JDJ. Emmett Duffy

J. Emmett Duffy

*This is an algorithmically generated author record based on publicly available information.

Current Organizations / Institutes

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Previous Organizations / Institutes

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J. Emmett Duffy has a total of 28 co-authors. Here are the top co-authors by number of shared publications:


Latest Publications

  • Open Access

    Marine biodiversity and ecosystem functioning: what’s known and what’s next?

    by Lars Gamfeldt, Jonathan S Lefcheck, Jarrett E K Byrnes, Bradley J Cardinale, J. Emmett Duffy, John N Griffin

    Marine ecosystems are experiencing rapid and pervasive loss of species. Understanding the consequences of species loss is critical to effectively managing these systems. Over the last several years, numerous experimental manipulations of species richness have been performed, yet existing quantitative syntheses have focused on a just a subset of processes measured in experiments and, as such, have not summarized the full data available from marine systems. Here, we present the results of a meta-analysis of 174 marine experiments from 42 studies that have manipulated the species richness of organisms across a range of taxa and trophic levels and analysed the consequences for various ecosystem processes (categorised as production, consumption or biogeochemical fluxes). Our results show that, generally, mixtures of species tend to enhance levels of ecosystem function relative to the average component species in monoculture, but have no or negative effect on functioning relative to the ‘highest-performing' species. These results are largely consistent with those from other syntheses, and extend conclusions to ecological functions that are most commonly measured in the marine realm (e.g. nutrient release from sediment bioturbation). For experiments that manipulated three or more levels of richness, we attempted to discern the functional form of the BEF relationship. We found that, for response variables categorised as consumption, a power-function best described the relationship, which is also consistent with previous findings. However, we identified a linear relationship between richness and production. Combined, our results suggest that losses of species will, on average, tend to alter the functioning of marine ecosystems. We outline several research frontiers that will allow us to more fully understand how, why, and when diversity may drive the functioning of marine ecosystems.


  • Open Access

    Marine biodiversity and ecosystem functioning: what’s known and what’s next?

    by Lars Gamfeldt, Jonathan S Lefcheck, Jarrett E K Byrnes, Bradley J Cardinale, J. Emmett Duffy, John N Griffin

    Marine ecosystems are experiencing rapid and pervasive loss of species. Understanding the consequences of species loss is critical to effectively managing these systems. Over the last several years, numerous experimental manipulations of species richness have been performed, yet existing quantitative syntheses have focused on a just a subset of processes measured in experiments and, as such, have not summarized the full data available from marine systems. Here, we present the results of a meta-analysis of 174 marine experiments from 42 studies that have manipulated the species richness of organisms across a range of taxa and trophic levels and analysed the consequences for various ecosystem processes (categorised as production, consumption or biogeochemical fluxes). Our results show that, generally, mixtures of species tend to enhance levels of ecosystem function relative to the average component species in monoculture, but have no or negative effect on functioning relative to the ‘highest-performing' species. These results are largely consistent with those from other syntheses, and extend conclusions to ecological functions that are most commonly measured in the marine realm (e.g. nutrient release from sediment bioturbation). For experiments that manipulated three or more levels of richness, we attempted to discern the functional form of the BEF relationship. We found that, for response variables categorised as consumption, a power-function best described the relationship, which is also consistent with previous findings. However, we identified a linear relationship between richness and production. Combined, our results suggest that losses of species will, on average, tend to alter the functioning of marine ecosystems. We outline several research frontiers that will allow us to more fully understand how, why, and when diversity may drive the functioning of marine ecosystems.

  • Open Access

    Decline and Local Extinction of Caribbean Eusocial Shrimp

    by J. Emmett Duffy, Kenneth S. Macdonald Iii, Kristin M. Hultgren, Tin Chi Solomon Chak, Dustin R. Rubenstein

    The tropical shrimp genus Synalpheus includes the only eusocial marine animals. In much of the Caribbean, eusocial species have dominated the diverse fauna of sponge-dwelling shrimp in coral rubble for at least the past two decades. Here we document a recent, dramatic decline and apparent local extinction of eusocial shrimp species on the Belize Barrier Reef. Our collections from shallow reefs in central Belize in 2012 failed to locate three of the four eusocial species formerly abundant in the area, and showed steep declines in colony size and increases in frequency of queenless colonies prior to their disappearance. Concordant with these declines, several nonsocial, pair-forming Synalpheus species increased in frequency. The decline in eusocial shrimp is explained in part by disappearance of two sponge species on which they specialize. Eusocial shrimp collections from Jamaica in 2012 showed similar patterns of decline in colony size and increased queenlessness compared with prior Jamaican collections. The decline and local extinction of eusocial shrimp happened against a backdrop of changes in coral assemblages during recent decades, and may reflect changes in abundance and quality of dead coral substratum and succession of the diverse cryptic organisms living within it. These changes document potentially worrisome declines in a unique taxon of eusocial marine animals.


  • Biofuels: Algae

    by J Emmett Duffy, Elizabeth A Canuel, Walter Adey, John P Swaddle


  • Kin structure, ecology and the evolution of social organization in shrimp: a comparative analysis

    by J. Emmett Duffy, Kenneth S. Macdonald

    Eusocial societies present a Darwinian paradox, yet they have evolved independently in insects, mole-rats and symbiotic shrimp. Historically, eusociality has been thought to arise as a response to ecological challenges, mediated by kin selection, but the role of kin selection has recently been questioned. Here we use phylogenetically independent contrasts to test the association of eusociality with ecological performance and genetic structure (via life history) among 20 species of sponge-dwelling shrimp (Synalpheus) in Belize. Consistent with hypotheses that cooperative groups enjoy an advantage in challenging habitats, we show that eusocial species are more abundant, occupy more sponges and have broader host ranges than non-social sister species, and that these patterns are robust to correction for the generally smaller body sizes of eusocial species. In contrast, body size explains less or no variation after accounting for sociality. Despite strong ecological pressures on most sponge-dwellers, however, eusociality arose only in species with non-dispersing larvae, which form family groups subject to kin selection. Thus, superior ability to hold valuable resources may favour eusociality in shrimp but close genetic relatedness is nevertheless key to its origin, as in other eusocial animals.


  • Open Access

    Why biodiversity is important to the functioning of real‐world ecosystems

    by J Emmett Duffy

    Controlled experiments have substantially advanced our understanding of the links between changing biodiversity and ecosystem functioning (BEF) in recent years. However, controversy continues regarding the relevance of BEF experiments to the complex ecosystems and large spatial and temporal scales of interest in conservation and management. Here, I address some of the persistent criticisms regarding experimental BEF research and argue that these have been overstated. Contrary to some suggestions, many putative artifacts attributed to experiments render their conclusions about BEF links stronger, rather than weaker. Like other broad ecological concepts, BEF focuses on general patterns, rather than looking at species‐level, applied conservation problems. Nevertheless, insights from BEF experiments conducted to date are likely to underestimate, rather than overestimate, the importance of biodiversity to ecosystem functioning and the provision of ecosystem services in the real world. These experiments suggest that managing ecosystems to promote biodiversity can have important practical benefits.


  • Top Cited Papers

    The functional role of biodiversity in ecosystems: incorporating trophic complexity

    by J. Emmett Duffy, Bradley J. Cardinale, Kristin E. France, Peter B. McIntyre, Elisa Thébault, Michel Loreau

    Understanding how biodiversity affects functioning of ecosystems requires integrating diversity within trophic levels (horizontal diversity) and across trophic levels (vertical diversity, including food chain length and omnivory). We review theoretical and experimental progress toward this goal. Generally, experiments show that biomass and resource use increase similarly with horizontal diversity of either producers or consumers. Among prey, higher diversity often increases resistance to predation, due to increased probability of including inedible species and reduced efficiency of specialist predators confronted with diverse prey. Among predators, changing diversity can cascade to affect plant biomass, but the strength and sign of this effect depend on the degree of omnivory and prey behaviour. Horizontal and vertical diversity also interact: adding a trophic level can qualitatively change diversity effects at adjacent levels. Multitrophic interactions produce a richer variety of diversity‐functioning relationships than the monotonic changes predicted for single trophic levels. This complexity depends on the degree of consumer dietary generalism, trade‐offs between competitive ability and resistance to predation, intraguild predation and openness to migration. Although complementarity and selection effects occur in both animals and plants, few studies have conclusively documented the mechanisms mediating diversity effects. Understanding how biodiversity affects functioning of complex ecosystems will benefit from integrating theory and experiments with simulations and network‐based approaches.


  • Two New Species of Sponge-Dwelling Snapping Shrimp from the Belizean Barrier Reef, with a Synopsis of the Synalpheus brooksi Species Complex

    by Kenneth S. Macdonald, J. Emmett Duffy

    Two new species of sponge-dwelling snapping shrimp in the genus Synalpheus are described. Synalpheus carpenteri is based on specimens collected from the Belizean Barrier Reef, the Exuma Islands of the Bahamas, and the Atlantic Coast of Panama, while Synalpheus ruetzleri is based on specimens collected from the Belizean Barrier Reef and the Atlantic Coast of Panama. Both species belong to a group of closely related shrimp (the “Synalpheus brooksi complex”) that includes Synalpheus brooksi, Synalpheus bousfieldi, Synalpheus chacei, and possibly additional undescribed species. All species in the complex are remarkably similar in morphology, but Synalpheus carpenteri is readily recognizable by its brilliant orange color in life, its habitation solely in sponges of the genus Agelas, its squat, wide-based telson, and the short lateral spines of its scaphocerite and basicerite. Synalpheus ruetzleri appears unique within the complex in possessing a well-developed blade on the scaphocerite. Specimens of Synalpheus brooksi and S. bousfieldi from Belize and other localities are also figured to facilitate separation of members of the brooksi complex.


  • Ecosystem consequences of diversity depend on food chain length in estuarine vegetation

    by J. Emmett Duffy, J. Paul Richardson, Kristin E. France

    Biodiversity and food chain length each can strongly influence ecosystem functioning, yet their interactions rarely have been tested. We manipulated grazer diversity in seagrass mesocosms with and without a generalist predator and monitored community development. Changing food chain length altered biodiversity effects: higher grazer diversity enhanced secondary production, epiphyte grazing, and seagrass biomass only with predators present. Conversely, changing diversity altered top‐down control: predator impacts on grazer and seagrass biomass were weaker in mixed‐grazer assemblages. These interactions resulted in part from among‐species trade‐offs between predation resistance and competitive ability. Despite weak impact on grazer abundance at high diversity, predators nevertheless enhanced algal biomass through a behaviourally mediated trophic cascade. Moreover, predators influenced every measured variable except total plant biomass, suggesting that the latter is an insensitive metric of ecosystem functioning. Thus, biodiversity and trophic structure interactively influence ecosystem functioning, and neither factor's impact is predictable in isolation.