• Investigations of mechanisms and modes of evolutionary diversity in coral reefs· Marine biodiversity and biogeography
• Ecology, phylogeny, and behavior commensal amphipod crustaceans
• Evolution of feeding tolerance to chemically-rich seaweeds by amphipod mesograzers
• Evolution of eusociality in marine invertebrates
• Use of morphological and molecular approaches in identifying global, basin, and regionally significant areas of marine biodiversity
• Scientific design and best science strategy for site selection of marine protected areas (MPA's)
• Application of scientific research tools in marine conservation
• Microvideo study of functional morphology and behavior in peracarid crustaceans
• Development and application of bioindicators in marine environments
• Investigations of natural and anthropogenic stressors in tropical and temperate marine environments
• Marine biodiversity policy development
• Monitoring and assessment of benthic marine communities
• Energetics and benthic population ecology of near shore coastal ecosystems
• Expeditions, surveys, and inventories of coral reef and tropical coastal systems

• Systematics, taxonomy, ecology, and phylogeny of tropical gammarid amphipod crustaceans
• Review of Marine Protected Areas
• Survey of introduced species in the marine environment
• Population dynamics of commensal amphipods

Selected Publications (Complete publication list)

White, K.N. & J.D. Thomas. Leucothoidae. In: Lowry, J.K. & Myers, A.A. (eds), Amphipoda of the Great Barrier Reef, Australia. Zootaxa. In press.

Richards, V.P., J.D. Thomas, M.J. Stanhope and M.S. Shivji. 2007. Genetic connectivity in the Florida reef system: comparative phylogeography of commensal invertebrates with contrasting reproductive strategies. Molecular Ecology 16(1):139-157.

Thomas, J.D. and K.N. Klebba. 2007. New species and host associations of commensal leucothoid amphipods from coral reefs in Florida and Belize (Crustacea: Amphipoda). Zootaxa: 1494: 1-44, 27 figures.

Thomas, J.D. and K.N. Klebba. 2006. Studies of commensal leucothoid amphipods: two new sponge-inhabiting species from south Florida and the western Caribbean. Journal of Crustacean Biology 26(1): 13-22.

Bernardo Vargas-Angel, Susan B. Colley, S, Michael Hoke, and James D.Thomas. 2005. The reproductive seasonality and gametogenic cycle of Acropora cervicornis in Broward County, Florida, U.S.A. Coral Reefs 25(1):110-122.

Richards, V. P., James D. Thomas, Michael J. Stanhope and Mahmood S. Shivji. 2004. High levels of gene flow in commensal, brooding marine amphipods: mitochondrial DNA variation in Florida populations of the Leucothoe spinicarpa species complex. 10th International Coral Reef Symposium, Okinawa, Japan, June 28 - July 2, 2004.

Vargas-Angel, B., J.D. Thomas, S.M. Hoke. 2003. High Latitude Acropora cervicornis thickets off Fort Lauderdale, Florida, USA. Coral Reefs 465-475.

Crowe, S.E. and J. D. Thomas. 2002. Abundance and Distribution of Commensal Amphipods from Common Marine Sponges of Southeast Florida. Special volume, Modern approaches to the study of Crustacea, Springer-Verlag.

Vargas-Angel, B. and J.D. Thomas. 2002. Sexual reproduction of Acropora cervicornis in nearshore waters off Broward County, Florida, USA. Coral Reefs 21:25-26.

Thomas, J.D. 2001. Preface. Proceedings of the National Coral Reef Institute's International Conference on Scientific Aspects of Coral Reef Assessment, Monitoring and Restoration. Bulletin of Marine Science, 69(2): ii-iv, 289-1056.

Thomas, J.D. 2001. Proceedings of the National Coral Reef Institute's International Conference on Scientific Aspects of Coral Reef Assessment, Monitoring and Restoration. Editor, Bulletin of Marine Science, 69(2): 287-1056.

Thomas, J.D., and R.E. Dodge. 1999. Quick Action Needed for World's Declining Coral Reefs. Results of the International Conference on Scientific Aspects of Coral Reef Assessment, Monitoring, and Restoration. Earth Systems Monitor, U.S. Dept. Commerce/NOAA, 10(1): 12-13, 16.

Thomas, J.D. 1999. Moolapheonoides utmas, new species, from Coral Reefs in the Madang Lagoon, Papua New Guinea (Amphipoda, Cyproideidae), Bulletin of Marine Science, 65(2):515-521, figures 1-3.

Thomas, J.D. and M. Ortiz. 1995. Leucothoe laurensi, n. sp., a new species of Leucothoid amphipod from Cuban Waters (Crustacea: Amphipoda: Leucothoidae). Proceedings of the Biological Society of Washington, 108(4):613-616, figs. 1-2.