Threats, Trends and Health of the Great Barrier Marine Park: A list of the most relevant papers published between 1996 and 2006.

Coral Reefs

Bellwood, D.R., Hughes, T.P., Folke, C., Nystroem, M. 2004, "Confronting the coral reef crisis", Nature, vol. 429, no. 6994, pp. 827-833.

De'ath, G. 2003, Analyses of crown-of-thorns starfish data from the fine-scale surveys and long-term monitoring program manta tow surveys, CRC Reef Technical Report no. 47, CRC Reef Research Centre, Townsville.

Doherty, P.J., Meekan, M.G., Miller, I.R., Osborne, K., Thompson, A.A. 1997, ‘Catastrophic loss of coral cover from reefs in the southern Great Barrier Reef and the impact on fish recruitment, In: Proceedings of the 8th International Coral Reef Symposium, Panama, 24-29 June 1996, Smithsonian Tropical Research Institute, Volume 1, pp 1005-1010.

Engelhardt, U., Miller, I.R., Lassig, B.R., Sweatman, H., Bass, D.K. 1997, ‘Crown-of-thorns starfish (Acanthaster planci) populations in the Great Barrier Reef World Heritage Area: status report 1995-96’, In: Wachenfeld, D., Oliver, J.K., Davis, K. (eds) State of the Great Barrier Reef World Heritage Area Workshop, Proceedings of a technical workshop held in Townsville, Queensland, Australia 27-29 November 1995, GBRMPA Workshop Series, no. 23, Great Barrier Reef Marine Park Authority, Townsville, pp 158-184.

Lourey, M.J., Ryan, D.A.J., Miller, I.R. 2000, ‘Rates of decline and recovery of coral cover on reefs impacted by, recovering from and unaffected by crown-of-thorns starfish Acanthaster planci: a regional perspective of the Great Barrier Reef’, Marine Ecology Progress Series 196:179-186.

Lunow, C.P., Helmke, S., Bullock, C. 2003, Fisheries long-term monitoring program: a summary of reef fish survey results 1999-2001, DPI Information Series no. QI103027, Department of Primary Industries and Fisheries, Brisbane.

Miller, I.R. 1996, ‘Black Band disease on the Great Barrier Reef’, Coral Reefs 15:58-66.

Miller, I.R., Coleman, G., Abdo, D. 2004, Crown-of-thorns starfish and coral surveys using the manta tow and SCUBA search techniques, Long-term Monitoring of the Great Barrier Reef, Standard Operational Procedure no. 8. (3rd ed.), Australian Institute of Marine Science, Townsville.
 
Miller, I.R., Coleman, G., Delean, S., Sweatman, H. 2004, Broadscale surveys of crown-of-thorns starfish along the Great Barrier Reef 1993-2003, Long-term Monitoring of the Great Barrier Reef, Project Data Report, Australian Institute of Marine Science, Townsville.

Ninio, R., Meekan, M.G., Done, T.J., Sweatman, H. 2000, ‘Temporal patterns in coral assemblages on the Great Barrier Reef from local to large spatial scales’, Marine Ecology Progress Series 194:65-74.

Osborne, K., Ninio, R., Sweatman, H. 1997, ‘The current status of sessile benthic organisms of the Great Barrier Reef’, In: Wachenfeld, D., Oliver, J.K., Davis, K. (eds) State of the Great Barrier Reef World Heritage Area Workshop, Proceedings of a technical workshop held in Townsville, Queensland, Australia 27-29 November 1995, GBRMPA Workshop Series no. 23, Great Barrier Reef Marine Park Authority, Townsville, pp 124-133.

Osborne, K., Thompson, A.A. 1997, ‘The regional relationship between damselfish communities and habitat on selected reef slopes of the Great Barrier Reef’, In: Proceedings of the 8th International Coral Reef Symposium, Panama, 24-29 June 1996, Smithsonian Tropical Research Institute, Panama City, Volume 2, pp 1167-1171.

Pandolfi, J.M., Bradbury, R.H., Sala, E., Hughes, T.P., Bjorndal, K.A., Cooke, R.G., McArdle, D., McClenachan, L., Newman, M.J.H., Paredes, G., Warner, R.R., Jackson, J.B.C. 2003, "Global Trajectories of the Long-Term Decline of Coral Reef Ecosystems", Science (Washington), vol. 301, no. 5635, pp. 955-958.

Pandolfi, J.M., Jackson, J. B. C., Baron, N., Bradbury, R.H., Guzman, H.M., Hughes, T.P., Kappel, C.V., Micheli, F., Ogden, J.C., Possingham, H.P. & Sala, E. 2005, "Are U.S. coral reefs on the slippery slope to slime?", Science, vol. 307, no. 18 March, pp. 1725-1726.

Sweatman, H. 1997, ‘Commercial fishes as predators of adult Acanthaster planci’, In: Proceedings of the 8th International Coral Reef Symposium, Panama, 24-29 June 1996, Smithsonian Tropical Research Institute, Panama City, Volume 1, pp 617-620.

Sweatman, H., Thompson, A.A., Cheal A.J. 1997, ‘The status of reef fishes on the Great Barrier Reef’, In: Wachenfeld, D., Oliver, J.K., Davis, K. (eds) State of the Great Barrier Reef World Heritage Area Workshop, Proceedings of a technical workshop held in Townsville, Queensland, Australia 27-29 November 1995, GBRMPA Workshop Series no.23, Great Barrier Reef Marine Park Authority, Townsville, pp 205-222.

Sweatman, H. (ed) 1997, Long-term monitoring of the Great Barrier Reef, AIMS Status Report no. 2, Australian Institute of Marine Science, Townsville.

Sweatman, H., Bass, D.K., Cheal, A., Coleman, G., Miller, I., Ninio, R., Osborne, K., Oxley, W.G., Ryan, D., Thompson, A., Tomkins, P. 1998, Long-term monitoring of the Great Barrier Reef, AIMS Status Report no. 3, Australian Institute of Marine Science, Townsville.

Sweatman, H., Cheal, A., Coleman, G., Fitzpatrick, B., Miller, I., Ninio, R., Osborne, K., Page, C., Ryan, D., Thompson, A., Tomkins, P. 2000, Long-term monitoring of the Great Barrier Reef, AIMS Status Report no. 4, Australian Institute of Marine Science, Townsville.

Sweatman, H., Cheal, A., Coleman, G., Delean, S., Fitzpatrick, B., Miller, I., Ninio, R., Osborne, K., Page, C., Thompson, A. 2001, Long-term monitoring of the Great Barrier Reef, AIMS Status Report no. 5, Australian Institute of Marine Science, Townsville.

Sweatman, H., Abdo, D., Burgess, S., Cheal, A., Coleman, G., Delean, S., Emslie, M., Miller, I., Osborne, K., Oxley, W., Page, C., Thompson, A. 2004, Long-term monitoring of the Great Barrier Reef, AIMS Status Report no. 6, Australian Institute of Marine Science, Townsville.

Sweatman, H., Wachenfeld, D.R. 2003, ‘A long-term monitoring program for the Great Barrier Reef and its value for managers – the AIMS reef monitoring program’, In: Wilkinson, C., Green, A., Almany, J., Dionne, S. (eds) Monitoring coral reef marine protected areas, Australian Institute of Marine Science, Townsville, pp 30-31.

Thompson, A.A., Mapstone, B.D. 2002, ‘Intra vs inter-annual variation in counts of reef fishes and interpretations of long term monitoring studies’, Marine Ecology Progress Series 232:247-257.

Water Quality 

Anthony, K.R.N. 1999, Sediment: stress factor or food source for reef corals?, Unpublished PhD Thesis, James Cook University, Townsville, Australia.

Anthony, K.R.N., Fabricius, K.E. 2000, ‘Shifting roles of heterotrophy and autotrophy in coral energetics under varying turbidity’, Journal of Experimental Marine Biology and Ecology 252:221-253.

Ayling, A.M., Ayling, A.L. 1998, The effect of the Daintree River flood plume on Snapper Island coral reefs, GBRMPA Research Publication no. 52, Great Barrier Reef Marine Park Authority, Townsville.

Ayling, A.M., Ayling, A.L. 1999, Medium term changes in coral populations of fringing reefs at Cape Tribulation, GBRMPA Research Publication no. 59, Great Barrier Reef Marine Park Authority, Townsville.

Bastidas, C., Benzie, J.A.H., Uthicke, S., Fabricius, K.E. 2001, ‘Genetic differentiation among populations of a broadcast spawning soft coral, Sinularia flexibilis, on the Great Barrier Reef’, Marine Biology 138:517-525. 

Bastidas, C., Benzie, J.A.H., Fabricius, K.E. 2002, ‘Genetic differentiation among populations of the brooding soft coral Clavularia sp. on the Great Barrier Reef’, Coral Reefs 21:233-241.

Berkelmans, R., Willis, B.L. 1999, ‘Seasonal and local spatial patterns in the upper thermal limits of corals on the inshore central Great Barrier Reef’, Coral Reefs 18:219-228.

Bramley, R.G.V., Muller, D.E. 1999, Water quality in the lower River Herbert - the CSIRO dataset, Technical Memorandum no. 16/99, CSIRO Land and Water, Canberra.

Brodie, J., De'ath, G., Furnas, M., Devlin, M., Waterhouse, J., Bainbridge, Z., Christie, C., Haynes, D., Wright, M. 2005 (In review), Long term chlorophyll monitoring in the Great Barrier Reef Lagoon: Status Report 2, 1993 2005, ACTFR Report No. 05/05, Australian Centre for Tropical Freshwater Research, James Cook University, Townsville.

Brodie, J.E., Fabricius, K.E., De'ath, G., Okaji, K. 2004, ‘Are increased nutrient inputs responsible for more outbreaks of crown-of-thorns starfish? An appraisal of the evidence’, In: Haynes, D., Schaffelke, B. (eds) Catchment to reef : water quality issues in the Great Barrier Reef Region, 9-11 March 2004, Townsville, Conference abstracts, CRC Reef Research Centre, Townsville, p. 12.

Brodie, J.E., Fabricius, K.E., Death, G., Okaji, K. 2005, ‘Are increased nutrient inputs responsible for more outbreaks of crown-of-thorns starfish? An appraisal of the evidence’, Marine Pollution Bulletin 51:266-278. 

Brodie, J., Furnas, M. 1994, ‘Long-term monitoring programs for eutrophication and the design of a monitoring program for the Great Barrier Reef’, Proceedings of the 7th International Coral Reef Symposium, 22-27 June 1992, University of Guam Press, Mangilao, pp 77-84.

Brodie, J., Furnas, M. 1996, ‘Cyclones, river flood plumes and natural water quality extremes in the central Great Barrier Reef’, In: Hunter, H.M., Eyles, A.G., Rayment, G..E. (eds) National Conference on Downstream Effects of Land Use, 26 - 28 April 1995, Department of Natural Resources, Queensland, Rockhampton, Australia, Department of Natural Resources, Queensland, Brisbane, pp 367-374.

Brodie, J., Furnas, M. 2004, ‘Status of inputs from Great Barrier Reef catchments and impacts on the Reef’, In: Dawson, N., Brodie, J., Rayment, G., Porter, C. (eds) Protecting the values of rivers, wetlands and the reef. Conference abstracts, papers, posters and presentations Townsville, Australia, Department of Natural Resources, Energy and Mines, Brisbane.

Brodie, J.E., Furnas, M.J., Steven, A.D.L., Trott, L.A., Pantus, F., Wright, M. 1997, ‘Monitoring chlorophyll in the Great Barrier Reef lagoon: trends and variability’, In: Lessios, H.A., MacIntyre, I.G. (eds), Proceedings of the 8th International Coral Reef Symposium, Balboa, Panama, Smithsonian Tropical Research Institute, Balboa, Volume 1, pp 797-802.

Brodie, J., Mitchell, A. 2005, ‘Nutrients in Australian tropical rivers: changes with agricultural developments and implications for receiving environments’, Marine and Freshwater Research 56:279-302.

Brodie, J., Mitchell, A. 2005, Sediments and nutrients in north Queensland tropical streams: changes with agricultural development and pristine status, ACTFR Report No. 05/05, Australian Centre for Tropical Freshwater Research, Townsville.

Brodie, J., Mitchell, A., Furnas, M., Haynes, D., Waterhouse, J., Ghonim, S., Morris, S., Yorkston, H., Audas, D. 2004, ‘Developing catchment pollutant load targets for the protection of the Great Barrier Reef’, In: Dawson, N., Brodie, J., Rayment, G., Porter, C. (eds) Protecting the values of rivers, wetlands and the reef. conference abstracts, papers, posters and presentations Townsville, Australia, Department of Natural Resources, Energy and Mines, Brisbane.

Brodie, J., Steven, A., McGill, R. 1994 ‘Spatial and temporal trends in chlorophyll in waters of the Great Barrier Reef Marine Park,’ In: The 6th Pacific Congress on Marine Science and Technology, PACON, James Cook University, Townsville, Australia, pp 77-85.

Bryce, S., Larcombe, P., Ridd, P. 1996, ‘Sediment transport in the Normanby River estuary, northern Great Barrier Reef Shelf, Australia’, In: Larcombe, P., Woolfe, K.J., Purdon, R.G. (eds) Great Barrier Reef: terrigenous sediment flux and human impacts, 2nd ed., CRC Reef Research Centre, Townsville, pp 40-44. 

Bryce, S., Larcombe, P., Ridd, P.V. 1998, ‘The relative importance of landward-directed tidal sediment transport versus freshwater flood events in the Normanby River estuary, Cape York Peninsula, Australia’, Marine Geology 149:55-78.

Burrage, D.M., Heron, M.L., Hacker, J.M., Miller, J.L., Stieglitz, T.C., Steinberg, C.R., Prytz, A. 2003, ‘Structure and influence of tropical river plumes in the Great Barrier Reef: application and performance of an airborne sea surface salinity mapping system’, Remote Sensing of Environment 85:204-220. 

Burrage, D.M., Heron, M.L., Hacker, J.M., Stieglitz, T.C., Steinberg, C.R., Prytz, A. 2002, ‘Evolution and dynamics of tropical river plumes in the Great Barrier Reef: an integrated remote sensing and in situ study’, Journal of Geophysical Research 107:1-17. 

Cavanagh, J.E., Burns, K.A., Brunskill, G.J., Coventry, R.J. 1999, ‘Organochlorine pesticide residues in soils and sediments of the Herbert and Burdekin River regions, North Queensland - implications for contamination of the Great Barrier Reef’, Marine Pollution Bulletin 39:367-375.

Chin, A., Ayling, A.M. 2000, ‘Disturbance and recovery cycles: long-term monitoring on 'unlucky' inshore fringing reefs in the Cairns section of the Great Barrier Reef Marine Park’, Reef Research 10:1.

De'ath, G., Fabricius, K.E. 2000, ‘Classification and regression trees: a powerful yet simple technique for the analysis of complex ecological data’, Ecology 81:3178-3192.

De'ath, G., Fabricius, K.E., Okaji, K., Brodie, J.E., Day, K. 2004, ‘Increased chlorophyll levels lead to increased frequency and severity of outbreaks of the crown-of-thorns starfish (Acanthaster planci) on the Great Barrier Reef’, In: Haynes, D., Schaffelke, B. (eds) Catchment to reef : water quality issues in the Great Barrier Reef Region, 9-11 March 2004, Townsville, Conference abstracts, CRC Reef Research Centre, Townsville, p. 19.

Devlin, M.J. 1997, ‘Offshore measurements late in the river plumes associated with Cyclone Sadie’, In: Steven, A. (ed) Cyclone Sadie flood plumes in the Great Barrier Reef Lagoon: composition and consequences, November 1994, GBRMPA Workshop Series no. 22, Great Barrier Reef Marine Park Authority, Townsville, pp 45-53.

Devlin, M., Waterhouse, J., Christie, C., Haynes, D., Brodie, J. 2000, Long-term chlorophyll monitoring in the Great Barrier Reef Lagoon, Status Report no 2, 1993-1999, Great Barrier Reef Marine Park Authority, Townsville.

Devlin, M., Waterhouse, J., Taylor, J.P., Brodie, J. 2001, Flood plumes in the Great Barrier Reef: spatial and temporal patterns in composition and distribution, GBRMPA Research Publication no. 68, Great Barrier Reef Marine Park Authority, Townsville.

Done, T.J., DeVantier, L.M., Turak, E.I., McCook, L.J., Fabricius, K.E. 1997, ‘Decadal changes in community structure in Great Barrier Reef coral reefs’, In: Wachenfeld, D., Oliver, J.K., Davis, K. (eds) State of the Great Barrier Reef World Heritage Area Workshop, proceedings of a technical workshop held in Townsville, Queensland, Australia 27-29 November 1995, GBRMPA Workshop Series no. 23, Great Barrier Reef Marine Park Authority, Townsville, pp 97-108.

Fabricius, K.E. 1996, ‘Ecosystem recovery after episodic disturbance: resilience of some coral reefs after Acanthaster outbreaks’, Senckenbergiana Maritima 27:227-235.

Fabricius, K.E. 1997, ‘Soft coral abundance in the central Great Barrier Reef: effects of Acanthaster planci, space availability, and aspects of the physical environment’, Coral Reefs 16:159-167.

Fabricius, K.E. 1998, ‘Reef invasion by soft corals: which taxa and which habitats?’, In: Greenwood, J.G., Hall, N.J. (eds) Proceedings of the Australian Coral Reef Society 75th Anniversary Conference, October 1997, Heron Island, Australia, University of Queensland, Brisbane, pp 77-90.

Fabricius, K.E. 1999 ‘Tissue loss and mortality in soft corals following mass bleaching’, Coral Reefs 18:54.

Fabricius, K.E. 2001, ‘Precious resources: the Great Barrier Reef, Queensland’, In: Australia beyond any price, Pan Macmillan Australia, Sydney, pp 66-75.

Fabricius, K.E. 2005, ‘Effects of terrestrial runoff on the ecology of corals and coral reefs: review and synthesis’, Marine Pollution Bulletin 50:125-146. 

Fabricius, K.E., Alderslade, P. 2001, Soft corals and sea fans, Australian Institute of Marine Science, Townsville.

Fabricius, K.E., De'ath, G. 1997, ‘Habitat optima of soft corals on the central Great Barrier reef: niche characterisation using regression tree analysis’, In: The Great Barrier Reef: science, use and management; a national conference: Proceedings, 25 - 29 November 1996, James Cook University, Townsville, Australia, Great Barrier Reef Marine Park Authority, Townsville, 2:167-174.

Fabricius, K.E., De'ath, G. 1997, ‘The effects of flow, depth and slope on cover of soft coral taxa and growth forms on Davies Reef, Great Barrier Reef’, In: Lessios, H.A., MacIntyre, I.G. (eds) Proceedings of the 8th International Coral Reef Symposium, Balboa, Panama, Smithsonian Tropical Research Institute, Balboa, Volume 2, pp 1071-1076.

Fabricius, K., De'ath, G. 1999, ‘Effects of sediment and river proximity on coral reef communities’, In: Heap, A.D. (ed) North Queensland Sedimentologists' 1st Annual Workshop: Extended Abstracts, Townsville, Australia, School of Earth Sciences, James Cook University, Townsville, pp 43-48.

Fabricius, K.E., De'ath, G. 2000, ‘Biodiversity on the Great Barrier Reef: large-scale patterns and turbidity-related local loss of soft coral taxa’, In: Wolanski, E. (ed) Oceanographic processes of coral reefs: physical and biological links in the Great Barrier Reef, CRC Press, Florida, pp 127-144.

Fabricius, K.E., De'ath, G. 2000, Soft coral atlas of the Great Barrier Reef, Australian Institute of Marine Science, Townsville.

Fabricius, K.E., De'ath, G. 2001, ‘Environmental factors associated with the spatial distribution of crustose coralline algae on the Great Barrier Reef’, Coral Reefs 19(4):303-309.

Fabricius, K.E., De'ath, G. 2004, ‘Identifying ecological change and its causes: a case study on coral reefs’, Ecological Applications 14:1448-1456.

Fabricius, K.E., De'ath, G., McCook, L.J., Turak, E.I., Williams, D.McB. 2004, ‘Coral, algae and fish communities on inshore reefs of the Great Barrier Reef : ecological gradients along water quality gradients’, In: Haynes, D., Schaffelke, B. (eds) Catchment to reef : water quality issues in the Great Barrier Reef Region, 9-11 March 2004, Townsville, Conference abstracts, CRC Reef Research Centre, Townsville, p. 24.

Fabricius, K.E., De'ath, G., McCook, L., Turak, E., Williams, D.McB. 2005, ‘Changes in algal, coral and fish assemblages along water quality gradients on the inshore Great Barrier Reef’, Marine Pollution Bulletin 51:384-398.

Fabricius, K.E., Dommisse, M. 2000, ‘Depletion of suspended particulate matter over coastal reef communities dominated by zooxanthellate soft corals’, Marine Ecology Progress Series 196:157-167. 

Fabricius, K.E., Wild, C., Wolanski, E., Abele, D. 2003, ‘Effects of transparent exopolymer particles (TEP) and muddy terrigenous sediments on the survival of hard coral recruits’, Estuarine Coastal and Shelf Science 56:1–9.

Fabricius, K.E., Wolanski, E. 2000, ‘Rapid smothering of coral reef organisms by muddy marine snow’, Estuarine Coastal and Shelf Science 50:115-120.

Fabricius, K.E., Yahel, G., Genin, A. 1998, ‘In situ depletion of phytoplankton by an azooxanthellate soft coral’, Limnology and Oceanography 43:354-356. 

Furnas, M. 2003, Catchments and corals: terrestrial runoff to the Great Barrier Reef, Australian Institute of Marine Science, Townsville.

Furnas, M., Brodie, J. 1996, ‘Current status of nutrient levels and other water quality parameters in the Great Barrier Reef’, In: Hunter, H., Eyles, A.G., Rayment, G. (eds), Downstream effects of land use, Department of Natural Resources and Mines, Brisbane, pp 9-22.

Furnas, M.J., Mitchell, A.W. 1996, ‘Nutrient inputs into the Central Great Barrier Reef (Australia) from subsurface intrusions of Coral Sea waters: a two-dimensional displacement model’, Continental Shelf Research 16:1127-1148. 

Furnas, M., Mitchell, A., Skuza, M. 1997, ‘Shelf-scale nitrogen and phosphorous budgets for the central Great Barrier Reef (16-19 S)’, In: Lessios, H.A., MacIntyre, I.G. (eds) Proceedings of the 8th International Coral Reef Symposium, Balboa, Panama, Smithsonian Tropical Research Institute, Balboa, Volume 1, pp 809-814.

Furnas, M., Mitchell. A. 1997, ‘Biological oceanography of the Great Barrier Reef’, In: The Great Barrier Reef. Science, use and management: a national conference: proceedings, 25 - 29 November 1996, James Cook University, Townsville, Australia, Great Barrier Reef Marine Park Authority, Townsville, Volume 1, pp 75-87. 

Furnas, M., Mitchell, A. 1999, ‘Event-related variability and inter-river differences in suspended sediment loads of tropical north eastern Queensland rivers’, In: Heap, A.D. (ed) North Queensland Sedimentologists' 1st Annual Workshop: Extended Abstracts, Townsville, Australia, School of Earth Sciences, James Cook University, Townsville, p. 96. 

Furnas, M., Mitchell, A. 2000, ‘Runoff of terrestrial sediment and nutrients into the Great Barrier Reef World Heritage Area’, In: Wolanski, E. (ed) Oceanographic processes of coral reefs: physical and biological links in the Great Barrier Reef, CRC Press, Florida, pp 37-51. 

Furnas, M., Mitchell, A., Skuza, M. 1997, ‘River inputs of nutrients and sediment to the Great Barrier Reef’, In: Wachenfeld, D.R., Oliver, J., Davis, K. (eds) State of the Great Barrier Reef World Heritage Area workshop: proceedings of a technical workshop held in Townsville, Australia, 27 - 29 November 1995, Townsville, Australia, Great Barrier Reef Marine Park Authority, Townsville, pp 46-68.

Furnas, M.J., Mitchell, A.W., Skuza, M., Wright, M. 2004, ‘River discharge of nutrients from dry tropical rivers of the Great Barrier Reef catchment’,. In: Haynes, D., Schaffelke, B.(eds) Catchment to reef : water quality issues in the Great Barrier Reef Region. 9-11 March 2004, Townsville, Conference abstracts. CRC Reef Research Centre, Townsville, p. 28.

Furnas, M.J., Skuza, M., Wright, M., Mitchell, A.W., Ghonim, S. 2004, ‘Regional variations in water column nutrients and other water quality parameters in Great Barrier Reef waters’, In: Haynes, D., Schaffelke, B.(eds) Catchment to reef : water quality issues in the Great Barrier Reef Region. 9-11 March 2004, Townsville: conference abstracts, CRC Reef Research Centre, Townsville, p. 29.

Furnas, M., Mitchell, A., Skuza, M., Brodie, J. 2005, ‘In the other 90%: phytoplankton responses to enhanced nutrient circulating in the Great Barrier Reef lagoon’, Marine Pollution Bulletin 51:253-265.

Gralton, C. 2002, Coral recovery on inshore reefs of the Palm Islands following the 1998 coral bleaching event, Unpublished BSc (Hons) Thesis, James Cook University, Townsville, Australia.

Greiner, R., Herr, A., Audas, D., Brodie, J., Creighton, C., Dorrington, B., Haynes, D., Roth, C. 2003, Assessment of relative risk of catchments with respect to pollution of the Great Barrier Reef World Heritage Area, CSIRO Land and Water, Townsville.

Harrington, L., Fabricius, K., De'ath, G., Negri, A. 2004, ‘Recognition and selection of settlement substrata determine post-settlement survival in corals’, Ecology 85:3428-3437.

Harrington, L., Fabricius, K.E., Eaglesham, G., Negri, A.P. 2005, ‘Synergistic effects of diuron and sedimentation on photosynthetic yields and survival of crustose coralline algae’, Marine Pollution Bulletin 51:415-427.

Harrington, L., Fabricius, K.E., Negri, A.P. 2004, ‘Synergistic effects of diuron and sedimentation on the photophysiology and survival of crustose coralline algae’, In: Haynes, D., Schaffelke, B. (eds) Catchment to reef : water quality issues in the Great Barrier Reef Region. 9-11 March 2004, Townsville, conference abstracts, CRC Reef Research Centre, Townsville, p. 32.

Halliday, I., Ley, J., Tobin, A., Garrett, R., Gribble, N., Meyer, D. 2002, The effects of net fishing: addressing biodiversity and bycatch issues in Queensland inshore waters, FRDC Report no. 97/206. Fisheries Research and Development Corporation, Canberra.

Haynes, D., Brodie, J., Devlin, M. 1998, ‘Long-term monitoring of chlorophyll concentrations in the Great Barrier Reef World Heritage Area’, In: Markwort, K.N., Maher, W.A. (eds), Proceedings of workshop on sampling nutrients in aquatic ecosystems: collecting valid and representative samples, held on 21 and 22 April 1997, University of Canberra, CRC for Freshwater Ecology, Canberra, pp 115-126.

Hunter, H., Walton, R.S. 1997, From land to river to reef lagoon: land use impacts on water quality in the Johnstone River catchment, Department of Natural Resources and Mines, Brisbane, Australia. 

Jompa, J., McCook, L.J. 1998, ‘Seaweeds save the reef? Sargassum canopy decreases coral bleaching on inshore reefs’, Reef Research 8:5. 

King, B., McAllister, F., Done, T.J. 2000, Modelling the impact of the Burdekin, Herbert, Tully and Johnstone River Plumes on the Central Great Barrier Reef, CRC Reef Technical Report no. 44, CRC Reef Research Centre, Townsville.

King, B., Spagnol, S., Wolanski, E., Done, T. 1998, ‘Modelling the mighty Burdekin River in flood’, In: Spalding, M.L., Blumberg, A.F. (eds) Coastal modelling: proceedings of the 5th International Conference, 22 - 24 October 1997, American Society of Civil Engineers, Alexandria, Virginia, USA, pp 103-115. 

Larcombe, P., Woolfe, K.J. 1999, ‘Terrigenous sediments as influences upon Holocene nearshore coral reefs, central Great Barrier Reef, Australia’, Australian Journal of Earth Sciences 46:141-154. 

Lough, J.M., Barnes, D.J., McAllister, F. 2002, ‘Luminescent lines in corals from the Great Barrier Reef provide spatial and temporal records of reefs affected by land runoff’, Coral Reefs 21:333-343.

McAllister, F., King, B., Done, T. 2000, The database of predicted river plume distributions (1966-1998) in the Central Great Barrier Reef Marine Park, Report to CRC Reef Research Centre, Australian Institute of Marine Science, Townsville, Australia.

McCook, L.J. 1996, ‘Effects of Herbivores and water quality on Sargassum distribution on the central Great Barrier Reef: cross-shelf transplants’,. Marine Ecology Progress Series 139:179-192. 

McCook, L.J. 1997, ‘Effects of herbivory on zonation of Sargassum spp within fringing reefs of the central Great Barrier Reef’, Marine Biology 129:713-722. 

McCook, L.J. 1999, ‘Macroalgae, nutrients and phase shifts on coral reefs: scientific issues and management consequences for the Great Barrier Reef’, Coral Reefs 18:357-367. 

McCook, L.J. 2001, ‘Competition between coral and algal turfs along a gradient of terrestrial runoff in the nearshore central Great Barrier Reef’, Coral Reefs 19:419-425.

McCook, L.J., Birrell, C., Diaz-Pulido, G., Willis, B.L. 2004, ‘Interactions between benthic algae, water quality and coral reef disturbance and recovery’, In: Haynes, D., Schaffelke, B. (eds) Catchment to reef : water quality issues in the Great Barrier Reef Region, 9-11 March 2004, Townsville, conference abstracts, CRC Reef Research Centre, Townsville, p. 45.

McCook, L., De'ath, G., Price, I.R. 2000, Macroalgal resources of the Great Barrier Reef II. Distribution patterns of the benthic macroalgae of Great Barrier Reef coral reefs, Unpublished report to the Great Barrier Reef Marine Park Authority, Townsville, Australia. 

McCook, L., Jompa, J., Diaz-Pulido, G., Mundy, C. 2000, Macroalgal resources of the Great Barrier Reef. Part 2: impacts of algae and terrestrial run-off on coral reefs, Report to the Great Barrier Reef Marine Park Authority. Townsville, Australia. 

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Walther, G. R., Post, E., Convey, P., Menzel, A., Parmesan, C., Beebee, T.R.J., Fromentin, J.M., Hoegh-Guldberg, O. Bairlein, F. 2002, Ecological responses to recent climate change’, Nature 416:389-395.

Ward, S., Harrison, P.J.,Hoegh-Guldberg, O. 2001, ‘Coral bleaching reduces reproduction of scleractinian corals and increases susceptibility to future stress’, Proceedings of the 9th International Symposium, Bali, October 23-27, 2000, Ministry of Environment, Indonesian Institute of Sciences, International Society for Reef Studies, Indonesia, Volume 2, pp 1123-1128.

Willis, B.L., Anthony, K.R.N., Berkelmans, R., Michalek-Wagner, K., Page, C., True, J. 2001, ‘Developing predictive and reactive tools for monitoring coral health’, JAMSTEC International Coral Reef Symposium, 23 - 24 February 2000, Tokyo, Japan, Japan Marine Science and Technology Centre, Tokyo.

Wooldridge, S., Done, T. 2004, ‘Learning to predict large-scale coral bleaching from past events: a Bayesian approach using remotely sensed data, in-situ data, and environmental proxies’, Coral Reefs 23(1):96–108.

Wooldridge, S., Done, T. 2003, ‘The use of bayesian belief networks to aid in the understanding and management of large-scale coral bleaching’, In: Post, D. (ed), Proceedings of the International Congress on Modelling and Simulation (MODSIM 2003). 14 - 17 July 2003, Townsville, Australia, Modelling and Simulation Society of Australia and New Zealand, Sydney. 

Fish and Fisheries 
Line

Adams, S., Mapstone, B.D., Russ, G.R., Davies, C.R. 2000, ‘Geographic variation in the sex ratio, sex specific size, and age structure of Plectropomus leopardus (Serranidae) between reefs open and closed to fishing on the Great Barrier Reef’, Canadian Journal of Fisheries and Aquatic Sciences 57:1448-1458.

Adams, S.A., Williams, A.J. 2001, ‘A preliminary test of the transitional growth spurt hypothesis using the protogynous coral trout, Plectropomus maculatus (Serranidae: Epinephelidae)’, Journal of Fish Biology 59:183-185.

Ayling, A.M., Ayling, A.L., Mapstone, B.D. 1992, ‘Possible effects of protection from fishing pressure on recruitment rates of the coral trout (Plectropomus leopardus: Serranidae)’, In: Hancock, D.A. (ed) Recruitment processes, Australian Society for Fish Biology workshop, Australian Government Publishing Service, Canberra, Volume 16, pp. 210-215.

Bean, K., Davies, C.R., Mapstone, B.D., Murchie, C.D., Williams, A.J. 2003, ‘Gonad development and evidence of protogyny in the red-throat emperor on the Great Barrier Reef’, Journal of Fish Biology 62:299-310.

Begg, G.A., Mapstone, B.D., Williams, A.J., Adams, S., Davies, C.R., Lou, D.C. 2005, ‘Multivariate life-history indices of exploited coral reef fish populations used to measure the performance of no-take zones in a marine protected area’, Canadian Journal of Fisheries and Aquatic Sciences 62:679-692.

Campbell, R.A., Mapstone, B.D., Smith, A.D.M. 2001, Large-scale experimental design for measuring the effects of line fishing on the Great Barrier Reef, Australia, Ecological Applications 11:1763-1777.

CRC Reef Research Centre 1995-1999, Effects of Line Fishing Newsletter nos. 1-11, 1995-2000, CRC Reef Research, Townsville.

CRC Reef Research Centre 2000-2005, Fishing and fisheries Newsletter no. 12-20, 2000-2005, CRC Reef Research, Townsville.

Davis, K.L.F., Russ, G.R., Williamson, D.H., Evans, R.D. 2004, ‘Surveillance and poaching on inshore reefs of the great barrier Reef Marine park’, Coastal Management 32(4):373-387.

Evans RD, Russ GR. 2004. Larger biomass of targeted reef fish in no-take marine reserves on the Great Barrier Reef, Australia. Aquatic Conservation: Marine and Freshwater Ecosystems 14:505-519.

Graham, N.A.J., Evans, R.D., Russ, G.R. 2003, ‘The effects of marine reserve protection on the trophic relationships of reef fishes on the Great Barrier Reef’, Environmental Conservation 30(2):200-208.
Jackson, J.B.C., Kirby, M.X., Berger, W.H., Bjorndal, K.A., Botsford, L.W., Bourque, B.J., Bradbury, R.H., Cooke, R., Erlandson, J., Estes, J.A., Hughes, T.P., Kidwell, S., Lange, C.B., Lenihan, H.S., Pandolfi, J.M., Peterson, C.H., Steneck, R.S., Tegner, M.J., Warner, R.R. 2001, “Historical Overfishing and the Recent Collapse of Coastal Ecosystems”, Science, vol. 293, no. 5530, pp. 629-637.

Jones, A., Mapstone, B.D., Davies, C.R. 1999, Report on the Effects of Line Fishing project: management strategy evaluation, First stakeholder workshop, Report to CRC Reef Research Centre, Townsville. 

Laursen, T., Russ, G.R., Higgs, J., Newman, S.J. 1999, ‘Age, growth and mortality of Gymnocranius audleyi (Pisces: Lethrinidae) on the Great Barrier Reef’, Asian Fisheries Science 12:187-200.

Little, L.R., Smith, A.D.M., McDonald, A.D., Punt, A.E., Mapstone, B.D., Pantus, F., Davies, C.R. 2005, ‘Effects of size and fragmentation of marine reserves and fisher infringements on the catch and biomass of coral trout, Plectropomus leopardus, on the Great Barrier Reef, Australia’, Fisheries Management and Ecology 12:177-188.

Lou, D.C., Mapstone, B.D., Russ, G.R., Davies, C.R., Begg, G.A. 2005, ‘Using otolith weight-age relationships to predict age-based metrics of coral reef fish populations at different spatial scales’, Fisheries Research 71:279-294.

Lou, D.C., Russ, G.R., Mapstone, B.D., Davies, C. 2003, ‘Effects of aquatic protection areas on the age structure of common coral trout (Plectropomus leopardus) in the Great Barrier Reef World Heritage Area of Australia’, In: Beumer J., Grant A., Smith D. (eds), Proceedings of the World Congress on Aquatic Protected Areas, Cairns, Australia, Australian Society for Fish Biology, Sydney, pp 93-100.

Mapstone, B.D. 1996, Design of experimental investigations of the effects of line and spear fishing on the Great Barrier Reef, CRC Reef Research Centre Technical Report no. 7, CRC Reef Research, Townsville.

Mapstone, B., Davies, C.R. 1998, ‘Science, fisheries and coral reefs – can management be done differently?’, In: Jones, G.P., Doherty, P.J., Mapstone, B.D., Howlett, L. (eds) ReeFish ’95: Recruitment and Population Dynamics of Coral Reef Fishes, CRC Reef Research Centre, Townsville, pp 268-271.

Mapstone, B.D., Davies, C.R., Little, L.R., Punt, A.E., Smith, A.D.M., Pantus, F., Lou, D.C., Williams, A.J., Jones, A., Ayling, A.M., Russ, G.R., McDonald, A.D. 2004, The effects of line fishing on the Great Barrier Reef and evaluations of alternative potential management strategies, CRC Reef Technical Report no. 52, CRC Reef Research Centre, Townsville.

Mapstone, B.D., Davies, C.R., Robertson, J.W. 1997, ‘The effects of line fishing on the Great Barrier Reef: available evidence and future directions’, In: The Great Barrier Reef. Science, use and management. A national conference, Proceedings, 25 - 29 November 1996, James Cook University, Townsville, Australia, Great Barrier Reef Marine Park Authority, Townsville, Volume 1, pp 178-192.

Mapstone, B.D., Davies, C.R., Slade, S.J., Jones, A., Kane, K.J., Williams, A.J. 2001, Effects of live fish trading and targeting spawning aggregations on fleet dynamics, catch characteristics, and resource exploitation by the Queensland commercial demersal reef line fishery, FRDC Report no. 96/138, Fisheries Research and Development Corporation, Canberra.

Russ, G.R., Lou, D.C., Ferreira, B.P. 1995, A long-term study on population structure of the coral trout, Plectropomus leopardus, on reefs open and closed to fishing in the central Great Barrier Reef, Australia, CRC Reef Technical Report no. 3, CRC Reef Research Centre, Townsville.

Russ, G.R., Lou, D.C., Ferreira, B.P. 1996, ‘Temporal tracking of a strong cohort in the population of a coral reef fish, the coral trout, Plectropomus leopardus (Serranidae: Epinephelinae), in the central Great Barrier Reef, Australia’, Canadian Journal of Fisheries and Aquatic Sciences 53:2745–2751.

Russ, G.R., Lou, D.C., Higgs, J., Ferreira, B.P. 1998, ‘Mortality rate of a cohort of the coral trout, Plectropomus leopardus, in zones of the Great Barrier Reef Marine Park closed to fishing’, Marine and Freshwater Research 49:507-511.

Russ, G.R., Lou, D.C., Slade, S.J., Wilson, D.T., Brown, I. 1997, The effects of management zoning and region on the age structure of the common coral trout on the Great Barrier Reef: baseline catch survey for the effects of Line fishing experiment, Report to CRC Reef Research Centre, November 1997, CRC Reef Research Centre, Townsville.

Russ, G.R., Lou, D.C., Slade, S.J., Wilson, D.T., Brown, I. 1998, The effects of the 1997 ELF line fishing manipulation on the age structure of the common coral trout, Report to CRC Reef Research Centre, June 1998, CRC Reef Research Centre, Townsville.

Russ, G.R., McCook, L.J. 1999, ‘Potential effects of a cyclone on benthic algal production and yield to grazers on coral reefs across the central Great Barrier Reef’, Journal of Experimental Marine Biology and Ecology 235:237-254.

St John, J., Russ, G.R., Brown, I., Squire, L. 2001, ‘The diet of the large coral reef serranid Plectropomus leopardus in two fishing zones on the Great Barrier Reef, Australia’, Fisheries Bulletin 99:180-192. 

Williams, A.J., Davies, C.R., Mapstone, B.D., Russ, G.R. 2003, ‘Scales of spatial variation in demography of a large coral reef fish – an exception to the typical model?’, Fisheries Bulletin 101:673-683.

Williams, A.J., Davies, C.R., Mapstone, B.D. 2005, ‘Variation in the periodicity and timing of increment formation in red throat emperor (Lethrinus miniatus) otoliths’, Marine and Freshwater Research 56:529-538.

Williams, A.J. 2003, Spatial patterns in population biology of a large coral reef fish: What role can movement play,? Unpublished PhD Thesis, James Cook University, Townsville, Australia.

Williamson DH, Russ GR, Ayling AM. 2004. No-take marine reserves increase abundance and biomass of reef fish on inshore fringing reefs of the Great Barrier Reef. Environmental Conservation 31 (2): 149-159.

Zeller, D., Russ, G.R. 2000, ‘Population estimates and size structure of Plectropomus leopardus (Pisces: Epinephelinae): mark-release-resighting’, Marine and Freshwater Research 51:221-222.

Trawl

Burridge, C.Y., Pitcher, C.R., and Wassenberg, T.J. 1997, ‘A comparison of interreef benthic communities in zones open and closed to trawling in the northern Great Barrier Reef [abstract]’, In: Hancock, D.A., Beumer, J.P. (eds) Developing and sustaining world fisheries resources: the state of science and management: 2nd World Fisheries Congress proceedings [book of abstracts], Brisbane, CSIRO Publishing, Collingwood, Victoria, p. 5.

Burridge, C.Y., Pitcher, C.R., Wassenberg, T.J., Poiner, I.R., Hill, B.J., 2003, ‘Measurement of the rate of depletion of benthic fauna by prawn (shrimp) otter trawls: an experiment in the Great Barrier Reef, Australia’, Fisheries Research 60(2-3):237-253.

Gribble, N.A. 2003, ‘GBR-prawn: modelling ecosystem impacts of changes in fisheries management of the commercial prawn (shrimp) trawl fishery in the far northern Great Barrier Reef’, Fisheries Research 65:493-506.

Pitcher, C.R., Burridge, C.Y., Wassenberg, T.J., Poiner, I.R. 1997, ‘The effects of prawn trawl fisheries on GBR [Great Barrier Reef] seabed habitats’, In: The Great Barrier Reef, science, use and management: a national conference: proceedings, James Cook University of North Queensland, Townsville, Qld., Great Barrier Reef Marine Park Authority, Townsville, pp 107-123.

Pitcher, C.R., Poiner, I.R., Hill, B.J., Burridge, C.Y. 2000, ‘Implications of the effects of trawling on sessile megazoobenthos on a tropical shelf in northeastern Australia’, ICES Journal of Marine Science 57(5):1359-1368.

Poiner, I., Glaister, J., Pitcher, R., Burridge, C., Wassenberg, T., Gribble, N., Hill, B., Blaber, S., Milton, D., Brewer, D., Ellis, N. 1998, Environmental effects of prawn trawling in the far Northern Section of the Great Barrier Reef Marine park, 1991-1996: final report to the Great Barrier Reef Marine Park Authority and Fisheries Research and Development Corporation, CSIRO Division of Marine Research, Cleveland, Qld. 2 volumes.

Robins, J.B. 1995, ‘Estimated catch and mortality of sea turtles caught in the east coast trawl fishery’, Biological Conservation 74:157-167.

Robins, J.B., Mayer, D.G. 1997, Monitoring the impact of trawling on sea turtle populations of the Queensland east coast, Final report from Queensland Department of Primary Industries to Fisheries Research and Development Corporation, FRDC, Canberra.

Stobutzki, I.C., Pitcher, C.R. 1999, ‘Assessing the response of bycatch communities to prawn trawling’, In: Buxton, C., Eayrs S.J. (eds) Establishing meaningful targets for bycatch reduction in Australian fisheries, Australian Society for Fish Biology: workshop proceedings, Hobart, Tasmania, Australian Society for Fish Biology, Sydney, pp 96-105.

Dugongs

Heinsohn, R., Lacy, R.R.C., Lindenmayer, D.B., Marsh, H., Kwan, D., Lawler, I.R. 2004 ‘Unsustainable harvest of dugongs in Torres Strait and Cape York (Australia) waters: two case studies using population viability analysis’, Animal Conservation 7:417-425.

Lawler, I, Marsh, H. 2000, Distribution and abundance of the dugong in Hervey Bay, Great Sandy Straits, November 1999, Report to Queensland Parks and Wildlife Service, Brisbane, Australia, James Cook University, Townsville.

Marsh, H., Corkeron, P.J., Lawler, I., Lanyon, J.M., Preen, A.R. 1996, The status of the dugong in the southern Great Barrier Reef Marine Park, GBRMPA Research Publication no. 41, Great Barrier Reef Marine Park Authority, Townsville.

Marsh, H., Corkeron, P.J. 1996, The status of the dugong in the northern Great Barrier Reef Marine Park, Unpublished report to Great Barrier Reef Marine Park Authority, Great Barrier Reef Marine Park Authority, Townsville.

Marsh, H., Corkeron, P.J. 1997, ‘The status of the dugong in the Great Barrier Reef Marine Park’, In: Wachenfeld, D.R., Oliver, J., Davis, K. (eds) State of the Great Barrier Reef World Heritage Area workshop: proceedings of a technical workshop held in Townsville, Australia, 27 - 29 November 1995, GBRMPA Workshop Series no.23, Great Barrier Reef Marine Park Authority, Townsville, pp 231-247.

Marsh, H., De’ath, G., Gribble, N., lane, B. 2001, Shark control records hindcast serious decline in dugong numbers off the urban coast of Queensland, GBRMPA Research Publication no. 70(Part 1), Great Barrier Reef Marine Park Authority, Townsville.

Marsh, H., De'ath, G., Gribble, N., Lane, B. 2005, ‘Historical marine population estimates: triggers or targets for conservation?:the dugong case study’, Ecological Applications 15(2):481-492.

Marsh, H., Eros, C., Corkeron, P.J., Breen, B. 1999 ‘A conservation strategy for dugongs: implications of Australian research’, Marine and Freshwater Research 50:979–990.

Marsh, H., Lawler, I. 2001, Dugong distribution and abundance in the southern Great Barrier Reef Marine Park and Hervey Bay: results of an aerial survey in October-December 1999, GBRMPA Research Publication no. 70(Part 2), Great Barrier Reef Marine Park Authority, Townsville.

Marsh, H., Lawler, I. 2002, Dugong distribution and abundance in the northern Great Barrier Reef Marine Park November 2000, GBRMPA Research Publication no. 77, Great Barrier Reef Marine Park Authority, Townsville. 

Marsh, H., Lawler, I.R., Kwan, D., Delean, S., Pollock, K., Alldredge, M. 2004, ‘An evaluation of the sustainability of an indigenous dugong fishery using aerial surveys and the potential biological removal technique’, Animal Conservation 7:435-447.