Research Overview

What mechanisms and processes underpin the high biodiversity of coral reefs?

How do large numbers of species coexist when they utilize the same, or very similar, resources? This has been one of the central motivating questions of ecology, particularly tropical ecology, for more than a century. I investigate mechanisms of coexistence, from tradeoffs between specialization and competitive dominance, to cryptic resource partitioning, to the role of different types of environmental fluctuations. This work involves formulation, empirical calibration, and analysis of ecological models at multiple scales: from individual physiology and energetics to species interactions, demography and connectivity.

What determines the commonness or rarity of different species in high-diversity ecosystems like coral reefs?

What makes some species common and others rare? Why do different species’ abundances vary from place to place to such different degrees? Modern biodiversity theories often make competing predictions about the degree to which coexisting species’ abundances vary, and about the spatial and temporal dynamics of those abundances. We apply contemporary biodiversity models to gain insights into the relative importance of factors such as environmental fluctuations and differences in species’ ecological traits in driving these patterns of commonness and rarity. Two dramatically different reef bioregions on either side of the Isthmus make Panama ideal comparative natural laboratory for such work: in the Tropical East Pacific, one group of corals overwhelmingly dominates in the marginal reef conditions there, while in the Caribbean, former community dominants have collapsed to a tiny fraction of their historical abundances.

How do fishing and management tools, such as marine reserves, impact exploited species and the broader functioning of reef ecosystems?

Fishing directly and profoundly impacts the abundances of the species that fishers target, but what impact does it have on the rest of the ecosystem, and how do contemporary management tools like no-take marine reserves mediate these impacts? Our group tackles a range of research problems related to these core questions, including how marine reserve networks influence the recovery of fished populations and fisheries yields, to identifying benchmarks for the sustainability of non-selective, multi-species fisheries, to understanding how levels of critical ecosystem functions depend on the extent and trophic structure of fishing.

How do reef ecosystems respond to climate change?

Today’s coral reefs respond to a very different environment than those to which modern coral reefs have been exposed for hundreds of thousands, and probably millions, of years. These dramatic changes in the physical and chemical environment have impacts that range from higher mortality and reduced growth and reproduction of organisms, to changes in the biogeochemical rates that determine whether reef structures grow or dissolve. This has profound implications for how reef organisms interact with each other, and how they will evolve in the coming decades and centuries. In addition to studying the ongoing changes experienced by today’s reefs, I am interested in using the fossil record to understand how profound environmental upheavals in the past led to reorganizations in the structure and functioning of marine ecosystems.


B.A. Earlham College, 1994

Ph.D., Stanford University, 1999.

Selected Publications

Hughes, T.P., J. T. Kerry, S.R. Connolly, J. G. Álvarez-Romero, C.M. Eakin, S.F. Heron, J. Moneghetti, M.A. Gonzalez. 2021. Emergent properties in the responses of tropical corals to recurrent climate extremes. Current Biology 31: 5393-5399.

Bairos-Novak, K.R., M.O Hoogenboom, M.J.H. van Oppen, and S.R. Connolly. 2021. Coral adaptation to climate change: meta-analysis reveals high heritability across multiple traits. Global Change Biology 27: 5594-5710. DOI 10.1111/gcb.15829.

Thibaut, L.M., and S.R. Connolly. 2020. Hierarchical modelling strengthens evidence for density-dependence in observational time series of population dynamics. Ecology 101:e02893. DOI 10.1002/ecy.2893.

Moneghetti, J., J. Figueiredo, A.H. Baird, and S.R. Connolly. 2019. High-frequency sampling and piecewise models reshape dispersal kernels of a common reef coral. Ecology 100: e02730. DOI: 10.1002/ecy.2730

Hopf, J. G.P. Jones, D.H. Williamson, and S.R. Connolly. 2019. Marine reserves stabilize fish populations and fisheries yields in disturbed coral reef systems. Ecological Applications 29: e01905. DOI: 10.1002/eap.1905.

Hughes, T.P., K.D. Anderson, S.R. Connolly, S.F. Heron, J.T. Kerry, J.M. Lough, A.H. Baird, J.K. Baum, M.L. Berumen, T.C. Bridge, D.C. Claar, C.M. Eakin, J.P. Gimour, N.A.J. Graham, H. Harrison, J.-P.A. Hobbs, A.S. Hoey, M. Hoogenboom, R.J. Lowe, M.T. McCullough, J.M. Pandolfi, M. Pratchett, V. Schoepf, G. Torda, S.K. Wilson. 2018. Spatial and temporal patterns of mass bleaching of corals in the Anthropocene. Science 359: 80-83. 

Connolly, S.R., S.A. Keith, R.K. Colwell, and C. Rahbek. 2017. Process, mechanism, and modelling in macroecology. Trends in Ecology and Evolution 32: 835-844.

Connolly, S.R., T.P. Hughes, and D.R. Bellwood. 2017. A unified model explains commonness and rarity on coral reefs. Ecology Letters 20: 477-486.

Hopf, J.K., G.P. Jones, D.H.Williamson, and S.R. Connolly. 2016. Synergistic effects of marine reserves and harvest controls on the abundance and catch dynamics of a coral reef fishery. Current Biology 26: 1543-1548.

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.

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.

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.

Thibaut, L.M.*, and S.R. Connolly*. 2013. Understanding diversity-stability relationships: toward a unified model of portfolio effects. Ecology Letters 16: 140-150.

Madin, J. S. and S. R. Connolly.  2006.  Ecological consequences of major hydrodynamic disturbances on coral reefs.  Nature 444: 477-480.

Dornelas, M.., S. R. Connolly, and T. P. Hughes.  2006.  Coral reef diversity refutes the neutral theory of biodiversity.  Nature 440: 80-82.

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