Faculty & Staff Profiles

James Darwin Thomas

Professor
thomasjd@nova.edu
Education
Areas of Research

My research area is conducting field research in marine biodiversity and biogeography of tropical and subtropical marine systems, with a primary focus on coral reefs. My specialty is documenting evolutionary diversity in coral reef and near-shore tropical marine ecosystems. In addition to my current position here at the NSUOC I have held previous posts as Curator of Crustacea at the Smithsonian National Museum of Natural History, Research Director for the National Coral Reef Institute, and Director of the Reef Foundation.  In the field, my research efforts involve the taxonomy, systematics, and ecology of amphipod crustaceans, especially commensal species that inhabit interior cavities of sponges, ascidians, and bivalve mollusks. Recent studies involved expeditions and student-involved research focusing on in-situ collection of potential hosts in Moorea, French Polynesia, Belize Barrier Reef, and deepwater habitats. These studies have yielded a wealth of new commensal species and host records now in various stages of publication and discovery.

Current students

MS Candidates
Abraham Smith

Publications

Thomas, J.D., and L. Watling. A new genus and species of Didymochelid amphipod from deep water hexactinellid sponges (Crustacea:Amphipoda:Didymocheliidae). Bulletin of the Yale Peabody Museum. In press.

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.

B. Vargas-Angel, S.B. Colley and J.D. Thomas. 2004. Reproductive seasonality and gametogenic cycle of Acropora cervicornisin Broward County, Florida, USA. (in press).

B. Vargas-Angel and J.D. Thomas. 2003. Sexual reproduction of Acropora cervicornis in near-shore waters off Fort Lauderdale, Florida, U.S.A. Coral Reefs 21(1):25-26.

S. E. Crowe 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, 12 pages.

Thomas, J.D. 2002. Book Review: Marine Protected Areas: Tools for Sustaining Ocean Ecosystems by; The Committee on the Evaluation, Design, and Monitoring of Marine Reserves and Protected Areas in the United States. Ocean Studies Board, Commission on Geosciences, Environment, and Resources. National Research Council (2001). Coral Reefs 21:226-228.

Thomas, J.D. 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. (Printed in Jan. 02).

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.(in press).

Sotka, E.E., M.E. Hay, and J.D. Thomas. 1998. Host-plant specialization by a non-herbivorous amphipod: advantages for the amphipod and costs for the seaweed. Oecologia, 25ms pp. (in press)

Thomas, J.D. 1997. Systematics and Phylogeny of the commensal amphipod family Anamixidae (Crustacea: Amphipoda). Records of the Australian Museum, Volume 49:35-98, figures 1-27-187.

Thomas, J.D. 1997. Ecology and behavior of Maxillipius commensalis, a gorgonophile amphipod from Madang, Papua New Guinea (Crustacea: Amphipoda: Maxillipiidae). Bulletin of Marine Science, 58(1):314-326, figs. 1-5.

Thomas, J.D.. 1996. Using Marine Invertebrates to Establish Research and Conservation Priorities. In Biodiversity II: Understanding and Protecting our Biological Resources. Chapter 24, 357:369. Eds. M.L. Reaka-Cudla, D. Wilson, and E.O. Wilson. National Academy Press, 551 pages.

Lowry, J.K., A.A.Myers, M. W. Jebb, and J.D.Thomas. 1995. Amphipoda (Crustacea) of the Madang Lagoon, Papua New Guinea. Geology Oceanography and Biology Series. Records of the Australian Museum, 174 pp.

Thomas, J.D. and L.D. McCann. 1995. Chapter 2. The Families Argissidae, Dexaminidae, Eusiridae, Gammaridae, Leucothoidae, Melphidippidae, Oedicerotidae, Pardaliscidae, Phoxocephalidae, Podoceridae, Stegocephalidae, Stenothoidae, Stilipedidae, Synopiidae, and Urothoidae. 116 pp, 94 figs. (galley). In: A Taxonomic Atlas to the Fauna of the Santa Maria Basin. Eds. L. Watling and P. Scott.

Watling, L. and J.D. Thomas. 1995. Chapter 1. Introduction to the Amphipoda. 20 pp, 30 figs. (galley). In : A Taxonomic Atlas to the Fauna of the Santa Maria Basin. Eds. L. Watling and P. Scott.

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.

Thomas, J.D. 1993. J. Laurens Barnard: a personal glimpse. Journal of Natural History 27:725-726.

Thomas, J.D. 1993. Biological monitoring and tropical biodiversity in marine environments: a critique with recommendations, and comments on the use of amphipods as bioindicators. Journal of Natural History. 27:795-806.

Thomas, J.D. 1992. Podocerus kleidus, new species, from the Florida Keys (Crustacea, Amphipoda, Dulichiidae). Bulletin of Marine Science51(3):309-314, figs. 1-3.

Thomas, J.D. 1992. J. Laurens Barnard (1928-1991). Journal of Crustacean Biology, 12(2):324-326.

Thomas, J.D. 1992. Podocerus chelonophilus, a testudinous amphipod newly recorded from the Western Atlantic Ocean. Bulletin of Marine Science 50(1):108-116, figs. 1-2.

Lowry, J.K., and J. D. Thomas. 1991. A new species of Cerapus from Cudjoe Channel, Lower Florida Keys, USA, with notes on male behaviour (Crustacea: Amphipoda: Corophioidea). Journal of Natural History 25:1461-1467, figs. 1-4.

Thomas, J.D., and J.L. Barnard. 1991. Guernea ipilya and G. yamminye, new species (Crustacea,Amphipoda,Dexaminidae), from the Great Barrier Reef, Australia. Memoirs of the Museum of Victoria 52 (2):299-310, figs. 1-6.

Barnard, J.L., K. Sandved, and J.D. Thomas. 1991. Tube building behavior of Grandidierella, and two species of Cerapus. Hydrobiologia 223:239 -254, 1 figure.

Thomas, J.D., and J.L. Barnard. 1991. Kamaka taditadi, a new marine species from Papua New Guinea (Crustacea, Amphipoda, Corophioidea) . Memoirs of the Museum of Victoria 52(2):311-318, figs. 1-3.

Barnard, J.L. and J.D. Thomas. 1991. Yhi yindi, a new genus and species of Paracalliopiidae from the Great Barrier Reef (Crustacea:Amphipoda). Memoirs of the Museum of Victoria 52(2):283-289, figs. 1-3.

Thomas, J.D., and J.L. Barnard. 1991. Wombalano yerang, a new genus and species of Corophiidae (Crustacea:Amphipoda) from the Great Barrier Reef, Australia. Memoirs of the Museum of Victoria 52(2):319-324, figs. 1-4.

Thomas, J.D., and J.L. Barnard. 1991. Two new species of Netamelita from the Caribbean Sea (Crustacea:Amphipoda:Gammaridea). Proceedings of the Biological Society of Washington, 104(3):583-592, figs. 1-5.

Thomas, J.D., and J.L. Barnard. 1991. A review of the genus Iphimedia (Crustacea:Amphipoda) with descriptions of three new species from Australia, Papua New Guinea and Florida. Invertebrate Taxonomy 5:469-485, figs. 1-9.

Thomas, J.D., and J.L. Barnard. 1991. Photis trapherus, a new elephantine species from the Caribbean Sea (Crustacea: Amphipoda). Proceedings of the Biological Society of Washington, 104(1):96-100, 3 figs. 1-3.

Thomas, J.D., and J.L. Barnard. 1991. Jerbarnia stocki, a new species from the Barrier Reef (Crustacea, Amphipoda). Beaufortia 41(24):169-176, figs. 1-3.

Thomas, J.D., and J.L. Barnard. 1990. Gitana dominica, a new species from the Caribbean Sea (Amphipoda: Amphilochidae). Proceedings of the Biological Society of Washington, 103(3):617-623, figs. 1-3.

Barnard, J.L., and J.D. Thomas. 1990. Ensayara jumanae, a new species from Belize, Caribbean Sea (Amphipoda, Lysianassidae). Proceedings of the Biological Society of Washington, 103(1):120-126, figs. 1-3.

Barnard, J.L. and J.D.Thomas. 1989. A new species, Ampelisca burkei, (Crustacea,Amphipoda) from Florida. Proceedings of the Biological Society of Washington, 102(2):375-384, figs. 1-5.

Barnard, J.L. and J.D.Thomas. 1989. Four new species of Synopiidae from the Carribean region (Crustacea:Amphipoda). Proceedings of the Biological Society of Washington, 102(2):362-374, figs. 1-6.

Thomas, J.D., and J.L. Barnard. 1989. Gammaropsis arawakia, a new species of marine Amphipoda (Crustacea) from Jamaica. Proceedings of the Biological Society of Washington, 102(1):89-94, figs. 1-3.

Thomas, J.D., and J.L. Barnard. 1989. Elasmopus balkomanus, a new species from the Florida Keys (Crustacea,Amphipoda). Proceedings of the Biological Society of Washington, 101(4):234-239, figs. 1-3.

Barnard, J.L., and J.D. Thomas. 1988. Ipanemidae, new family, Ipanema talpa, new genus and species, from the surf zone of Brazil (Crustacea:Amphipoda:Haustoroidea). Proceedings of the Biological Society of Washington, 101(3):614-621, figs. 1-4.

Barnard, J.L., and J.D. Thomas. 1988. Vadosiapus copacabanus, a new genus and species of Exoedicerotidae from Brazil (Crustacea,Amphipoda). Proceedings of the Biological Society of Washington. 101(2):366-374, figs. 1-3.

Barnard. J.L., J.D. Thomas, K.B. Sandved. 1988. Behavior of gammaridean Amphipods (Crustacea): Corophium Grandidierella Podocerus, and Gibberosus (American Megaluropus) in Florida. Crustaceana, Special Supplement No. 13:234-244.

Thomas, J.D. 1987. Audulla chelifera (Indo-Pacific) from the Caribbean Sea (Crustacea:Amphipoda). Proceedings of the Biological Society of Washington, 100(2):364-370, figs. 1-4.

Barnard, J.L., and J.D. Thomas. 1987. A new species of Chevalia from the Caribbean Sea. Proceedings of the Biological Society of Washington, 100(3): 532-542, figs. 1-5.

Barnard, J.L. and J.D. Thomas. 1987. New species of Neomegamphopus from tropical America (Marine Amphipoda, Crustacea). Proceedings of the Biological Society of Washington, 100(1):147-163, figs. 1-6.

Thomas, J.D., and J.L. Barnard. 1986. Two species of Hornellia (subgenus Metaceradocus) from the Florida Keys and Belize (Amphipoda,Melphidippoidea). Bulletin of Marine Science, 38(3):477-486, figs 1-6.

Thomas, J.D., and J.L. Barnard. 1986. New genera and species of the Megaluropus group (Amphipoda,Megaluropidae) from American Seas. Bulletin of Marine Science, 38(3):442-476, figs. 1-15.

Barnard, J.L., J.D. Thomas, and J. Clark. 1986. Coral Reef Amphipods of Jamaica. in, Caribbean Coral Reef Ecosystems, Report 1986, National Museum of Natural History, K. Ruetzler, editor, p.48.

1986. A comparison of amphipod fauna from mangrove and coral reef habitats. Caribbean Coral Reef Ecosystems, Report 1986, National Museum of Natural History, K. Ruetzler, editor, p. 19.

1986. Diel migration of amphipods from coral reef substrates. Caribbean Coral Reef Ecosystems, Report 1986, National Museum of Natural History, K. Ruetzler, editor, p.42.

Thomas, J.D., and J.L. Barnard. 1985. A new marine genus of the Maera group (Crustacea:Amphipoda) from Belize. Proceedings of the Biological Society of Washington, 98(3):630-635, figs. 1-3.

Thomas, J.D., and J.L. Barnard. 1985. Two new species of two new gammaridan genera (Crustacea:Amphipoda) from the Florida Keys. Proceedings of the Biological Society of Washington, 98(1):191-203, figs. 1-7.

Thomas, J.D., and J.L. Barnard. 1985. Perioculodes cerasinus, n. sp., the first record of the genus from the Caribbean Sea (Amphipoda:Oedicerotidae). Proceedings of the Biological Society of Washington, 98(1):98-106, figs. 1-3.

Barnard, J.L., and J.D.Thomas. 1984. Two new species of the Siphonoecetes complex from the Arabian Gulf and Borneo (Crustacea:Amphipoda). Proceedings of the Biological Society of Washington, 97(4):864-881, figs. 1-9.

Thomas, J.D., and J.L. Barnard. 1984. Acanthohaustorius pansus, a new species of sand-burrowing amphipod from Looe Key Reef, Florida Keys, with redescription and distribution data of Acanthohaustorius bousfieldi Frame, 1980 (Amphipoda: Haustoriidae). Proceedings of the Biological Society of Washington, 97(4):909-926, figs. 1-9.

Thomas, J.D. 1983. Discovery of a majid host for the commensal amphipod Stenothoe symbiotica Shoemaker, 1956. Bulletin of Marine Science, 34(3):484-485.

Barnard, J.L., and J.D. Thomas. 1983. A new species of Amphilochus from the gorgonian Ptergorgia anceps in the Caribbean Sea. Festschrift for Dr. Pillai. Selected Papers on Crustacea:179-187, figs. 1-4./P>

Thomas, J.D. 1983. Curidia debrogania, a new genus and species of amphipod (Crustacea:Ochlesidae) from the barrier reefs of Belize. Proceedings of the Biological Society of Washington, 96(1):127-133, figs. 1-3.

Thomas, J.D., and J.L. Barnard. 1983. Transformation of the Leucothoides morph to the Anamixis morph (Amphipoda). Journal of Crustacean Biology, 3(1): 154-157.

Thomas, J.D., and J.L. Barnard. 1983. The Platyischnopiidae of the Americas (Crustacea:Amphipoda). Smithsonian Contributions to Zoology, 375:1-33, figs. 1-12.

Thomas, J.D., and G. W. Taylor. 1981. Mouthpart morphology and feeding strategies of the commensal amphipod Anamixis hanseni Stebbing. Bulletin of Marine Science, 31(2):462-467, figs. 1-5.

Thomas, J.D. 1979. Occurrence of the amphipod Leucothoides pottsi Shoemaker in the tunicate Ecteinascidia turbinata Herdman from Big Pine Key, Florida. Crustaceana, 37(1):107-109.

Thomas, J.D. 1979. Redescription of the wood-rasping amphipod Tropichelura gomezi Ortiz, with notes on its ecology. Proceedings of the Biological Society of Washington, 92(4):863-872, figs. 1-4.

Thomas, J.D.,and R.W. Heard. 1979. A new species of Cerapus Say 1817 (Crustacea:Amphipoda) from the northern Gulf of Mexico with notes on its ecology. Proceedings of the Biological Society of Washington, 92(1):98-105, figs. 1-4.

Thomas, J.D. 1976. A survey of gammarid amphipods of the Barataria Bay, Louisiana region. Contributions to Marine Science, 20:87-111.

Thomas, J.D. 1976. Benthos, in Louisiana Offshore Oil Port, An Environmental Baseline Study, 3:32pp.

Thomas, J.D. 1971. Studies on the fishes of Barataria Bay, Louisiana, an estuarine community. Coastal Studies Bulletin, 6:56-66.

Thomas, J.D. 1970. Some notes on fish collected in the Barataria Bay, Louisiana Region. Coastal Studies Institute Bulletin, 5:35-42.

Abstracts

Thomas, J.D. 2006. Marine Hotspots Revisited. Association of Limnologists and Oceanographers and The Oceanic Society Annual meeting, February 20-24, 2006, Honolulu, Hawaii.

Thomas, J.D. 2005. Unexplored diversity and cryptic species in Leucothoid amphipods: Status, progress, and needs. XII International Colloquium on Amphipoda, National University of Ireland, Cork, July 24-26.

Thomas, J.D. 2004. Marine hotspots revisited. In: Shallow water reefs as predictors of diversity in deep-sea coral. Association of Limnologists and Oceanographers and The Oceanic Society Annual meeting, 15-20 February 2004, Honolulu, Hawaii.

Thomas, J.D. 2002. Predicting biodiversity "hotspots" in coral reefs: combining amphipod phylogenies and geotectonics as a proxy to identify areas of composite evolutionary diversity, International Society for Reef Studies, Cambridge, England, September 3-7.

Thomas, J.D. 2001. Establishing research and conservation priorities in coral reef ecosystems: the risk assessment paradigm, Florida Association of Benthologists (FAB), Long Key, FL, October 16-19.

Thomas, J.D. 2000. A new model for identifying evolutionary diversity in coral reefs using marine invertebrates: A synthesis of geology and biodiversity. Abstract, 9th International Coral Reef Symposium, Biodiversity Mini-symposium, Bali, Indonesia, October 23-27.

Thomas, J.D., and J.L Robinson. 2000. Measure of mesobenthic reef diversity: A pilot study using 3-dimensional artificial substrates as a surrogate for natural substrate. Abstract 9th International Coral Reef Symposium, Bali, Indonesia, October 23-27.

Thomas, J.D., R.E. Dodge, and D.S. Gilliam. 2000. Occurrence of staghorn coral (Acropora cervicornis) outcrops at high latitudes in near shore waters of Ft. Lauderdale, FL., USA. Abstract 9th International Coral Reef Symposium, Bali, Indonesia, October 23-27.

Thomas, J.D. 2000. "A model for siting marine protected areas in coral reefs: A synthesis of geology and biodiversity" Society of Integrative and Comparative Biology, Atlanta, GA, 6-8 January, 2000.

Thomas, J.D. 1998. "Non-indigenous species in managed reef systems: is there a problem?" Society of Integrative and Comparative Biology, Boston, MA, 4-6 January, 1998.

Thomas, J.D. 1998. " Bioinvasions of marine invertebrates in coral reef systems: is it happening?" Benthic Ecology Meeting, Melbourne, FL, 12-15 March, 1998.

Sotka, Erik, M.E. Hay and J.D. Thomas. 1997. "How to specialize on a plant without eating it: an unusual amphipod-seaweed association and its negative effects on the host ", Benthic Society Annual Meeting, Portland Maine, April 1997.

Sotka, Erik, M.E. Hay and J.D. Thomas. 1997. "How to specialize on a plant without eating it: an unusual amphipod-seaweed association and its negative effects on the host ", Annual Meeting, Ecological Society of America, Albuquerque, NM, August 1997.

Thomas, J.D.. 1996. Extreme Levels of Marine Invertebrate Biodiversity in New Guinea, in, Coral Reefs: Global Change and Biodiversity Loss. AAAS Annual Meetieng and Science Innovation Exposition, (AIMSIE) Baltimore, Maryland, February 8-13.

Guidebooks & Keys

Thomas, J.D. and L.D. McCann. 1995. Chapter 2. The Families Argissidae, Dexaminidae, Eusiridae, Gammaridae, Leucothoidae, Melphidippidae, Oedicerotidae, Pardaliscidae, Phoxocephalidae, Podoceridae, Stegocephalidae, Stenothoidae, Stilipedidae, Synopiidae, and Urothoidae. 116 pp, 94 figs. (galley). In: A Taxonomic Atlas to the Fauna of the Santa Maria Basin. L. Watling and P. Scott, editors.

Watling, L. and J.D. Thomas. 1995. Chapter 1. Introduction to the Amphipoda. 20 pp, 30 figs. (galley). In : A Taxonomic Atlas to the Fauna of the Santa Maria Basin. L. Watling and P. Scott, editors.

Thomas, J.D. 1993. Identification Manual for the Marine Amphipoda: (Gammaridea) I. Common Coral Reef and Rocky Bottom Amphipods of South Florida. Florida Department of Environmental Protection:83 pp, figs. 1-101.

Thomas, J.D. 1984. Illustrated guidebook to the shallow water gammaridean amphipods of the Arabian Gulf. ARAMCO annual report, 1984. 102 pages, 63 figs.