Publications

Our Harbour Our Asset

SIMS Associate Fellow Caroline Hoisington 

An overview of economic activities and values associated with Australia’s most iconic harbour and its use by the city that surrounds it. Sydney Institute of Marine Science Technical Report – Our Harbour Our Asset

Oceanography in the Days of Sail

Prof Ian Jones & Joyce Jones

The waters of the Pacific have played an important part in the development of the science of oceanography. Expeditions organised in the days of sail power were conducted in the face of hardships and dangers unknown today.

This book will be of interest to those drawn by the romance of the sea: to sailors, yachtsmen, and hydrographers. Click here to read the e-book.

Journal Articles

See below for a selection of SIMS journal articles:

  • Agüera, A., & Byrne, M. (2018). A dynamic energy budget model to describe the reproduction and growth of invasive starfish Asterias amurensis in southeast Australia. Biological Invasions.
  • Bugnot, A., Hose, G., Walsh, C., Floerl, O., French, K., & Dafforn, K. et al. (2018). Urban impacts across realms: Making the case for inter-realm monitoring and management. Science of The Total Environment, 648, 711-719. doi: 10.1016/j.scitotenv.2018.08.134
  • Brodie, S., Lédée, E., Heupel, M., Babcock, R., Campbell, H., & Gledhill, D. et al. (2018). Continental-scale animal tracking reveals functional movement classes across marine taxa. Scientific Reports, 8(1).
    Chan, K., Sewell, M., & Byrne, M. (2018). Revisiting the larval dispersal black box in the Anthropocene. ICES Journal of Marine Science. doi: 10.1093/icesjms/fsy097
  • Couturier, L., Newman, P., Jaine, F., Bennett, M., Venables, WN., Cagua, EF., Townsend, K., Weeks, S., Richardson, A. (2018). Variation in occupancy and habitat use of Mobula alfredi at a major aggregation site. Marine Ecology Progress Series, 599, 125-145, doi:10.3354/meps12610
  • Espinel-Velasco, N., Hoffmann, L., Agüera, A., Byrne, M., Dupont, S., & Uthicke, S. et al. (2018). Effects of ocean acidification on the settlement and metamorphosis of marine invertebrate and fish larvae: a review. Marine Ecology Progress Series, 606, 237-257. doi: 10.3354/meps12754
  • Foo, S., Deaker, D., & Byrne, M. (2018). Cherchez la femme – impact of ocean acidification on the egg jelly coat and attractants for sperm. The Journal of Experimental Biology, 221(13), jeb177188. doi: 10.1242/jeb.177188
  • Heery, E., Dafforn, K., Smith, J., Ushiama, S., & Mayer-Pinto, M. (2018). Not all artificial structures are created equal: Pilings linked to greater ecological and environmental change in sediment communities than seawalls. Marine Environmental Research, 142, 286-294. http://dx.doi: 10.1016/j.marenvres.2018.08.012
  • Hoenner, X., Huveneers, C., Steckenreuter, A., Simpfendorfer, C., Tattersall, K., & Jaine, F. et al. (2018). Australia’s continental-scale acoustic tracking database and its automated quality control process. Scientific Data, 5, 170206. http://dx.doi.org/10.1038/sdata.2017.206
  • Kienker, S., Coleman, R., Morris, R., Steinberg, P., Bollard, B., & Jarvis, R. et al. (2018). Bringing harbours alive: Assessing the importance of eco-engineered coastal infrastructure for different stakeholders and cities. Marine Policy, 94, 238-246. doi: 10.1016/j.marpol.2018.04.028
  • Lachnit, T., Dafforn, K., Johnston, E., & Steinberg, P. (2018). Contrasting distributions of bacteriophages and eukaryotic viruses from contaminated coastal sediments. Environmental Microbiology. http://dx.doi: 10.1111/1462-2920.14340
  • Lamare, M., Harianto, J., Uthicke, S., Agüera, A., Karelitz, S., & Pecorino, D. et al. (2018). Larval thermal windows in native and hybrid Pseudoboletia progeny (Echinoidea) as potential drivers of the hybridization zone. Marine Ecology Progress Series, 598, 99-112. doi: 10.3354/meps12601
  • Lawson, C., Suthers, I., Smith, J., Schilling, H., Stewart, J., Hughes, J., & Brodie, S. (2018). The influence of ontogenetic diet variation on consumption rate estimates: a marine example. Scientific Reports, 8(1). http://dx.doi: 10.1038/s41598-018-28479-7
  • Lee, K., Roughan, M., Harcourt, R., & Peddemors, V. (2018). Environmental correlates of relative abundance of potentially dangerous sharks in nearshore areas of southeastern Australia. Marine Ecology Progress Series, 599, 157-179. https://doi.org/10.3354/meps12611
  • Martino, C., Costa, C., Roccheri, M., Koop, D., Scudiero, R., & Byrne, M. (2018). Gadolinium perturbs expression of skeletogenic genes, calcium uptake and larval development in phylogenetically distant sea urchin species. Aquatic Toxicology, 194, 57-66. http://dx.doi.org/10.1016/j.aquatox.2017.11.004
  • Marzinelli, E., Qiu, Z., Dafforn, K., Johnston, E., Steinberg, P., & Mayer-Pinto, M. (2018). Coastal urbanisation affects microbial communities on a dominant marine holobiont. Npj Biofilms and Microbiomes, 4(1). http://dx.doi.org/10.1038/s41522-017-0044-z
  •  Pauthenet, E., Roquet, F., Madec, G., Guinet, C., Hindell, MA., McMahon, C., Harcourt, R., Nerini, D. (2018). Seasonal meandering of the Polar Front upstream of the Kerguelen Plateau, Geophysical Research Letters, 45 (18), 9774-9781, doi:10.1029/2018GL079614
  • Porter, A., Ferrari, R., Kelaher, B., Smith, S., Coleman, R., Byrne, M., & Figueira, W. (2018). Marine infrastructure supports abundant, diverse fish assemblages at the expense of beta diversity. Marine Biology, 165(7). doi: 10.1007/s00227-018-3369-0
  • Rohner, C., Richardson, A., Jaine, F., Bennett, M., Weeks, S., & Cliff, G. et al. (2018). Satellite tagging highlights the importance of productive Mozambican coastal waters to the ecology and conservation of whale sharks. Peerj, 6, e4161. doi: 10.7717/peerj.4161
    Rowe, C., Figueira, W., Raubenheimer, D., Solon-Biet, S., & Machovsky-Capuska, G. (2018). Effects of temperature on macronutrient selection, metabolic and swimming performance of the Indo-Pacific Damselfish (Abudefduf vaigiensis). Marine Biology, 165(11). http://dx.doi: 10.1007/s00227-018-3435-7
  • Schilling, H., Reis-Santos, P., Hughes, J., Smith, J., Everett, J., & Stewart, J. et al. (2018). Evaluating estuarine nursery use and life history patterns of Pomatomus saltatrix in eastern Australia. Marine Ecology Progress Series. http://dx.doi.org/10.3354/meps12495
  • Sequeira, A., Rodriguez, J., Eguiluz, V., Harcourt, R., Hindell, MA., Sims, DW., Duarte, CM., Costa, D., Fernandez-Gracia, J., Ferreira, LC., Hays, GC., Heupel, M., Meekan, MG., et, al. (2018). Convergence of marine megafauna movement patterns in coastal and open oceans, Proceedings of the National Academy of Sciences of the United States of America, 115 (12), 3072-3077. doi:10.1073/pnas.1716137115
  • Stewart, J.D., Jaine, F.R., Armstrong, A.O., Bennett, M.B., Burgess, K.B., Stevens, G.M., et al. (2018) Research priorities to support effective manta and devil ray conservation. Frontiers in Marine Science, 5 (314), 1-27. https://doi.org/10.3389/fmars.2018.00314
  • Turnbull, J., Shah Esmaeili, Y., Clark, G., Figueira, W., Johnston, E., & Ferrari, R. (2018). Key drivers of effectiveness in small marine protected areas. Biodiversity and Conservation. http://dx.doi.org/10.1007/s10531-018-1532-z Udyawer, V., Dwyer, R., Hoenner, X., Babcock, R., Brodie, S.,Taylor, M., et al. (2018). A standardised framework for analysing detection data from automated tracking arrays. Animal Biotelemetry, 6(1). doi: 10.1186/s40317-018-0162-2
  • Waltham, N., & Dafforn, K. (2018). Ecological engineering in the coastal seascape. Ecological Engineering, 120, 554-559. http:dx.doi: 10.1016/j.ecoleng.2018.07.028
  • Beck, H., Feary, D., Nakamura, Y., & Booth, D. (2017). Temperate macroalgae impacts tropical fish recruitment at forefronts of range expansion. Coral Reefs, 36(2), 639-651. http://dx.doi.org/10.1007/s00338-017-1553-1.
  • Dafforn, K. (in press). Eco-engineering and management strategies for marine infrastructure to reduce establishment and dispersal of non-indigenous species. Management Of Biological Invasions, 8(2), 153-161. http://dx.doi.org/10.3391/mbi.2017.8.2.03.
  • Everett, J., van Sebille, E., Taylor, M., Suthers, I., Setio, C., Cetina-Heredia, P., & Smith, J. (2017). Dispersal of Eastern King Prawn larvae in a western boundary current: New insights from particle tracking. Fisheries Oceanography. http://dx.doi.org/10.1111/fog.12213.
  • Harrison, D. (2017). Global negative emissions capacity of ocean macronutrient fertilization. Environmental Research Letters, 12(3), 035001. http://dx.doi.org/10.1088/1748-9326/aa5ef5.
  • Heery, E., Bishop, M., Critchley, L., Bugnot, A., Airoldi, L., & Mayer-Pinto, M. et al. (2017). Identifying the consequences of ocean sprawl for sedimentary habitats. Journal of Experimental Marine Biology and Ecology, 492, 31-48. http://dx.doi.org/10.1016/j.jembe.2017.01.020.
  • Kohli, G., Haslauer, K., Sarowar, C., Kretzschmar, A., Boulter, M., & Harwood, D. et al. (2017). Qualitative and quantitative assessment of the presence of ciguatoxin, P-CTX-1B, in Spanish Mackerel ( Scomberomorus commerson ) from waters in New South Wales (Australia). Toxicology Reports, 4, 328-334. http://dx.doi.org/10.1016/j.toxrep.2017.06.006.
  • Lawes, J., Dafforn, K., Clark, G., Brown, M., & Johnston, E. (in press). Multiple stressors in sediments impact adjacent hard substrate habitats and across biological domains. Science of The Total Environment, 592, 295-305. http://dx.doi.org/10.1016/j.scitotenv.2017.03.083.
  • Levin, R., Suggett, D., Nitschke, M., van Oppen, M., & Steinberg, P. (2017). Expanding the Symbiodinium (Dinophyceae, Suessiales) Toolkit Through Protoplast Technology. Journal Of Eukaryotic Microbiology, 64(5), 588-597. http://dx.doi.org/10.1111/jeu.12393.
  • Levin, R., Voolstra, C., Agrawal, S., Steinberg, P., Suggett, D., & van Oppen, M. (2017). Engineering Strategies to Decode and Enhance the Genomes of Coral Symbionts. Frontiers In Microbiology, 8. http://dx.doi.org/10.3389/fmicb.2017.01220.
  • Puritz, J., Keever, C., Addison, J., Barbosa, S., Byrne, M., & Hart, M. et al. (2017). Life-history predicts past and present population connectivity in two sympatric sea stars. Ecology and Evolution, 7(11), 3916-3930. http://dx.doi.org/10.1002/ece3.29.
  • Ainley LB, Vergés A, Bishop MJ (in press) Congruence of intraspecific variability in leaf traits for two co-occurring estuarine angiosperms. Oecologia (accepted, 8 April, 2016)
  • Armansin, N., Lee, K., Huveneers, C., Harcourt, R. 2016. Integrating social network analysis and fine-scale positioning to characterise the associations of a benthic shark. Animal Behaviour 115 (2016) 245e258.
  • Bain KF and Poore AGB. 2016. Use of near infrared reflectance spectroscopy (NIRS) to quantify diet mixing in a marine generalist herbivore. Marine Biology 163: 79.
  • Baird DJ; Van Den Brink PJ; Chariton AA; Dafforn KA; Johnston EL, 2016, ‘New diagnostics for multiply stressed marine and freshwater ecosystems: Integrating models, ecoinformatics and big data’, Marine and Freshwater Research, vol. 67, no. 4, pp. 391 – 392, http://dx.doi.org/10.1071/MF15330
  • Banks JL; Hutchings P; Curley B; Hedge L; Creese B; Johnston E, 2016, ‘Biodiversity conservation in Sydney Harbour’, Pacific Conservation Biology, vol. 22, no. 2, pp. 98 – 109,http://dx.doi.org/10.1071/PC15048
  • Bishop MJ, Mayer-Pinto M, Airoldi L, Firth LB, Morris RL, Loke LHL, Hawkins SJ, Naylor LA, Coleman RA, Chee SY, Dafforn KA (in press) Effects of ocean sprawl on ecological connectivity: impacts and solutions. J Exp Mar Biol Ecol (accepted, 29 May, 2016) Invited review
  • Bugnot AB, Coleman RA, Figueira WF & Marzinelli EM (2016) Effects of the receiving assemblage and disturbance on the colonisation of an invasive species. Marine Biology In press (accepted 31/05/2016)
  • Dafforn KA; Johnston EL; Ferguson A; Humphrey CL; Monk W; Nichols SJ; Simpson SL; Tulbure MG; Baird DJ, 2016, ‘Big data opportunities and challenges for assessing multiple stressors across scales in aquatic ecosystems’, Marine and Freshwater Research, vol. 67, no. 4, pp. 393 – 413,http://dx.doi.org/10.1071/MF15108
  • Domínguez-Tejo E; Metternicht G; Johnston E; Hedge L, 2016, ‘Marine Spatial Planning advancing the Ecosystem-Based Approach to coastal zone management: A review’, Marine Policy, vol. 72, pp. 115 – 130, http://dx.doi.org/10.1016/j.marpol.2016.06.023
  • Edge KJ; Johnston EL; Dafforn KA; Simpson SL; Kutti T; Bannister RJ, 2016, ‘Sub-lethal effects of water-based drilling muds on the deep-water sponge Geodia barretti’, Environmental Pollution, vol. 212, pp. 525
  • Evans SM, Sinclair E, Poore AGB, Bain KF, Vergés A. 2016. Genotypic richness predicts phenotypic variation in an endangered clonal plant. PeerJ 4:e1633. 534, http://dx.doi.org/10.1016/j.envpol.2016.02.047
  • Flood M, Stobutzki I, Andrews J, Ashby C, Begg G, Fletcher R, Gardner C, Georgeson L, Hansen S, Hartmann K, Hone P, Larcombe J, Maloney L, Moore A, Roach J, Roelofs A, Sainsbury K, Saunders T, Sloan S, Smith T, Stewart J, Wise B (2016). Multijurisdictional fisheries performance reporting: how Australia’s nationally standardised approach to assessing stock status compares. Fisheries Research – In Press
  • Hughes LE and Poore AGB. 2016. Biancolina japonica Ishimaru 1996: first record of this burrowing amphipod from Australia and a review of host use in the genus Biancolina (Amphipoda: Peracarida: Crustacea). Marine Biodiversity Records 9:32.
  • Hughes, J.M., Rowland, A.J., Stewart, J., Gill, H.S. (2016). Discovery of a specialised anatomical structure in some physoclistous carangid fishes which permits rapid ascent without barotrauma. Marine Biology.
  • Hughes, J.M., Stewart, J., Gillanders, B.M., Collins, D., & Suthers, I.M. (2016). Relationship between otolith chemistry and age in a widespread pelagic teleost Arripis trutta: influence of adult movements on stock structure and implications for management. Marine and Freshwater Research.
  • Gonçalves P, Anderson KA, Thompson EL, Melwani AR, Parker L, Ross PM, Raftos DA. 2016. Rapid transcriptional acclimation following transgenerational exposure of oysters to ocean acidification. Molecular Ecology. In Press.
  • Green TJ, Chataway T, Melwani AR, Raftos DA. 2016. Proteomic analysis of hemolymph from poly(I:C)-stimulated Crassostrea gigas. Fish & Shellfish Immunology 48: 39-42
  • Hays GC, Ferreira LC, Sequeira AMM, Meekan MG, Duarte CM, Bailey H, Bailleul F, Bowen WD, Cayley MJ, Costa DP, Eguiluz VM, Fossette S, Friedlaender AS, Gales N, Gleiss AC, Gunn J, Harcourt R, Hazen E, Heithaus MR, Heupel M, Holland K, Horning M, Jonsen I, Kooyman G, Lowe CG, Madsen PT, Marsh H, Phillips R, Righton D, Ropert- Coudert Y, Sato K, Shaffer S, Simpfendorfer CA, Sims DW, Skomal G, Takahashi A, Trathan PN, Wikelski M, Womble J, Thums M. 2016. Key questions in marine megafauna movement ecology. Trends in Ecology and Evolution DOI: 10.1016/j.tree.2016.02.015
  • Heery HC, Bishop MJ, Critchley L, Bugnot AB, Airoldi L, Mayer-Pinto M, Sheehan EV, Coleman RA, Loke LHL, Johnston EJ, Komyakova V, Morris RL, Strain EMA, Naylor LA, Dafforn KA (in press) Identifying the consequences of ocean sprawl for sedimentary habitats. J Exp Mar Biol Ecol (accepted, 29 May, 2016) Invited review
  • Henschke N, JD Everett, A Richardson, IM Suthers. 2016. Rethinking the role of salps in the ocean. Trends in Ecology and Evolution. 14 June 2016
  • Henschke N, JD Everett, IM Suthers. 2016. An observation of two oceanic salp swarms in the Tasman Sea: Thetys vagina and Cyclosalpa affinis. Marine Biodiversity Records in press.
  • Hindell, M.A., McMahon, C.R., Bester, M.N., Boehme, L., Costa, D., Fedak, M.A., Guinet, C., Herraiz-Borreguero, L., Harcourt, R.G., Huckstadt, L., Kovacs, K., M., Lydersen, C., McIntyre, T., Muelbert, M.M.C., Patterson, T., Roquet, F., Williams, G. & Charrassin, J.B. 2016. Circumpolar habitat use in the southern elephant seal: implications for foraging success and population trajectories. Ecosphere 7(5):e01213. 10.1002/ecs2.1213
  • Hughes JM, Stewart J, Gillanders BM, Collins D and Suthers IM. 2016. Relationship between otolith chemistry and age in a widespread pelagic teleost Arripis trutta: influence of adult movements on stock structure and implications for management. Marine & Freshwater Research 67: 224-237
  • Huveneers, C., Simpfendorfer, Colin; Kim, S., Semmens, J., Hobday, A., Pederson, H., Stieglitz, T., Vallee, R., Webber, D., Heupel, M., Peddemors, V., Harcourt, R. 2016. The influence of environmental parameters on the performance and detection range of acoustic receivers. Methods in Ecology and Evolution. DOI: 10.1111/2041-210X.12520.
  • Keller K, AS Steffe, M Lowry, JJ Murphy and IM Suthers. 2016. Monitoring boat-based recreational fishing effort at a nearshore artificial reef with a shore-based camera. Fisheries Research: 181: 84-92.
  • Lawes JC; Clark GF; Johnston EL, 2016, ‘Contaminant cocktails: Interactive effects of fertiliser and copper paint on marine invertebrate recruitment and mortality’, Marine Pollution Bulletin, vol. 102, no. 1, pp. 148 – 159, http://dx.doi.org/10.1016/j.marpolbul.2015.11.040
  • Lawes JC; Neilan BA; Brown MV; Clark GF; Johnston EL, 2016, ‘Elevated nutrients change bacterial community composition and connectivity: high throughput sequencing of young marine biofilms’,Biofouling: the journal of bioadhesion and biofilm research, vol. 32, no. 1, pp. 57 – 69,http://dx.doi.org/10.1080/08927014.2015.1126581
  • Masood M, Raftos DA, Nair SV. 2016 Two oyster species that show differential susceptibility to virus infection also show differential proteomic responses to generic dsRNA. Journal of Proteome Research. 15(6):1735-46.
  • Melwani AR, Thompson EL, Raftos DA. 2016. Differential proteomic response of Sydney rock oysters (Saccostrea glomerata) to prolonged environmental stress. Aquatic Toxicology. 173:53-62.
  • McAfee D, Cole VJ, Bishop MJ (2016) Latitudinal gradients in ecosystem engineering by oysters vary across habitats. Ecology 97:929-939
  • McGowan, J., Beger, M., Lewison, R., Harcourt, R., Campbell, H., Priest, M., Dwyer, R., Lin, H-Y., Lentini, P., Dudgeon, C., McMahon, C., Watts, M., Possingham, H. 2016. Linking research using animal-borne telemetry with the needs of conservation management. Journal of Applied Ecology. DOI: 10.1111/1365-2664.1275
  • Nicastro A, Lee KM, Bishop MJ (in press) Assimilation of organic matter by two benthic consumers across gradients of latitude and of nutrient enrichment. Mar Freshwater Res (accepted, 4 May, 2016)
  • Payne, N. L., Smith, J. A., van der Meulen, D. E., Taylor, M. D., Watanabe, Y. Y., Takahashi, A., Marzullo, T. A., Gray, C. A., Cadiou, G., Suthers, I. M. (2016), Temperature dependence of fish performance in the wild: links with species biogeography and physiological thermal tolerance. Functional Ecology, 30: 903–912. doi: 10.1111/1365-2435.12618.
  • Poore AGB, Graham S, Byrne M and Dworjanyn SA. 2016. Effects of ocean warming and lowered pH on algal growth and palatability to a grazing gastropod. Marine Biology 163: 99.
  • Raftos DA, Melwani AR, Haynes PA, Muralidharan S, Birch GF, Amaral V, Thompson EL, Taylor DA. 2016. The Biology of Environmental Stress: Molecular Biomarkers in Sydney Rock Oysters (Saccostrea glomerata). Environmental Science: Processes & Impacts. DOI: 10.1039/C6EM00322B.
  • Schaeffer A, M Roughan, T Austin, JD Everett, D Griffin, B Hollings, E King, A Mantovanelli, S Milburn, B Pasquer, C Pattiaratchi, R Robertson, D Stanley, IM Suthers and D White. 2016. Mean hydrography on the continental shelf from 26 repeat glider deployments along Southeastern Australia (Paper #SDATA-15-00212A),
  • Schnell, A. K., Smith, C. L., Hanlon, R. T., Hall, K., Harcourt, R. 2016. Cuttlefish perform multiple agonistic displays to communicate a hierarchy of threats. Behavioral Ecology and Sociobiology. DOI: 10.1007/s00265-016-2170-7
  • Stelling-Wood TP, Clark GF and Poore AGB. 2016. Responses of ghost crabs to human modification of urban sandy beaches. Marine Environmental Research 116: 32-40.
  • Thompson EL, Parker L, Amaral V, Bishop, MJ, O’Connor WA, Raftos DA (2016) Wild populations of Sydney rock oysters differ in their proteomic responses to elevated carbon dioxide. Mar Freshwater Res http://dx.doi.org/10.1071/MF15320
  • Williams, G.D., Herraiz-Borreguero, L., Roquet, F., Tamura, T., Ohshima, K., Fukamachi, Y., Fraser, A. D., Gao, L., Chen, H., McMahon, C. R. Harcourt, R., Hindell, M. 2016. The suppression of Antarctic Bottom Water formation by melting ice shelves in Prydz Bay. Nature Communications DOI 10.1038/ncomms12577
  • Ushiama S, JA Smitha, IM Suthers, M Lowry and EL Johnston. 2016. The effects of substrate material and surface orientation on the developing epibenthic community on a designed artificial reef. Biofouling in press. Accepted 29 July16