Publications

Reef Restoration and Adaptation

Journal Articles

Anthony KRN, Helmstedt KJ, Bay LK, Fidelman P, Hussey KE, Lundgren P, et al. (2020) Interventions to help coral reefs under global change—A complex decision challenge. PLoS ONE 15(8): e0236399. https://doi.org/10.1371/journal.pone.0236399

Bay, L. K., & Howells, E. J. (2021). Mapping the future for coral reefs. eLife, 10, e72978. https://doi.org/10.7554/eLife.72978

Condie, S. A., Bay, L. K., Harrison, H. B., & Lough, J. M. (2020). Large-scale interventions may delay decline of the Great Barrier Reef. Royal Society Open Science, 7(11), 201296. https://doi.org/10.1098/rsos.201296

McLeod IM, Hein MY, Babcock R, Bay L, Bourne DG, Cook N, et al. (2022) Coral restoration and adaptation in Australia: The first five years. PLoS ONE 17(11): e0273325. https://doi.org/10.1371/journal.pone.0273325

Bay, L. K., Gilmour, J. P., Muir, B., & Hardisty, P. E. (2023). Management approaches to conserve Australia’s marine ecosystem under climate change. Science, 381(6658), 631–636. https://doi.org/10.1126/science.adi3023

Peixoto, R.S., Voolstra, C.R., Baums, I.B. et al. The critical role of coral reef restoration in a changing world. Nat. Clim. Chang. 14, 1219–1222 (2024). https://doi.org/10.1038/s41558-024-02202-z

Ecological Intelligence for Reef Restoration

Journal Articles and Book Chapters

Ferrari, R., Lachs, L., Pygas, D. R., Humanes, A., Sommer, B., Figueira, W. F., Edwards, A. J., Bythell, J. C., & Guest, J. R. (2021). Photogrammetry as a tool to improve ecosystem restoration. Trends in Ecology & Evolution, 36(12), 1093–1101. https://doi.org/10.1016/j.tree.2021.07.004

  • This article discusses how photogrammetry can enhance ecosystem restoration by enabling precise, non-invasive monitoring and measurement of restoration success indicators.

Riginos, C., & Beger, M. (2021). Incorporating genetic measures of connectivity and adaptation in marine spatial planning for corals. In C. R. Voolstra & R. B. Ramos (Eds.), Coral reef conservation and restoration in the omics age (pp. 15–35). Springer. Incorporating Genetic Measures of Connectivity and Adaptation in Marine Spatial Planning for Corals | SpringerLink 

  • This chapter explores how incorporating genetic data on connectivity and adaptive potential can enhance marine spatial planning strategies for coral conservation and resilience.

Lachs, L., Humanes, A., Pygas, D. R., Bythell, J. C., Mumby, P. J., Ferrari, R., Figueira, W. F., Beauchamp, E., East, H. K., Edwards, A. J., Golbuu, Y., Martinez, H. M., Sommer, B., van der Steeg, E., & Guest, J. R. (2023). No apparent trade-offs associated with heat tolerance in a reef-building coral. Communications Biology, 6, Article 400. https://doi.org/10.1038/s42003-023-04758-6

  • This study suggests that within coral populations, trade-offs between heat tolerance and growth or fecundity may not be significant barriers to natural adaptation or the success of assisted evolution interventions.

Meziere, Z., Popovic, I., Prata, K., Ryan, I., Pandolfi, J., & Riginos, C. (2024). Exploring coral speciation: Multiple sympatric Stylophora pistillata taxa along a divergence continuum on the Great Barrier Reef. Evolutionary Applications, 17(1), e13644. https://doi.org/10.1111/eva.13644

  • This article investigates the genomic diversity and divergence among Stylophora pistillata coral taxa on the Great Barrier Reef.

Buccheri, E., Ricardo, G. F., Babcock, R. C., Mumby, P. J., & Doropoulos, C. (2023). Fertilisation kinetics among common Indo-Pacific broadcast spawning corals with distinct and shared functional traits. Coral Reefs, 42(6), 1351–1363. https://doi.org/10.1007/s00338-023-02431-2

  • This study examines how sperm concentration and gamete contact time affect fertilisation success in various coral species, providing insights valuable for coral reef management and restoration efforts.

Álvarez-Noriega, M., Marrable, I., Noonan, S. H. C., Barneche, D. R., & Ortiz, J. C. (2023). Highly conserved thermal performance strategies may limit adaptive potential in corals. Proceedings of the Royal Society B: Biological Sciences, 290(1994), 20221703. https://doi.org/10.1098/rspb.2022.1703

  • This study examines the thermal performance curves of four common coral species, revealing that while interspecific differences exist, intraspecific variation is minimal.

Fabricius, K. E., Crossman, K., Jonker, M., Mongin, M., & Thompson, A. (2023). Macroalgal cover on coral reefs: Spatial and environmental predictors, and decadal trends in the Great Barrier Reef. PLOS ONE, 18(1), Article e0279699. https://doi.org/10.1371/journal.pone.0279699

  • This study examines macroalgal cover on coral reefs, identifying spatial patterns, environmental drivers, and long-term trends in the Great Barrier Reef.

Richards, T. J., McGuigan, K., Aguirre, J. D., Humanes, A., Bozec, Y.-M., Mumby, P. J., & Riginos, C. (2023). Moving beyond heritability in the search for coral adaptive potential. Global Change Biology, 29(6), 1569–1581. https://doi.org/10.1111/gcb.16719x

  • This article explores the limitations of focusing solely on heritability when assessing coral adaptation potential, advocating for broader quantitative genetic approaches to better predict coral responses to environmental changes.

Wolfe, K. M., Boström‐Einarsson, L., McLeod, I. M., & Suggett, D. J. (2023). Hidden biodiversity in coral rubble: A hierarchical structuring approach reveals the value of microhabitats for reef restoration. Ecological Monographs, 93(3), Article e1586. https://doi.org/10.1002/ecm.1586  

  • This study employs hierarchical structuring theory to uncover the biodiversity within coral rubble habitats, highlighting their significance for reef restoration efforts.

Remmers, T., Grech, A., Roelfsema, C., Gordon, S., Lechene, M., & Ferrari, R. (2024). Close-range underwater photogrammetry for coral reef ecology: A systematic literature review. Coral Reefs, 43(1), 35–52. https://doi.org/10.1007/s00338-023-02445-w

  • This systematic review analyses how close-range underwater photogrammetry has been used in coral reef ecology, highlighting its growing role in accurately measuring reef structure, monitoring change, and informing conservation efforts.

Lechene, M. A. A., Figueira, W. F., Murray, N. J., Aston, E. A., Gordon, S. E., & Ferrari, R. (2024). Evaluating error sources to improve precision in the co-registration of underwater 3D models. Ecological Informatics, 81, 102632. https://doi.org/10.1016/j.ecoinf.2024.102632

  • This study identifies and quantifies key sources of error in aligning underwater 3D models to improve the precision and reliability of temporal comparisons in reef monitoring.

Webber, K., Fabricius, K., Wilson, S. K., & Hoey, A. S. (2024). The influence of Sargassum biomass and thallus density on the recruitment of coral reef fishes. Coral Reefs, 43, 687–699. https://doi.org/10.1007/s00338-024-02494-9

  • This study examines how variations in Sargassum biomass and thallus density affect the recruitment of coral reef fishes, highlighting the importance of macroalgal structural complexity in reef ecosystems.

Fabricius, K. E., Cooley, S. R., Golbuu, Y., Riginos, C., Gonzalez-Rivero, M., Heron, S. F., Mead, D., Cinner, J., & Schaffelke, B. (2024). Research priorities to support coral reefs during rapid climate change. PLOS Climate, 3(7), e0000435. https://doi.org/10.1371/journal.pclm.0000435

  • This article identifies key research priorities to help coral reefs adapt to and survive rapid climate change, emphasizing the urgent need for integrated, cross-disciplinary approaches.

Martin, C. C., McClure, E. C., Webber, K., Burgo, M., & Hoey, A. S. (2024). Utilisation of macroalgal habitats by juvenile rabbitfishes on an inshore reef. Coral Reefs, 43, 1843–1855. https://doi.org/10.1007/s00338-024-02581-x

  • This study investigates the distribution, feeding behaviour, diet, and predation risk of juvenile rabbitfish in macroalgal habitats on Orpheus Island, Great Barrier Reef.

Álvarez-Noriega, M., Ortiz, J. C., Ceccarelli, D. M., Emslie, M. J., Fabricius, K. E., Jonker, M. J., Puotinen, M., Robson, B. J., Roelfsema, C. M., Sinclair-Taylor, T. H., & Ferrari, R. (2025). Spatial variation in upper limits of coral cover on the Great Barrier Reef. Global Ecology and Biogeography, 34(1), e13928. https://doi.org/10.1111/geb.13928            

  • This study analyses 32 years of coral cover data from the Great Barrier Reef to identify environmental factors influencing the maximum sustainable coral cover, revealing that upper limits are generally lower than previously assumed and vary spatially across the reef system.

Riginos, C., Popovic, I., Meziere, Z., Garcia, V., Byrne, I., Howitt, S. M., Ishida, H., Bairos-Novak, K., Humanes, A., Scharfenstein, H., Richards, T., Briggs, E., Clark, V., Lei, C., Khan, M., & Prata, K. E. (2024). Cryptic species and hybridisation in corals: Challenges and opportunities for conservation and restoration. Peer Community Journal, 4, e106. https://doi.org/10.24072/pcjournal.492  

  • This study investigates the prevalence of cryptic coral groups and assesses evidence for their permeability to gene flow via a structured literature review of genomic studies.

Remmers, T., Boutros, N., Wyatt, M., Gordon, S., Toor, T., Roelfsema, C., Fabricius, K., Grech, A., Lechene, M. A. A., & Ferrari, R. (2025). RapidBenthos: Automated segmentation and multi-view classification of coral reef communities from photogrammetric reconstruction. Methods in Ecology and Evolution, 16(2), 427–441. https://doi.org/10.1111/2041-210X.14477

  • This study introduces RapidBenthos, a machine learning workflow that automates the segmentation and classification of coral reef communities from photogrammetric reconstructions, significantly reducing manual analysis time and enhancing scalability for reef monitoring.

P.J. Mumby, G. Sartori, E. Buccheri, C. Alessi, H. Allan, C. Doropoulos, G. Rengiil, & G. Ricardo, Allee effects limit coral fertilization success, Proc. Natl. Acad. Sci. U.S.A. 121 (52) e2418314121, https://doi.org/10.1073/pnas.2418314121 (2024) 

  • This study investigates how low coral colony densities can lead to reduced fertilisation success, highlighting the presence of Allee effects in coral reproduction and the implications for reef restoration efforts.

Álvarez-Noriega, M., Aston, E., Becker, M., Fabricius, K. E., Figueira, W. F., Gordon, S., Krensel, R., Lechene, M. A. A., Remmers, T., Toor, M., & Ferrari, R. (2025). Challenging paradigms around the role of colony size, taxa, and environment on bleaching susceptibility. Global Change Biology, 31(2), e70090. https://doi.org/10.1111/gcb.70090

  • This study reveals that bleaching susceptibility is influenced by complex interactions among colony size, taxonomic identity, and environmental factors, challenging existing assumptions about uniform patterns of bleaching vulnerability.

Drake, M. A., Noonan, S. H. C., Alvarez-Noriega, M., Rashid, A. R., & Fabricius, K. E. (2025). Current velocity, water quality, and benthic taxa as predictors for coral recruitment rates on the Great Barrier Reef. PLOS ONE, 20(3), e0319521. https://doi.org/10.1371/journal.pone.0319521

  • This study analysed coral recruit densities, revealing that recruitment success is significantly influenced by factors such as current velocity, sedimentation, depth, and pH levels.

Matias, A. M. A., Popovic, I., Thia, J. A., Cooke, I. R., Torda, G., Lukoschek, V., Bay, L. K., Kim, S. W., & Riginos, C. (2023). Cryptic diversity and spatial genetic variation in the coral Acropora tenuis and its endosymbionts across the Great Barrier Reef. Evolutionary Applications, 16(2), 293–310. https://doi.org/10.1111/eva.13435

  • This study analysed the genetic diversity of Acropora tenuis and its symbiotic algae across the Great Barrier Reef. Results suggest the presence of cryptic species, and found that symbiont diversity varied with reef location, highlighting the influence of environmental factors on coral-symbiont associations.

Briggs, N. D., Page, C. A., Giuliano, C., Alessi, C., Hoogenboom, M., Bay, L. K., & Randall, C. J. (2024). Dissecting coral recovery: Bleaching reduces reproductive output in Acropora millepora. Coral Reefs, 43(3), 557–569. https://doi.org/10.1007/s00338-024-02483-y

  • This study shows that coral bleaching significantly reduces the reproductive output of Acropora millepora, even in colonies that appear visually recovered.

Ani, C. J., Haller-Bull, V., Gilmour, J. P., & Robson, B. J. (2024). Connectivity modelling identifies sources and sinks of coral recruitment within reef clusters. Scientific Reports, 14, Article 13564. https://doi.org/10.1038/s41598-024-64388-8

  • This study used connectivity modelling to identify which reefs act as key sources and sinks for coral larvae within clusters, helping to guide more effective coral restoration strategies.

Sun, C., Steinberg, C., Klein Salas, E., Mellin, C., Babcock, R. C., Schiller, A., Cantin, N. E., Stella, J. S., Baird, M. E., Condie, S. A., Hobday, A. J., Herzfeld, M., Jones, N. L., Zhang, X., Chamberlain, M. A., Fiedler, R., Green, C., & Steven, A. D. L. (2024). Climate refugia in the Great Barrier Reef may endure into the future. Science Advances, 10(48), eado6884. https://doi.org/10.1126/sciadv.ado6884

  • This study utilised high-resolution ocean modelling to investigate the persistence of climate refugia in the Great Barrier Reef.

Hsu, T.-H. T., Gordon, S., Ferrari, R., Hoey, A. S., & Figueira, W. F. (2025). Optimizing remote underwater video sampling to quantify relative abundance, richness, and corallivory rates of reef fish. Coral Reefs, 44, 435–449. https://doi.org/10.1007/s00338-024-02613-6

  • This study found that analysing a subset of remote underwater video frames can accurately estimate reef fish abundance and feeding behavior while significantly reducing processing time.

Aston, E. A., Duce, S., Hoey, A. S., & Ferrari, R. (2022). A protocol for extracting structural metrics from 3D reconstructions of corals. Frontiers in Marine Science, 9, 854395. https://doi.org/10.3389/fmars.2022.854395

  • This study presents a standardised method and accompanying scripts for reconstructing 3D models of coral colonies from in-situ images, with metrics facilitating reproducible assessments of coral ecological functions.

Ferrari, R., Leon, J. X., Davies, A. J., Burns, J. H. R., Sandin, S. A., Figueira, W. F., & Gonzalez-Rivero, M. (2022). Editorial: Advances in 3D habitat mapping of marine ecosystem ecology and conservation. Frontiers in Marine Science, 8, 827430. https://doi.org/10.3389/fmars.2021.827430

  • This editorial introduces a collection of research articles focusing on the application of 3D technologies in marine ecosystem ecology and conservation.

Guillaume, A. S., Ferrari, R., Selmoni, O., Mocellin, V. J. L., Denis, H., Naugle, M., Howells, E., Bay, L. K., & Joost, S. (2025). Harnessing multiscale topographic environmental variables for regional coral species distribution models. Ecology and Evolution, 15(4), e71292. https://doi.org/10.1002/ece3.71292

Greenwood, J., Sun, C. J., Doropoulos, C., Thomson, D., Baird, M., Porobic, J., & Condie, S. (2025). Passive retention of simulated larvae on coral reefs. Royal Society Open Science, 12(5). https://doi.org/10.1098/rsos.241708  

  • This study used hydrodynamic simulations to show that coral reef physical features, like size and shape, significantly influence the passive retention of larvae, with implications for reef connectivity and restoration planning.
Standard Operating Procedures
Developing, implementing and testing fine scale hydrodynamical models in the context of larval supply and restoration
  • Describes how to develop, implement, and validate hydrodynamical models and Lagrangian particle tracking models that can inform reef restoration and conservation activities
Plankton tow sampling to estimate coral larvae relative abundance
  • Outlines plankton tow and laboratory plankton sorting procedures so that future sampling techniques remain consistent.
In-Situ Experiments to Estimate Fertilisation Success During Coral Spawning
  • Describes various approaches to assess coral fertilisation success in situ from small coral patch outplants.
Standard Operation Procedure Series: Field Photogrammetry in 4D:

Overview and In-Field Workflow

  • Outlines procedures for in-field image collection to reconstruct 3D models and 2D orthomosaics of benthic communities.

3D Model

  • ProcessingDetails the workflow for processing collected images into accurate 3D models, including software and hardware specifications.

Digitisation and 2D metric extraction

  • Provides guidelines for extracting quantitative metrics from 3D models to assess coral structures.
Photogrammetry and Benthic Orthomosaics
EcoRRAP SketchFab Collection
EcoRRAP Benthic Orthomosaics:
  • 3D models and 2D orthomosaics of complex reef ecosystems allow for the extraction of metrics such as coral volume, surface area, and the spacing between colonies.

Traditional Owner and Stakeholder Engagement
and Regulation

Journal Articles

Vella, K., Baresi, U., Lockie, S., & Taylor, B. (2021). Challenges and opportunities for assisted regional ecosystem adaptation: International experience and implications for adaptation research. PLOS ONE, 16(9), Article e0257868. https://doi.org/10.1371/journal.pone.0257868

  • This study reviews international experiences with regional ecosystem adaptation and highlights challenges and opportunities to guide future research and policy

Curnock, M. I., Arya, R., Chamberland, E., Chartrand, K., Edmondson, J., Fisher, E. E., Forster, R., Lockie, S., Loder, J., Nembhard, D., & Scott, A. (2024). Reef visitors’ observation of assisted coral recovery devices in situ reduces concern about their use. PLOS ONE, 19(11), e0313345. https://doi.org/10.1371/journal.pone.0313345

  • This study found that when reef visitors observed assisted coral recovery devices in the water, their concerns about using such technologies significantly decreased, suggesting in situ exposure can improve public acceptance.

Lockie, S., Graham, V., Taylor, B., Baresi, U., Maclean, K., Paxton, G., & Vella, K. (2024). Conceptualizing social risk in relation to climate change and assisted ecosystem adaptation. Risk Analysis. https://doi.org/10.1111/risa.17635

  • This paper proposes a framework for understanding the social risks associated with climate change and assisted ecosystem adaptation

Lockie, S., Bartelet, H. A., Ritchie, B. W., Demeter, C., Taylor, B., & Sie, L. (2024). Australians support multi-pronged action to build ecosystem resilience in the Great Barrier Reef. Biological Conservation, 299, 110789. https://doi.org/10.1016/j.biocon.2024.110789

  • This study found strong public support across Australia for a wide range of actions—including large-scale restoration and resilience-building measures—to protect the Great Barrier Reef, with trust in science closely linked to support for intervention.

Kong, T. M., Taylor, B., & Graham, V. (2024). Why partner? Harnessing value from collaborative sustainable business models to restore coral reefs at scale. PLOS ONE, 19(12), e0315094. https://doi.org/10.1371/journal.pone.0315094

  • This study explores how collaborative sustainable business models can create and capture value for large-scale coral reef restoration, emphasizing the strategic benefits of partnering across sectors.

Paxton, G., Lockie, S., & Backhaus, V. (2024). Articulating futures: Community storylines and assisted ecosystem adaptation in the Great Barrier Reef. Environmental Science & Policy, 162, 103944. https://doi.org/10.1016/j.envsci.2024.103944

  • This paper examines how community-generated storylines can shape and support socially acceptable pathways for assisted ecosystem adaptation in the Great Barrier Reef.

Baresi, U., Baum, C. M., Fischer, T. B., Lockie, S., Piggott-McKellar, A., Graham, V., & Ristovski, Z. (2024). A call for strategic assessments of regional applications of solar radiation management: Exploring the challenges and opportunities from marine cloud brightening and albedo surface modification. Environmental Impact Assessment Review, 110, 107701. https://doi.org/10.1016/j.eiar.2024.107701

  • This paper advocates for strategic environmental assessments of regional solar radiation management methods—such as marine cloud brightening—highlighting both their potential and the complex challenges they pose for governance and impact evaluation.

Baresi, U., Eberhard, R., Vella, K., Gooch, M., Piggott-McKellar, A., Luna Calibeo, D., Lockie, S., Taylor, B., Bohensky, E., Brooksbank, L., Curnock, M., Graham, V., Kong, T., Lyons, I., Maclean, K., Paxton, G., Schmitt, K., Siehoyono Sie, L., & Stone-Jovicich, S. (2025). Community engagement for novel ecosystem restoration and assisted adaptation interventions: Observations and lessons from the Australian Reef Restoration and Adaptation Program. Society & Natural Resources, 38(6), 626–645. https://doi.org/10.1080/08941920.2025.2463088

  • This paper shares reflections from the Reef Restoration and Adaptation Program on community engagement in novel and large-scale ecosystem restoration and climate adaptation interventions.

Bartelet, H. A., Lockie, S., Ritchie, B. W., Demeter, C., Sie, L., & Taylor, B. (2025). Public support for novel interventions to protect, restore, and accelerate adaptation to climate change in the Great Barrier Reef. Ocean and Coastal Management, 260, Article 107489. https://doi.org/10.1016/j.ocecoaman.2024.107489

  • This study reveals strong public support for innovative interventions aimed at protecting, restoring, and accelerating climate adaptation in the Great Barrier Reef, highlighting trust in science as a key factor influencing acceptance.
Reports and Guidelines

Taylor B, Hussey K, Fidelman P, Vella K, Maclean K, Newlands M, Ritchie B, Lockie S, Lacey J, McGrath C, Baresi U, Barber M, Koopman D (2019) Reef Restoration and Adaptation Program: Engagment and Regulatory Dimensions. A report provided to the Australian Government by the Reef Restoration and Adaptation Program (23pp)

Taylor B, Vella K, Maclean K, Newlands M, Ritchie B, Lockie S, Lacey J, Baresi U, Barber M, Siehoyono Sie L, Martin M, Marshall N, Koopman D (2019) Reef Restoration and Adaptation Program: Stakeholder, Traditional Owner and Community Engagement Assessment. A report provided to the
Australian Government by the Reef Restoration and Adaptation Program (95 pp)

Sie, L., Ritchie, B. W., & Lockie, S. (2022). Australian attitudes toward the protection and restoration of the Great Barrier Reef: Summary findings. Reef Restoration and Adaptation Program.

Williams, Liana; Stone-Jovicich, Samantha; Bohensky, Erin. Reef Restoration and Adaptation Program (RRAP) Best Practice Engagement – Participatory Community Panels. Townsville: CSIRO; 2021. csiro:EP2021-3271. https://doi.org/10.25919/xwk9-5c81 

Shumway, N., Foster, R., Head, B. and Fidelman, P. (2024). Governance Principles for Novel Reef Interventions. Reef Restoration and Adaptation Program. (33 pp).

Taylor, B.M., Bohensky, E., Curnock, M., Kong, T., Stone-Jovicich, S., Vella, K. Lockie, S. and Loder, J. (2024) Reef Restoration and Adaptation Program – Synthesis of best-practice engagement activities in RRAP Phase 1: objectives, findings and future directions.

Fidelman, P., McGrath, C., Newlands, M., & Dobbs, K. (2019). Regulatory implications of coral reef restoration and adaptation under a changing climate. Environmental Science & Policy, 100, 221–229. https://doi.org/10.1016/j.envsci.2019.04.016 

Shumway, N., Foster, R., Head, B., & Fidelman, P. (2023). Policy solutions needed for the future of coral reefs. BioScience, 73(11), 778–780. https://doi.org/10.1093/biosci/biad092

Shumway, N., Foster, R., & Fidelman, P. (2025). The governance of marine and coral reef restoration: Lessons and paths forward for novel interventions. Environmental Science & Policy, 164, 103999. https://doi.org/10.1016/j.envsci.2025.103999

Foster, R., Shumway, N., Harrison, D., & Fidelman, P. (2025). Governing marine cloud brightening for ecosystem conservation under a warming climate. Earth System Governance, 17, 100235. https://doi.org/10.1016/j.esg.2024.100235

Fact Sheets

Social research to support responsible adaptation

Modelling and Decision Support

Journal Articles

Stoeckl, N., Condie, S., & Anthony, K. (2021). Assessing changes to ecosystem service values at large geographic scale: A case study for Australia’s Great Barrier Reef. Ecosystem Services, 51, 101352. https://doi.org/10.1016/j.ecoser.2021.101352

Condie, S. A., Anthony, K. R. N., Babcock, R. C., Baird, M. E., Beeden, R., Fletcher, C. S., Gorton, R., Harrison, D., Hobday, A. J., Plagányi, É. E., & Westcott, D. A. (2021). Large-scale interventions may delay decline of the Great Barrier Reef. Royal Society Open Science, 8(4), 201296. https://doi.org/10.1098/rsos.201296

Richards, T. J., McGuigan, K., Aguirre, J. D., Humanes, A., Bozec, Y., Mumby, P. J., … & Riginos, C. (2023). Moving beyond heritability in the search for coral adaptive potential. Global Change Biology, 29(14), 3869-3882. https://doi.org/10.1111/gcb.16719

Pascoe, S., Anthony, K., Scheufele, G., & Pears, R. J. (2024). Identifying coral reef restoration objectives: A framework. Ocean & Coastal Management, 251, 107081. https://doi.org/10.1016/j.ocecoaman.2024.107081

Cresswell, A.K., Haller-Bull, V., Gonzalez-Rivero, M. et al. Capturing fine-scale coral dynamics with a metacommunity modelling framework. Sci Rep 14, 24733 (2024). https://doi.org/10.1038/s41598-024-73464-y

Yu, J., Baker, P., Cox, S. J., Petridis, R., Freebairn, A. C., Mirza, F., Thomas, L., Tickell, S., Lemon, D., & Rezvani, M. (2023). Provena: A provenance system for large distributed modelling and simulation workflows. In Proceedings of the 25th International Congress on Modelling and Simulation (MODSIM2023). Modelling and Simulation Society of Australia and New Zealand. https://mssanz.org.au/modsim2023/files/yu90.pdf

Crocker, R., Robson, B. J., Ani, C., Anthony, K., & Iwanaga, T. (2024). Synthetic data for reef modelling. Ecological Informatics, 82, 102698. https://doi.org/10.1016/j.ecoinf.2024.102698

Ani, C.J., Haller-Bull, V., Gilmour, J.P. et al. Connectivity modelling identifies sources and sinks of coral recruitment within reef clusters. Sci Rep 14, 13564 (2024). https://doi.org/10.1038/s41598-024-64388-8

Sun, C., Steinberg, C., Klein Salas, E., Mellin, C., Babcock, R. C., Schiller, A., Cantin, N. E., Stella, J. S., Baird, M. E., Condie, S. A., Hobday, A. J., Herzfeld, M., Jones, N. L., Zhang, X., Chamberlain, M. A., Fiedler, R., Green, C., & Steven, A. D. L. (2024). Climate refugia in the Great Barrier Reef may endure into the future. Science Advances, 10(48), eado6884. https://doi.org/10.1126/sciadv.ado6884

Stoeckl, N., Costanza, R., Dorji, N., Kubiszewski, I., Limenih, B., Tian, J., & Yamazaki, S. (2025). Valuing the reciprocating services that humans can provide to ecosystems. Ecological Indicators, 174, 113496. https://doi.org/10.1016/j.ecolind.2025.113496

Translation to Deployment

Journal Articles

Gibbs MT, Gibbs BL, Newlands M, Ivey J (2021) Scaling up the global reef restoration activity: Avoiding ecological imperialism and ongoing colonialism. PLoS ONE 16(5): e0250870. https://doi.org/10.1371/journal.pone.0250870

Gibbs, M. T. (2021). Technology requirements, and social impacts of technology for at-scale coral reef restoration. Technology in Society, 66, 101622. https://doi.org/10.1016/j.techsoc.2021.101622

Gibbs, M. T., & Newlands, M. (2021). Restoration heralds’ new management challenges for coral reefs. Marine Policy, 136, 104911. https://doi.org/10.1016/j.marpol.2021.104911

Gibbs, M.T. Developing a regional-scale reef restoration activity for the tropics. Reg Environ Change 21, 99 (2021). https://doi.org/10.1007/s10113-021-01843-6  

Lippmann RB, Helmstedt KJ, Gibbs MT, Corry P (2023) Optimizing facility location, sizing, and growth time for a cultivated resource: A case study in coral aquaculture. PLoS ONE 18(3): e0282668. https://doi.org/10.1371/journal.pone.0282668

Gibbs, M., Jackel, K., Ames, J., & McLeod, I. (2024). How the incentives of participating organizations influence the current scales of coral reef restoration activities. Aquatic Conservation: Marine and Freshwater Ecosystems, 34(1), e4077. https://doi.org/10.1002/aqc.4077

Gibbs, M. T. (2025). Oceanographic‐informed coral out‐planting density for coral reef restoration activities. Restoration Ecology, 33(1), e14315. https://doi.org/10.1111/rec.14315

Enhanced Corals and Treatments

Journal Articles and Book Chapters

Howells, E.J., Bay, L.K., Bay, R.A. (2022). Identifying, Monitoring, and Managing Adaptive Genetic Variation in Reef-Building Corals under Rapid Climate Warming. In: van Oppen, M.J.H., Aranda Lastra, M. (eds) Coral Reef Conservation and Restoration in the Omics Age. Coral Reefs of the World, vol 15. Springer, Cham. https://doi.org/10.1007/978-3-031-07055-6_4

Randall, C.J., Speaks, J.E., Lager, C. et al. Rapid counting and spectral sorting of live coral larvae using large-particle flow cytometry. Sci Rep 10, 12919 (2020). https://doi.org/10.1038/s41598-020-69491-0

Randall CJ, Negri AP, Quigley KM, Foster T, Ricardo GF, Webster NS, Bay LK, Harrison PL, Babcock RC, Heyward AJ (2020) Sexual production of corals for reef restoration in the Anthropocene. Mar Ecol Prog Ser 635:203-232 https://doi.org/10.3354/meps13206

Macadam, A., Nowell, C. J., & Quigley, K. (2021). Machine Learning for the Fast and Accurate Assessment of Fitness in Coral Early Life History. Remote Sensing, 13(16), 3173. https://doi.org/10.3390/rs13163173

Roepke, L. K., Brefeld, D., Soltmann, U., Randall, C. J., Negri, A. P., & Kunzmann, A. (2022). Applying behavioral studies to the ecotoxicology of corals: A case study on Acropora millepora. Frontiers in Marine Science, 9, 1002924. https://doi.org/10.3389/fmars.2022.1002924

Maire, J., Buerger, P., Chan, W. Y., Deore, P., Dungan, A. M., Nitschke, M. R., & van Oppen, M. J. H. (2022). Effects of ocean warming on the underexplored members of the coral microbiome. Integrative and Comparative Biology, 62(6), 1700–1709. https://doi.org/10.1093/icb/icac005

“Scharfenstein, H. J., Chan, W. Y., Buerger, P., Humphrey, C., & van Oppen, M. J. H. (2022). Evidence for de novo acquisition of microalgal symbionts by bleached adult corals. The ISME Journal, 16(6), 1676–1679. https://doi.org/10.1038/s41396-022-01203-0

Howells, E.J., Bay, L.K., Bay, R.A. (2022). Identifying, Monitoring, and Managing Adaptive Genetic Variation in Reef-Building Corals under Rapid Climate Warming. In: van Oppen, M.J.H., Aranda Lastra, M. (eds) Coral Reef Conservation and Restoration in the Omics Age. Coral Reefs of the World, vol 15. Springer, Cham. https://doi.org/10.1007/978-3-031-07055-6_4

van Oppen, M.J.H., Nitschke, M.R. (2022). Increasing Coral Thermal Bleaching Tolerance via the Manipulation of Associated Microbes. In: van Oppen, M.J.H., Aranda Lastra, M. (eds) Coral Reef Conservation and Restoration in the Omics Age. Coral Reefs of the World, vol 15. Springer, Cham. https://doi.org/10.1007/978-3-031-07055-6_8

“Thatcher, C., Høj, L., & Bourne, D. G. (2022). Probiotics for coral aquaculture: Challenges and considerations. Current Opinion in Biotechnology, 73, 380–386. https://doi.org/10.1016/j.copbio.2021.09.009

Scharfenstein, H., Alvarez‐Roa, C., Peplow, L. M., Buerger, P., Chan, W. Y., & Oppen, M. J. H. v. (2023). Chemical mutagenesis and thermal selection of coral photosymbionts induce adaptation to heat stress with trait trade‐offs. Evolutionary Applications, 16(9), 1549-1567. https://doi.org/10.1111/eva.13586

Matias, A. M. A., Popovic, I., Thia, J. A., Cooke, I., Torda, G., Lukoschek, V., … & Riginos, C. (2022). Cryptic diversity and spatial genetic variation in the coral acropora tenuis and its endosymbionts across the great barrier reef. Evolutionary Applications, 16(2), 293-310. https://doi.org/10.1111/eva.13435

Chan, W. Y., Meyers, L., Rudd, D., Topa, S. H., & Oppen, M. J. H. v. (2023). Heat‐evolved algal symbionts enhance bleaching tolerance of adult corals without trade‐off against growth. Global Change Biology, 29(24), 6945-6968. https://doi.org/10.1111/gcb.16987

Quigley, K.M., Alvarez-Roa, C., Raina, JB. et al. Heat-evolved microalgal symbionts increase thermal bleaching tolerance of coral juveniles without a trade-off against growth. Coral Reefs 42, 1227–1232 (2023). https://doi.org/10.1007/s00338-023-02426-z

Turnlund, A. C., Vanwonterghem, I., Botté, E. S., Randall, C. J., Giuliano, C., Kam, L., Bell, S., O’Brien, P., Negri, A. P., Webster, N. S., & Lurgi, M. (2023). Linking differences in microbial network structure with changes in coral larval settlement. ISME Communications, 3(1), 114. https://doi.org/10.1038/s43705-023-00320-x

Madin, J. S., McWilliam, M., Quigley, K., Bay, L. K., Bellwood, D., Doropoulos, C., Fernandes, L., Harrison, P., Hoey, A. S., Mumby, P. J., Ortiz, J. C., Richards, Z. T., Riginos, C., Schiettekatte, N. M. D., Suggett, D. J., & van Oppen, M. J. H. (2023). Selecting coral species for reef restoration. Journal of Applied Ecology, 60(8), 1537–1544. https://doi.org/10.1111/1365-2664.14447

Chan, W. Y., Rudd, D., & van Oppen, M. J. H. (2023). Spatial metabolomics for symbiotic marine invertebrates. Life Science Alliance, 6(8), e202301900. https://doi.org/10.26508/lsa.202301900

Riginos, C.; Popovic, I.; Meziere, Z.; Garcia, V.; Byrne, I.; Howitt, S. M.; Ishida, H.; Bairos-Novak, K.; Humanes, A.; Scharfenstein, H.; Richards, T.; Briggs, E.; Clark, V.; Lei, C.; Khan, M.; Prata, K. E. Cryptic species and hybridisation in corals: challenges and opportunities for conservation and restoration. Peer Community Journal, Volume 4 (2024), article no. e106. https://doi.org/10.24072/pcjournal.492

Briggs, N.D., Page, C.A., Giuliano, C. et al. Dissecting coral recovery: bleaching reduces reproductive output in Acropora millepora. Coral Reefs 43, 557–569 (2024). https://doi.org/10.1007/s00338-024-02483-y

Meziere, Z., Popovic, I., Prata, K. E., Ryan, I., Pandolfi, J. M., & Riginos, C. (2024). Exploring coral speciation: multiple sympatric stylophora pistillata taxa along a divergence continuum on the great barrier reef. Evolutionary Applications, 17(1). https://doi.org/10.1111/eva.13644

Selmoni, O., Bay, L. K., Exposito-Alonso, M., & Cleves, P. A. (2024). Finding genes and pathways that underlie coral adaptation. Trends in Genetics, 40(3), 213–227. https://doi.org/10.1016/j.tig.2024.01.003

Naugle, M.S., Denis, H., Mocellin, V.J.L. et al. Heat tolerance varies considerably within a reef-building coral species on the Great Barrier Reef. Commun Earth Environ 5, 525 (2024). https://doi.org/10.1038/s43247-024-01649-4

Scharfenstein, H., Peplow, L. M., Alvarez‐Roa, C., Nitschke, M. R., Chan, W. Y., Buerger, P., … & Oppen, M. J. H. v. (2024). Pushing the limits: expanding the temperature tolerance of a coral photosymbiont through differing selection regimes. New Phytologist, 243(6), 2130-2145. https://doi.org/10.1111/nph.19996

Nitschke, M. R., Abrego, D., Allen, C. E., Alvarez-Roa, C., Boulotte, N. M., Buerger, P., Chan, W. Y., Fae Neto, W. A., Ivory, E., Johnston, B., Meyers, L., Parra, C., Peplow, L., Perez, T., Scharfenstein, H. J., & van Oppen, M. J. H. (2024). The use of experimentally evolved coral photosymbionts for reef restoration. Trends in Microbiology, 32(8), 708–719. https://doi.org/10.1016/j.tim.2024.05.008

Denis, H., Bay, L. K., Mocellin, V. J. L., Naugle, M. S., Lecellier, G., Purcell, S. W., Berteaux-Lecellier, V., & Howells, E. J. (2024). Thermal tolerance traits of individual corals are widely distributed across the Great Barrier Reef. Proceedings of the Royal Society B: Biological Sciences, 291(2030), 20240587. https://doi.org/10.1098/rspb.2024.0587

Macadam, A., Morgans, C., Cheok, J., Damjanovic, K., Ciampaglia, M., Toor, M., Laffy, P., Cooke, I. R., Strugnell, J. M., & Quigley, K. M. (2025). Assessing the potential for “assisted gene flow” to enhance heat tolerance of multiple coral genera over three key phenotypic traits. Biological Conservation, 306, 111155. https://doi.org/10.1016/j.biocon.2025.111155

Turnlund, A.C., O’Brien, P.A., Rix, L. et al. Understanding the role of micro-organisms in the settlement of coral larvae through community ecology. Mar Biol 172, 43 (2025). https://doi.org/10.1007/s00227-025-04607-6

Ivory, E.A., Mieog, J.C., Nitschke, M.R. et al. Interactions among wildtype and heat-evolved photosymbionts shape performance of coral recruits. Coral Reefs 44, 643–655 (2025). https://doi.org/10.1007/s00338-025-02632-x

O’Brien, P.A., Bell, S.C., Rix, L. et al. Light and dark biofilm adaptation impacts larval settlement in diverse coral species. Environmental Microbiome 20, 11 (2025). https://doi.org/10.1186/s40793-025-00670-0

Saper, J., Raina, JB., Humphrey, C., Høj, L., Bourne, D.G. (2025). Microbial Processes and Nutrient Uptake in the Coral Holobiont and Reef Ecosystems. In: Peixoto, R.S., Voolstra, C.R. (eds) Coral Reef Microbiome. Coral Reefs of the World, vol 20. Springer, Cham. https://doi.org/10.1007/978-3-031-76692-3_9

Project Reports

Prokaryote treatments and coral nutrition: Feasibility of research and recommendations

  • This report discusses how RRAP-funded projects have progressed towards addressing bottlenecks in coral production through the identification of bacterial inducers to enhance coral settlement, and the development of bacterial probiotics and coral diets to support the survival, growth, and health of coral spat and juveniles 

Assessment and interpretation of Symbiodiniaceae community composition in adult coral

  • A report on the inoculation of two coral species (Platygyra daedalea and Galaxea fascicularis) with heat-evolved Cladocopium and Durusdinium and their long-term persistence in an experimental mesocosm system over nearly two years.

Coral Aquaculture and Deployment

Journal Articles

Randall, C.J., Giuliano, C., Mead, D. et al. Immobilisation of living coral embryos and larvae. Sci Rep 9, 14596 (2019). https://doi.org/10.1038/s41598-019-51072-5

Randall, C. J., Speaks, J. E., Lager, C., Hagedorn, M., Llewellyn, L., Pulak, R., Thompson, J., Bay, L. K., Mead, D., Heyward, A. J., & Negri, A. P. (2020). Rapid counting and spectral sorting of live coral larvae using large-particle flow cytometry. Scientific Reports, 10, Article 12919. https://doi.org/10.1038/s41598-020-69491-0

Randall, C. J., Negri, A. P., Quigley, K. M., Foster, T., Ricardo, G. F., Webster, N. S., Bay, L. K., Harrison, P. L., Babcock, R. C., & Heyward, A. J. (2020). Sexual production of corals for reef restoration in the Anthropocene. Marine Ecology Progress Series, 635, 203–232. https://doi.org/10.3354/meps13206

Randall, C. J., Giuliano, C., Heyward, A. J., & Negri, A. P. (2021). Enhancing coral survival on deployment devices with microrefugia. Frontiers in Marine Science, 8, 662263. https://doi.org/10.3389/fmars.2021.662263

Roepke, L. K., Brefeld, D., Soltmann, U., Randall, C. J., Negri, A. P., & Kunzmann, A. (2022). Antifouling coatings can reduce algal growth while preserving coral settlement. Scientific Reports, 12, Article 15935. https://doi.org/10.1038/s41598-022-19997-6

Roepke, L. K., Brefeld, D., Soltmann, U., Randall, C. J., Negri, A. P., & Kunzmann, A. (2022). Applying behavioral studies to the ecotoxicology of corals: A case study on Acropora millepora. Frontiers in Marine Science, 9, Article 1002924. https://doi.org/10.3389/fmars.2022.1002924

Briggs, N.D., Page, C.A., Giuliano, C. et al. Dissecting coral recovery: bleaching reduces reproductive output in Acropora millepora. Coral Reefs 43, 557–569 (2024). https://doi.org/10.1007/s00338-024-02483-y

Abdul Wahab, M.A., Ferguson, S., Snekkevik, V.K. et al. Hierarchical settlement behaviours of coral larvae to common coralline algae. Sci Rep 13, 5795 (2023). https://doi.org/10.1038/s41598-023-32676-4

Randall, C.J., Giuliano, C., Stephenson, B. et al. Larval precompetency and settlement behaviour in 25 Indo-Pacific coral species. Commun Biol 7, 142 (2024). https://doi.org/10.1038/s42003-024-05824-3

Ramsby, B.D., Emonnot, F., Flores, F. et al. Low light intensity increased survival of coral spat in aquaculture. Coral Reefs 43, 627–640 (2024). https://doi.org/10.1007/s00338-024-02489-6

Jeong, S. Y., Gabrielson, P. W., Hughey, J. R., Hoey, A. S., Cho, T. O., Abdul Wahab, M. A., & Diaz-Pulido, G. (2023). New branched Porolithon species (Corallinales, Rhodophyta) from the Great Barrier Reef, Coral Sea, and Lord Howe Island. Journal of Phycology, 59(5), 1025–1041. https://doi.org/10.1111/jpy.13387

Pratchett, M. S., Baird, A. H., & Pratchett, D. J. (2022). Settlement cue selectivity by larvae of the destructive crown-of-thorns starfish. Biology Letters, 18(11), 20220399. https://doi.org/10.1098/rsbl.2022.0399

Randall, C. J., Giuliano, C., Allen, K., Bickel, A., Miller, M., & Negri, A. P. (2022). Site mediates performance in a coral‐seeding trial. Restoration Ecology, 30(6), e13745. https://doi.org/10.1111/rec.13745

Severati, A., Nordborg, M., Heyward, A., Abdul Wahab, M., Brunner, C. A., Montalvo-Proaño, J., & Negri, A. P. (2024). The AutoSpawner system – Automated ex situ spawning and fertilisation of corals for reef restoration. Journal of Environmental Management, 366, 121886. https://doi.org/10.1016/j.jenvman.2024.121886

Whitman, T.N., Hoogenboom, M.O., Negri, A.P. et al. Coral-seeding devices with fish-exclusion features reduce mortality on the Great Barrier Reef. Sci Rep 14, 13332 (2024). https://doi.org/10.1038/s41598-024-64294-z

Fong, J., Ramsby, B.D., Flores, F. et al. Effects of material type and surface roughness of settlement tiles on macroalgal colonisation and early coral recruitment success. Coral Reefs 43, 1083–1096 (2024). https://doi.org/10.1007/s00338-024-02526-4

Neil, R.C., Heyward, A., Bourne, D.G. et al. Let the fish do the cropping: identifying fish grazers to improve coral aquaculture. Coral Reefs 44, 749–758 (2025). https://doi.org/10.1007/s00338-024-02612-7

Curnock, M. I., Arya, R., Chamberland, E., Chartrand, K., Edmondson, J., Fisher, E. E., Forster, R., Lockie, S., Loder, J., & Nembhard, D. (2024). Reef visitors’ observation of assisted coral recovery devices in situ reduces concern about their use. PLOS ONE, 19(11), e0313345. https://doi.org/10.1371/journal.pone.0313345

Whitman, T. N., Jurriaans, S., Lefevre, C., Sims, C. A., Radford, B., Puotinen, M., Hoogenboom, M. O., Negri, A. P., & Randall, C. J. (2025). Seeded Acropora digitifera corals survive best on wave-exposed reefs with grazing from small fishes. Restoration Ecology, 1–12. Advance online publication. https://doi.org/10.1111/rec.70016

Neil, R. C., Barton, J. A., Dougan, W., Dworjanyn, S., Heyward, A., Mos, B., Bourne, D. G., & Humphrey, C. (2024). Size matters: Microherbivores make a big impact in coral aquaculture. Aquaculture, 581, 740402. https://doi.org/10.1016/j.aquaculture.2023.740402

Fong, J., Jackson, T.L., Flores, F. et al. The interplay of temperature, light, and substrate type in driving growth and reproduction of an important tropical crustose coralline alga. J Appl Phycol 36, 3133–3145 (2024). https://doi.org/10.1007/s10811-024-03312-z

Neil, R. C., Barton, J. A., Heyward, A., Francis, D. S., Nankervis, L., Mock, T. S., Bourne, D. G., & Humphrey, C. (2025). Improving coral grow-out through an integrated aquaculture approach. Aquaculture Nutrition, 2025(1), 1–13. https://doi.org/10.1155/anu/1446195

Standard Operating Procedures

Nordborg, F.M., Brunner, C.A., Severati, A., Negri, A.P., Stephenson, S., Abdul-Wahab, A.M. (2024). Standard Operating Procedure: Optimised larval settlement in a high throughput coral aquaculture facility. SOP prepared for the Reef Restoration and Adaptation Program. Australian Institute of Marine Science,
Townsville QLD. Pp 41.

Moving Corals

Journal Articles and Book Chapters

Doropoulos, C., & Roff, G. (2022). Coloring coral larvae allows tracking of local dispersal and settlement. PLOS Biology, 20(12), e3001907. https://doi.org/10.1371/journal.pbio.3001907

Doropoulos, C., & Vanderklift, M. A. (2022). Harvesting coral spawn slicks for reef restoration. In S. M. Hamylton, P. Hutchings, & O. Hoegh-Guldberg (Eds.), Coral reefs of Australia: Perspectives from beyond the water’s edge (pp. 273–279). CSIRO Publishing. https://doi.org/10.1071/9781486315499

Gouezo, M., Doropoulos, C., Slawinski, D., Cummings, B., & Harrison, P. (2023). Underwater macrophotogrammetry to monitor in situ benthic communities at submillimetre scale. Methods in Ecology and Evolution, 14(9), 2494–2509. https://doi.org/10.1111/2041-210X.14175

Langley, C., Harrison, P. L., & Doropoulos, C. (2024). Optimizing initial stocking densities of wild coral spawn slicks for mass production of larvae and settled corals for restoration. Restoration Ecology, 32(7), e14239. https://doi.org/10.1111/rec.14239

Waters, C., Harrison, P. L., Gouezo, M., Severati, A., & Doropoulos, C. (2025). Early-stage coral survivorship using wild larval assemblages on coral seeding devices for reef restoration. Restoration Ecology, 33(3), e14387. https://doi.org/10.1111/rec.14387

Gouezo, M., Langlais, C., Beardsley, J., Roff, G., Harrison, P. L., Thomson, D. P., & Doropoulos, C. (2025). Going with the flow: Leveraging reef-scale hydrodynamics for upscaling larval-based restoration. Ecological Applications, 35(3), e70020. https://doi.org/10.1002/eap.70020

Harrison, P. L. (2024). Sexual reproduction of reef corals and application to coral restoration. In Oceanographic processes of coral reefs (2nd ed., pp. 19). CRC Press. https://doi.org/10.1201/9781003320425-32

Rubble Stabilisation

Journal Articles

Ceccarelli, D. M., McLeod, I. M., Boström-Einarsson, L., Bryan, S. E., Chartrand, K. M., Emslie, M. J., Gibbs, M. T., Gonzalez Rivero, M., Hein, M. Y., Heyward, A., Kenyon, T. M., Lewis, B. M., Mattocks, N., Newlands, M., Schläppy, M.-L., Suggett, D. J., & Bay, L. K. (2020). Substrate stabilisation and small structures in coral restoration: State of knowledge, and considerations for management and implementation. PLOS ONE, 15(10), e0240846. https://doi.org/10.1371/journal.pone.0240846

Lewis, B. M., Suggett, D. S., Prentis, P. J., & Nothdurft, L. D. (2022). Cellular adaptations leading to coral fragment attachment on artificial substrates in Acropora millepora (Am-CAM). Scientific Reports, 12, Article 18431. https://doi.org/10.1038/s41598-022-23134-8

Kenyon, T. M., Mumby, P. J., Callaghan, D. P., Baldock, T. E., & Doropoulos, C. (2023). Coral rubble dynamics in the Anthropocene and implications for reef recovery. Limnology and Oceanography, 68(12), 2955–2969. https://doi.org/10.1002/lno.12254

Harris, D. L., Webster, J. M., Vila-Concejo, A., Duce, S., Leon, J. X., & Hacker, J. (2023). Defining multi-scale surface roughness of a coral reef using a high-resolution LiDAR digital elevation model. Geomorphology, 439, 108852. https://doi.org/10.1016/j.geomorph.2023.108852

Kenyon, T. M., Harris, D., Baldock, T., Callaghan, D., Doropoulos, C., Webb, G., Newman, S. P., & Mumby, P. J. (2023). Mobilisation thresholds for coral rubble and consequences for windows of reef recovery. Biogeosciences, 20(20), 4339–4357. https://doi.org/10.5194/bg-20-4339-2023

Kenyon, T. M., Jones, C., Rissik, D., Brassil, W., Callaghan, D. P., Mattocks, N., & Baldock, T. E. (2025). Bio-degradable ‘reef bags’ used for rubble stabilisation and their impact on rubble stability, binding, coral recruitment and fish occupancy. Ecological Engineering, 210, 107433. https://doi.org/10.1016/j.ecoleng.2024.107433

Kenyon TM, Eigeland K, Wolfe K, et al. Material Legacies on Coral Reefs: Rubble Length and Bed Thickness Are Key Drivers of Rubble Bed Recovery. Glob Chang Biol. 2024;30(11):e17574. doi:10.1111/gcb.17574

Deng, W., Kenyon, T., Eigeland, K., Callaghan, D. P., & Baldock, T. E. (2025). Structural and hydrodynamic modelling of the probability of breakage of branching and plate coral colonies. Coastal Engineering, 195, 104647. https://doi.org/10.1016/j.coastaleng.2024.104647

Liu, D., Callaghan, D. P., Wuppukondur, A., & Baldock, T. E. (2025). A probabilistic coral rubble mechanical instability model applied with field observations from the Great Barrier Reef. Coastal Engineering, 195, 104655. https://doi.org/10.1016/j.coastaleng.2024.104655

Kenyon, T. M., Mumby, P. J., Webb, G. E., Dove, S., Newman, S. P., & Doropoulos, C. (2025). Trajectories and agents of binding in stabilized and unstabilized coral rubble across environmental gradients. Ecosphere, 16(2), e70195. https://doi.org/10.1002/ecs2.70195

Liu, D., Callaghan, D. P., & Baldock, T. E. (2025). Accelerating coral rubble instability assessments with machine learning: Insights from the Great Barrier Reef. Applied Ocean Research, 158, Article 104580. https://doi.org/10.1016/j.apor.2025.104580

Liu, D., Callaghan, D. P., & Baldock, T. E. (2025). Quantifying the impact of future climate change on the risk of coral rubble instability across the Great Barrier Reef by 2100. Journal of Environmental Management, 386, Article 125716. https://doi.org/10.1016/j.jenvman.2025.125716

Cheung, Mandy W.M., Chaloupka, Milani, Mumby, Peter J., and Callaghan, David P. (2025). The spatial risk of cyclone wave damage across the Great Barrier Reef. Ecological Informatics 89 103175 103175-89. https://doi.org/10.1016/j.ecoinf.2025.103175

Deng, W., Kenyon, T., Eigeland, K., Callaghan, D. P., & Baldock, T. E. (2025). Structural and hydrodynamic modelling of the probability of breakage of branching and plate coral colonies. Coastal Engineering, 195, 104647. https://doi.org/10.1016/j.coastaleng.2024.104647

Guidelines

A Practical Guide to Restoration and Rehabilitationof Rubble on Coral Reefs

Cryopreservation

Journal Articles

Zuchowicz, N., Daly, J., Bouwmeester, J. et al. Assessing coral sperm motility. Sci Rep 11, 61 (2021). https://doi.org/10.1038/s41598-020-79732-x

Hobbs, R. J., O’Brien, J. K., Bay, L. K., Severati, A., Spindler, R., Henley, E. M., Quigley, K. M., Randall, C. J., van Oppen, M. J. H., Carter, V., Zuchowicz, N., Hagedorn, M., & Daly, J. (2022). A decade of coral biobanking science in Australia – transitioning into applied reef restoration. Frontiers in Marine Science, 9, 960470. https://doi.org/10.3389/fmars.2022.960470

Daly, J., Hobbs, R.J., Zuchowicz, N. et al. Cryopreservation can assist gene flow on the Great Barrier Reef. Coral Reefs 41, 455–462 (2022). https://doi.org/10.1007/s00338-021-02202-x

Daly, J., Bouwmeester, J., Perry, R., Page, C., Khosla, K., Kangas, J., Lager, C., Hardy, K., Bischof, J. C., & Hagedorn, M. (2023). The first proof of concept demonstration of nanowarming in coral tissues. Advanced Sustainable Systems, 7(10), 2300303. https://doi.org/10.1002/adsu.202300303

Daly, J., Hobbs, R., Severati, A., Nordborg, M., Bay, L., Zuchowicz, N., Hagedorn, M., & O’Brien, J. (2023). Maximizing the utility of cryopreservation as an enabling technology in coral reef recovery and resilience. Cryobiology, 113, 104672. https://doi.org/10.1016/j.cryobiol.2023.104672

Powell-Palm, M.J., Henley, E.M., Consiglio, A.N. et al. Cryopreservation and revival of Hawaiian stony corals using isochoric vitrification. Nat Commun 14, 4859 (2023). https://doi.org/10.1038/s41467-023-40500-w

Page, C., Perry, R., Lager, C. V. A., Daly, J., Bouwmeester, J., Henley, E. M., & Hagedorn, M. (2023). Tank fouling community enhances coral microfragment growth. PeerJ, 11, e15723. https://doi.org/10.7717/peerj.15723

Daly, J., Hobbs, R., Zuchowicz, N., Hagedorn, M., & O’Brien, J. K. (2024). A semi-automated workflow for the cryopreservation of coral sperm to support biobanking and aquaculture. Journal of Visualized Experiments, 208, e66233. https://doi.org/10.3791/66233

Daly, J., Van Issum, H., Cummins, M., Evans-Illidge, E., Randall, C. J., Boyd, S., … O’Brien, J. K. (2024). Cross-cultural approach to biobanking of living coral cells on Woppaburra sea Country in the southern inshore Great Barrier Reef. Australasian Journal of Environmental Management, 32(1), 6–21. https://doi.org/10.1080/14486563.2024.2401567

Guo, Z., Zuchowicz, N., Bouwmeester, J., Joshi, A. S., Neisch, A. L., Smith, K., Daly, J., Etheridge, M. L., Finger, E. B., Kodandaramaiah, S. B., Hays, T. S., Hagedorn, M., & Bischof, J. C. (2024). Conduction-dominated cryomesh for organism vitrification. Advanced Science, 11(3), Article 2303317. https://doi.org/10.1002/advs.202303317

Lager, C. V. A., Perry, R., Daly, J., Page, C., Mizobe, M., Bouwmeester, J., Consiglio, A. N., Carter, J., Powell-Palm, M. J., & Hagedorn, M. (2024). Cryophysiology of coral microfragments: Effects of chilling and cryoprotectant toxicity. PeerJ, 12, e18447. https://doi.org/10.7717/peerj.18447

Cooling and Shading

Journal Articles

Baird ME, Green R, Lowe R, Mongin M, Bougeot E (2020) Optimising cool-water injections to reduce thermal stress on coral reefs of the Great Barrier Reef. PLoS ONE 15(10): e0239978. https://doi.org/10.1371/journal.pone.0239978

Tagliafico A, Baker P, Kelaher B, Ellis S and Harrison D (2022) The Effects of Shade and Light on Corals in the Context of Coral Bleaching and Shading Technologies. Front. Mar. Sci. 

Liu, F., Mao, F., Rosenfeld, D. et al. Opposing comparable large effects of fine aerosols and coarse sea spray on marine warm clouds. Commun Earth Environ 3, 232 (2022).

Medcraft, C., Hernandez-Jaramillo, D. C., Harrison, L., Braga, R. C., Butcherine, P., Harrison, D. P. (2023): Size distributions of sea salt aerosols for marine cloud brightening over the Great Barrier Reef, XXVIII General Assembly of the International Union of Geodesy and Geophysics (IUGG) (Berlin 2023) https://doi.org/10.57757/IUGG23-2107

Butcherine, Peter & Tagliafico, Alejandro & Ellis, Sophia & Kelaher, Brendan & Hendrickson, Conor & Harrison, Daniel. (2023). Intermittent shading can moderate coral bleaching on shallow reefs. Frontiers in Marine Science. 10. 10.3389/fmars.2023.1162896

Hernandez-Jaramillo, D. C., Medcraft, C., Braga, R. C., Rosenfeld, D., Harrison, D. (2023): Estimating the portion of Marine Cloud Brightening sea-salt aerosols that activate when incorporated into low-lying marine clouds: preliminary results, XXVIII General Assembly of the International Union of Geodesy and Geophysics (IUGG) (Berlin 2023).
https://doi.org/10.57757/IUGG23-2669

Eckert, C.; Monteforte, K.I.; Harrison, D.P.; Kelaher, B.P. Exploring Meteorological Conditions and Microscale Temperature Inversions above the Great Barrier Reef through Drone-Based Measurements. Drones 2023, 7, 695. https://doi.org/10.3390/drones7120695

Hernandez-Jaramillo, D.C. et al (2023) Evaporative Cooling Does Not Prevent Vertical Dispersion of Effervescent Seawater Aerosol for Brightening Clouds. Environmental Science & Technology 2023 57 (49), 20559-20570. DOI: 10.1021/acs.est.3c04793

Harrison D P (2024) An Overview of Environmental Engineering Methods for Reducing Coral Bleaching Stress in Oceanographic Processes of Coral Reefs. Physical and Biological Links in The Great Barrier Reef. Ed. Wolanski E, Kingsford MJ, CRC Press, Boca Raton, Fla.

Harrison D P (2024) An Overview of Environmental Engineering Methods for Reducing Coral Bleaching Stress in Oceanographic Processes of Coral Reefs. Physical and Biological Links in The Great Barrier Reef. Ed. Wolanski E, Kingsford MJ, CRC Press, Boca Raton, Fla. 

Zhao, W., Huang, Y., Siems, S., Manton, M., and Harrison, D.: Interactions between trade wind clouds and local forcings over the Great Barrier Reef: a case study using convection-permitting simulations, Atmos. Chem. Phys., 24, 5713–5736, https://doi.org/10.5194/acp-24-5713-2024, 2024.

Ryan Robert G., Eckert Christian, Kelaher Brendan P., Harrison Daniel P., Schofield Robyn (2024) Boundary layer height above the Great Barrier Reef studied using drone and Mini-Micropulse LiDAR measurements. Journal of Southern Hemisphere Earth Systems Science 74, ES24008. https://doi.org/10.1071/ES24008 

Ellis, Sophia & Butcherine, Peter & Tagliafico, Alejandro & Hendrickson, Conor & Kelaher, Brendan & Schulz, Kai & Harrison, Daniel. (2024). Shading responses are species-specific in thermally stressed corals. Frontiers in Marine Science. 11. 10.3389/fmars.2024.1333806.

Jiayue Yu, Sebastian Galindo-Lopez, Bosen Wang, Agisilaos Kourmatzis, Matthew J. Cleary, Analysis of the explicit volume diffusion subgrid closure for the Σ−Y model to interfacial flows over a wide range of Weber numbers, International Journal of Multiphase Flow, Volume 179, 2024,
104914, ISSN 0301-9322, https://doi.org/10.1016/j.ijmultiphaseflow.2024.104914.

Diana C. Hernandez-Jaramillo, Chris Medcraft, Ramon Campos Braga, Peter Butcherine, Adrian Doss, Brendan Kelaher, Daniel Rosenfeld, Daniel P. Harrison, New airborne research facility observes sensitivity of cumulus cloud microphysical properties to aerosol regime over the Great Barrier Reef. Environmental Science: Atmospheres, Volume 4, Issue 8,
2024, https://doi.org/10.1039/d4ea00009a

Eckert C, Hernandez-Jaramillo DC, Medcraft C, Harrison DP, Kelaher BP. Drone-Based Measurement of the Size Distribution and Concentration of Marine Aerosols above the Great Barrier Reef. Drones. 2024; 8(7):292. https://doi.org/10.3390/drones8070292

Richards, L.S., Siems, S.T., Huang, Y. et al. The meteorological drivers of mass coral bleaching on the central Great Barrier Reef during the 2022 La Niña. Sci Rep 14, 23867 (2024). https://doi.org/10.1038/s41598-024-74181-2

Scofield, J.M.P.; Prime, E.L.; Flores, F.; Severati, A.; Mongin, M.; Bougeot, E.; Baird, M.E.; Negri, A.P.; Qiao, G.G. The Development of a Floating Mono-Particle “Sun Shield” to Protect Corals from High Irradiance during Bleaching Conditions. J. Mar. Sci. Eng. 2024, 12, 1809. https://doi.org/10.3390/jmse12101809

Conor Hendrickson, Peter Butcherine, Alejandro Tagliafico, Sophia L. Ellis, Daniel P. Harrison, Brendan P. Kelaher, Combining shading and lipid-enriched diets as an adaption tool to reduce coral bleaching, Journal of Experimental Marine Biology and Ecology, Volume 572, 2024,
151988, ISSN 0022-0981, https://doi.org/10.1016/j.jembe.2024.151988.

U. Baresi, C.M. Baum, T.B. Fischer, S. Lockie, A. Piggott-McKellar, V. Graham, E. Bohensky, L.B. Fritz, N. Shumway, D.P. Harrison, R. Foster, B.K. Sovacool, K. Vella, Z. Ristovski, A call for strategic assessments of regional applications of solar radiation management: Exploring the challenges and opportunities from marine cloud brightening and albedo surface modification, Environmental Impact Assessment Review,
Volume 110, 2025, 107701, ISSN 0195-9255, https://doi.org/10.1016/j.eiar.2024.107701.

Ramon C. Braga, Daniel Rosenfeld, Diana Hernandez, Chris Medcraft, Avichay Efraim, Manuel Moser, Johannes Lucke, Adrian Doss, Daniel Harrison, Cloud processing dominates the vertical profiles of aerosols in marine air masses over the Great Barrier Reef,
Atmospheric Research, 2025, https://doi.org/10.1016/j.atmosres.2025.107928

Deschaseaux, Elisabeth & Dunne, Erin & Schulz, Kai & Eyre, Bradley & Harrison, Daniel. (2025). The Central Great Barrier Reef as a Net Source of Climatically Relevant Biogenic Volatile Organic Compounds. Journal of Geophysical Research: Oceans. 130. 10.1029/2024JC021192.

Virah-Sawmy, D., Beck, F. J., Sturmberg, B. Ignore variability, overestimate hydrogen production – Quantifying the effects of electrolyzer efficiency curves on hydrogen production from renewable energy sources,
International Journal of Hydrogen Energy, Volume 72, 2024,https://doi.org/10.1016/j.ijhydene.2024.05.360

Virah-Sawmy, D., Sturmberg, B.Socio-economic and environmental impacts of renewable energy deployments: A review, Renewable and Sustainable Energy Reviews, Volume 207, 2025, https://doi.org/10.1016/j.rser.2024.11495

Virah-Sawmy, D., Sturmberg, B., Harrison, D. P., Assessing the availability and feasibility of renewable energy on the Great Barrier Reef-Australia,
Energy Reports, Volume 13, 2025, Pages 2035-2065, ISSN 2352-4847, https://doi.org/10.1016/j.egyr.2025.01.036

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