Professor John Pandolfi


School of Biological Sciences
Faculty of Science
+61 7 336 53050


Ecological dynamics of coral reef ecosystems over broad spatial and temporal scales.

Dr Pandolfi is a Professor in Palaeoecology and Marine Studies.

Research Interests include (for more information, see Research Interests):

1) Long-term ecology of coral reefs

2) Using Historical Ecology to guide reef management actions

3) The palaeoecological, evolutionary, and extinction dynamics of Indo-Pacific reef corals

4) Hybridization, extinction, and evolution in a Caribbean reef coral species complex

Research Interests

  • Long-term ecology of coral reefs
    The overarching goal of this research program is to integrate long-term ecological and environmental time series data over broad spatial scales to discover the major past and predicted future influences of natural variability, human impact, and climate change on coral reef resilience. This research program enables direct linkage among physical variables and biological responses, attempts to parse out the effects of human versus natural variability, provide natural baselines with which managers can use as goals for restoration, unveils processes that contribute to the resilience of coral reefs over long time frames and changing environmental conditions, and fosters new understanding of the role of climate change in coral reef ecology.
  • Using Historical Ecology to guide reef management actions
    Recent findings from sites distributed throughout the tropical world point to the immense importance of understanding historical events when attempting to tease apart factors that have or may influence present coral reef biodiversity. For example, large-scale changes in climate that have occurred in the past 400,000 years (e.g. Younger Dryas event; 11.6 ka) have the potential to help us understand the current rapid changes in global climate. Data will be obtained using the Quaternary fossil record (past 2 MA), archaeological records (thousands to tens of thousands of years), historical records, government records of fishing practices and stocks, environmental proxies derived from living and fossil corals, and modern ecological surveys. Taken together, these databases provide a holistic view of changing environments and ecology on coral reefs against which the acquisition of present day data can be evaluated. Correlation of reef decline with specific human and environmental impacts over time provides an insight into the processes that are most important in local reef settings. When these processes are uncovered, specific steps can be taken to ameliorate or reverse the decline. Major projects will gather data from the Great Barrier Reef, from across a species diversity and sea surface temperature gradient from Indonesia in the west to Fiji in the eastern part of the Indo-Pacific ocean, and from a latitudinal gradient along the Western Australian coastline.
  • The palaeoecological, evolutionary, and extinction dynamics of Indo-Pacific reef corals
    The Miocene epoch, 24 - 5 million years before present (mybp), was a time of great environmental and evolutionary change in coral reefs - whole oceans with their component reef biota were obliterated, extinction rates were high, and, near the end of the epoch, the modern Atlantic and Indo-Pacific coral faunas evolved separately. In the Indo-Pacific Ocean, major global climatic and tectonic events resulted in the breakdown of established reef ecosystems and an overall loss of species diversity. The subsequent recovery, during the Miocene to Pliocene transition (10 - 5 mybp), was characterized by increased rates of speciation and the overall ecological re-organization of coral reef communities. The major result of this community re-organization was a dramatic shift from reefs dominated by corals with a massive growth form to those dominated by coral species with a branching architecture. This post-Miocene ascendance of large scale Acropora assemblages opened up new ecospace for the evolution of the myriad of creatures that now comprise our modern coral reefs - not only the most complex and diverse communities in the sea, but also some of the most threatened. In this research programme we examine the ecological context of the great architectural shift in community structure in Indo-Pacific coral reefs that occurred during the Miocene to Pliocene. Studies will document changes in the patterns of coral species associations, and the rate at which those changes occurred, from a number of reef environments. The decline in coral species with a massive growth form and the rapid evolution of branching coral species and their rise to dominance within reef communities will be studied in relation to concurrent broad scale geological events (tectonic, climatic and oceanographic). This research will increase our understanding of how ecological factors influence the survival of coral reef ecosystems when they are subject to significant environmental fluctuations over prolonged intervals of time. Because the Pliocene coral fauna has very similar characteristics to living coral reefs, the study will help us to understand the nature and significance of shifts in community composition in modern reefs affected by human activities.
  • Hybridization, extinction, and evolution in a Caribbean reef coral species complex
    Recent molecular analyses indicate that many reef coral species belong to hybridizing species complexes or ��syngameons.�� Such complexes consist of numerous genetically distinct species or lineages, which periodically split and/or fuse as they extend through time. During splitting and fusion, morphologic intermediates form and species overlap. Here we focus on processes associated with lineage fusion, and the recognition of such hybridization in the fossil record. Our approach involves comparing patterns of ecologic and morphologic overlap in genetically characterized modern species with fossil representatives of the same or closely related species. We also consider the long-term consequences of past hybridization on the structure of modern-day species boundaries. Our studies involve the species complex Montastraea annularis s.l., where we also conduct parallel studies on its long-term evolutionary history, palaeoecology, and rates of origination and extinction.


  • Doctor of Philosophy, Calif., Davis
  • Master of Science, Wis.,
  • Bachelor of Science, University of Notre Dame Australia


View all Publications


  • Doctor Philosophy

  • Doctor Philosophy

  • (2019) Doctor Philosophy

View all Supervision


Book Chapter

  • Pandolfi, J. M. (2018). Succession. In Encyclopedia of Ecology (pp. 616-623) : Elsevier. doi:10.1016/B978-0-444-63768-0.00547-3

  • Thurstan, Ruth H., Pandolfi, John M. and zu Ermgassen, Philine S.E. (2017). Animal forests through time: historical data to understand present changes in marine ecosystems. In Marine animal forests: the ecology of benthic biodiversity hotspots (pp. 947-963) Cham, Switzerland: Springer International Publishing. doi:10.1007/978-3-319-21012-4_31

  • Thurstan, Ruth H., Pandolfi, John M. and zu Ermgassen, Philine S. E. (2016). Animal forests through time: historical data to understand present changes in marine ecosystems. In Sergio Rossi, Lorenzo Bramanti, Andrea Gori and Covadonga Orejas Saco del Valle (Ed.), Marine animal forests (pp. 1-17) Cham, Switzerland: Springer International Publishing. doi:10.1007/978-3-319-17001-5_31-1

  • Budd, A. F. and Pandolfi, J. M. (2016). Contrasting patterns of speciation in reef corals and their relationship to population connectivity. In Warren D. Allmon and Margaret M. Yacobucci (Ed.), Species and speciation in the fossil record (pp. 217-237) Chicago: University of Chicago Press.

  • Thurstan, Ruth H., Buckley, Sarah M. and Pandolfi, John M. (2016). Oral histories: informing natural resource management using perceptions of the past. In Kathleen Schwerdtner Máñez and Bo Poulsen (Ed.), Perspectives on oceans past: a handbook of marine environmental history (pp. 155-173) Dordrecht , The Netherlands: Springer . doi:10.1007/978-94-017-7496-3_9

  • Pandolfi, John M. and Sampayo, Eugenia M. (2015). Adaptation of coral symbiosis to climate change. In Judith L. Bronstein (Ed.), Mutualism (pp. 246-248) Oxford, United Kingdom: Oxford Univerisity Press.

  • Jackson, Jeremy B. C., Donovan, Mary K., Cramer, Katie L., Lam, Vivian Y. Y., Bak, Rolf P. M., Chollett, Iliana, Connolly, Sean R., Cortés, Jorge, Dustan, Phil, Eakin, C. Mark, Friedlander, Alan M., Greenstein, Benjamin J., Heron, Scott F., Hughes, Terry, Miller, Jeff, Mumby, Peter, Pandolfi, John M., Rogers, Caroline S., Steneck, Robert, Weil, Ernesto, Alemu I, Jahson B., Alevizon, William S., Arias-González, Jesús Ernesto, Atkinson, Andrea, Ballantine, David L., Bastidas, Carolina, Bouchon, Claude, Bouchon-Navaro, Yolande, Box, Steve, Brathwaite, Angelique, Bruno, John F., Caldow, Chris, Carpenter, Robert C., Charpentier, Bernadette H., Causey, Billy, Chiappone, Mark, Claro, Rodolfo, Cróquer, Aldo, Debrot, Adolphe O., Edmunds, Peter, Fenner, Douglas, Fonseca, Ana, Ford, Marcia C., Forman, Kirah, Forrester, Graham E., Garza-Pérez, Joaquín R., Gayle, Peter M. H., Grimsditch, Gabriel D., Guzmán, Hector M., Harborne, Alastair R., Hardt, Marah J., Hixon, Mark, Idjadi, Joshua, Jaap, Walter, Jeffrey, Christopher F. G., Johnson, Ayana Elizabeth, Jordán-Dahlgren, Eric, Koltes, Karen, Lang, Judith C., Loya, Yossi, Majil, Isaias, Manfrino, Carrie, Maréchal, Jean-Philippe, McCoy, Croy M. R., McField, Melanie D., Murdoch, Thaddeus, Nagelkerken, Ivan, Rodriguez-Ramirez, Alberto, Ruttenberg, Benjamin I., Ruzicka, Rob, Sandin, Stuart, Shulman, Myra J., Smith, Struan R., Smith, Tyler B., Sommer, Brigitte, Stallings, Chris, Torres, Rubén E., Tunnell Jr., John W., Vermeij, Mark J. A., Williams, Ivor D. and Witman, Jon D. (2014). Part I: Overview and synthesis for the wider Caribbean region. In Jeremy Jackson, Mary Donovan, Katie Cramer and Vivian Lam (Ed.), Status and trends of Caribbean coral reefs: 1970-2012 (pp. 55-154) Washington, DC, United States: Global Coral Reef Monitoring Network.

  • Pandolfi, John M. (2011). Historical ecology of coral reefs. In Hopley, D. (Ed.), Encyclopedia of Modern Coral Reefs: Structure, Form and Process 1 ed. (pp. 554-558) Berlin, Germany: Springer-Verlag. doi:10.1007/978-90-481-2639-2_94

  • Pandolfi, John. M. (2011). The paleoecology of coral reefs. In Zvy Dubinsky and Noga Stambler (Ed.), Coral reefs: An ecosystem in transition (pp. 13-24) Dordrecht, Netherlands: Springer. doi:10.1007/978-94-007-0114-4

  • Pandolfi, J. M. (2008). Succession. In Sven Erik Jørgensen and Brian Fath (Ed.), Encyclopedia of Ecology (pp. 3416-3424) Oxford: Elsevier. doi:10.1016/B978-008045405-4.00547-4

  • Pandolfi, J.M. and Kelley, R. (2008). The Great Barrier Reef in Time and Space: Geology and Palaeobiology. In Hutchings, P.A., Kingsford, M.J. and Hoegh-Guldberg, O. (Ed.), The Great Barrier Reef: Biology, Environment and Management (pp. 17-27) Collingwood, Victoria: CSIRO Publishing.

  • Pandolfi, J. M. (2007). Ancient Reefs. In Palaeobiology II (pp. 307-309) : Wiley Blackwell. doi:10.1002/9780470999295ch.69

  • Pandolfi, J. M. and Greenstein, B. J. (2007). Using the past to understand the future: palaeoecology of coral reefs. In Johnson, J. E. and Marshall, P. A. (Ed.), Climate Change and the Great Barrier Reef: A Vulnerability Assessment (pp. 717-744) Townsville, Queensland: Great Barrier Reef Marine Park Authority and The Australian Greenhouse Office.

  • Pandolfi, J. M. and Jackson, B. C. (2006). Broad-scale Patterns in Pleistocene Coral Reef Communities from the Caribbean: Implications for Ecology and Management. In Richard B. Aronson (Ed.), Geological Approaches to Coral Reef Ecology (pp. 201-236) New York: Springer Science and Business Media, LLC.

  • Roy, K. and Pandolfi, J. M. (2005). Responses of Marine Species and Ecosystems to Past Climate Change. In Thomas E. Lovejoy and Lee Hannah (Ed.), Climate Change and Biodiversity 1 ed. (pp. 160-175) New Haven & London: Yale University Press.

  • Blake, S. G. and Pandolfi, J. M. (2004). Chapter 12 Geology of selected islands of the Pitcairn group, Southern Polynesia. In (pp. 407-431) : Elsevier. doi:10.1016/S0070-4571(04)80034-7

  • Pandolfi, J. M. (1995). Geomorphology of the Uplifted Pleistocene Atoll At Henderson Island, Pitcairn Group. In The Pitcairn Island: biogeography, ecology and prehistory (pp. 63-77) London, United Kingdom: Academic Press. doi:10.1111/j.1095-8312.1995.tb01078.x

Journal Article

Conference Publication

  • Richardson, Anthony J., Brown, Christopher J., Brander, Keith, Bruno, John F., Buckley, Lauren, Burrows, Michael T., Duarte, Carlos M., Halpern, Benjamin S., Hoegh-Guldberg, Ove, Holding, Johnna, Kappel, Carrie V., Kiessling, Wolfgang, Moore, Pippa J., O'Connor, Mary I., Pandolfi, John M., Parmesan, Camille, Schoeman, David S., Schwing, Frank, Sydeman, William J. and Poloczanska, Elvira S. (2012) Climate change and marine life. Biology Letters, 8 6: 907-909. doi:10.1098/rsbl.2012.0530

  • Reymond, Claire E., Uthicke, Sven and Pandolfi, John M. (2012). Tropical Foraminifera as indicators of water quality and temperature. In: D. Yellowlees and T. P. Hughes, Proceedings of the 12th International Coral Reef Symposium. 12th International Coral Reef Symposium, Cairns, QLD, Australia, (). 9-13 July 2012.

  • Beger, Maria, Babcock, Russ, Booth, David J., Bucher, Daniel, Condie, Scott A., Creese, Bob, Cvitanovic, Christopher, Dalton, Steve J., Harrison, Peter, Hoey, Andrew, Jordan, Alan, Loder, Jennifer, Malcolm, Hamish, Purcell, Steven W., Roelfsema, Chris, Sachs, Patrick, Smith, Stephen D. A., Sommer, Brigitte, Stuart-Smith, Rick, Thomson, Damian, Wallace, Carden C., Zann, Maria and Pandolfi, John M. (2011) Research challenges to improve the management and conservation of subtropical reefs to tackle climate change threats. Ecological Management & Restoration, 12 1: e7-e10. doi:10.1111/j.1442-8903.2011.00573.x

  • Best, M. M. R., Burniaux, P. and Pandolfi, J. M. (2004). Experimental Bivalve Taphonomy in Reefs of Madang Lagoon, Papua New Guinea. In: M. Best and J.-B. Caron, Canadian Paleontology Conference Proceedings No. 2: Canadian Paleontology Conference 2004. 14th Canadian Paleontology Conference, Huntsman Marine Science Centre in St. Andrews, New Brunswick, Canada, (8-12). 23-26 September 2004.

  • Estrada Alvarez, L. M., Edinger, E. N. and Pandolfi, J. M. (2004). Taphonomy of modern corals from Madang lagoon, Papua New Guinea. In: M. Best and J.-B. Caron, Canadian Paleontology Conference Proceedings No. 2: Canadian Paleontology Conference 2004. 14th Canadian Paleontology Conference, Huntsman Marine Science Centre in St. Andrews, New Brunswick, Canada, (23-28). 23-26 September 2004.

Other Outputs

Grants (Administered at UQ)

PhD and MPhil Supervision

Current Supervision

  • Doctor Philosophy — Principal Advisor

    Other advisors:

  • Doctor Philosophy — Principal Advisor

    Other advisors:

  • Doctor Philosophy — Principal Advisor

  • Doctor Philosophy — Principal Advisor

    Other advisors:

  • Doctor Philosophy — Principal Advisor

  • Doctor Philosophy — Associate Advisor

    Other advisors:

  • Doctor Philosophy — Associate Advisor

    Other advisors:

Completed Supervision