Books and Monographs published (all formally refereed):

Vergara S, McManus JW, Kesner-Reyes KN, Menez LAB, Funk RZ, Evangelista RC, Noordeloos M, Serrano AMB, Rull MFSJ, Alarcon VL, Meneses ABT, Glorioso JR. (2000) ReefBase 2000: Improving policies for sustainable management of coral reefs. Ver.2000. ICLARM, , Manila, Philippines (also 3 previous versions of this CD and manual with various co-authors).

Bryant D, Burke L, McManus J, Spalding M (1998) Reefs at Risk: a Map-Based Indicator of Threats to the World's Coral Reefs. World Resources Institute. NY. 56 p.

McManus JW, Ablan MC, Vergara SG, Menez LAB, Vallejo BM, Kesner KP, Gorospe MG, Halmarick L (1997) The ReefBase Survey Manual. ICLARM. 61 p.

Jameson SC, McManus JW, Spalding MD (1995) State of the Reefs: Regional and Global Perspectives. International Coral Initiative (ICRI) Secretariat Background Paper, U.S. State Department. 32 p.

McManus JW, Nanola C, Reyes R, Kesner K (1992) Resource Ecology of the Bolinao System. ICLARM Studies and Reviews 22, 117 p.

McManus JW (1985) Descriptive community dynamics: background and an application to tropical fisheries management. Ph.D. dissertation, Graduate School of , University of Rhode Island. Published by University Microfilms. 217 p.

Formally Refereed Journal Articles:

Yñiguez A, McManus JW, Collado-Vides L (2015). Consequences of morphological plasticity and fragmentation on two-dimensional space occupation of coral reef macroalgae. Ecological Modelling 309–310:128–142

Zhu L, Qualls WA, Marshall JM, Arheart KL, DeAngelis DL, McManus JW, Traore SF, Doumbia S, Schlein Y, Muller GC, Beier JC (2015) A spatial individual-based model predicting a great impact of copious sugar sources and resting sites on survival of Anopheles gambiae and malaria parasite transmission. Malaria Journal (2015) 14:59, (open access 15 pages), DOI 10.1186/s12936-015-0555-0.

Cooper WT, Lirman D, Van Groningen MP, Parkinson JE, Herlan J, McManus, JW (Accepted) Assessing techniques to enhance early post-settlement survival of corals in situ for reef restoration. Bull Mar Sci Brown CH, Mohr DC, Gallo CG, Mader, Palinkas L, Wingood G, Prado G, Kellam SG, Pantin H, Poduska J, Gibbons R, McManus J, Ogihara M, Valente T, Wulczyn F, Czaja S, Sutcliffe G, Villamar J, Jacobs CL (2013) A Computational Future for Preventing HIV in Minority Communities: How Advanced Technology Can Improve Implementation of Effective Programs. J Acquir Immune Defic Syndr 63(Suppl 1):S72-S84

Brown CH, Kellam SG, Kaupert S, Muthen BO, Wang W, Muthen LK, Chamberlain P, PoVey CL, Cady R, Valente TW, Ogihara M, Prado GJ, Pantin HM, Gallo CG, Szapocznik J, Czaja SJ, McManus JW (2011) Partnerships for the Design, Conduct, and Analysis of Effectiveness, and Implementation Research: Experiences of the Prevention Science and Methodology Group. Adm Policy Ment Health (Published Online December 10, 2011) DOI 10.1007/s10488-011-0387-3

McManus JW, Shao K-T, Lin SY (2010) Toward establishing a Spratly Islands International Marine Peace Park: ecological importance and supportive collaborative activities with an emphasis on the role of Taiwan. Ocean Development and International Law 41:270-280.

Yniguez AT, McManus JW, Collado-Vides L (2010) Capturing the dynamics in benthic structures: environmental effects on morphology in the macroalgal genera Halimeda and Dictyota. Marine Ecology Progress Series 411:17-32.

Brandt M, McManus JW (2009) Dynamics and impact of the coral disease white plague: insights from a simulation model. Disease of Aquatic Organisms 87: 117–133. doi: 10.3354/dao02137.

Brandt M, McManus JW (2009). Disease incidence is related to bleaching severity in reef- building corals. Ecology 90(10): 2859-2867.

Yniguez, A, McManus JW, DeAngelis, D.L. (2008) Allowing macroalgae growth forms to emerge: use of an agent-based model to understand the growth and spread of macroalgae in Florida coral reefs, with emphasis on Halimeda tuna. Ecological Modelling 216: 60–74. doi:10.1016/j.ecolmodel.2008.04.016.

McManus JW, Polsenberg JF (2004) Coral-Algal Phase-Shifts on Coral Reefs: Ecological and Environmental Aspects. Progress in Oceanography 60:263-279.

Chen CA, Ablan MCA, McManus JW, Bell JD, Tuan VS, Cabanban AS, Tsao KS (2004) Variable numbers of tandem repeats (VNTRs), heteroplasmy, and sequence variation of the mitochondrial control region in the threespot dascyllus, Dascyllus trimaculatus (Perciformes : Pomacentridae) Zoological Studies 43 (4): 803-812. Chen CA, Ablan MCA, McManus JW, Bell JD, Tuan VS, Cabanban AS, Tsao KS (2004) Population structure and genetic variability of six bar wrasse (Thallasoma hardwicki) in northern South China Sea revealed by mitochondrial control region sequences Marine Biotechnology 6 (4): 312-326.

McManus JW, Menez LAB, Reyes KNK, Vergara SG, Ablan MC (2000) Coral reef fishing and coral-algal phase shifts: implications for global reef status. ICES Journal of Marine Science, 57(3): 572-578.

Pollnac RB, McManus JW, del Rosario AE, Banzon AS, Vergara SG, Gorospe MLG (2000) Unexpected relationships between coral reef health and socio-economic in the Philippines: ReefBase/RAMP applied. Marine & Freshwater Research 51:529-533.

Kleypas J, McManus JW, Menez LAB (1999) Environmental limits to coral reef development: Where do we draw the line? American Zoologist. 39:146-159.

McManus JW (1997) Tropical marine fisheries and the future of coral reefs: a brief review with emphasis on Southeast Asia. Coral Reefs 16 Suppl. S121-S127. Also in Proc. 8th Int. Coral Reef Symp. 1: 229-134.

McManus JW, Nanola CL, Reyes RB (1997) Effects of some destructive fishing methods on coral cover and potential rates of recovery. Environmental Management. 21(1): 69-78.

Maragos JE, Crosby MP, McManus JW (1996) Coral reefs and biodiversity: a critical and threatened relationship. Oceanography 9(1):83-99.

McManus JW (1994) The Spratly Islands: A ? Ambio 23(3):181-186

Campos WL, del Norte AGC, McManus JW (1994) Yield estimates, catch, effort and fishery potential of the reef flat in Cape Bolinao, Philippines. J Applied Ichthyol. 10:82-95.

Saila SB, Kocic VL, McManus JW (1993) Modelling the effects of destructive fishing practices on tropical coral reefs. Mar Ecol Prog Ser 94:51-60.

McManus JW, Pauly D (1990) On measuring ecological stress: variations on a theme by R.M. Warwick. 106:305–308.

McManus JW (1988) Coral reefs of the ASEAN Region: status and management. Ambio 17(3):189–193.

McManus JW, Wenno JJ (1981) Coral Communities in Outer Ambon Bay, Indonesia: a general assessment survey. Bulletin of Marine Science. 31(3):574–580 Formally Refereed Proceedings and Chapters:

McManus J (2001) Coral Reefs. p. 524-534 In: J.H. Steele, S.A. Thorpe and K.K. Turekian (eds.) Encyclopedia of Ocean Sciences. Academic Press, London. 2000 pp.

McManus JW (1998) Marine reserves and biodiversity: Toward 20% by 2020. p. 25-29. In McManus, J. W., van Zwol, C., Garces, L.R. and Sadacharan, D. (eds). A Framework for Future Training in Marine and Coastal Protected Area Management. ICLARM Conf. Proc. 57, 54 p.

McManus JW, Noordelos M (1998) Toward a global inventory of coral reefs (GICOR): Remote sensing, international cooperation and ReefBase. Proc. 5th Internat. Conf. Remote Sensing of the Marine Environment, San Diego, Ca. pp. I-83 - I-89.

McManus JW (1998) ReefBase: Status and plans. p. 131-138. In: Hatziolos, M.E., Hooten, A. J. and Fodor, M. (eds). Coral Reefs: Challenges and Opportunities for Sustainable Management. Proceedings. The World Bank.

Coronado GU, McManus JW (1997) Mapper: a mapping tool for database systems with coral reef applications. Proc. 8th Intl. Coral Reef Symp. 2:1561-1564.

Eakin CM, McManus JW, Spalding MD, Jameson SC (1997) Coral reef status around the world: where are we and where do we go from here? Proc. 8th Int. Coral Reef Symp. 1: 277- 282.

McManus JW, Ablan MC (1997) ReefBase: a global database of coral reefs and their resources. Proc. 8th Intl. Coral Reef Symp. 2:1541-1544.

McManus JW, Menez LAB (1997) Potential effects of a Spratly Island Marine Park. Proc. 8th Intl. Coral Reef Symp. 2:1943-1948.

McManus JW (1997) Ecological Community Structure Analysis: Applications in Fisheries Management. pp. 133-142. In: Silvestre, G. and Pauly, D. (eds.). Status and Management of Coastal Fisheries in Tropical Asia. ICLARM Workshop Proc. ICLARM, Manila, Philippines.

McManus JW (1996) Marine bottomfish communities from the Indian Ocean coast of Bali to mid-Sumatra. p. 91-101. In: D. Pauly and P. Martosubroto (eds.) Baseline studies of Biodiversity: the Marine Fisheries of Western Indonesia. ICLARM Stud. and Rev. 23, 231 p.

McManus JW (1996) Social and economic aspects of reef fisheries and their management. Chapter 10. p. 249-181. In: N. Polunin and C. Roberts (eds.) Coral Reef Fisheries. Chapman and Hall. 477 p. McManus JW, Nanola CL, del Norte AGC, Reyes RB, Pasamonte JPN, Armada NP, Gomez ED, Alino PM (1996) Coral reef fishery sampling methods. Chapter 5. p. 226-270. In: V.F. Gallucci, S.B. Saila, D.J. Gustafson and B.J. Rothschild (eds) Stock Assessment: Quantitative Methods and Applications for Small-scale Fisheries. CRC Lewis Publishers, New York. 527 p.

Saila SB, McKenna JE, Formacion S, Silvestre G, McManus J (1996) Empirical methods and models for multispecies stock assessment. Chapter 8. p. 403-472. In: V.F. Gallucci, S.B. Saila, D.J. Gustafson and B.J. Rothschild (eds) Stock Assessment: Quantitative Methods and Applications for Small-scale Fisheries. CRC Lewis Publishers, New York. 527 p.

McManus JW (1996) Assessing the coral reefs of the world: a multifaceted strategy. In: Proceedings of the NOAA/NOS Coral Reef Remote Sensing Monitoring Workshop. Key Biscayne, Florida.

McManus JW, Vallejo B, Menez LAB, Coronado G (1995) ReefBase: an international database on coral reefs. In: Marine/Coastal Biodiversity in the Tropical Region (workshop proceedings). East-West Center, Honolulu.

McManus JW (1995) Future prospects for artificial reefs in the Philippines. In: J.L. Munro and M.C. Balgos (eds.) Artificial Reefs in the Philippines. ICLARM Conf. Proc. 49.

McManus JW (1995) Coastal marine fisheries, mollusk culture and seaweed culture in Southeast Asia: Integrated planning and precautions. In: ADSEA '94: Aquaculture Development in Southeast Asia. (workshop proceedings). Southeast Asian Fisheries Development Council (SEAFDEC), Iloilo, Philippines.

McManus JW (1995) Large and Small Scale Protected Areas: Planning, Investment and Intergenerational Quality of Life. p. 60-71. In: A.J. Hooten and M.E. Hatziolos (eds.) Sustainable Financing Mechanisms for Coral Reef Conservation: Proceedings of a Workshop. Environmentally Sustainable Development Proceedings Series No. 9. World Bank. 116 p.

McManus JW, Nanola C, Reyes R, Kesner K (1995) The Bolinao Coral Reef Resource System. p. 193-204 In: M.A.Juinio-Me–ez and G.F. Newkirk (eds) Philippine Coastal Resources Under Stress. Coastal Resources Research Network and Marine Science Institute, University of the Philippines, Diliman, Quezon City, Philippines. 240 p.

Alino P, McManus L, Fortes M, McManus J, Trono G, Nanola C, Jacinto G (1994) Initial parameter estimation of a reef flat ecosystem in Bolinao, Pangasinan, Northwestern Philippines. p. 252-258. In: V. Christensen and D. Pauly (eds.) Trophic Models of Aquatic Ecosystems. ICLARM Conference Proceedings No. 26. 390 p.

McManus JW (1994) Suggestions for future Philippine-Australian coral reef research. p. 68- 71. In: J.L. Munro and P.E. Munro (eds.) The Management of Coral Reef Resource Systems. ICLARM Conf. Proc. 44, 129 p.

McManus JW (1993) Managing seagrass fisheries in Southeast Asia: an introductory review. In: M.D. Fortes and N. Wirjoatmodjo (eds.) Seagrass Resources in Southeast Asia. UNESCO- ROSTEA. (workshop proceedings). Jakarta, Indonesia. 361 p.

Jaranilla HS, McManus JW (1992) Applications of jackknife estimations of species richness and diversity to a coral reef fish community in Bolinao, Philippines. Proc. First National Symposium in Marine Science (Phillippines). p. 225–223.

McManus JW, Cabanban AS (1992) Coral reef recruitment studies in Southeast Asia: background and implications. p.7-18. In: Workshop on Coral and Fish Recruitment (proceedings). ASEAN-Australia Project: Living Coastal Resources. Townsville, Australia. 90 p. del Norte AGC, McManus JW, Nanola CL, Cabansag J, Campos WL (1989) Overfishing on a Philippine Coral Reef: a glimpse of the future. In Coastal Zone '89: Proceedings of the 6th Symposium on Coastal and Ocean Management, 1989. 5:3087–3097.

McManus JW (1989) Earth Observing system and coral reef fisheries. In Coastal Zone '89: Proceedings of the 6th Symposium on Coastal and Ocean Management, 1989. 5:4936– 4949.

McManus JW (1989) Zonation among demersal fishes of Southeast Asia: The southwest shelf of Indonesia. In Coastal Zone '89: Proceedings of the 6th Symposium on Coastal and Ocean Management, 1989. 2:1011–1022.

Nanola CL, McManus JW, Campos WL, del Norte AGC, Reyes RB, Cabansag JBP, Pasamonte, JN (1989) Spatio–Temporal variations in community structure on a heavily fished forereef slope in Bolinao, Philippines. pp. 377–380. In: Hirano, R. and I. Hanyu, eds. The Second Asian Fisheries Forum. 991 p. Asian Fisheries Society, Manila, Philippines.

McManus JW, Ferrer EM, Campos WL (1988) A village–level approach to coastal adaptive management and resource assessment (CAMRA). Proceedings of the 6th International Coral Reef Symposium. 2:381–386. McManus JW (1986) Depth zonation in a demersal fishery in the Samar Sea, Philippines, p. 483–486. In J.L. Maclean, L.B. Dizon and L.V. Hosillos (eds.) The First Asian Fisheries Forum. Asian Fisheries Society, Manila, Philippines.

McManus JW (1985) Marine speciation, tectonics and sea–level changes in Southeast Asia. Proceedings of the 5th International Coral Reef Congress. 4:133–138.

McManus JW, Miclat RI, Palaganas VP 1981. Coral and fish community structure of Sombrero Island, Batangas, Philippines. Proceedings of the 4th International Coral Reef Symposium. 2:263–269.

Sy JC, Herrera FS, McManus JW (1981) Coral Community structure of a fringing reef at Mactan Island, Cebu, Philippines. Proceedings of the 4th International Coral Reef Symposium. 2:263–269.

Glenn C, McManus JW, Talaue LL, Alino PM, Banzon VF (1981) Distributions of living foraminifers on a portion of Apo Reef, , Philippines. Proceedings of the 4th International Coral Reef Symposium. 2:775–780.

Other Reports:

Ablan MCA, McManus JW, Viswanathan K (2004). Indicators for management of coral reefs and their applications to marine protected areas. NAGA: The WorldFish Center Quarterly Vol.27, No. 1&2 : 31-39.

Ablan MCA, McManus JW, Chen CA, Shao KT, Bell J, Cabanban AS, Tuan VS, Jarayabhand, P, Suharsono, Alcala A, Arthana IW (2003) Enhancing the resilience of coral reef resources: Could genetic marking contribute to increasing the resilience of coral reef resources? IHDP Update 2/2003. International Human Dimensions Programme on Global Environmental Change.

McManus JW (2002) Contributing Author to: Burke L et al (2002) Reefs at Risk Southeast Asia. World Resources Institute. 72 p

McManus JW (2002) The global importance of Philippine coral reefs. pp. 7-8. In: Alino PM, Miclat EFB, Nanola CL, Roa-Quiaouit HA, Campos RT (eds) Atlas of Philippine coral reefs. Goodwill Trading Co., Inc. Manila, Philippines

McManus J (Compiler 2002) Report from the Information Needs Working Group. In: Bruckner, AW (ed) pp. 54-58. NOAA Technical Memorandum NMFS-OPR-24, Silver Spring, MD. 199 pp. Ablan MCA, McManus JW, Chen CA, Shao KT, Bell J, Cabanban AS, Tuan VS, Arthana IW (2002) Meso-scale Transboundary Units for the Management of Coral Reefs in the South China Sea Area. NAGA- The WorldFish Center Quarterly. Vol.25, No. 3&4 (July - December 2002) pp 4-9

Dickman C, McManus JW (2002) Priorities for Caribbean coral reef research: an overview of the results from an international workshop of the National Center for Caribbean Coral Reef Research (NCORE). in Report of the Regional Workshop for Tropical Americas, Cancun, Mexican. June 12, 2002 - June 14, 2002. International Coral Reef Initiative (ICRI). Pp. 120- 128.

McManus JW (2001) The death of a coral reef: Bolinao. pp. 95-97. In: Talbot, F. and Wilkinson, C. Coral reefs, and seagrasses: a handbook for managers.

McManus JW, Vergara S (1999) ReefBase 3.0 and the ReefBase Aquanaut system. in: Maragos JE, Grober-Dunsmore R (eds), Proceedings of the Hawaii Coral Reef Monitoring Workshop, June 9-11, 1998, Honolulu, Hawaii, pp.159-172.

McManus JW, Ablan MCA (1995) ReefBase: toward informed coral reef management. EU Bulletin 8(3):22.

Wells S, McManus JW (1994) ReefBase - a global database of coral reef systems and their resources. Naga 17(1):16. (reprinted in at least 10 newsletters and 1 journal (Marine Pollution Bulletin)).

McManus JW (1993) Coral Reefs: What happened to management science? Reef Encounter. 13 July. pp. 7-8.

McManus JW (1993) Problems with percent composition analyses. Reef Encounter. 13 July. pp. 9-10.

McManus JW, Nanola C, Reyes R, Kesner K (1993) Ecological Effects of Harvesting on a Philippine Fringing Reef. Final Technical Report I. Project REEF. Marine Science Institute, University of the Philippines and Philippine Department of Agriculture. 50 pp.

McManus JW, Nanola C, Reyes R, Kesner K (1993) The Proposed Bolinao Marine Reserve/Park System: Ecological and Reef Use Factors. Final Technical Report II. Project REEF. Marine Science Institute, University of the Philippines and Philippine Department of Agriculture. 15 pp. McManus JW (1993) TACO: Table Analysis by Classification of Ordinations. Final Technical Report IV. Project REEF. Marine Science Institute, University of the Philippines and Philippine Department of Agriculture. 61 pp.

McManus JW (1992) The Spratly Islands: a marine park alternative. Naga - The ICLARM Quarterly 15(3):4-8.

McManus JW, Nanola C, Reyes R, Kesner K (1992) Resource Ecology of the Bolinao Coral Reef System: A Summary of an upcoming book. Naga - The ICLARM Quarterly 15(3):43-45.

McManus JW (1990) A search for new methods for fish stock assessment and management, the FSA–CRSP. Overview and Philippine activities. Fishbyte. 8(1):45–46.

McManus JW (1990) Ecological Computer Programs: the importance of being friendly. Naga - The ICLARM Quarterly 13(2):5–8.

McManus JW (1990) Recommendations for the future development of the Magellanes School of Fisheries. ICMRD Report. Philippine Gov. 10 p.

McManus JW (1989) The proposed Philippine Fisheries Sector Program: a preliminary evaluation. ORAD – U.S. AID/Philippines Report. 10 p.

McManus JW (1984) Fishpak HP–85/87: A set of programs for the storage and preliminary analysis of fisheries survey data. Technical Reports of the Department of Marine Fisheries No. 4. College of Fisheries, University of the Philippines in the Visayas, and the German Agency for Technical Cooperation (GTZ). 110 pp. del Norte AGC, Nanola CL, Campos WL, McManus JW, Reyes RB, Cabansag JBP (1989) Results of the Bolinao Reef Fishery Survey (September 1986–June 1988). Data Report of the Multispecies Field Studies Component, Fish Stock Assessment Collaborative Research Support Program (FSA–CRSP). Parts I & II. Marine Science Institute, University of the Philippines, Diliman, Q.C., Philippines. approx. 1000 pp. plus diskettes.

Nanola CL, del Norte AGC, Campos WL, McManus JW, Reyes RB, Cabansag JBP (1989) Results of the Bolinao Reef Slope Visual Census (July 1987 – June 1988). Data Report of the Multispecies Field Studies Component, Fish Stock Assessment Collaborative Research Support Program (FSA–CRSP). Marine Science Institute, University of the Philippines, Diliman, Q.C., Philippines. approx. 500 pp. plus diskettes. del Norte AGC, Nanola CL, McManus JW, Reyes RB, Pasamonte JN (1990) Results of the Bolinao Reef Fishery Survey (July 1988 – June 1989). Data Report of the Multispecies Field Studies Component, Fish Stock Assessment Collaborative Research Support Program (FSA– CRSP). Parts I, II & III. Marine Science Institute, University of the Philippines, Diliman, Q.C., Philippines. Approx. 1,500 pp. plus diskettes.

Nanola CL, del Norte AGC, McManus JW, Reyes RB, Pasamonte JN (1990) Results of the Bolinao Reef Slope Visual Census (July 1988 – June 1989). Data Report of the Multispecies Field Studies Component, Fish Stock Assessment Collaborative Research Support Program (FSA–CRSP) Parts I & II. Marine Science Institute, University of the Philippines, Diliman, Q.C., Philippines. Approx. 1,000 pp. plus diskettes.

McManus JW, Roa PA (1988) Finding gradients and groups of stations and species. Fishbyte 6(1):19

McManus JW (1987) Getting the most out of tropical fisheries. Maritimes 31(3):14–15.

McManus JW (1980) Philippine coral exports: the coral drain. ICLARM Newsletter (now Naga) 3(1):18–21.

'78–83 Ten technical reports for Philippine Government, U.S. AID/Indonesia, United Nations, Cities Service Oil Co., International Center for Living Aquatic Resources Management, Marcopper Mining Corporation and others.

Cooper WT, Lirman D, Van Groningen MP*, Parkinson JE*, Herlan J*, McManus JW (2014) Assessing techniques to enhance early post-settlement survival of corals in situ for reef restoration. Bull Mar Sci 90(2):651–664. Brown CH, Mohr DC, Gallo CG, Mader, Palinkas L, Wingood G, Prado G, Kellam SG, Pantin H, Poduska J, Gibbons R, McManus J, Ogihara M, Valente T, Wulczyn F, Czaja S, Sutcliffe G, Villamar J, Jacobs CL (2013) A Computational Future for Preventing HIV in Minority Communities: How Advanced Technology Can Improve Implementation of Effective Programs. J Acquir Immune Defic Syndr 63(Suppl 1):S72-S84