People and ecosystems

Understanding of the links between coral reef ecosystems, the goods and services they provide to people, and the wellbeing of human societies.


Ecosystem dynamics: past, present and future

Examining the multi-scale dynamics of reefs, from population dynamics to macroevolution


Responding to a changing world

Advancing the fundamental understanding of the key processes underpinning reef resilience.

Coral Bleaching

Coral Bleaching

Coral Reef Studies

From 2005 to 2022, the main node of the ARC Centre of Excellence for Coral Reef Studies was headquartered at James Cook University in Townsville, Queensland (Australia)

Menu Image Menu Image Menu Image Menu Image Menu Image Menu Image Menu Image
ResearchersResearchers StudentsStudents AdjunctsAdjuncts AlumniAlumni ManagementManagement
Sean Connolly

Sean Connolly


Australian Professorial Fellow (2008-2012)
Associate Professor James Cook University (2007-)
Senior Lecturer JCU (2003-2006), Lecturer J.C.U. (2000-2003)
Postdoctoral Fellow, Research Training Group in the Analysis of Biological Diversification, University of Arizona, USA (1999-2000).

PhD, Biological Sciences Stanford University, USA • B.A., Biology Earlham College, USA

Program 2: Understanding and Managing Coral Reef Biodiversity

James Cook University

+61 (0)7 4781 4242

Research Interests

My research group uses a combination of mathematical modelling and empirical work, to address fundamental questions about the origin and maintenance of biodiversity, and also to understand the ecological impacts of environmental changes caused by human activity, such as overfishing and climate change. Mostly, but not exclusively, we use coral reefs as a study system.

Our ongoing work spans a broad range of processes and scales, from the determinants of global-scale patterns in species richness to the energetics of individual organisms. Key research areas include:

Species Richness Gradients on Coral Reefs.—We are investigating the effects of historical and contemporary environmental factors on coral reef biodiversity. Increasingly, we are moving beyond traditional randomization and correlative approaches that focus only on patterns in species richness, and towards approaches that allow testing of multiple predictions – not only species richness, but the full distribution of species range sizes and locations that give rise to those predictions. A key part of this is building hypothesized mechanisms into process-based models in which species ranges arise dynamically in response to the geographical distribution of environmental conditions (habitat availability, temperature, etc.).

Commonness, Rarity, and Biodiversity on Coral Reefs.—We are using patterns of species richness and relative abundance in coral reef assemblages to test a variety of general models of community dynamics suitable for high-diversity assemblages like coral reefs. Most previous tests of biodiversity theory have focused on a single prediction (for instance, the species-abundance distribution at the level of individual sites), which is problematic because very different mechanistic assumptions often lead to similar or even identical predictions. To overcome this, we are exploring analytical approximations that identify shared predictions of models that make similar core assumptions about mechanism, and exploiting hierarchically-structured empirical data sets to test multiple predictions of biodiversity simultaneously. This gives us much greater power to distinguish between competing explanations.

Community ecology.—We address a broad range of questions in community ecology. Current projects include the interactive effects of heterospecific aggression and dietary specialization on community structure in butterflyfishes, the relationship between biodiversity and the temporal stability of ecosystem functioning, dispersal-mediated mechanisms of species coexistence, effects of habitat engineering by damselfishes on benthic community structure and dynamics, and the role of demographic tradeoffs in the coexistence of reef coral species.

Population Dynamics, Marine Protected Areas, and Extinction Risk on Coral Reefs.—Coral reef fisheries provide sustenance and income to millions of people worldwide. Increasing human population size, and the globalisation of fish markets, are increasing the pressure on many coral reef species, including those that are directly targeted or indirectly affected by fishing activities. We are using population models to investigate a variety of questions related to the viability of coral reef species subject to fishing pressure. Key recent and ongoing topics include robust estimation of population viability in coral reef shark populations, and determining the effects of no-take marine reserves on sustainable yields of reef fish species.

Physiological Ecology of Reef Corals.—Physical environmental conditions influence population and community dynamics mainly through their effects on the physiology of individual organisms –by influencing their acquisition and expenditure of energy, and their responses to encounters with symbionts, competitors, prey, predators, and pathogens. Our work in this area focuses on going beyond simple “canned” analyses of laboratory experiments that examine individual colony responses to environmental stress, to the calibration of population-dynamic models that allow us to understand how environmental variables like light, temperature, and ocean acidity influence the energy budgets of coral colonies, and consequently their lifetime growth, survival, and reproductive output. By linking coral demography to calibrated responses of organisms to environmental conditions, we are in a much better position to anticipate likely responses to environmental changes, such as increases in coastal runoff, temperature, and ocean acidification.

Publications online


Selected Publications



Australian Research Council Pandora

Partner Research Institutions

Partner Partner Partner Partner
Coral Reef Studies