MacNeil, M. Aaron, Graham, Nicholas A.J., Cinner, Joshua E., Wilson, Shaun K., Williams, Ivor D., Maina, Joseph, Newman, Steven, Friedlander, Alan M., Jupiter, Stacy, Polunin, Nicholas V.C., and McClanahan, Tim R. (2015) Recovery potential of the world's coral reef fishes. Nature, 520 (7547). pp. 341-357.

Graham, Nicholas A.J., Jennings, Simon, MacNeil, M. Aaron, Mouillot, David, and Wilson, Shaun K. (2015) Predicting climate-driven regime shifts versus rebound potential in coral reefs. Nature, 518 (7537). pp. 94-97.

McClanahan, T.R., Graham, N.A.J., MacNeil, M.A., and Cinner, J.E. (2015) Biomass-based targets and the management of multispecies coral reef fisheries. Conservation Biology, 29 (2). pp. 409-417.

MacNeil, M. Aaron, and Connolly, Sean R. (2015) Multi-scale patterns and processes in reef fish abundance. In: Mora, Camilo, (ed.) Ecology of Fishes on Coral Reefs. Cambridge University Press, Cambridge, UK, pp. 116-124.

Connolly, Sean R., Macneil, M. Aaron, Caley, M. Julian, Knowlton, Nancy, Cripps, Ed, Hisano, Mizue, Thibaut, Loïc M., Bhattacharya, Bhaskar D., Benedetti-Cechi, Lisandro, Brainard, Russell E., Brandt, Angelika, Bulleri, Fabio, Ellingsen, Kari E., Kaiser, Stefanie, Kröncke, Ingrid, Linse, Katrin, Maggi, Elena, O'Hara, Timothy D., Plaisance, Laetititia, Poore, Gary C.B., Sarkar, Santosh K., Satpathy, Kamala, Schückel, Ulrike, Williams, Alan, and Wilson, Robin S. (2014) Commonness and rarity in the marine biosphere. Proceedings of the National Academy of Sciences of the United States of America, 111 (23). pp. 8524-8529.

Macneil, M. Aaron, and Cinner, Joshua E. (2013) Hierarchical livelihood outcomes among co-managed fisheries. Global Environmental Change, 23 (6). pp. 1393-1401.

McClanahan, Tim R., Donner, Simon D., Maynard, Jeffrey A., MacNeil, M. Aaron, Graham, Nicholas A.J., Maina, Joseph, Baker, Andrew C., Alemu, Jahson B., Beger, Maria, Campbell, Stuart J., Darling, Emily S., Eakin, C. Mark, Heron, Scott F., Jupiter, Stacy D., Lundquist, Carolyn J., McLeod, Elizabeth, Mumby, Peter J., Paddack, Michelle J., Selig, Elizabeth R., and van Woesik, Robert (2012) Prioritizing key resilience indicators to support coral reef management in a changing climate. PLoS ONE, 7 (8). e42884. pp. 1-7.

Cinner, Joshua E., McClanahan, Tim R., MacNeil, M. Aaron, Graham, Nicholas A.J., Daw, Tim M., Mukminin, Ahmad, Feary, David A., Rabearisoa, Ando L., Wamukota, Andrew, Jiddawi, Narriman, Campbell, Stuart J., Baird, Andrew H., Januchowski-Hartley, Fraser A., Hamed, Salum, Lahari, Rachael, Morove, Tau, and Kuange, John (2012) Comanagement of coral reef social-ecological systems. Proceedings of the National Academy of Sciences of the United States of America, 109 (14). pp. 5219-5222.

Cappo, Mike, Stowar, Marcus, Stieglitz, Thomas, Lawrey, Eric, Johansson, Charlotte, and Macneil, Aaron (2012) Measuring and communicating effects of MPAs on deep "shoal" fisheries. In: Proceedings of the 12th International Coral Reef Symposium. 18A_1. pp. 1-5. From: 12th International Coral Reef Symposium, 9-13 July 2012, Cairns, QLD, Australia.

Hussey, N.E., MacNeil, M.A., Olin, J. A., McMeans, B. C., Kinney, Michael, Chapman, D. D., and Fisk, A. T. (2012) Stable isotopes and elasmobranchs: tissue types, methods, applications and assumptions. Journal of Fish Biology, 80 (5). pp. 1449-1484.

McClanahan, Tim R., Graham, Nicholas A.J., MacNeil, M. Aaron, Muthiga, Nyawira A., Cinner, Joshua E., Bruggemann, J. Henrich, and Wilson, Shaun K. (2011) Critical thresholds and tangible targets for ecosystem-based management of coral reef fisheries. Proceedings of the National Academy of Sciences of the United States of America, 108 (41). pp. 17230-17233.

Graham, Nicholas A.J., Chabanet, Pascal, Evans, Richard D., Jennings, Simon, Letourneur, Yves, MacNeil, M. Aaron, McClanahan, Tim R., Öhman, Marcus C., Polunin, Nicholas V.C., and Wilson, Shaun K. (2011) Extinction vulnerability of coral reef fishes. Ecology Letters, 14 (4). pp. 341-348.

MacNeil, M. Aaron, Graham, Nicholas A.J., Cinner, Joshua E., Dulvy, Nicholas K., Loring, Philip A., Jennings, Simon, Polunin, Nicholas V., Fisk, Aaron T., and McClanahan, Tim R. (2010) Transitional states in marine fisheries: adapting to predicted global change. Philosophical Transactions of the Royal Society B: Biological Sciences, 365 (1558). pp. 3753-3763.

MacNeil, M. Aaron, and Graham, Nicholas A.J. (2010) Enabling regional management in a changing climate through Bayesian meta-analysis of a large-scale disturbance. Global Ecology and Biogeography , 19 (3). pp. 412-421.

MacNeil, M. Aaron, Graham, Nicholas A.J., Polunin, Nicholas V.C., Kulbicki, Michel, Galzin, Rene, Harmelin-Vivien, Mireille, and Rushton, Steven P. (2009) Hierarchical drivers of reef-fish metacommunity structure. Ecology, 90 (1). pp. 252-264.

MacNeil, M.A., Graham, N.A.J., Conroy, M.J., Fonnesbeck, C.J., Polunin, N.V.C., Rushton, S.P., Chabanet, P., and McClanahan, T.R. (2008) Detection heterogeneity in underwater visual-census data. Journal of Fish Biology, 73 (7). pp. 1748-1763.

Graham, Nicholas A.J., McClanahan, Timothy R., MacNeil, M. Aaron, Wilson, Shaun K., Polunin, Nicholas V.C., Jennings, Simon, Chabanet, Pascale, Clark, Susan, Spalding, Mark D., Letourneur, Yves, Bigot, Lionel, Galzin, René, Öhman, Marcus C., Garpe, Kajsa C., Edwards, Alasdair J., and Sheppard, Charles R.C. (2008) Climate warming, marine protected areas and the ocean-scale integrity of coral reef ecosystems. PLoS ONE, 3 (8). e3039. - .