Publications by Year
Malerba, M.A., S.R. Connolly, and K. Heimann. In press. An experimentally validated nitrate-ammonium-phytoplankton model including effects of starvation length and ammonium inhibition on nitrate. Ecological Modelling, accepted 22 Aug 2015.
Hopf, J.K., G.P. Jones, D.H. Williamson, and S.R. Connolly. In press. Fishery consequences of marine reserved: short-term pain for longer-term gain. Ecological Applications, accepted 18 Aug 2015.
Freilich, M.A. and S.R. Connolly. In press. Phylogenetic community structure when competition and environmental filtering determine abundances. Global Ecology and Biogeography, accepted 18 Jul 2015.
Hughes, T.P., D.S. Cameron, A. Chin, S.R. Connolly, J.C. Day, G.P. Jones, L. McCook, P. McGinnity, P.J. Mumby, R.J.Pears, R.L. Pressey, G.R. Russ, J. Tanzer, A. Tobin, M.A.L. Young. In Press. A critique of claims for negative impacts of Marine Protected Areas on fisheries. Ecological Applications, accepted 27 Jun 2015.
Casey, J.M., J.H. Choat, and S.R. Connolly. 2015. Coupled dynamics of territorial damselfishes and juvenile corals on the reef crest. Coral Reefs 34: 1-11.
Casey, J.M., S.R. Connolly, and T.D. Ainsworth. 2015. Coral transplantation triggers shift in microbiome and promotion of coral disease associated potential pathogens. Scientific Reports 5: 11903. DOI 10.1038/srep11903.
MacNeil, M.A. and S.R. Connolly. 2015. Multi-scale patterns and processes in reef fish abundance. Pages 116-124 in Mora, C., editor. Ecology of fishes on coral reefs. Cambridge University Press, Cambridge, UK.
Malerba, M.E., S.R. Connolly, and K. Heimann. 2015. Standard flow cytometry as a rapid and non-destructive proxy for cell nitrogen quota. Journal of Applied Phycology, in press. DOI 10.1007/s10811-015-0642-1.
Ban, S.S., N.A.J. Graham, and S.R. Connolly. 2014. Evidence for multiple stressor interactions and effects on coral reefs. Global Change Biology 20: 681-697.
Casey, J.M., T.D. Ainsworth, J.H. Choat, and S.R. Connolly. 2014. Farming behaviour of reef fishes increases the prevalence of coral disease associated microbes and the prevalence of black band disease. Proceedings of the Royal Society of London, Series B 281: 20141032.
Connolly, S.R., M.A. MacNeil, M.J. Caley, N. Knowlton, E. Cripps, M. Hisano, L.M. Thibaut, B.D. Bhattacharya, L. Benedetti-Cecchi, R.E. Brainard, A. Brandt, F. Bulleri, K.E. Ellingsen, S. Kaiser, I. Kröncke, K. Linse, E. Maggi, T. O’Hara, L. Plaisance, G.C.B. Poore, S.K. Sarkar, K.K. Satpathy, U. Schückel, A. Williams, R.S. Wilson. 2014. Commonness and rarity in the marine biosphere. Proceedings of the National Academy of Sciences, USA 111: 8524-8529. (Reviewed by Faculty of 1000)
Figueiredo, J., A.H. Baird, S. Harii, and S.R. Connolly. 2014. Increased local retention of reef coral larvae as a result of ocean warming. Nature Climate Change 4: 498-502.
Highes, T.P., D.R. Bellwood, S.R. Connolly, H.V. Cornell, and R.H. Karlson. 2014. Double jeopardy and global extinction risk in corals and reef fishes. Current Biology 24: 1-6.
Keith, S.A., A.P. Kerswell, and S.R. Connolly. 2014. Global diversity of marine macroalgae: environmental conditions explain less variation in the tropics. Global Ecology and Biogeography 23: 517-529.
Madin, J.S., A.H. Baird, M. Dornelas, and S.R. Connolly. 2014. Mechanical vulnerability explains size-dependent mortality of reef corals. Ecology Letters 17: 1008-1015.
Ban, S.S., N.A.J. Graham, and S.R. Connolly. 2013. Relationships between temperature, bleaching, and white syndrome on the Great Barrier Reef. Coral Reefs 32: 1-12.
Blowes, S.A., M.S. Pratchett, and S.R. Connolly. 2013. Heterospecific aggression and dominance in a guild of coral-feeding fishes: the roles of dietary ecology and phylogeny. American Naturalist 182(2): 157-168.
Chan, N.C.S. and S.R. Connolly. 2013. Sensitivity of coral calcification to ocean acidification: a meta-analysis. Global Change Biology 19(1): 282-290.
Connolly, S.R. and M.A. Kosnik. 2013. Fossil record. Pages 537-544 in Levin, S.A., editor. Encyclopedia of Biodiversity, 2nd edition, Volume 3. (Revised and updated from Connolly 2001.) Academic Press, Waltham, MA, USA.
Figueiredo, J., A.H. Baird, and S.R. Connolly. 2013. Synthesizing larval competence dynamics and reef-scale retention reveals a high potential for self-recruitment in corals. Ecology 94(3): 650-659.
Graham, E.M., A.H. Baird, B.L. Willis, and S.R. Connolly. 2013. Effects of delayed settlement on post-settlement growth and survival of scleractinian coral larvae. Oecologia 173(2): 431-438.
Graham, E.M., A.H. Baird, S.R. Connolly, M.A. Sewell, and B.L. Willis. 2013. Rapid declines in metabolism explain extended coral larval longevity. Coral Reefs 32(2): 539-549. (Winner of the 2013 “Best Paper Award” for Coral Reefs)
Hughes, T.P., S.R. Connolly, and S.A. Keith. 2013. Geographic ranges of reef corals (Cnidaria: Anthozoa: Scleractinia) in the Indo-Pacific. Ecology (Data Paper) 94: 1659. Ecological Archives E094-150.
Keith, S.A. and S.R. Connolly. 2013. Effects if diversity-dependent colonization-extinction dynamics on the mid-domain effect. Global Ecology and Biogeography 22(7): 773-783.
Keith, S.A., A.H. Baird, T.P. Hughes, J.S. Madin, and S.R. Connolly. 2013. Faunal breaks and species composition of Indo-Pacific corals: the role of plate tectonics, environment, and habitat distribution. Proceedings of the Royal Society of London, Series B 280(1763): 20130818.
Thibaut, L.M. and S.R. Connolly. 2013. Understanding diversity-stability relationships: towards a unified model of portfolio effects. Ecology Letters 16: 140-150.
Barbosa, M., S.R. Connolly, M. Hisano, M. Dornelas, and A.E. Magurran. 2012. Fitness consequences of female multiple mating: a direct test of indirect benefits. BMC Evolutionary Biology 12: 185.
Blowes, S.A. and S.R. Connolly. 2012. Risk-spreading, connectivity, and optimal reserve spacing. Ecological Applications 22: 311-321.
Bode, M, S.R. Connolly, and J.M. Pandolfi. 2012. Species differences drive non-neutral structure in Pleistocene coral communities. American Naturalist 180(5): 577-588.
Chan, N.C.S., S.R. Connolly, and B.D. Mapstone. 2012. Effects of sex change on the implications of marine reserves for fisheries. Ecological Applications 22: 778-791.
Connolly, S.R., M.A. Lopez-Yglesias, and K.R.N. Anthony. 2012. Food availability promotes rapid recovery from thermal stress in a scleractinian coral. Coral Reefs 31(4): 951-960.
Connolly, S.R. and L.M. Thibaut. 2012. A comparative analysis of alternative approaches to fitting species abundance models. Journal of Plant Ecology 5: 32-45.
Figueiredo, J. and S.R. Connolly. 2012. Dispersal-mediated Coexistence under Recruitment Limitation and Displacement Competition. Ecological Modelling 243: 133-142.
Hobbs, J-P.A., G.P. Jones, P.L. Munday, S.R. Connolly, and M. Srinivasan. 2012. Biogeography and the structure of coral reef fish communities on isolated islands. Journal of Biogeography 39: 130-139.
Keith, S.A., T.J. Webb, K. Böhning-Gaese, S.R. Connolly, N.K. Dulvy, F. Eigenbrod, K.E. Jones, T. Price, D.W. Redding, I.P.F. Owens, and N.J.B. Isaac. 2012. What is macroecology? Biology Letters 8: 904-906.
Madin, J.S., M.O. Hoogenboom, and S.R. Connolly. 2012. Integrating physiological and biomechanical drivers of population growth over environmental gradients on coral reefs. Journal of Experimental Biology 215: 968-976.
Madin, J.S., T.P. Hughes, and S.R. Connolly. 2012. Calcification, storm damage and population resilience of tabular corals under climate change. PLoS ONE 7(10): e46637.
Malerba, M.E., S.R. Connolly, and K. Heimann. 2012. Nitrate-nitrite dynamics and phytoplankton growth: Formulation and experimental evaluation of a dynamic model. Limnology and Oceanography 57(5): 1555-1571.
Thibaut, L.M., S.R. Connolly, and H.P.A. Sweatman. 2012. Diversity and stability of herbivorous fishes on coral reefs. Ecology 93: 891-901.
Cetina-Heredia, P. and S. R. Connolly. 2011. A simple approximation for larval retention around reefs. Coral Reefs 30: 593-605.
Connolly, S.R. and M. Dornelas. 2011. Fitting and empirical evaluation of models for species abundance distributions. In Magurran, A.E. and B. McGill, editors. Biological diversity: frontiers in measurement and assessment. Oxford University Press, Oxford, UK.
Hisano, M., S.R. Connolly, and W.D. Robbins. 2011. Population growth rates of reef sharks with and without fishing on the Great Barrier Reef: robust estimation with multiple models. PLoS ONE 6: e25028, doi: 10.1371/journal.pone.0025028.
Hoogenboom, M.O., S.R. Connolly, and K.R.N. Anthony. 2011. Biotic and abiotic correlates of tissue quality for common scleractinian corals. Marine Ecology Progress Series 438: 119-128.
Karlson, R.H., S.R. Connolly, and T.P. Hughes. 2011. Spatial variance in abundance and occupancy of corals across broad geographical scales. Ecology 92: 1282-1291.
Pandolfi, J.M., S.R. Connolly, D.J. Marshall, and A.L. Cohen. 2011. Projecting coral reef futures under global warming and ocean acidification. Science 333: 418-422.
Connolly, S.R. and A.H. Baird. 2010. Estimating dispersal potential for marine larvae: dynamic models applied to scleractinian corals. Ecology 91: 3572-3583.
Penin, L., F. Michonneau, A.H. Baird, S.R. Connolly, M.S. Pratchett, M. Kayal, and M. Adjeroud. 2010. Early post-settlement mortality and the structure of coral assemblages. Marine Ecology Progress Series 408: 55-64.
Salomon, Y., S.R. Connolly, and L. Bode. 2010. Effects of asymmetric dispersal on the coexistence of competing species. Ecology Letters 13: 432–441.
Almany, G.R., S.R. Connolly, D.D. Heath, J.D. Hogan, G.P. Jones, L.J. McCook, M. Mills, R.L. Pressey, D.H. Williamson. 2009. Connectivity, biodiversity conservation, and the design of marine reserve networks for coral reefs. Coral Reefs 28: 339-351.
Connolly, S.R. 2009. Macroecological theory and the analysis of species richness gradients. Pages 279-309 in Witman, J. and K. Roy, editors. Marine Macroecology. University of Chicago Press, Chicago, USA.
Connolly, S.R., M. Dornelas, D.R. Bellwood, and T.P. Hughes. 2009. Testing species-abundance models: a new bootstrap approach applied to Indo-Pacific coral reefs. Ecology 90: 3138-3149.
Elmhirst, T., S.R. Connolly, and T.P. Hughes. 2009. Connectivity, regime shifts, and the resilience of coral reefs. Coral Reefs 28: 949–957.
Gotelli, N.J., M.J. Anderson, H.T. Arita, A. Chao, R.K. Colwell, S.R. Connolly, D.J. Currie, R.R. Dunn, G.R. Graves, J.L. Green, J.-A. Grytnes, Y.-H. Jiang, W. Jetz, S.K. Lyons, C.M. McCain, A.E. Magurran, C. Rahbek, T.F.L.V.B. Rangel, J. Soberón, C.O. Webb, and M.R. Willig. 2009. Patterns and causes of species richness: a general simulation model for macroecology. Ecology Letters 12: 873–886.
Hoogenboom, M.O. and S.R. Connolly. 2009. Defining fundamental niche dimensions of corals: synergistic effects of colony size, light and flow. Ecology 90: 767-780.
Hoogenboom, M.O., S.R. Connolly, and K.R.N. Anthony. 2009. Effects of photo acclimation on the light niche of corals: a process-based approach. Marine Biology 156: 2493–2503.
Belmaker, J., Y. Ziv, N. Shashar, and S.R. Connolly. 2008. Regional variation in the hierarchical partitioning of alpha and beta diversity in coral-dwelling fishes. Ecology 89: 2829-2840.
Dornelas, M. and S.R. Connolly. 2008. Multiple modes in a coral species abundance distribution. Ecology Letters 11: 1008–1016.
Graham, E.M., A.H. Baird, and S.R. Connolly. 2008. Survival dynamics of scleractinian coral larvae and implications for dispersal. Coral Reefs 27: 529-539.
Hoogenboom, M.O., S.R. Connolly, and K.R.N. Anthony. 2008. Interactions between morphological and physiological plasticity optimize energy acquisition in corals. Ecology 89: 1144-1154.
Madin, J.S., M.J. O’Donnell, and S.R. Connolly. 2008. Climate-mediated changes to post-disturbance coral assemblages. Biology Letters 4: 490–493.
Anthony, K.R.N., S.R. Connolly, and O. Hoegh-Guldberg. 2007. Bleaching, energetics, and coral mortality risk: Effects of temperature, light, and sediment regime. Limnology and Oceanography 52(2): 716-726.
Dornelas, M.A., S.R. Connolly, and T.P. Hughes. 2006. Coral reef diversity refutes the neutral theory of biodiversity. Nature 440: 80-82.
Hoogenboom, M.O., K.R.N. Anthony, and S.R. Connolly. 2006. Energetic costs of photoinhibition in corals. Marine Ecology Progress Series 313: 1-12.
Madin, J.S. and S.R. Connolly. 2006. Ecological consequences of major hydrodynamic disturbances on coral reefs. Nature 444: 477-480.
Madin, J.S., K.P. Black, and S.R. Connolly. 2006. Scaling water motion on coral reefs: from regional to organismal scales. Coral Reefs 25: 635-644.
Robbins, W., M. Hisano, S.R. Connolly, and J.H. Choat. 2006. Ongoing collapse of coral reef shark populations. Current Biology 16: 2314-2319.
Anthony, K.R.N., M. Hoogenboom, and S.R. Connolly. 2005. Adaptive variation in coral geometry and the optimization of internal colony light climates. Functional Ecology 19: 17-26.
Bellwood, D.R., T.P. Hughes, S.R. Connolly, and J. Tanner. 2005. Environmental and geometric constraints on Indo-Pacific coral reef biodiversity. Ecology Letters 8: 643-651.
Connolly, S.R. 2005. Process-based models of species distributions and the mid-domain effect. American Naturalist 166: 1-11.
Connolly, S.R., T.P. Hughes, D.R. Bellwood, and R.H. Karlson. 2005. Community structure of corals and reef fishes at multiple scales. Science 309: 1363-1365.
Anthony, K.R.N. and S.R. Connolly. 2004. Environmental limits to growth: physiological niche boundaries of corals along turbidity-light gradients. Oecologia 141: 373-384.
Connolly, S.R. and S. Muko. 2003. Space pre-emption, size-dependent competition, and the coexistence of clonal growth forms. Ecology 84: 2979-2988.
Connolly, S.R., D.R. Bellwood, and T.P. Hughes. 2003. Indo-Pacific biodiversity of coral reefs: deviations from a mid-domain model. Ecology 84: 2178-2190.
Hughes, T.P., A. Baird, D.R. Bellwood, M. Card, S.R. Connolly, et al. 2003. Climate change, human impacts, and the resilience of coral reefs. Science 301: 929-933.
Anthony, K.R.N., S.R. Connolly, and B.L. Willis. 2002. Comparative analysis of energy allocation to tissue and skeletal growth in corals. Limnology and Oceanography 47: 1417-1429.
Connolly, S.R. and A.I. Miller. 2002. Global Ordovician faunal transitions in the marine benthos: ultimate causes. Paleobiology 28: 26-40.
Connolly, S.R. and A.I. Miller. 2001. Global Ordovician faunal transitions in the marine benthos: proximate causes. Paleobiology 27: 779-795.
Connolly, S.R., B.A. Menge, and J. Roughgarden. 2001. A latitudinal gradient in recruitment of intertidal invertebrates in the northeast Pacific Ocean. Ecology 82: 1799-1813.
Connolly, S.R. and J. Roughgarden. 1999. Theory of marine communities: competition, predation, and recruitment-dependent interaction strength. Ecological Monographs 66: 277-296.
Connolly, S.R. and J. Roughgarden. 1998. A latitudinal gradient in Northeast Pacific intertidal community structure: evidence for an oceanographically-based synthesis of marine community theory. The American Naturalist 151: 311-326.