Underlined names indicate Humphries Lab members. Links to the publication are provided at the end of each citation in brackets.

2024

[64] Caldwell IR, McClanahan TR, Oddenyo RM, Graham NAJ, Beger M, Vigliola L, Sandin SA, Friedlander AM, Randriamanantsoa B, Wantiez L, Green AL, Humphries AT, Hardt M, Caselle JE, Feary DA, Karkarey R, Jadot C, Hoey AS, Eurich JG, Wilson SK, Crane NL, Tupper M, Ferse SCA, Maire E, Mouillot D, Cinner JE (in press) Protection efforts have resulted in ~10% of existing fish biomass on coral reefs. Proceedings of the National Academy of Sciences 121 (42) e2308605121. [doi]

[63] Fahlevy K, Prabowo B, Manik NWK, Carvalho PG, Humphries AT, Subhan B, Madduppa H (2024) Coral communities distribution in the context of site’s reef formation type in Wakatobi National Park, Indonesia. Ocean Science Journal 59:29. [pdf]

[62] Borbee EM, Puspa I, Restiana E, Setiawan F, Madduppa H, Humphries AT, Lane CE (2024) Surface currents shape protist community structure across the Indo-Pacific. Journal of Phycology 00:1-18. [pdf]

[61] Shen EW, Borbee EM, Carvalho PG, Setiawan F, Subhan B, Madduppa H, Humphries AT, Lane CE (2024) Preliminary characterization of coral reef diversity using environmental DNA in a hyper-diverse context. Regional Studies in Marine Science 71:103432. [pdf]

2023

[60] Dimarchopoulou D, Wibisono E, Saul S, Carvalho PG, Nugraha A, Mous PJ, Humphries AT (2023) Combining catch-based indicators suggests overexploitation and poor status of Indonesia's deep demersal fish stocks. Fisheries Research 268:106854. [pdf]

[59] Humphries AT, Dimarchopoulou D, Stergiou KI, Tsikliras AC, Palomares MD, Bailly N, Nauen CE, Luna S, Banasihan LP, Froese R, Pauly D (2023) Measuring the scientific impact of FishBase after three decades. Cybium 47(3):213-224. [pdf]

[58] Heinichen M, Innes-Gold A, Langan J, Richman T, Collie J, Humphries AT (2023) Describing the diet of a generalist feeder: the striped searobin (Prionotus evolans) from Narragansett Bay, Rhode Island (U.S.). Environmental Biology of Fishes 106:697–706. [pdf]

[57] Lavaud R, Ullman D, Venolia C, Thornber C, Green-Gavrielidis L, Humphries AT (2023) Production potential of seaweed and shellfish integrated aquaculture in Narragansett Bay (Rhode Island, U.S.) using an ecosystem model. Ecological Modelling 481:110370. [pdf]

[56] Kamau-Mbuthia E, Lesorogol C, Wamukota A, Humphries AT, Sarange C, Mbeyu R, Cheupe C, Cheupe J, Nunez-Garcia A, Blackmore I, Iannotti L (2023) Sustainable aquatic food systems: multisectoral analysis of determinants of child nutrition in coastal Kenya. Frontiers in Sustainable Food Systems 7:1091339. [doi] [pdf]

[55] Borbee E, Ayu IP, Carvalho PG, Restiana E, Setiawan F, Subhan B, Humphries AT, Madduppa H, Lane CE (2023) Rubble fields shape planktonic protist communities in Indonesia at a local scale. Journal of Eukaryotic Microbiology 70(2):e12954. [pdf]

[54] Roberts N, Mengge B, Oaks B, Sari N, Irsan I, Humphries AT (2023) Fish consumption pathways and food security in an Indonesian fishing community. Food Security 15:1-19. [pdf]

2022

[53] Galligan BP, McClanahan TR, Humphries AT (2022) Nutrient capture and sustainable yield maximized by a gear modification in artisanal fishing traps. Environmental Research Letters 17:124035. [doi] [pdf]

[52] Blackmore I, Wamukota A, Kamau-Mbuthia E, Humphries AT, Lesorogol C, Cohn R, Sarange C, Mbogholi F, Obata C, Cheupe C, Cheupe J, Sherburne L, Chapnick M, Cartmill MK, Iannotti L (2022) Samaki Salama - promoting healthy child growth and sustainable fisheries in coastal Kenya: a study protocol. Frontiers in Public Health 10:934806. [doi] [pdf]

[51] Pratomo A, Bengen DG, Zamani NP, Lane CE, Humphries AT, Borbee E, Subhan B, Madduppa H (2022) Diversity and distribution of Symbiodiniaceae detected on coral reefs of Lombok (Indonesia) using environmental DNA metabarcoding. PeerJ 10:e14006. [doi] [pdf]

[50] Roberts N, Mengge B, Rifadly Utina M, Muhatar F, Anugerah, Icwardanhi A, Muhammad Zulkifli R, Humphries AT (2022) Patron-client relationships shape value chains in an Indonesian island-based fisheries system. Marine Policy 143(105142):1-12. [pdf]

[49] Arizi EK, Collie J, Castro K, Humphries AT (2022) Fishing characteristics and catch composition of the sardinella fishery in Ghana indicate urgent management is needed. Regional Studies in Marine Science 52:102348. [pdf]

[48] Wibisono E, Mous P, Firmana E, Humphries AT (2022) A crew-operated data recording system for length-based stock assessment of Indonesia's deep demersal fisheries. PLoS ONE 17(2):e0263646. [doi] [pdf]

[47] Heinichen M, McManus C, Lucey S, Aydin K, Humphries AT, Innes-Gold A, Collie J (2022) Incorporating temperature-dependent fish bioenergetics into a Narragansett Bay food web model. Ecological Modelling 466:109911. [pdf]

[46] Cartmill MK, Blackmore I, Sarange C, Mbeyu R, Cheupe C, Cheupe J, Kamau-Mbuthia E, Iannotti L, Wamukota A, Humphries AT, Lesorogol C (2022) Fish and complementary feeding practices for young children: Qualitative research findings from coastal Kenya. PLoS ONE 17(3):e0265310. [doi] [pdf]

[45] Humphries AT, Gorospe KD, Innes-Gold A, McNamee J, McManus C, Oviatt C, Collie J (2022) In pursuit of ecosystem-based management for Narragansett Bay: an overview of previous models and roadmap for future research. Coastal Management 50(3):262-283. [doi] [pdf]

[44] Santoso P, Setiawan F, Subhan B, Arafat D, Bengen DG, Sani LMI, Humphries AT, Madduppa H (2022) Influence of coral reef rugosity on fish communities in marine reserves around Lombok Island, Indonesia. Environmental Biology of Fishes 105:105-117. [pdf]

[43] Carvalho PG, Humphries AT (2022) Gear restrictions create conservation and fisheries tradeoffs for management. Fish and Fisheries 23:183-194. [pdf]

[42] Iannotti LL, Blackmore I, Cohn R, Chen F, Gyimah EA, Chapnick M, Humphries AT (2022) Aquatic animal foods for nutrition security and child health. Food and Nutrition Bulletin 43(2):127-147. [pdf]

2021

[41] Dimarchopoulou D, Mitsutaku M, Prayoga MR, Zeller D, Vianna GMS, Humphries AT (2021) Responses in fisheries catch data to a warming ocean along a latitudinal gradient in the western Pacific Ocean. Environmental Biology of Fishes 105:1347-1362. [pdf]

[40] Viducic K, Natanson L, Winton M, Humphries AT (2021) Reproductive characteristics for the blue shark (Prionace glauca) in the North Atlantic Ocean. Fishery Bulletin 120:26-38. [pdf]

[39] Drew J, Kahn B, Locatelli N, Airey M, Humphries AT (2021) Examining stakeholder perceptions of oyster ecosystem services using fuzzy cognitive mapping. Conservation Science and Practice 3(11):e531. [doi] [pdf]

[38] Dimarchopoulou D, Mous P, Firmana E, Wibisono E, Coro G, Humphries AT (2021) Exploring the status of the Indonesian deep demersal fishery using length-based stock assessments. Fisheries Research 243:106089. [pdf]

[37] Carvalho PG, Setiawan F, Fahlevy K, Subhan B, Madduppa H, Zhu G, Humphries AT. (2021) Fishing and habitat condition differentially affect size spectra slopes of coral reef fishes. Ecological Applications e2345. [doi] [pdf]

[36] Innes-Gold A, Pavlowich T, Heinichen M, McManus C, McNamee J, Collie J, Humphries AT (2021) Exploring social-ecological tradeoffs in fisheries using a coupled food web and human behavior model. Ecology and Society 26(2):40. [doi] [pdf]

[35] Refulio-Coronado SM, Lacasse KM, Dalton T, Humphries AT, Basu S, Uchida H, Uchida E (2021) Coastal and marine socio-ecological systems: A systematic review of the literature. Frontiers in Marine Science 8:648006. [doi] [pdf]

[34] Vandenberg J, Humphries AT, Garcia-Quijano C, Moore A, Pollnac R, Abdullah S. (2021) Assessing indicators and limitations of food security objectives in coral reef restoration. Conservation and Society 19(1):68-79. [doi] [pdf]

[33] Wibisono E, Puggioni G, Firmana E, Humphries AT. (2021) Identifying hotspots for spatial management of the Indonesian deep-slope demersal fishery. Conservation Science and Practice e356. [doi] [pdf]

2020

[32] McClanahan TR, Maina JM, Darling ES, Guillaume MM, Muthiga NA, D’agata SD, Leblond J, Arthur R, Jupiter SD, Wilson SK, Mangubhai S, Ussi AM, Humphries AT, Patankar V, Shedrawi G, Julius P, Ndagala J, Grimsditch G. (2020) Large geographic variability in the resistance of corals to thermal stress. Global Ecology and Biogeography 00:1-19 [doi] [pdf]

[31] Innes-Gold A, Heinichen M, Gorospe KD, Truesdale C, Collie J, Humphries AT. (2020) Modeling 25 years of food web changes in Narragansett Bay as a tool for ecosystem-based management. Marine Ecology Progress Series 654:17-33. [pdf]

[30] McClanahan TR, Darling ES, Maina JM, Muthiga NA, D’agata S, Leblong J, Arthur R, Jupiter SD, Wilson SK, Mangubhai S, Ussi AM, Guillaume MM, Humphries AT, Patankar V, Shedrawi G, Pagu J, Grimsditch G. (2020) Highly variable taxa-specific coral bleaching response to thermal stresses. Marine Ecology Progress Series 648:135-151. [doi] [pdf]

[29] Venolia CT, Lavaud R, Green-Gavrielidis L, Thornber C, Humphries AT. (2020) Modeling the growth of sugar kelp (Saccharina latissima) in aquaculture systems using dynamic energy budget theory. Ecological Modelling 430:109151. [pdf]

[28] Humphries AT, McClanahan TR, McQuaid CD. (2020) Algal turf consumption by sea urchins and fishes is mediated by fisheries management on coral reefs in Kenya. Coral Reefs 39:1137-1146. [pdf]

[27] Gorospe KD, Josephs LI, Humphries AT. (2020) Using seafood traceability to teach the complexities of natural resource management and sustainability. CourseSource 7:1-9. [doi] [pdf]

2019

[26] La Peyre MK, Marshall DA, Miller LS, Humphries AT. (2019) Oyster reefs in northern Gulf of Mexico estuaries harbor diverse fish and decapod crustacean assemblages: a meta-synthesis. Frontiers in Marine Science 6:666. [doi] [pdf]

[25] Humphries AT, Josephs LI, La Peyre M, Hall S, Dowty-Beech R. (2019) Vulnerability of resource-users in Louisiana’s oyster fishery to environmental hazards. Ecology and Society 24(3):37. [doi] [pdf] [infographic]

[24] McClanahan TR, Darling ES, Maina JM, Muthiga NA, D’agata S, Jupiter S, Arthur R, Wilson SK, Mangubhai S, Nand Y, Usi AM, Humphries AT, Patankar VJ, Guillaume MM, Keith SA, Shedrawi G, Pagu J, Grimsditch G, Ndagala J, Leblond J. (2019) Evaluating temperature patterns and mechanisms influencing coral bleaching during the 2016 El Niño. Nature Climate Change 9:769-774. [pdf]

[23] Gorospe KD, Carvalho PG, Josephs LI, Humphries AT (2019) Sustainable seafood certification labels: the case for and against Atlantic menhaden. National Socio-Environmental Synthesis Center’s Teaching Socio-Environmental Synthesis with Case Studies. 43 pp. [teaching lesson plan]

[22] Humphries AT, Gorospe KD, Carvalho PG, Yulianto I, Kartawaijaya T, Campbell SJ (2019) Catch composition and selectivity of fishing gears in a multi-species Indonesian coral reef fishery. Frontiers in Marine Science 6:378. [doi] [pdf]

[21] Carvalho PG, Jupiter SD, Januchowski-Hartley FA, Goetze J, Claudet J, Weeks R, Humphries AT, White C. (2019) Optimized fishing through periodically harvested closures. Journal of Applied Ecology 00:1-10. [pdf]

[20] McLeod IM, zu Ermgassen PSE, Gillies C, Hancock B, Humphries AT (2019) Can bivalve habitat restoration improve degraded estuaries? In E Wolanski, J Day, M Elliott, and R Ramachandran (Ed.) Coasts and Estuaries – The Future. Elsevier, Amsterdam. pp. 427-442. [pdf]

2018

[19] Merrill NH, Mulvaney KK, Martin DM, Chintala MM, Berry W, Gleason T, Balogh S, Humphries AT (2018) A resilience framework for chronic exposures: water quality and ecosystem services in coastal social-ecological systems. Coastal Management 46(4):242-258. [pdf]

[18] Josephs LI, Humphries AT (2018) Identifying social factors that undermine support for nature-based coastal management. Journal of Environmental Management 212:32-38. [pdf]

2017

[17] Woodson R, Borel J, Dillard H, Ejeta G, Glickman D, Keenum M, Leshner A, Simon LA, Humphries AT, + others (2017) The Challenge of Change: harnessing university discovery, engagement, and learning to achieve food and nutrition security. US Association of Public & Land-Grant Universities. 144 pp. [pdf]

[16] Quan WM, Fan R, Wang Y, Humphries AT (2017) Long-term oyster recruitment and growth are not influenced by substrate type in China: implications for sustainable oyster reef restoration. Journal of Shellfish Research 36:79-86. [pdf]

[15] Coen LT, Humphries AT (2017) Bivalve-generated marine habitats: their value and related monitoring, restoration, and enhancement efforts. In S Stuart and S Murphy (Ed.) Routledge Handbook of Ecological and Environmental Restoration. Routledge, Oxon. pp.274-294. [pdf]

2016

[14] Oczkowski AJ, Gumbley T, Carter BJ, Carmichael RH, Humphries AT (2016) Establishing an anthropogenic nitrogen baseline using Native American shell middens. Frontiers in Marine Science 3:79. [doi] [pdf] [art]

[13] Humphries AT, Ayvazian SG, Carey J, Hancock BT, Grabbert S, Cobb D, Strobel CJ and Fulweiler RW (2016) Directly measured denitrification reveals oyster aquaculture and restored oyster reefs remove nitrogen at comparable high rates. Frontiers in Marine Science 3:74. [doi] [pdf]

Pre-2016 / URI

[12] Humphries AT, McQuaid CD, McClanahan TR (2015) Context-dependent diversity-effects of seaweed consumption on coral reefs in Kenya. PLoS ONE 10(12):e0144204. [doi] [pdf]

[11] La Peyre MK, Serra KT, Joyner TA, Humphries AT (2015) Assessing shoreline exposure and oyster habitat suitability maximizes potential success for restored oyster reefs. PeerJ 3:e1317. [doi] [pdf]

[10] Humphries AT, La Peyre MK (2015) Oyster reef restoration supports increased nekton biomass and potential commercial fishery value. PeerJ 3:e1111. [doi] [pdf]

[9] Humphries AT, McClanahan TR, McQuaid CD (2014) Differential impacts of coral reef herbivores on algal succession in Kenya. Marine Ecology Progress Series 504:119-132. [pdf] 

[8] La Peyre MK, Humphries AT, Casas SM, La Peyre JL (2014) Temporal variation in the development of ecosystem services from oyster reef restoration. Ecological Engineering 63:34-44. [pdf] 

[7] Cinner JE, Huchery C, Darling ES, Humphries AT, Graham NAJ, Hicks CC, Marshall N, McClanahan TR (2013) Evaluating social and ecological vulnerability of coral reef fisheries to climate change. PLoS ONE 8(9):e74321. [doi] [pdf]

[6] Cinner JE, McClanahan TR, Wamukota A, Darling ES, Humphries AT, Hicks CC, Huchery C, Marshall N, Hempson T, Graham NAJ, Bodin O, Daw T, Allison E (2013) Social-ecological vulnerability of coral reef fisheries to climate shocks. FAO Fisheries and Aquaculture Circular No. 1082. Rome, FAO. 64 pp. [pdf] 

[5] McClanahan TR, Humphries AT (2012) Differential and slow life history responses of fishes to coral reef closures. Marine Ecology Progress Series 469:121-131. [pdf] 

[4] Quan WM, Humphries AT, Shi LY, Chen YQ (2012) Oyster and benthic macrofaunal development on a restored oyster reef in the Yangtze River estuary, China. Journal of Shellfish Research 31(3):1-12. [pdf] 

[3] Quan WM, Humphries AT, Shi LY, Chen YQ (2012) Trophic transfer at a restored intertidal oyster reef in the Yangtze River estuary using stable isotope analysis. Estuaries and Coasts 35(1):109-120. [pdf] 

[2] Humphries AT, La Peyre MK, Decossas GA (2011) The effect of structural complexity, prey density, and predator-free space on prey survivorship at oyster reef mesocosms. PLoS ONE 6(12):e28339. [doi] [pdf]

[1] Humphries AT, La Peyre MK, Kimball ME, Rozas LP (2011) Testing the effect of habitat structure and complexity on nekton assemblages using experimental oyster reefs. Journal of Experimental Marine Biology and Ecology 409(1):172-179. [pdf]