Our Research

Connolly Lab

Most of the ongoing research in the laboratory falls under one of the following broad research themes:

Commonness, Rarity, and Biodiversity in High-Diversity Systems

Explaining patterns in the occurrence and abundance of species – why some species are common, why others are rare, why some species tend to be correlated in occurrence or abundance with each other, and why they do or do not co-occur (i.e., what determines species coexistence), are among ecology’s most fundamental questions. They are particularly challenging in highly diverse systems, where species-by-species parameterization of community dynamics models is unfeasible. In current work, we are:

  • Fitting process-based community dynamics models to highly replicated species-level time series of coral reef fishes, to understand how species interactions and response diversity (differential responses of species’ demographic rates to environmental fluctuations) shape the dynamics of relative abundances of fishes on coral reefs, and the ecosystem functions provided by reef fishes.
  • Testing species coexistence mechanisms in reef-building corals during the early post-settlement demographic bottleneck. This work involves spawning corals, and then rearing and settling larvae in different densities across multiple species, to determine how intraspecific and interspecific settlement patterns, and post-settlement interactions, may influence the relative strength of intraspecific and interspecific competition.
  • Developing new theoretical models of coral species interactions, to quantify the extent to which different mechanisms, such as differential susceptibility to hydrodynamic dislodgment, intraspecific spatial aggregation in settlement coupled with neighborhood competition, temporal storage effects, and habitat partitioning, contribute to coral species coexistence.

This research theme is currently supported by a Rubinoff Big Bet award.

Collaborators on different aspects of this work include Joana Figueiredo (Nova Southeastern University), and Mike Emslie and Mariana Álvarez-Noriega (Australian Institute of Marine Science).

Resistance and Resilience of Coral Reefs in the Eastern Tropical Pacific

The Eastern Tropical Pacific (ETP) contains some of the most marginal coral reef habitat in the world, with only an estimated 350-800 km2 of reef in the entire region, a highly variable temperature regime due to the El Niño-Southern Oscillation, and an ocean chemistry that is marginal for the calcification process by which corals build their skeleton (and which make up much of the matrix of coral reefs). The ETP is by far the most depauperate region in the Indo Pacific, for example including less than 50 currently recognized species of reef-building corals (compared to, for example, ~600 on Australia’s Great Barrier Reef). Nevertheless, according to Resource Watch, around 2.5 million people in this region depend on reefs for nutrition or income, and tourists spend around US$500 on reef-associated tourism, making these relatively small areas of outsized importance in the region.

Most shallow-water reefs in this region are dominated by two species from a single genus, Pocillopora. Our work in this system focuses on the resistance and resilience of these corals to environmental stress, particularly temperature stress, and the extent to which corals’ acclimation or adaptation to different regional environmental conditions across the ETP (or example, regions with seasonal upwelling and associated large swings in temperature with regions that experience relatively warm water year-round) influence their ability to cope with change. The core of our work in this area over the last four years has been the Rohr Reef Resilience Program, a project that also involves the Symbiosis and Resilience Lab and the laboratory of Mark Torchin. The project involves characterizing community change in the reef benthos from photomosaics and 3D models of reef structure, in the fish community via visual and video census, in the coral microbiome via genomic analysis, as well as the dynamics of photosynthetic performance and physiological condition of corals. The work has also involved common-garden experiments in which corals from different regions are exposed to the same environmental conditions, to compare their responses.

Most recently, we have been following the 2023-2024 mass bleaching event and its aftermath in Panama, using high-frequency sampling to resolve how a coral’s species identity, and the composition of its microbiome, influence its susceptibility to bleaching and bleaching-induced mortality.

This project consists principally of the Rohr Reef Resilience Project (supported by the Mark and Rachel Rohr Foundation), with additional funding from the Smithsonian Institution’s Life on a Sustainable Planet initiative.

Collaborators on different aspects of this work include Dr Davey Kline (Pacific Blue Foundation), Drs Alan Forman and Nicolas Duprey (Max Planck Institute of Chemistry), Dr Inti Keith (Charles Darwin Foundation, Galapagos), Drs Juan José Alvaredo and Cindy Fernandez (University of Costa Rica), Dr Mike Connelly (National Human Genome Research Institute), Dr Andrea Quattrini (Smithsonian National Museum of Natural History), Dr Miguel Mies (University of San Paolo), Dr Matan Yuval (University of Haifa), and Prof Rowan Barrett (McGill University).

Anthropogenic Impacts on Coral Reefs at Regional to Global Scales

The structure and dynamics of coral reef ecosystems are heavily impacted by a range of human activities, from fishing, to coastal development and associated runoff of sediment, nutrients, and toxic chemicals, to mass coral bleaching and reductions in coral calcification rates linked to the rapidly accelerating impacts of global warming and ocean acidification. Our lab has been involved in analysis and modeling for a wide range of studies of these types of anthropogenic impacts, including population modeling (for example, to investigate the effects of no-take marine areas on the dynamics of coral trout populations in the Great Barrier Reef), meta-analysis (effects of acidification: Chan and Connolly 2013; heritability of temperature tolerance: Bairos-Novak et al. 2021, and long-term global trends in the structure of the coral reef benthos: Tebbett et al. 2023), and analyses of mass coral bleaching events on the Great Barrier Reef and globally (Hughes et al 2017, 2018, 2021; Eakin et al. in review).

Typically, we analyze existing databases, or databases assembled by teams of collaborators. Consequently, we do not have any current funding sources of our own for this work.

There have been numerous external collaborators in this work over the years. However, particularly notable collaborating organizations include James Cook University (Prof Terry Hughes, Prof Dave Bellwood and members of the Reef Function Hub), and NOAA’s Coral Reef Watch.

Marine Ecological and Evolutionary Transformations in the Fossil Record

The emergence of the Isthmus of Panama, a geological event that transpired over many millions of years and culminated with closure of the seaway between the Pacific and Caribbean around 3 million years ago, produced profound changes in the marine environments on either side of the Isthmus. The fossil record of these changes is particularly well-preserved in the Caribbean, where productivity collapsed, substantial extinction and origination of taxa occurred, and major transformations in marine ecosystems (such as the emergence of extensive areas of coral reef) took place. The Panama Paleontology Project (PPP), founded at STRI by Jeremy Jackson and Anthony Coates, collected enormous amounts of data documenting this transformation. Working with the laboratory of Aaron O’Dea, we are revitalizing the PPP, to examine shifts in the structure and dynamics of marine metacommunities that bridge ecological and evolutionary time scales. This work will help us learn how marine communities collapse and reorganize during periods of rapid environmental change (such as the world is currently experiencing).

This project is currently funded by support from the Smithsonian Institution’s Life on a Sustainable Planet initiative.

Our key external collaborator in this work is Dr Jon Todd of the London Natural History Museum, but ultimately we expect to involve all of the researchers who contributed to the PPP.

Commonness and rarity in microbial assemblages

It is becoming increasingly apparent that microbial organisms play crucial roles in the functioning of ecosystems, but of course they cannot be surveyed with traditional ecological sampling protocols. Instead, we rely on sequencing-based approaches, which come with their own set of biases that include sequence amplification, sequencing errors, and other factors that can make the relative abundances of sequences in genomic data sets very different from the relative abundances of the organisms themselves in the environment from which they have been sampled. We are working with the Symbiosis and Resilience Lab to develop new sampling theory for sequence data that allows estimates of the relative abundances of the organisms from which those sequences have been extracted.

Photos by: Aaron O’Dea, Ana Endara and Ed Roberts. Artwork by: Victoria Glynn.