chua, Gladys, Tobin, Andrew J., Fisk, Aaron T., Simpfendorfer, Colin A., and Heupel, Michelle R. (2018) Integrating complementary methods to improve diet analysis in fishery‐targeted species. Ecology and Evolution, 8 (18). pp. 9503-9515.

Grant, Michael I., Smart, Jonathan J., White, William T., Chin, Andrew, Baje, Leontine, and Simpfendorfer, Colin A. (2018) Life history characteristics of the silky shark Carcharhinus falciformis from the central west Pacific. Marine and Freshwater Research, 69 (4). pp. 562-573.

Woodings, Laura N., Murphy, Nicholas P., Doyle, Stephen R., Hall, Nathan E., Robinson, Andrew J., Liggins, Geoffrey W., Green, Bridget S., Cooke, Ira R., Bell, James J., and Strugnell, Jan M. (2018) Outlier SNPs detect weak regional structure against a background of genetic homogeneity in the Eastern Rock Lobster, Sagmariasus verreauxi. Marine Biology, 165 (12). 185.

Campbell, Matthew J., McLennan, Mark F., Courtney, Anthony J., and Simpfendorfer, Colin A. (2018) Post-release survival of two elasmobranchs, the eastern shovelnose ray (Aptychotrema rostrata) and the common stingaree (Trygonoptera testacea), discarded from a prawn trawl fishery in southern Queensland, Australia. Marine and Freshwater Research, 69 (4). pp. 551-561.

Smart, Jonathan J., Punt, André E., Espinoza, Mario, White, William T., and Simpfendorfer, Colin A. (2018) Refining mortality estimates in shark demographic analyses: a Bayesian inverse matrix approach. Ecological Applications, 28 (6). pp. 1520-1533.

Diopere, Eveline, Vandamme, Sara G., Hablutzel, Pascal I., Cariani, Alessia, Van Houdt, Jeroen, Rijnsdorp, Adriaan, Tinti, Fausto, FishPopTrace Consortium, Volckaert, Filip A.M., and Maes, Gregory E. (2018) Seascape genetics of a flatfish reveals local selection under high levels of gene flow. ICES Journal of Marine Science, 75 (2). pp. 675-689.

Goncalves, Priscila, Jones, David B., Thompson, Emma L., Parker, Laura M., Ross, Pauline M., and Raftos, David A. (2017) Transcriptomic profiling of adaptive responses to ocean acidification. Molecular Ecology, 26 (21). pp. 5974-5988.

Smart, Jonathan J., Chin, Andrew, Tobin, Andrew J., White, William T., Kumasi, Brian, and Simpfendorfer, Colin A. (2017) Stochastic demographic analyses of the silvertip shark (Carcharhinus albimarginatus) and the common blacktip shark (Carcharhinus limbatus) from the Indo-Pacific. Fisheries Research, 191. pp. 95-107.

Smart, Jonathan J., Chin, Andrew, Baje, Leontine, Tobin, Andrew J., Simpfendorfer, Colin A., and White, William T. (2017) Life history of the silvertip shark Carcharhinus albimarginatus from Papua New Guinea. Coral Reefs, 36 (2). pp. 577-588.

Simpfendorfer, Colin A., and Dulvy, Nicholas K. (2017) Bright spots of sustainable shark fishing. Current Biology, 27 (3). R97-R98.

D'Alberto, Brooke M., Chin, Andrew, Smart, Jonathan J., Baje, Leontine, White, William, and Simpfendorfer, Colin A. (2017) Age, growth and maturity of oceanic whitetip shark (Carcharhinus longimanus) from Papua New Guinea. Marine and Freshwater Research, 68 (6). pp. 1118-1129.

Wakefield, Corey B., O'Malley, Joseph M., Williams, Ashley J., Taylor, Brett M., Nichols, Ryan S., Halafihi, Tuikolongahau, Humphreys, Robert L., Kaltavara, Jeremie, Nichol, Simon J., and Newman, Stephen J. (2017) Ageing bias and precision for deep-water snappers: evaluating nascent otolith preparation methods using novel multivariate comparisons among readers and growth parameter estimates. ICES Journal of Marine Science, 74 (1). pp. 193-203.

Eddy, Tyler D., Lotze, Heike K., Fulton, Elizabeth A., Coll, Marta, Ainsworth, Cameron H., de Araújo, Júlio Neves, Bulman, Catherine M., Bundy, Alida, Christensen, Villy, Field, John C., Gribble, Neil A., Hasan, Mejs, Mackinson, Steve, and Townsend, Howard (2017) Ecosystem effects of invertebrate fisheries. Fish and Fisheries, 18 (1). pp. 40-53.

Clifton, Julian, and Foale, Simon (2017) Extracting ideology from policy: analysing the social construction of conservation priorities in the Coral Triangle region. Marine Policy, 82. pp. 189-196.

Fabinyi, Michael, Dressler, Wolfram H., and Pido, Michael D. (2017) Fish, trade and food security: moving beyond 'availability' discourse in marine conservation. Human Ecology, 45 (2). pp. 177-188.

Pazmiño, Diana A., Maes, Gregory E., Simpfendorfer, Colin A., Salinas-de-León, Pelayo, and van Herwerden, Lynne (2017) Genome-wide SNPs reveal low effective population size within confined management units of the highly vagile Galapagos shark (Carcharhinus galapagensis). Conservation Genetics, 18 (5). pp. 1151-1163.

Matley, J.K., Heupel, M.R., Fisk, A.T., Simpfendorfer, C.A., and Tobin, A.J. (2017) Measuring niche overlap between co-occurring Plectropomus spp. using acoustic telemetry and stable isotopes. Marine and Freshwater Research, 68 (8). pp. 1468-1478.

Steckenreuter, Andre, Hoenner, Xavier, Huveneers, Charlie, Simpfendorfer, Colin, Buscot, Marie J., Tattersall, Katherine, Babcock, Russel, Heupel, Michelle, Meekan, Mark, van den Broek, James, McDowall, Phillip, Peddemors, Victor, and Harcourt, Robert (2017) Optimising the design of large-scale acoustic telemetry curtains. Marine and Freshwater Research, 68 (8). pp. 1403-1413.

Matley, J.K., Tobin, A.J., Simpfendorfer, C.A., Fisk, A.T., and Heupel, M.R. (2017) Trophic niche and spatio-temporal changes in the feeding ecology of two sympatric species of coral trout (Plectropomus leopardus and P-laevis). Marine Ecology-Progress Series, 563. pp. 197-210.

Taylor, Matthew D., Babcock, Russel, Simpfendorfer, Colin A., and Crook, David A. (2017) Where technology meets ecology: acoustic telemetry in contemporary Australian aquatic research and management. Marine and Freshwater Research, 68 (8). pp. 1397-1402.

Lédée, Elodie J.I., Heupel, Michelle R., Tobin, Andrew J., Mapleston, Amos, and Simpfendorfer, Colin A. (2016) Movement patterns of two carangid species in inshore habitats characterised using network analysis. Marine Ecology Progress Series, 553. pp. 219-232.

Harry, Alastair V., Saunders, Richard J., Smart, Jonathan J., Yates, Peter M., Simpfendorfer, Colin A., and Tobin, Andrew J. (2016) Assessment of a data-limited, multi-species shark fishery in the Great Barrier Reef Marine Park and south-east Queensland. Fisheries Research, 177. pp. 104-115.

Smart, Jonathan J., Chin, Andrew, Baje, Leontine, Green, Madeline E., Appleyard, Sharon A., Tobin, Andrew J., Simpfendorfer, Colin A., and White, William T. (2016) Effects of including misidentified sharks in life history analyses: a case study on the grey reef shark Carcharhinus amblyrhynchos from Papua New Guinea. PLoS ONE, 11 (4). e0153116. pp. 1-18.

Espinoza, Mario, Heupel, Michelle R., Tobin, Andrew J., and Simpfendorfer, Colin A. (2016) Evidence of partial migration in a large coastal predator: opportunistic foraging and reproduction as key drivers? PLoS ONE, 11 (2). e0147608. pp. 1-22.

Angell, Alex R., Mata, Leonardo, de Nys, Rocky, and Paul, Nicholas A. (2016) The protein content of seaweeds: a universal nitrogen-to-protein conversion factor of five. Journal of Applied Phycology, 28 (1). pp. 511-524.

Yates, Peter M., Tobin, Andrew J., Heupel, Michelle R., and Simpfendorfer, Colin A. (2016) Benefits of marine protected areas for tropical coastal sharks. Aquatic Conservation: marine and freshwater ecosystems , 26 (6). pp. 1063-1080.

Matley, J.K., Fisk, A.T., Tobin, A.J., Heupel, M.R., and Simpfendorfer, C.A. (2016) Diet-tissue discrimination factors and turnover of carbon and nitrogen stable isotopes in tissues of an adult predatory coral reef fish, Plectropomus leopardus. Rapid Communications in Mass Spectrometry, 30 (1). pp. 29-44.

Nash, Kirsty L., and Graham, Nicholas A.J. (2016) Ecological indicators for coral reef fisheries management. Fish and Fisheries, 17 (4). pp. 1029-1054.

Dulvy, Nicholas K., Davidson, Lindsay N.K., Kyne, Peter M., Simpfendorfer, Colin, Harrison, Lucy R., Carlson, John K., and Fordham, Sonja V. (2016) Ghosts of the coast: global extinction risk and conservation of sawfishes. Aquatic Conservation: marine and freshwater ecosystems , 26 (1). pp. 134-153.

Hamilton, Richard J., Almany, Glenn R., Stevens, Don, Bode, Michael, Pita, John, Peterson, Nate A., and Choat, J. Howard (2016) Hyperstability masks declines in bumphead parrotfish (Bolbometopon muricatum) populations. Coral Reefs, 35 (3). pp. 751-763.

Smart, Jonathan J., Chin, Andrew, Tobin, Andrew J., and Simpfendorfer, Colin A. (2016) Multimodel approaches in shark and ray growth studies: strengths, weaknesses and the future. Fish and Fisheries, 17 (4). pp. 955-971.

Cameron, Leo, Baumgartner, Lee, Butler, Gavin, Burcher, Daniel, and Lou, Dong-chun (2016) Using otolith microchemistry to differentiate between stocked and unstocked Australian bass (Percalates novemaculeata). Fisheries Research, 183. pp. 86-91.

Munroe, S.E.M., Simpfendorfer, C.A., and Heupel, M.R. (2016) Variation in blacktip shark movement patterns in a tropical coastal bay. Environmental Biology of Fishes, 99 (4). pp. 377-389.

Book Chapter

Phang, Key-Seem, Pung, Qi-En, and Loh, Jiun-Yan (2022) Advances in shrimp aquaculture technology. In: Loh, Jiun Yan, Soo, Michelle Oi-Yoon, Gunasekaran, Baskaran, and Andin, Victor Charlie, (eds.) Advances in Aquaculture. UCSI Press, Kuala Lumpur, Malaysia, pp. 29-37.

Johnson, Johanna E., Bell, Johann D., Allain, Valerie, Hanich, Quentin, Lehodey, Patrick, Moore, Brad R., Nicol, Simon, Pickering, Tim, and Senina, Inna (2018) The Pacific Island region: fisheries, aquaculture and climate change. In: Phillips, Bruce F., and Pérez-Ramírez, Mónica, (eds.) Climate Change Impacts on Fisheries and Aquaculture: a global analysis. Wiley-Blackwell, Hoboken, NJ, USA, pp. 333-379.

Thesis

Saleh, Alzayat (2023) Novel deep learning architectures for marine and aquaculture applications. PhD thesis, James Cook University.

Campbell, Matthew John (2022) Assessing ecological risk posed to common rays by prawn trawling. PhD thesis, James Cook University.

Rennie, Benjamin (2022) Broodstock conditioning techniques, filtration rate and bioremediatory ability of the tropical Blacklip rock oyster (Saccostrea echinata). Masters (Research) thesis, James Cook University.

Schlaff, Audrey M. (2020) Multi-scale patterns in movement and space use of sharks on inshore reefs. PhD thesis, James Cook University.