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Villacorta Rath, Cecilia, Espinoza, Thomas, Cockayne, Bernie, Schaffer, Jason, and Burrows, Damien (2022) Environmental DNA analysis confirms extant populations of the cryptic Irwin’s turtle within its historical range. BMC Ecology and Evolution, 22. 57.

Morrissey, Scott J., Jerry, Dean R., and Kingsford, Michael J. (2022) Genetic Detection and a Method to Study the Ecology of Deadly Cubozoan Jellyfish. Diversity, 14 (12). 1139.

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Doll, Peter C., Messmer, Vanessa, Uthicke, Sven, Doyle, Jason R., Caballes, Ciemon F., and Pratchett, Morgan S. (2021) DNA-based detection and patterns of larval settlement of the corallivorous crown-of-thorns sea star (Acanthaster sp.). Biological Bulletin, 241 (3). pp. 271-285.

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Villacorta-Rath, Cecilia, Hoskin, Conrad J., Strugnell, Jan M., and Burrows, Damien (2021) Long distance (>20 km) downstream detection of endangered stream frogs suggests an important role for eDNA in surveying for remnant amphibian populations. PeerJ, 9. e12013.

Kwong, Lok Ting, Villacorta-Rath, Cecilia, Doyle, Jason, and Uthicke, Sven (2021) Quantifying shedding and degradation rates of environmental DNA (eDNA) from Pacific crown-of-thorns seastar (Acanthaster cf. solaris). Marine Biology, 168. 85.

Orbán, László, Shen, Xueyan, Phua, Norman, and Varga, László (2021) Toward genome-based selection in Asian seabass: what can we learn from other food fishes and farm animals? Frontiers in Genetics, 12. 506754.

Tol, S.J., Harrison, M., Groom, R., Gilbert, J., Blair, D., Coles, R., and Congdon, B.C (2021) Using DNA to distinguish between faeces of Dugong dugon and Chelonia mydas: non-invasive sampling for IUCN-listed marine megafauna. Conservation Genetics Resources, 13. pp. 115-117.

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Villacorta Rath, Cecilia, Adekunle, Adeshina I., Edmunds, Richard C., Strugnell, Jan M., Schwarzkopf, Lin, and Burrows, Damien (2020) Can environmental DNA be used to detect first arrivals of the cane toad, Rhinella marina, into novel locations? Environmental DNA, 2 (4). pp. 635-646.

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Jin, Young K., Kininmonth, Stuart, Lundgren, Petra B., van Oppen, Madeleine J.H., and Willis, Bette L. (2020) Predicting the spatial distribution of allele frequencies for a gene associated with tolerance to eutrophication and high temperature in the reef-building coral, Acropora millepora, on the Great Barrier Reef. Coral Reefs, 39. pp. 147-158.

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Ramirez Flores, Omar, Birtles, Alastair, Pazmino, Diana, Zenger, Kyall R., and Van Herwerden, Lynne (2019) Dwarf minke whales from the South Pacific share a matrilineal lineage distinct from Balaenoptera acutorostrata acutorostrata and B. a. scammoni. Australian Mammalogy, 41 (2). pp. 231-240.

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Villacorta-Rath, Cecilia, Souza, Carla A., Murphy, Nicholas P., Green, Bridget S., Gardner, Caleb, and Strugnell, Jan M. (2018) Temporal genetic patterns of diversity and structure evidence chaotic genetic patchiness in a spiny lobster. Molecular Ecology, 27 (1). pp. 54-65.

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Yang, Yuchen, Li, Jianfang, Yang, Shuhuan, Li, Xinnian, Fang, Lu, Zhong, Cairong, Duke, Norman C., Zhou, Renchao, and Shi, Suhua (2017) Effects of Pleistocene sea-level fluctuations on mangrove population dynamics: a lesson from Sonneratia alba. BMC Evolutionary Biology, 17. 22. pp. 1-14.

Raeymaekers, Joost A.M., Chaturvedi, Anurag, Hablützel, Pascal I., Verdonck, Io, Hellemans, Bart, Maes, Gregory, De Meester, Luc, and Volckaert, Filip A.M. (2017) Adaptive and non-adaptive divergence in a common landscape. Nature Communications, 8. 267.

Strugnell, Jan M., Allcock, A. Louise, and Watts, Phillip C. (2017) Closely related octopus species show different spatial genetic structures in response to the Antarctic seascape. Ecology and Evolution, 7 (19). pp. 8087-8099.

Nelson, Joel T., Wilson, Robert E., McCracken, Kevin G., Cumming, Graeme S., Joseph, Leo, Guay, Patrick-Jean, and Peters, Jeffrey L. (2017) Divergence and gene flow in the globally distributed blue-winged ducks. Journal of Avian Biology, 48 (5). pp. 640-649.

McKnight, Donald T., Schwarzkopf, Lin, Alford, Ross A., Bower, Deborah S., and Zenger, Kyall R. (2017) Effects of emerging infectious diseases on host population genetics: a review. Conservation Genetics, 18. pp. 1235-1245.

Souza, Carla A., Murphy, Nicholas, Villacorta-Rath, Cecilia, Woodings, Laura N., Ilyushkina, Irina, Hernandez, Cristian E., Green, Bridget S., Bell, James J., and Strugnell, Jan (2017) Efficiency of ddRAD target enriched sequencing across spiny rock lobster species (Palinuridae: Jasus). Scientific Reports, 7 (1). 6781.

Momigliano, P., Harcourt, R., Robbins, W.D., Jaiteh, V., Mahardika, G.N., Sembiring, A., and Stow, A. (2017) Genetic structure and signatures of selection in grey reef sharks (Carcharhinus amblyrhynchos). Heredity, 119. pp. 142-153.

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.

Bernatchez, Louis, Wellenreuther, Maren, Araneda, Cristián, Ashton, David T., Barth, Julia M.I., Beacham, Terry D., Maes, Gregory E., Martinsohn, Jann T., Miller, Kristina M., Naish, Kerry A., Ovenden, Jennifer R., Primmer, Craig R., Suk, Ho Young, Therkildsen, Nina O., and Withler, Ruth E. (2017) Harnessing the power of genomics to secure the future of seafood. Trends in Ecology and Evolution, 32 (9). pp. 665-680.

Neuditschko, Markus, Raadsma, Herman W., Khatkar, Mehar S., Jonas, Elisabeth, Steinig, Eike J., Flury, Christine, Signer-Hasler, Heidi, Frischknecht, Mirjam, von Niederhausem, Ruedi, Leeb, Tosso, and Rieder, Stefan (2017) Identification of key contributors in complex population structures. PLoS One, 12 (5). e0177638. pp. 1-19.

Silva, C.N.S., McFarlane, S.E., Hagen, I.J., Rönnegård, L., Billing, A.M., Kvalnes, T., Kemppainen, P., Rønning, B., Ringsby, T.H., Sæther, B-E., Qvarnström, A., Ellegren, H., Jensen, H., and Husby, A. (2017) Insights into the genetic architecture of morphological traits in two passerine bird species. Heredity, 119. pp. 197-205.

Almany, Glenn R., Planes, Serge, Thorrold, Simon R., Berumen, Michael L., Bode, Michael, Saenz-Agudelo, Pablo, Bonin, Mary C., Frisch, Ashley J., Harrison, Hugo B., Messmer, Vanessa, Nanninga, Gerrit B., Priest, Mark A., Srinivasan, Maya, Sinclair-Taylor, Tane, Williamson, David H., and Jones, Geoffrey P. (2017) Larval fish dispersal in a coral-reef seascape. Nature Ecology & Evolution, 1 (6). pp. 1-4.

Harrison, Hugo B., Pratchett, Morgan S., Messmer, Vanessa, Saenz-Agudelo, Pablo, and Berumen, Michael L. (2017) Microsatellites reveal genetic homogeneity among outbreak populations of crown-of-thorns starfish (Acanthaster cf. solaris) on Australia's Great Barrier Reef. Diversity, 9 (1). 16.

Roura, Álvaro, Doyle, Stephen R., Nande, Manuel, and Strugnell, Jan M. (2017) You are what you eat: a genomic analysis of the gut microbiome of captive and wild Octopus vulgaris paralarvae and their zooplankton prey. Frontiers in Physiology, 8. 362.

Villacorta-Rath, Cecilia, Ilyushkina, Irina, Strugnell, Jan M., Green, Bridget S., Murphy, Nicholas P., Doyle, Stephen R., Hall, Nathan E., Robinson, Andrew J., and Bell, James J. (2016) Outlier SNPs enable food traceability of the southern rock lobster, Jasus edwardsii. Marine Biology, 163 (11). 223.

Li, Xinnian, Duke, Norman C., Yang, Yuchen, Huang, Lishi, Zhu, Yuxiang, Zhang, Zhang, Zhou, Renchao, Zhong, Cairong, Huang, Yelin, and Sia, Suhua (2016) Re-evaluation of phylogenetic relationships among species of the mangrove genus Avicennia from Indo-West Pacific based on multilocus analyses. PLoS ONE, 11 (10). e0164453. pp. 1-14.

Yan, Yu-Bin, Duke, Norm C., and Sun, Mei (2016) Comparative analysis of the pattern of population genetic diversity in three Indo-West Pacific Rhizophora mangrove species. Frontiers in Plant Science, 7. 1434. pp. 1-17.

Hodge, Jennifer R., and Bellwood, David R. (2016) The geography of speciation in coral reef fishes: the relative importance of biogeographical barriers in separating sister-species. Journal of Biogeography, 43 (7). pp. 1324-1335.

Bonin, Mary C., Harrison, Hugo B., Williamson, David H., Frisch, Ashley J., Saenz-Agudelo, Pablo, Berumen, Michael L., and Jones, Geoffrey P. (2016) The role of marine reserves in the replenishment of a locally impacted population of anemonefish on the Great Barrier Reef. Molecular Ecology, 25 (2). pp. 487-499.

Yang, Yuchen, Duke, Norman C., Peng, Fangfang, Li, Jianfang, Yang, Shuhuan, Zhong, Cairong, Zhou, Renchao, and Shi, Suhua (2016) Ancient geograpical barriers drive differentiation among Sonneratia caseolaris populations and recent divergence from S. Ianceolata. Frontiers in Plant Science, 7. 1618. pp. 1-14.

Cooper, W.E., Kudo, H., and Duke, Norman C. (2016) Bruguiera hainesii C.G.Rogers (Rhizophoraceae), an endangered species recently discovered in Australia. Austrobaileya, 9 (4). pp. 481-488.

Le Port, A., Roycroft, E.J., Thakur, V., and Lavery, S.D. (2016) Characterisation of eleven new polymorphic microsatellite markers for the coastal stingray Dasyatis brevicaudata (Dasyatidae Hutton 1875), and cross-amplification in seven dasyatid species. Biochemical Systematics and Ecology, 65. pp. 234-237.

Bhattacharya, Debashish, Agrawal, Shobhit, Aranda, Manuel, Baumgarten, Sebastian, Belcaid, Mahdi, Drake, Jeana L., Erwin, Douglas, Foret, Sylvain, Gates, Ruth D., Gruber, David F., Kamel, Bishoy, Lesser, Michael P., Levy, Oren, Liew, Yi Jin, MacManes, Matthew, Mass, Tali, Medina, Monica, Mehr, Shaadi, Meyer, Eli, Price, Dana C., Putnam, Hollie M., Qiu, Huan, Shinzato, Chuya, Shoguchi, Eiichi, Stokes, Alexander J., Tambutté, Sylvie, Tchernov, Dan, Voolstra, Christian R., Wagner, Nicole, Walker, Charles W., Weber, Andreas P.M., Weis, Virginia, Zelzion, Ehud, Zoccola, Didier, and Falkowski, Paul G. (2016) Comparative genomics explains the evolutionary success of reef-forming corals. eLife, 5. e13288. pp. 1-26.

Lukoschek, Vimoksalehi, Riginos, Cynthia, and van Oppen, Madeleine J.H. (2016) Congruent patterns of connectivity can inform management for broadcast spawning corals on the Great Barrier Reef. Molecular Ecology, 25 (13). pp. 3065-3080.

Lawn, R.J., and Bielig, L.M. (2016) Expression of amphicarpy in Vigna lanceolata morphotypes and their hybrids and implications for cultivar development. Crop & Pasture Science, 67 (9). CP16087. pp. 978-987.

Sherman, Craig D.H., York, Paul H., Smith, Timothy M., and Macreadie, Peter I. (2016) Fine-scale patterns of genetic variation in a widespread clonal seagrass species. Marine Biology, 163 (4). 82.

Guo, Zixiao, Huang, Yelin, Chen, Yongmei, Duke, Norman C., Zhong, Cairong, and Shi, Sugua (2016) Genetic discontinuities in a dominant mangrove Rhizophora apiculata (Rhizophoraceae) in the Indo-Malesian region. Journal of Biogeography, 43. pp. 1856-1868.

Jin, Young K,, Lundgren, Petra, Lutz, Adrian, Raina, Jean-Baptiste, Howells, Emily J., Paley, Allison S., Willis, Bette L., and Van Oppen, Madeleine J.H. (2016) Genetic markers for antioxidant capacity in a reef-building coral. Science Advances, 2. e1500842. pp. 1-7.

Tang, Lei Stanley, Smith-Keune, Carolyn, Grice, Anthony C., Moloney, James M., and Hardesty, Britta Denise (2016) Genetic structure and diversity of the black-throated finch (Poephila cincta) across its current range. Australian Journal of Zoology, 64 (6). pp. 375-384.

Silva, Catarina N.S., and Gardner, Jonathan P.A. (2016) Identifying environmental factors associated with the genetic structure of the New Zealand scallop: linking seascape genetics and ecophysiological tolerance. ICES Journal of Marine Science, 73 (7). pp. 1925-1934.

Ma, Jun, He, Jun-Jun, Liu, Guo-Hua, Blair, David, Liu, Li-Zhi, Liu, Yi, and Zhu, Xing-Quan (2016) Mitochondrial genome of Ogmocotyle sikae and implications for phylogenetic studies of the Notocotylidae trematodes. Infection, Genetics and Evolution, 37. pp. 208-214.

Delghandi, Madjid, Afzal, Hasifa, Al Hinai, Manal Saif Nasser, Al-Breiki, Rafaida Dhuhai Gharib, Jerry, Dean R., and Dao, Hoc Tan (2016) Novel polymorphic microsatellite markers for Panulirus ornatus and their cross-species primer amplification in Panulirus homarus. Animal Biotechnology, 27 (4). pp. 310-314.

Yin, Mingbo, Li, Hongyan, Blair, David, Xu, Bin, Feng, Zheng, and Hu, Wei (2016) Temporal genetic diversity of Schistosoma japonicum in two endemic sites in China revealed by microsatellite markers. Parasites & Vectors, 9. 36. pp. 1-5.

Oliva, Jessica Lee, Wong, Yen T., Rault, Jean-Loup, Appleton, Belinda, and Lill, Alan (2016) The oxytocin receptor gene, an integral piece of the evolution of Canis familaris from Canis lupus. Pet Behaviour Science, 2. pp. 1-15.

Noonan, Sam H.C., Fabricius, Katharina E., and Humphrey, Craig (2013) Symbiodinium Community Composition in Scleractinian Corals Is Not Affected by Life-Long Exposure to Elevated Carbon Dioxide. PLoS ONE, 8 (5). e63985.

Book Chapter

Pujolar, José Martin, and Maes, Gregory E. (2016) Evolutionary genomics of North Atlantic eels: current status and perspectives. In: Arai, Takaomi, (ed.) Biology and Ecology of Anguillid Eels. CRC Press, Boca Raton, FL, USA, pp. 36-51.

Report

Pratchett, Morgan S., Caballes, Ciemon F., Burn, Deborah, Doll, Peter C., Chandler, Josie F., Doyle, Jason R., and Uthicke, Sven (2022) Scooter-assisted large area diver-based (SALAD) visual surveys to test for renewed outbreaks of crown-of-thorns starfish (Acanthaster cf. solaris) in the northern Great Barrier Reef. Report. Australian Government.

Thesis

Cooper, Madalyn K. (2022) Resolving the global distribution of sawfishes (family Pristidae) using environmental DNA. PhD thesis, James Cook University.

Tol, Samantha (2020) Relative importance of different seagrass re-establishment strategies in tropical Queensland, Australia. PhD thesis, James Cook University.

Creative Work

van de Pol, M., Brouwer, L., and Cockburn, A. (2020) R package hiphop: parentage assignment using bi-allelic genetic markers. Statistical software. [Creative Work]