SERC Marine Biodiversity Lab Publication List
(* student co-author) 

2014    Reynolds, P.L., J.P. Richardson, and J.E. Duffy. In revision. Field experimental evidence that grazers mediate transition between microalgal and seagrass dominance. Limnology and Oceanography.
 
2013    Byrnes, J.E.K., L. Gamfeldt, F. Isbell, J.S. Lefcheck*, J.N. Griffin, A. Hector, B.J. Cardinale, D.U. Hooper, L.E. Dee, J.E. Duffy.In press. Investigating the relationship between biodiversity and ecosystem multifunctionality: Challenges and solutions. Methods in Ecology and Evolution.
 
2013    Staudinger M.D., S.L. Carter, M.S. Cross, N.S. Dubois, J.E. Duffy, C. Enquist, R. Griffis, J.J. Hellmann, J.J. Lawler, J. O’Leary, S.A. Morrison, L. Sneddon, B.A. Stein, L.M. Thompson, and W. Turner. In press. Biodiversity in a changing climate: a synthesis of current and projected trends in the United States. Frontiers in Ecology and the Environment.
 
2013    Stuart-Smith, R.D., A.E. Bates, J.S. Lefcheck*, J.E. Duffy, and 14 others. 2013. Integrating abundance and functional traits reveals new global hotspots of fish diversity. Nature 501:539-542.
 
2013    Duffy, J.E., L.A. Amaral-Zettler, D.G. Fautin, G. Paulay, T.A. Rynearson, H.M. Sosik, and J.J. Stachowicz. 2013. Envisioning a marine biodiversity observation network. BioScience, 63:350-361.
 
2013    Howard, J. and 65 others. 2013. Oceans and Marine Resources in a Changing Climate. Oceanography and Marine Biology: Annual Review 51:71-192.
 
2013    Ruckelshaus, M., S. Doney, H. Galindo, J. Barry, F. Chan, J.E. Duffy, C. English, S. Gaines, J. Grebmeier, A. Hollowed, N. Knowlton, J. Polovina, N. Rabalais, B. Sydeman, L. Talley. 2013. Securing ocean benefits in the face of climate change. Marine Policy 40:154-159.
 
2013    Whalen*, M.A., J.E. Duffy, and J.B. Grace. 2013. Field experimental evidence for mesograzer control of primary producers in a seagrass bed food web. Ecology 94:510-520.
 
2013    Lefcheck*, J.S., M.A. Whalen*,T.M. Davenport*, J.P. Stone*, and J.E. Duffy. 2013. Diet mixing effects on consumer fitness: A meta-analysis. Ecology, 94:565–572.
 
2013    Duffy, J.E., K.S. Macdonald III, K.M. Hultgren, T.C.S. Chak*, and D. R. Rubenstein. 2013. Decline and local extinction of Caribbean eusocial shrimp. PLoS One 8(2):e54637.
 
2013    Duffy, J.E., A.R. Hughes, an P.-O. Moksnes. 2013. Ecology of seagrass communities. In: Bertness, M.D., J.F. Bruno, B.D. Silliman, and J.J. Stachowicz, editors. Marine Community Ecology and Conservation. Sinauer, In press.
 
2012    Naeem, S., J.E. Duffy, and E. Zavaleta. 2012. The Functions of Biological Diversity in an Age of Extinction. Science 336:1401-1406.
 
2012    Cardinale, B.J., J.E. Duffy, A. Gonzalez, D.U. Hooper, C. Perrings, P. Venail, A. Narwani, G.M. Mace, D. Tilman, D.A. Wardle, A.P. Kinzig, G.C. Daily, M. Loreau, J.B. Grace, A. Larigauderie, D. Srivastava, and S. Naeem. 2012. Biodiversity loss and its impact on humanity. Nature 486:59-67 (doi:10.1038/nature11148).
 
2012    Hooper, D.U., E.C. Adair, B.J. Cardinale, J.E.K. Byrnes, B.A. Hungate, K.L. Matulich, A. Gonzalez, J.E. Duffy, L. Gamfeldt, and M.I. O’Connor. 2012. A global synthesis reveals biodiversity loss as a major driver of ecosystem change. Nature 486:105-108 (doi:10.1038/nature11118).
 
2012    Poore, A.G.B., A.H. Campbell, R.A. Coleman, G.J. Edgar, V. Jormalainen, P.L. Reynolds, E.E. Sotka, J.J. Stachowicz, R.B. Taylor, M.A. Vanderklift, and J.E. Duffy. 2012. Global patterns in the impact of marine herbivores on benthic primary producers. Ecology Letters 15:912-922. 
 
2012    Hultgren, K.M., and J.E. Duffy. 2012. Phylogenetic community ecology and the role of social dominance in sponge-dwelling shrimp. Ecology Letters, 15: 704–713 (doi: 10.1111/j.1461-0248.2012.01788.x).
 
2012    Blake*, R.E. and J.E. Duffy. 2012. Changes in biodiversity and environmental stressors influence community structure of an experimental eelgrass (Zostera marina) system. Marine Ecology Progress Series 470:41-54.
 
2011    Doney, S.C., M. Ruckelshaus, J.E. Duffy, J.P. Barry, F. Chan, C.A. English, H.M. Galindo, J.M. Grebmeier, A.B. Hollowed, N. Knowlton, J. Polovina, N.N. Rabalais, W.J. Sydeman, L.D. Talley. 2011. Climate Change Impacts on Marine Ecosystems. Annual Review of Marine Science 4:11-37 (DOI: 10.1146/annurev-marine-041911-111611)
 
2011    Douglass*, J.G., J.E. Duffy, and E.A. Canuel. 2011. Food web structure in a Chesapeake Bay eelgrass bed as determined through gut contents and 13C and 15N isotope analysis. Estuaries and Coasts 34:701–711 (DOI: 10.1007/s12237-010-9356-4)
 
2011    Wu, X., J.E. Duffy, P.B. Reich, and S. Sun. 2011. A brown-world cascade in the dung decomposer food web of an alpine meadow: Effects of predator interactions and warming. Ecological Monographs 81:313–328.
 
2011    Hultgren, K.M., K.S. Macdonald III, and J.E. Duffy. 2011. Sponge-dwelling snapping shrimp (Alpheidae: Synalpheus) of Barbados, West Indies, with a description of a new eusocial species. Zootaxa 2834:1-16.
 
2011    Cardinale, B.J, K. Matulich, D.U. Hooper, J.E. Byrnes, J.E. Duffy, L. Gamfeldt, P. Balvanera, M.I. O’Connor, and A. Gonzalez. 2011. The functional role of producer diversity in ecosystems. American Journal of Botany 98: 572-592(doi: 10.3732/ajb.1000364)
 
2011    Hultgren, K.M. and J.E. Duffy. 2011. Multi-locus phylogeny of sponge-dwelling snapping shrimp (Caridea: Alpheidae: Synalpheus) supports morphology-based species concepts. Journal of Crustacean Biology 31:352-360 (DOI: 10.1651/10-3382.1)
 
2011    Long, Z.T., J.F. Bruno, and J.E. Duffy. 2011. Food chain length and omnivory determine the stability of a marine subtidal food web. Journal of Animal Ecology 80: 586-594. 
 
2010    Duffy, J.Edoi: 10.1098/rspb.2009.1483). and K.S. Macdonald III. 2010. Kin structure, ecology, and the evolution of social organization in shrimp: A comparative analysis. Proceedings of the Royal Society of London B Biological Sciences 277:575–584 (
 
2010    Douglass*, J.G., K.E. France*, J.P. Richardson, and J.E. Duffy. 2010. Seasonal and interannual change in a Chesapeake Bay eelgrass community: insights into biotic and abiotic control of community structure. Limnology and Oceanography. 55:1499–1520 (DOI: 10.4319/lo.2010.55.4.1499)
 
2010    Blake*, R.E. and J.E. Duffy. 2010. Grazer diversity affects resistance to multiple stressors in an experimental seagrass ecosystem. Oikos. 119:1625–1635 (DOI: 10.1111/j.1600-0706.2010.18419.x)
 
2010    Foley, M.M., B.S. Halpern, F. Micheli, M.H. Armsby, M.R. Caldwell, C.M. Crain, E. Prahler, D. Sivas, N. Rohr, M.W. Beck, M.H. Carr, L.B. Crowder, J.E. Duffy, S.D. Hacker, K. McLeod, C.H. Peterson, H.M. Regan, M.H. Ruckelshaus, P.A. Sandifer, R.S. Steneck. 2010. Guiding ecological principles for marine spatial planning. Marine Policy 34:955–966.
 
2010    Duffy, J.E. 2010. Social biology of Crustacea. In: M. Breed and J. Moore, editors. Encyclopedia of Animal Behavior. Elsevier, Oxford. Pp 421-429.
 
2010    Duffy, J.E. 2010. Sea changes: structure and functioning of emerging marine communities. Pages 95-114 in: H.A. Verhoef and P.J. Morin (editors). Community Ecology. Processes, Models and Applications. Oxford University Press.
 
2010    Hultgren, K.M. and J.E. Duffy. 2010. Sponge host characteristics shape the community structure of their shrimp associates. Marine Ecology Progress Series 407: 1–12.
 
2010    Hultgren, K.M., K.S. Macdonald III, and J.E. Duffy. 2010. Sponge-dwelling snapping shrimp of Curaçao, with descriptions of three new species. Zootaxa 2372: 221–262.
 
2010    Duffy, J.E. 2010. Biodiversity effects: trends and exceptions – a reply to Wardle and Jonsson. Frontiers in Ecology and the Environment 8:11-12.
 
2009    Duffy, J.E. 2009. Why biodiversity is important to functioning of real-world ecosystems. Frontiers in Ecology and the Environment 7:437-444.
 
2009    Duffy, J.E., D.S. Srivastava, J. McLaren, M. Sankaran, J. Griffin, M. Emmerson, M. Solan, and K.E. Jones. 2009. Forecasting decline in ecosystem services under realistic scenarios of extinction. Pages 60-77 in: Naeem, S., D.E. Bunker, A. Hector, and C. Perrings (editors). Biodiversity, Ecosystem Functioning, and Human Wellbeing: An Ecological and Economic Perspective. Oxford University Press.
 
2009    Cardinale, B.J., J.E. Duffy, D.S. Srivastava, M. Loreau, M. Thomas, and M. Emmerson. 2009. Towards a Food-web perspective on biodiversity and ecosystem functioning. Pages 105-120 in: Naeem, S., D.E. Bunker, A. Hector, and C. Perrings (editors). Biodiversity, Ecosystem Functioning, and Human Wellbeing: An Ecological and Economic Perspective. Oxford University Press.
 
2009    Duffy, J.Ehttp://www.actionbioscience.org/biodiversity/duffy.html). . 2009. The future of marine fish resources. AIBS Action BioScience (
 
2009    Spivak*, A.C., E.A. Canuel, J.E. Duffy, and J.P. Richardson. 2009. Nutrient enrichment and food web composition affect ecosystem metabolism in an experimental seagrass habitat. PLoS One 4(10): e7473:1-13.
 
2009    Macdonald III, K.S., K. Hultgren, and J.E. Duffy. 2009. The sponge-dwelling snapping shrimps (Crustacea, Decapoda, Alpheidae, Synalpheus) of Discovery Bay, Jamaica, with descriptions of four new species. Zootaxa 2199:1-57.
 
2009    Srivastava, D.S., B.J. Cardinale, A.L. Downing, J.E. Duffy, C. Jouseau, M. Sankaran, and J.P. Wright. 2009. Diversity has stronger top-down than bottom-up effects on decomposition. Ecology 90:1073-1083.
 
2009    Cardinale, B.J., D. Srivastava, J.E. Duffy, J. Wright, A. Downing, M. Sankaran, C. Jouseau, M. Cadotte, I. Carroll, J. Weis, A. Hector, and M. Loreau. 2009. Effects of biodiversity on the functioning of ecosystems: A summary of 164 experimental manipulations of species richness. Ecology 90:854 (Ecological Archives E090-060).
 
2009    Spivak*, A.C., E.A. Canuel, J.E. Duffy, J.G. Douglass, and J.P. Richardson. 2009. Community composition and nutrient availability alter sediment organic matter composition in a seagrass bed: a field experiment. Marine Ecology Progress Series 376: 55–67.
 
2008    Bruno J.F., K.E. Boyer, J.E. Duffy, and S.C. Lee. 2008. Relative and interactive effects of plant and grazer richness in a benthic marine community. Ecology 89:2518-2528.
 
2008    Douglass*, J.G., J.E. Duffy, and J.F. Bruno. 2008. Herbivore and predator diversity interactively affect ecosystem properties in marine macroalgal communities. Ecology Letters 11:598-608.
 
2008    Rubenstein, D.R., B.V. McCleery, and J.E. Duffy. 2008. Microsatellite development suggests evidence of polyploidy in the social sponge-dwelling snapping shrimp Zuzalpheus brooksi. Molecular Ecology Resources 8:890-894.
 
2008    Tóth, E. and J.E. Duffy. 2008. Influence of sociality on allometric growth and morphological differentiation in sponge-dwelling alpheid shrimp. Biological Journal of the Linnean Society 94:527-540.
 
2008    Duffy, J.E. 2008. General ecology: Association. Pages 269-272 in: Encyclopedia of Ecology. Elsevier, Oxford, UK.
 
2007    Stachowicz, J.J., J.F. Bruno, and J.E. Duffy. 2007. Understanding the effects of marine biodiversity on community and ecosystem processes. Annual Review of Ecology, Evolution, and Systematics, 38:739-766. (featured as Must-Read [6.0] paper in Faculty of 1000)
 
2007    Duffy, J.E. and M. Thiel, editors. 2007. Evolutionary ecology of social and sexual systems: Crustaceans as model organisms. Oxford University Press.
 
2007    Thiel, M. and J.E. Duffy. 2007. The behavioral ecology of crustaceans. A primer in taxonomy and functional biology. In: Duffy, J.E. and M. Thiel, editors. Evolutionary ecology of social and sexual systems: Crustaceans as model organisms. Oxford University Press, pp 3-28.
 
2007    Duffy, J.E. 2007. The evolution of eusociality in sponge-dwelling shrimp. In: Duffy, J.E. and M. Thiel, editors. Evolutionary ecology of social and sexual systems: Crustaceans as model organisms. Oxford University Press, pp 387-409.
 
2007    Duffy, J.E.Thiel. 2007. Sexual and social behavior of Crustacea: A way forward. In: Duffy, J.E. and M. Thiel, editors. Evolutionary ecology of social and sexual systems: Crustaceans as model organisms. Oxford University Press, pp 461-473. and M.
 
2007    Long, Z.T., J.F. Bruno, and J.E. Duffy. 2007. Biodiversity mediates productivity through different mechanisms at adjacent trophic levels. Ecology 88:2821-2829.
 
2007    Douglass*, J.G., J.E. Duffy, A.C. Spivak*, and J.P. Richardson. 2007. Nutrient versus consumer control of community structure in a Chesapeake Bay eelgrass habitat. Marine Ecology Progress Series 348:71-83.
 
2007    Spivak*, A.C., E.A. Canuel, J.E. Duffy, and J.P. Richardson. 2007. Top-down and bottom-up controls on sediment organic matter composition in an experimental seagrass ecosystem. Limnology and Oceanography 52: 2595-2607.
 
2007    Ríos*, R. and J.E. Duffy. 2007. A review of the sponge-dwelling snapping shrimp from Carrie Bow Cay, Belize, with description of Zuzalpheus, new genus, and six new species (Crustacea: Decapoda: Alpheidae). Zootaxa 1602:1-89.
 
2007    Worm, B., E.B. Barbier, N. Beaumont, J.E. Duffy, C. Folke, B.S. Halpern, J.B.C. Jackson, H.K. Lotze, F. Micheli, S.R. Palumbi, E. Sala, K.A. Selkoe, J.J. Stachowicz, and R. Watson. 2007. Response to comments on “Impacts of biodiversity loss on ocean ecosystem services”. Science 316:1282-1284.
 
2007    Duffy, J.E., B.J. Cardinale, K.E. France*, P.B. McIntyre, E. Thébault, and M. Loreau. 2007. The functional role of biodiversity in food webs: Incorporating trophic complexity. Ecology Letters 10:522-538.
 
2007    Canuel, E.A., A.C. Spivak*, E.J. Waterson*, and J.E. Duffy. 2007. Biodiversity and food web structure influence short-term accumulation of sediment organic matter in an experimental seagrass system. Limnology and Oceanography 52: 590-602.
 
2006    Worm, B., E.B. Barbier, N. Beaumont, J.E. Duffy, C. Folke, B.S. Halpern, J.B.C. Jackson, H.K. Lotze, F. Micheli, S.R. Palumbi, E. Sala, K.A. Selkoe, J.J. Stachowicz, and R. Watson. 2006. Impacts of biodiversity loss on ocean ecosystem services. Science 314:787-790. (featured as Must-Read [6.0] paper in Faculty of 1000)
 
2006    Cardinale, B.J., Srivastava, D.S., Duffy, J.E., Wright, J.P., Downing, A.L., Sankaran, M. and Jouseau, C. 2006. Effects of biodiversity on the functioning of trophic groups and ecosystems: A meta-analysis. Nature 443:989-992. (featured as Must-Read [6.0] paper in Faculty of 1000)
 
2006    France*, K.E. and J.E. Duffy. 2006. Biodiversity, dispersal, and scale interactively affect stability of ecosystem function in seagrass metacommunities. Nature 441:1139-1143. (featured as Must-Read [4.8] paper in Faculty of 1000)
 
2006    Valentine, J.F. and J.E. Duffy. 2006. The central role of grazing in seagrass ecology. In: A.W.D. Larkum, R.J. Orth, and C.M. Duarte (eds). Seagrasses: Biology, Ecology, and Conservation. Springer, Amsterdam, pp. 463-501.
 
2006    Bruno, J.F., S.C. Lee*, J.S. Kertesz*, R.C. Carpenter, Z.T. Long, and J.E. Duffy. 2006. Partitioning the effects of algal species identity and richness on benthic marine primary production. Oikos 115:170-178. 
 
2006    Macdonald, K.S. III and J.E. Duffy. 2006. Two new species of sponge-dwelling snapping shrimp from the Belizean Barrier Reef, and a synopsis of the Synalpheus brooksi species complex. American Museum Novitates, 3543: 1-22.
 
2006    Macdonald, K.S. III, R. Ríos*, and J.E. Duffy. 2006. Biodiversity, host specificity, and dominance by eusocial species among sponge-dwelling alpheid shrimp on the Belize Barrier Reef. Diversity and Distributions 12:165-178.
 
2006    Duffy, J.E. 2006. Biodiversity and the functioning of seagrass ecosystems. Marine Ecology Progress Series 311:233-250 (Invited).
 
2006    Duffy, J.E. and J.J. Stachowicz. 2006. Why biodiversity is important to oceanography: potential roles of genetic, species, and trophic diversity in pelagic ecosystem processes. Marine Ecology Progress Series 311:179-189.
 
2006    France*, K.E. and J.E. Duffy. 2006. Consumer diversity mediates invasion dynamics at multiple trophic levels. Oikos 113:515-529.
 
2005    Duffy, J.E., J.P. Richardson, and K.E. France*. 2005. Ecosystem consequences of diversity depend on food chain length in estuarine vegetation. Ecology Letters 8:301-309. (featured as Must-Read [6.0] paper in Faculty of 1000)
 
2005    Tóth, E. and J.E. Duffy. 2005. Coordinated group response to nest intruders in social shrimp. Biology Letters 1:49-52 (featured in Research Highlights section of Nature, 3 Mar 2005, p. 36; New York Times 15 March 2005).
 
2005    Bruno, J.F., K.E. Boyer, J.E. Duffy, S.C. Lee*, and J.S. Kertes*. 2005. Effects of macroalgal species identity and richness on primary production in benthic marine communities. Ecology Letters 8:1165-1174.
 
2005    Macdonald*, K.S. III, L. Yampolsky, and J.E. Duffy. 2005. Molecular and Morphological Evolution of the amphipod radiation of Lake Baikal. Molecular Phylogenetics and Evolution 35:323-343.
 
2004    Rhode*, J.M. and J.E. Duffy. 2004. Relationships between bed age, bed size, and genetic structure in Chesapeake Bay (Virginia, USA) eelgrass (Zostera marina L). Conservation Genetics 5: 1-11.
 
2004    Rhode*, J.M. and J.E. Duffy. 2004. Seed Production from the Mixed Mating System of Chesapeake Bay (USA) Eelgrass (Zostera marina L; Zosteraceae). American Journal of Botany 91:192-197.
 
2004    Morrison, C. L., R. Ríos*, and J.E. Duffy. 2004. Phylogenetic evidence for an ancient rapid radiation of Caribbean sponge-dwelling snapping shrimps (Synalpheus). Molecular Phylogenetics and Evolution 30:563-581.
 
2003    Worm, B. and J.E. Duffy. 2003. Biodiversity, productivity, and stability in real food webs. Trends in Ecology and Evolution 18:628-632.
 
2003    Duffy, J.E. 2003. Biodiversity loss, trophic skew, and ecosystem functioning. Ecology Letters 6:680-687 (Top 20 most cited papers in Ecology Letters, as of July 2006).
 
2003    Duffy, J.E., J.P. Richardson, and E.A. Canuel. 2003. Grazer diversity effects on ecosystem functioning in seagrass beds. Ecology Letters 6:637-645 (featured in Editor’s Choice section of Science, 1 Aug 2003, p. 569).
 
2003    Duffy, J.E. 2003. The ecology and evolution of eusociality in sponge-dwelling shrimp. Pp. 217-252 in: T. Kikuchi, S. Higashi, and N. Azuma (editors). Genes, Behaviors, and Evolution in Social Insects. University of Hokkaido Press, Sapporo, Japan. (Also published in Japanese translation in the journal Seibutsu no Kagaku, Iden (Life Science, Heredity) April 2003, translated by A. Noriko & S. Higashi).
 
2003    Sagasti*, A., J.E. Duffy, and L.C. Schaffner. 2003Effects of stress on recruitment: estuarine epifauna recruit despite hypoxic stress. Marine Biology 142: 111-122.
 
2002    Duffy, J.E. 2002Biodiversity and ecosystem function: the consumer connection. Oikos99: 201-219 (6th most cited paper in Oikos, as of July 2006; ISI top 1% of citations in field from 2002).
 
2002    Duffy, J.E., C.L. Morrison, and K.S. Macdonald*. 2002Colony defense and behavioral differentiation in the eusocial shrimp Synalpheus regalis. Behavioral Ecology and Sociobiology 51:488-495.
 
2001    Duffy, J.E. and A.M. Harvilicz†. 2001. Species-specific impacts of grazing amphipods in an eelgrass-bed community. Marine Ecology Progress Series 223:201-211.
2001    Duffy, J.E., K.S. Macdonald*, J.M. Rhode*, and J.D. Parker*. 2001. Grazer diversity, functional redundancy, and productivity in seagrass beds: an experimental test. Ecology 82:2417-2434.
2001    Parker*, J.D., J.E. Duffy, and R.J. Orth. 2001. Plant species diversity and composition: experimental effects on marine epifaunal assemblages. Marine Ecology Progress Series 224:55-67. 
 
2001    Sagasti*, A., L.C. Schaffner, and J.E. Duffy. 2001. Effects of periodic hypoxia on mortality, feeding and predation in an estuarine epifaunal community.Journal of Experimental Marine Biology and Ecology 258:257-283.
 
2000    Duffy, J.E., C.L. Morrison, and R. Ríos*. 2000. Multiple origins of eusociality among sponge-dwelling shrimps (Synalpheus). Evolution 54:503-516.
 
2000    Duffy, J.E. and M.E. Hay. 2000. Strong impacts of grazing amphipods on the organization of a benthic community. Ecological Monographs 70:237-263.
 
2000    Duffy, J.E. and M.E. Hay. 2000. Ecology and evolution of marine consumer-prey interactions. Pages 131-157 in: Bertness, M.D., S. Gaines, and M.E. Hay (editors). Marine Community Ecology. Sinauer Associates.
 
2000    Sagasti*, A., L.C. Schaffner, and J.E. Duffy. 2000. Epifaunal communities thrive in an estuary with hypoxic episodes. Estuaries 23:474-487.
 
1999    Ríos*, R. and J.E. Duffy. 1999. Description of Synalpheus williamsi, a new species of sponge-dwelling shrimp (Crustacea: Decapoda: Alpheidae), with remarks on its first larval stage. Proceedings of the Biological Society of Washington 112:541-552.
 
1999    Duffy, J.E. and K.S. Macdonald*. 1999. Colony structure of the social snapping shrimp, Synalpheus filidigitus, in Belize. Journal of Crustacean Biology 19:283-292.
 
1998    Duffy, J.E. 1998. On the frequency of eusociality in snapping shrimps with description of a new eusocial species. Bulletin of Marine Science 63:387-400.
 
1996    Duffy, J.E. 1996. Eusociality in a coral-reef shrimp. Nature 381:512-514. (News & Views Commentary by J. Seger and N.A. Moran, pp. 473-474).  
 
1996    Duffy, J.E. 1996. Resource-associated population subdivision in a symbiotic coral-reef shrimp. Evolution 50:360-373.
 
1996    Duffy, J.E. 1996. Specialization, species boundaries, and the radiation of sponge-dwelling alpheid shrimp. Biological Journal of the Linnean Society 58:307-324.
 
1996    Duffy, J.E. 1996. Synalpheus regalis, new species, a sponge-dwelling shrimp from the Belize Barrier Reef, with comments on host specificity in SynalpheusJournal of Crustacean Biology16:564-573. 
 
1994    Duffy, J.E. and M.E. Hay. 1994. Herbivore resistance to seaweed chemical defense: the roles of mobility and predation risk. Ecology 75:1304-1319.
 
1994    Pennings, S.C., S.R. Pablo, V.J. Paul, and J.E. Duffy. 1994. Effects of sponge secondary metabolites in different diets on feeding by three groups of consumers. Journal of Experimental Marine Biology and Ecology180:737-
 
1993    Duffy, J.E. 1993. Genetic population structure in two tropical sponge-dwelling shrimps that differ in dispersal potential. Marine Biology 90:127-138.
 
1992    Duffy, J.E. 1992. Host use patterns and demography in a guild of tropical sponge-dwelling shrimps. Marine Ecology Progress Series 90:127-138.
 
1992    Duffy, J.E. and V.J. Paul. 1992. Prey nutritional quality and the effectiveness of chemical defenses against tropical reef fishes. Oecologia 90:333-339.
 
1991    Duffy, J.E. and M.E. Hay. 1991. Host plants as food and shelter: determinants of food choice in an herbivorous marine amphipod. Ecology 72: 1286-1298.
 
1991    Duffy, J.E. and M.E. Hay. 1991. Amphipods are not all created equal: a reply to Bell. Ecology 72:354-358.
 
1990    Duffy, J.E. 1990. Amphipods on seaweeds: partners or pests? Oecologia 83:267-276.
 
1990    Duffy, J.E. and M.E. Hay. 1990. Seaweed adaptations to herbivory. BioScience 40:368-376.
 
1990    Hay, M.E., J.E. Duffy, and W. Fenical. 1990. Host-plant specialization decreases predation on a marine amphipod: an herbivore in plant's clothing. Ecology 71:733-743.
 
1990    Hay, M.E., J.E. Duffy, V.J. Paul, P.E. Renaud, and W. Fenical. 1990. Specialist herbivores reduce their susceptibility to predation by feeding on the chemically defended seaweed Avrainvillea longicaulis. Limnology and Oceanography 35:1734-1743.
 
1989    Hay, M.E., J.R. Pawlik, J.E. Duffy, and W. Fenical. 1989. Seaweed-herbivore-predator interactions: host-plant specialization reduces predation on small herbivores. Oecologia 81:418-427.
 
1988    Hay, M.E., J.E. Duffy, and W. Fenical. 1988. Seaweed chemical defense: among-compound and among-herbivore variance. Proceedings of the Sixth International Coral Reef Symposium, Townsville, Australia 3:43-48.
 
1988    Hay, M.E., J.E. Duffy, W. Fenical, and K. Gustafson. 1988. Chemical defense in the seaweed Dictyopteris delicatula: differential effects against reef fishes and amphipods. Marine Ecology Progress Series 48:185-192.
 
1987    Hay, M.E., J.E. Duffy, C.A. Pfister, and W. Fenical. 1987. Chemical defense against marine herbivores: are amphipods insect equivalents? Ecology 68:1567-1580.
 
1987    Paul, V.J., M.E. Hay, J.E. Duffy, W. Fenical, and K. Gustafson. 1987. Chemical defense in the seaweed Ochtodes secundiramea (Montagne) Howe (Rhodophyta): effects of its monoterpenoid components upon diverse coral-reef herbivores. Journal of Experimental Marine Biology and Ecology 114:249-260.
 
1984    Duffy, J.E. and S. Tyler. 1984. Quantitative differences in mitochondrial ultrastructure of a thiobiotic and an oxybiotic turbellarian. Marine Biology 83:95-102.