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Edmunds, P.J., S. Comeau, C.A. Lantz, A. Andersson, C. Briggs, A. Cohen, J.-P. Gattuso, J.M. Grady, K. Gross, M. Johnson, E.B. Muller, J.B. Ries, S. Tambutte, E. Tambutte, A. Venn and R.C. Carpenter. In Press. Integrating the effects of ocean acidification across functional scales on tropical coral reefs. BioScience.
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Holbrook, S.J. 2016. Kelp forests, coral reefs and the LTER Program: Synergies and impacts on a scientific career. Chapter 27 In: L.R. Walker and M.R. Willig (eds). Long-Term Environmental Research: Changing the Nature of Scientists. Oxford University Press.
Lenihan, H.S., J.L. Hench, S.J. Holbrook, R.J. Schmitt and M. Potoski. In Press. Hydrodynamics influence coral performance through simultaneous direct and indirect effects. Ecology.
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Davies, N., D. Field, D. Gavaghan, S.J. Holbrook, S. Planes, M. Troyer, M. Bonsall, J. Claudet, G. Roderick , R.J. Schmitt, L. Amaral Zettler,V. Berteaux, H.C. Bossin, C. Cabasse, A. Collin, J. Deck, T. Dell, J. Dunne, R. Gates, M. Harfoot, J.L. Hench, M. Hopuare, P. Kirch, G. Kotoulas, A. Kosenkov, A. Kusenko, J.J. Leichter, H. Lenihan, A. Magoulas, N. Martinez, C. Meyer, B. Stoll, B. Swalla, D.M. Tartakovsky, H.T. Murphy, S. Turyshev, F. Valdvinos, R. Williams, S. Wood. In Press. Simulating social-ecological systems: the Island Digital Ecosystem Avatars (IDEA) consortium. Gigascience.
Leenhardt, P., M. Lauer, R.M. Moussa, S.J. Holbrook, A. Rassweiler, R.J. Schmitt and J. Claudet. In Press. Complexities and uncertainties in transitioning small-scale coral reef fisheries. Frontiers in Marine Science.
Putnam, H.M., Davidson, J. and R.D. Gates. 2016. Ocean acidification influences DNA methylation and phenotypic plasticity in environmentally susceptible corals. Integrative and Comparative Biology 56 (Supplement 1):e177-e177.
Sogin, E.M., H.M. Putnam, P.E. Anderson and R.D. Gates. 2016. Metabolomic signatures of increases in temperature and ocean acidification from the reef-building coral, Pocillopora damicornis. Metabolomics 12:UNSP 71.
Sternberg, D.R., H.R. Nelson and P.J. Edmunds. 2016. Asexual budding and aggregated spatial distribution of fungiid corals from disturbed reefs in Moorea, French Polynesia. Integrative and Comparative Biology 56 (Supplement 1):e212-e212.
Andersson, A.J., D.I. Kline, P.J. Edmunds, S.D. Archer, N. Bednarsek, R.C Carpenter, M. Chadsey, P. Goldstein, A.G. Grottoli, T.P. Hurst, A.L. King, J.E. Kubler, I.B. Kuffner, K.R.M. Mackey, B.A. Menge, A. Paytan, U. Riebesell, A. Schnetzer, M.E. Warner and R.C Zimmerman. 2015. Understanding ocean acidification on organismal to ecological scales. Oceanography.28:16-27.
Beijbom, O., P.J. Edmunds, C. Roelfsema, J. Smith, D.I. Kline, B.P. Neal, M.J. Dunlap, V. Moriarty, T-Y Fan, C.-J. Tan, S. Chan, T. Treibitz, A. Gamst, B.G. Mitchell and D. Kriegman. 2015. Towards automated annotation of benthic survey images: Variability of human experts and operational modes of automation. PLoS One 10:e0130312.
Bramanti, L., M. Iannelli, T.-Y. Fan and P.J. Edmunds. 2015. Using demographic models to project the effects of climate change on scleractinian corals: Pocillopora damicornis as a case study. Coral Reefs 34:505-515.
Brewin, R.J.W., S. Sathyendranath, D. Muller, C. Brockmann, P.Y. Deschamps, E. Devred, R. Doerffer, N.Fomferra, B. Franz, M. Grant, S. Groom, A. Horseman, C. Hu, H. Krasemann, Z. Lee, S. Maritorena, F. Meelin, M. Peters, T. Platt, P. Regner, T. Smyth, F. Steinmetz, J. Swinton, J. Werdell, G.N. White III. 2015. The ocean colour climate change initiative: III. A round-robin comparison on in-water bio-optical algorithms. Remote Sensing of Environment 162:271-294.
Briggs, A.A. 2015. The effects of ocean acidification, temperature, and light on the physiology and ecology of tropical crustose coralline algae. MS Thesis, California State University Northridge, Northridge, CA.
Brown, A. and R.C. Carpenter. 2015. Water flow influences the mechanisms and outcomes of interactions between massive Porites and coral reef algae. Marine Biology 162:459-468.
Forsman, Z., G.M. Wellington, G.E. Fox and R.J. Toonen. 2015. Clues to unraveling the coral species problem: distinguishing species from geographic variation in Porites across the Pacific with molecular markers and microskeletal traits. PeerJ 3:e751.
Herdman, L.M.M., J.L. Hench and S.G. Monismith. 2015. Heat balances and thermally-driven lagoon-ocean exchanges on a tropical coral reef system (Moorea, French Polynesia). Journal of Geophysical Research: Oceans 120:1233-1252.
Holbrook, S.J., R.J. Schmitt, V. Messmer, A.J. Brooks, M. Srinivasan, P.L. Munday and G.P. Jones. 2015. Reef fishes in biodiversity hotspots are at greatest risk from loss of coral species. PLoS One 10:e0124054
Pratchett, M.S., K.D. Anderson, M.O. Hoogenboom, E. Widman, A.H. Baird, J.M. Pandolfi, P.J. Edmunds and J.M. Lough. 2015. Spatial, temporal and taxonomic variation in coral growth-implications for the structure and function of coral reef ecosystems. In Hughes, R.N., J.P. Smith and A.C. Dale (Eds.), Oceanography and marine biology: An Annual Review, Volume 53. Pp 215-295. Palo Alto, CA. CRC Press.
Putnam, H.M. and R.D. Gates. 2015. Preconditioning in the reef-building coral Pocillopora damicornis and the potential for trans-generational acclimatization in coral larvae under future climate change conditions. Journal of Experimental Biology 218:2365-2372.
Rivest, E.B. and G.E. Hofmann. 2015. Effects of temperature and high pCO2 on lipid use and biological parameters of planulae of Pocillopora damicornis. Submitted to Journal of Experimental Marine Biology and Ecology 473:43-52.
Tsounis, G., H. Lasker and P.J. Edmunds. 2015. Octocoral success in degrading reefs: A case study in St. John, US Virgin Islands. In: Proceedings of the Society for Integrative and Comparative Biology. West Palm Beach, FL. Integrative and Comparative Biology 55 (Supplement 1):E186-E186.
Adam, T.C., A.J. Brooks, S.J. Holbrook, R.J. Schmitt, L. Washburn and G. Bernardi. 2014. How will coral reef fish communities respond to climate-driven disturbances? Insight from landscape-scale perturbations. Oecologia 176:285–296.
Antoine, D., M. Babin, J.F. Berthon, A. Bricaud, B. Gentili, H. Loisel, S. Maritorena and D. Stramski. 2014. Shedding light on the sea: Andre Morel’s legacy to optical oceanography. Annual Review of Marine Science 6:1-21.
Beijbom, O., M. Saberian, D. Kriegman and N. Vasconcelos. 2014. Guess Averse Loss functions for cost-sensitive multiclass boosting. In: Proceedings of the 31st International Conference on Machine Learning (ICML), Beijing, China 2014. Xing, E.P. and T. Jebara Eds. Journal of Machine Learning Research, Workshop and Conference Proceeding Volume 32. 9 Pp.
Bowen, B.W., K. Shanker, N. Yasuda, M.C.D. Malay, S. von der Heyden, G. Paulay, L.A. Rocha, K.A. Selkoe, P.H. Barber, S.T. Williams, H.A. Lessios, E.D. Crandall, G. Bernardi, C.P. Meyer, K.E. Carpenter and R.J. Toonen. 2014. Phylogeography unplugged: Comparative surveys in the genomic era. Bulletin of Marine Science 90: 13-46.
Clausing, R.J., C. Annunziata, G. Baker, C. Lee, S.J. Bittick and P. Fong. 2014. Effects of sediment depth on algal turf height are mediated by interactions with fish herbivory on a fringing reef. Marine Ecology Progress Series 517:121-129.
Comeau, S., P.J. Edmunds, N.B. Spindel and R.C. Carpenter. 2014. Fast coral reef calcifiers are more sensitive to ocean acidification in short-term laboratory incubations. Limnology and Oceanography 59:1081-1091.
Comeau, S., P.J. Edmunds, N.B. Spindel and R.C. Carpenter. 2014. Diel pCO2 oscillations modulate the response of the coral Acropora hyacinthus to ocean acidification. Marine Ecology Progress Series 501:99-111.
Comeau, S., R.C. Carpenter and P.J. Edmunds. 2014. Effects of irradiance on the response of the coral Acropora pulchra and the calcifying alga Hydrolithon reinboldii to temperature elevation and ocean acidification. Journal of Experimental Marine Biology and Ecology 453:28-35.
Comeau S., R.C. Carpenter, Y. Nojiri, H.M. Putnam, K. Sakai and P.J. Edmunds. 2014. Pacific-wide contrast highlights resistance of reef calcifiers to ocean acidification. Proceedings of the Royal Society B – Biological Sciences 281:20141339.
Edmunds, P. J., S.C. Burgess, H.M. Putnam, M.L. Baskett, L. Bramanti, N.S. Fabina, X. Han, M.P. Lesser, J.S. Madin, C.B. Wall, D.M. Yost and R.D. Gates. 2014. Evaluating the causal basis of ecological success within the scleractinia: an integral projection model approach. Marine Biology 161:2719-2734.
Edmunds, P.J., X. Pochon, D.R. Levitan, D.M. Yost, M. Belcaid, H.M. Putnam and R.D. Gates. 2014. Long-term changes in Symbiodinium communities in Orbicella annularis in St. John, US Virgin Islands. Marine Ecology Progress Series 506:129-144.
Edmunds P.J., M. Adjeroud, M.L. Baskett, I.B. Baums, A.F. Budd, R.C. Carpenter, N. Fabina, T.-Y. Fan, E.C. Franklin, K. Gross, X. Han, L. Jacobson, J.S. Klaus, T.R. McClanahan, J.K. O’Leary, M.J.H. van Oppen, X. Pochon, H.M. Putnam, T.B. Smith, M.I. Stat, H. Sweatman, R. van Woesik, and R.D. Gates. 2014. Persistence and change in community composition of reef corals through past, present, and future climates. PLoS One 9:e107525.
Gibbin, E.M., H.M. Putnam, S.K. Davy and R.D. Gates. 2014. Intracellular pH and its response to CO2-driven seawater acidification in symbiotic versus non-symbiotic coral cells. Journal of Experimental Biology 217:1963-1969.
Hillard, H. and R.C. Carpenter. 2014. Acidification and algae: do they have interactive effects on corals?. In: Proceedings of the Society of Integrative and Comparative Biology. Austin, TX. Integrative and Comparative Biology 54 (Supplement 1):E91-E91.
Kelly, L.W., G. J. Williams, K.L. Barott, C.A. Carlson, E.A. Dinsdale, R.A. Edwards, A.F. Haas, M. Haynes, Y.W. Lim, T. McDole, C.E. Nelson, E. Sala, S.A. Sandin, J.E. Smith, M.J.A. Vermeij, M. Youle and F. Rohwer. 2014. Local genomic adaption of coral and algal-associated microbiomes to gradients of natural variability and anthropogenic stressors. Proceedings of the National Academy of Sciences 111:10227-10232.
Keyse, J., E.D. Crandall, R.J. Toonen, C.P. Meyer, E.A. Treml and C. Riginos. 2014. The scope of published population genetic data for Indo-Pacific marine fauna and future research opportunities in the region. Bulletin of Marine Science 90:47-78.
Leichter, J.J., M.D. Stokes, L.I. Vilchis and J. Fiechter. 2014. Regional synchrony of tempertaure variation and internal wave forcing along the Florida Keys reef tract. Journal of Geophysical research: Oceans 119:548-558.
Lenz, E.A., D. Brown, C. Didden, A. Arnold, and P.J. Edmunds. 2014. The distribution of hermit crabs and their gastropod shells on shallow reefs off St. John, US Virgin Islands. Bulletin of Marine Science 90:681-692.
Levitan, D.R., P.J. Edmunds and K.E. Levitan. 2014. What makes a species common? No evidence of density-dependent recruitment or mortality of the sea urchin Diadema antillarum after the 1983-1984 mass mortality. Oecologia 175:117-128
Marti-Puig, P., Z.H. Forsman, R.D. Haverkort-Yeh, I.S.S. Knapp, J.E. Maragos and R. J. Toonen. 2014. Extreme phenotypic polymorphism in the coral genus Pocillopora; Micro-morphology corresponds to mitochondrial groups, while colony morphology does not. Bulletin of Marine Science 90:211-231.
Muller, E.B. and R.M. Nisbet. 2014. Dynamic energy budget modeling reveals the potential of future growth and calcification for the coccolithophore Emiliania huxleyi in an acidified ocean. Global Change Biology 20:2031-2038.
Padilla-Gamino, J.L. 2014. Kupe and the corals – French/Paumotu electronic edition. LTER Schoolyard Children’s Book Series. Taylor Trade Publishing; an imprint of Rowman & Littlefield. Lanham, MD. 32pp.
Padilla-Gamino J.L., L. Hedouin, R.G. Waller, D. Smith, W. Truong and R.D. Gates. 2014. Sedimentation and the reproductive biology of the Hawaiian reef-building coral Montipora capitata. Biological Bulletin 226:8-18.
Pochon, X., R.D. Gates, D. Vik and P.J. Edmunds. 2014. Molecular characterization of symbiotic algae (Symbiodinium spp.) in soritid foraminifera (Sorites orbiculus) and a scleractinian coral (Orbicella annularis) from St John, US Virgin Islands. Marine Biology 161:2307-2318.
Rivest, E.B. 2014. The effects of elevated ocean acidity and temperature on the physiological integrity of the larvae of the cauliflower coral, Pocillopora damicornis. PhD Dissertation, University of California Santa Barbara, Santa Barbara, CA.
Sogin, M., P. Anderson, P. Williams, C.-S. Chen and R.D. Gates. 2014. Application of 1H-NMR metabolomic profiling for reef-building corals. PLoS One 9:e111274.
Valentino, L.M. 2014. The effects of ocean acidification on bioerosion in the back reef of Moorea, French Polynesia. MS Thesis, California State University Northridge, Northridge, CA.
Von der Heyden, S., M. Berger, R. J. Toonen, L. van Herwerden, M. A. Juinio-Menez, R. Ravago-Gotanco, C. Fauvelot and G. Bernardi. 2014. The application of genetics to marine management and conservation: Examples from the Indo-Pacific. Bulletin of Marine Science 90:123-158.
Zamudio, S.L. 2014. Impacts of temperature-induced maternal effects on larval phenotype, settlement, and post-settlement growth of brooding scleractinian corals. MS Thesis, California State University Northridge, Northridge, CA.
Alldredge, A.L., S.J. Holbrook, R.J. Schmitt, A.J. Brooks and H. Stewart. 2013. Skeletal growth of four scleractinian corals is not enhanced by in situ mesozooplankton enrichment. Marine Ecology Progress Series 489:143-153.
Bramanti, L. and P.J. Edmunds. 2013. Demographic models can forcast climate change effects on scleractinian corals: the Pocillopora damicornis case study. In: Proceedings of the Society of Integrative and Comparative Biology. San Francisco, CA. Integrative and Comparative Biology 53 (Supplement 1):E22-E22.
Carr, M.H., D.P. Malone, M.A. Hixon, S.J. Holbrook and R.J. Schmitt. 2013. How SCUBA changed our understanding of nature: underwater breakthroughs in reef fish ecology. Smithsonian Contributions to the Marine Sciences 39:157-167.
Comeau, S., P.J. Edmunds, N.B. Spindel and R.C. Carpenter. 2013. The responses of eight coral reef calcifiers to increasing partial pressure of CO2 do not exhibit a tipping point. Limnology and Oceanography 58:388-398.
Comeau, S., R.C. Carpenter and P.J. Edmunds. 2013. Response to: Coral reef calcification – carbonate, bicarbonate and proton flux under conditions of increasing ocean acidification. Proceedings of the Royal Society B – Biological Sciences 280:20131153.
Cumbo, V.R., P.J. Edmunds, C.B. Wall and T.-Y. Fan. 2013. Brooded coral larvae differ in their response to high temperature and elevated pCO2 depending on the day of release. Marine Biology 160:2903-2917
Cumbo, V.R., T.-Y. Fan and P.J. Edmunds. 2013. Effects of exposure duration on the response of Pocillopora damicornis larvae to elevated temperature and high pCO2. Journal of Experimental Marine Biology and Ecology 439:100-107.
Dufault, A.M., A. Ninokawa, L. Bramanti, V.R. Cumbo, T.-Y. Fan and P.J. Edmunds. 2013. The role of light in mediating the effects of ocean acidification on coral calcification. Journal of Experimental Biology 216:1570-1577.
Edmunds, P.J. and T.-Y. Fan. 2013. Evidence that high pCO2 affects coral recruits through perturbed protein metabolism. In: Proceedings of the Society of Integrative and Comparative Biology. San Francisco, CA. Integrative and Comparative Biology 53 (Supplement 1):E60-E60.
Edmunds P.J., V.R. Cumbo and T.-Y. Fan. 2013. Metabolic costs of larval settlement and metamorphosis in the coral Seriatopora caliendrum under ambient and elevated pCO2. Journal of Experimental Marine Biology and Ecology 443:33-38.
Fabina, N.S., H.M. Putnam, E.C. Franklin, M. Stat and R.D. Gates. 2013. Symbiotic specificity, association patterns, and function determine community responses to global changes: Defining critical research areas for coral-Symbiodinium symbioses. Global Change Biology 19:3306-3316.
Hofmann, G.E., C.A Blanchette, E.B. Rivest and L. Kapsenberg. 2013. Taking the pulse of marine ecosystems: The importance of coupling long-term physical and biological observations in the context of global change biology. Oceanography 26:140-148.
Leichter, J.J., A.L., Alldredge, G. Bernardi, A.J. Brooks, C.A. Carlson, R,C. Carpenter, P.J. Edmunds, M.R. Fewings, K.M. Hanson, J.L. Hench, S.J. Holbrook, C.E. Nelson, R.J. Schmitt, R.J. Toonan, L Washburn and A.S.J. Wyatt. 2013. Biological and physical interactions on a tropical island coral reef: Transport and retention processes on Moorea, French Polynesia. Oceanography 26:52-63.
Lenz, E.A. and P.J. Edmunds. 2013. Evidence that octocorals are increasing in population density in the Caribbean. In: Proceedings of the Society of Integrative and Comparative Biology. San Francisco, CA. Integrative and Comparative Biology 53 (Supplement 1):E317-E317.
Padilla-Gamino, J.L., R.R. Bidigare, D.J. Barshis, A. Alamaru, L. Hedouin, X. Hernandez-Pech, F. Kandel, S.L.Soon, M.S. Roth, L.J. Rodrigues, A.G. Grottoli, C. Portocarrero, S.A. Wagenhauser, F. Buttler and R.D. Gates. 2013. Are all eggs created equal? A case study from the Hawaiian reef-building coral Montipora capitata. Coral Reefs 32:137-152.
Page, H.M., A.J. Brooks, M. Kulbicki, R. Galzin, R.J. Miller, D. Reed, R.J. Schmitt, S.J. Holbrook and C. Koennigs. 2013. Stable isotopes reveal trophic relationships and diet of consumers in temperate kelp forest and coral reef ecosystems. Oceanography 26:180-189.
Putnam, H.M., A.B. Mayfield, T.-Y. Fan, C.-S. Chen and R.D. Gates. 2013. The physiological and molecular responses of larvae from the reef-building coral Pocillopora damicornis exposed to near-future increases in temperatures and pCO2. Marine Biology 160:2157-2173.
Rivest, E.B., C.-S. Chen, T.-Y. Fan, H.-H. Li, P.J. Edmunds and G.E. Hofmann. 2013. Energetic consequences of ocean acidification and warming for coral larvae. In: Proceedings of the Society of Integrative and Comparative Biology. San Francisco, CA. Integrative and Comparative Biology 53 (Supplement 1):E360-E360.
Stat M, X. Pochon, E.C. Franklin, J.F. Bruno, K.S. Casey, E.R. Selig and R.D. Gates. 2013. The distribution of the thermally tolerant symbiont lineage (Symbiodinium clade D) in corals from Hawaii: correlations with host and the history of ocean thermal stress. Ecology and Evolution 3:1317-1329.
Stewart, H.L., N.N. Price, S.J. Holbrook, R.J. Schmitt and A.J. Brooks. 2013. Determinants of the onset and strength of mutualistic interactions between branching corals and associate crabs. Marine Ecology Progress Series 493:155-163.
Treibitz, T., B.P. Neal, D.I. Kline, O. Beijbom, P.L.D. Roberts, G.B. Mitchell and D. Kriegman. 2013. Wide field-of-view daytime fluorescence imaging of coral reefs. Proceedings of the MTS/IEEE Oceans '13 Conference. San Diego, CA, Sept 23-27, 2013. 5 Pp.
Wall, C.B. and P.J. Edmunds. 2013. Elevated pCO2 increases ammonium excretion in juvenile colonies of the scleractinian Seriatopora caliendrum. In: Proceedings of the Society of Integrative and Comparative Biology. San Francisco, CA. Integrative and Comparative Biology 53 (Supplement 1):E389-E389.
Werdell, P.J., B.A. Franz, S.W. Bailey, G.C. Feldman, E. Boss, V.E. Brando, M. Dowell, T. Hirata, S.J. Lavender, Z. Lee, H. Loisel, S. Maritorena, F. Mélin, T.S. Moore, T.J. Smyth, D. Antoine, E. Devred, O. Hembise Fanton d’Andon, and A. Mangin. 2013. Generalized ocean color inversion model for retrieving marine inherent optical properties. Applied Optics 52: 2019-2037.
Zamudio, S., L. Bramanti and P.J. Edmunds. 2013. Temperature-induced maternal effects on the phenotype of larvae released by the brooding coral Pocillopora damicornis. In: Proceedings of the Society of Integrative and Comparative Biology. San Francisco, CA. Integrative and Comparative Biology 53 (Supplement 1):E233-E233.
Beijbom, O, P.J. Edmunds, D.I. Kline, G.B. Mitchell and D. Kriegman. 2012. Automated annotation of coral reef survey images. Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition. (CVPR), Providence Rhode Island, June, 2012. 8 Pp.
Beldade, R., S.J. Holbrook, R.J. Schmitt, S. Planes, D. Malone and G. Bernardi. 2012. Larger female fish contribute disproportionately more to self-replenishment. Proceedings of the Royal Society of London. Series B, Biological Sciences 279:2116-2121.
Buenau, K.E., Price, N.N., Nisbet, R,M. 2012. Size dependence, facilitation, and microhabitats mediate space competition between coral and crustose coralline algae in a spatially explicit model. Ecological Modelling 237: 23-33.
Collin, A., J.L. Hench and S. Planes. 2012. A novel spaceborne proxy for mapping coral cover. In Yellowlees, D. and T.P. Hughes (eds.). Proceedings of the 12th International Coral Reef Symposium, Cairns, Australia, 9-13 July 2012. ICRS12 Proceedings 5 Pp.
Comeau, S., R.C. Carpenter and P.J. Edmunds. 2012. Coral reef calcifiers buffer their response to ocean acidification using both bicarbonate and carbonate. Proceedings of the Royal Society B – Biological Sciences 280:20122374.
Dufault, A.M., V.R. Cumbo, T.-Y. Fan and P.J. Edmunds. 2012. Effects of diurnally oscillating pCO2 on the calcification and survival of coral recruits. Proceedings of the Royal Society B – Biological Sciences 279:2951-2958.
Edmunds, P.J. D.B. Brown and V. Moriarty. 2012. Interactive effects of ocean acidification and temperature on two scleractinian corals from Moorea, French Polynesia. Global Change Biology 18:2173-2183.
Franklin, E.C., M. Stat, X. Pochon, H.M. Putnam and R.D. Gates. 2012. GeoSymbio: A hybrid, cloud-based web application of global geospatial bioinformatics and ecoinformatics for Symbiodinium-host symbioses. Molecular Ecology Resources 12:369-373.
Jaroensutasinee, K., M. Jaroensutasinee, S. Bainbridge, T. Fountain, S. J. Holbrook and M. Nekrasov. 2012. CREON – Integrating disparate sources of remote coral reef sensor data. In Yellowlees, D. and T.P. Hughes (eds.). Proceedings of the 12th International Coral Reef Symposium, Cairns, Australia, 9-13 July 2012. ICRS12 Proceedings 5 Pp.
Johnson, M.D. and R.C. Carpenter. 2012. Ocean acidification and warming decrease calcification in the crustose coralline alga Hydrolithon onkodes and increases susceptibility to grazing. Journal of Experimental Marine Biology and Ecology 434:94-101.
Krueger, T. and R.D. Gates. 2012. Cultivating endosymbionts - host environmental mimics support the survival of Symbiodinium C15 ex hospite. Journal of Experimental Marine Biology and Ecology 413:169-176.
Mayfield, A.B., P.-H. Chan, H.M. Putnam, C.-S. Chen and T.-Y. Fan. 2012. The effects of a variable temperature regime on the physiology of the reef-building coral Seriatopora hystrix: results from a laboratory-based reciprocal transplant. Journal of Experimental Biology 215:4183-4195.
Padilla-Gamino, J.L., X. Pochon, C. Bird, G.T. Concepcion and R.D. Gates. 2012. From parent to gamete: vertical transmission of Symbiodinium (Dinophyceae) ITS2 sequence assemblages in the reef building coral Montipora capitata. PLoS One 7(6): e38440.
Padilla-Gamino J.L., K.M. Hanson, M. Stat, and R.D. Gates. 2012. Phenotypic plasticity of the coral Porites rus: acclimatization responses to a turbid environment. Journal of Experimental Marine Biology and Ecology 435:71-80.
Pochon, X., H.M. Putnam, F. Burki and R.D. Gates. 2012. Identifying and characterizing alternative molecular markers for the symbiotic and free-living dinoflagellate genus Symbiodinium. PLoS One 7(1):e29816.
Putnam H.M., M. Stat, X. Pochon and R.D. Gates. 2012. Endosymbiotic flexibility associates with environmental sensitivity in scleractinian corals. Proceedings of the Royal Society B – Biological Sciences 279:4352-4361.
Siegel, D.A., D. Antoine, M.J. Behrenfeld, O. Hembise Fanton d’Andon, E. Fields, B.A. Franz, P. Goryl, S. Maritorena, C.R. McClain, M. Wang, and J.A. Yoder. 2012. Global ocean phytoplankton. In Blunden, J. and D.S. Arndt (eds.) State of the Climate in 2011. Bulletin of the American Meteorological Society 93:S107-S110.
Stat, M., A.C. Baker, D.G. Bourne, A.M.S. Correa, Z. Forsman, M.J. Huggett, X. Pochon, D. Skillings, R.J. Toonen, M.J.H. van Oppen and R.D. Gates. 2012. Molecular delineation of species in the coral holobiont. in M. Lesser, editor. Advances in Marine Biology Vol. 63, Amsterdam, The Netherlands. Academic Press. 65 pp.
Adam, T.C., R.J. Schmitt, S.J. Holbrook, A.J. Brooks, P.J. Edmunds, R.C. Carpenter and G. Bernardi. 2011. Herbivory, connectivity and ecosystem resilience: response of a coral reef to a large-scale perturbation. PLoS One 6(8):e23717.
Antoine D., D.A. Siegel, T. Kostadinov, S. Maritorena, N.B. Nelson, B. Gentili, V. Vellucci, and N. Guillocheau. 2011. Variability in optical particle backscattering in contrasting bio-optical oceanic regimes. Limnology and Oceanography 56:955-973.
Franklin, E.C., M. Stat, X. Pochon, H.M. Putnam and R.D. Gates. 2011. Rapid development of a hybrid web application for synthesis science of Symbiodinium with Google Apps. In Jones, M. and C. Gries (eds.), Proceedings of the Environmental Information Management Conference 2011. Pp.44-48.
Gates, R.D. and T.D. Ainsworth. 2011. The nature and taxonomic composition of coral symbiomes as drivers of performance limits in scleractinian corals. Journal of Experimental Marine Biology and Ecology 408:94-101.
Haas, A.F., C.E. Nelson, L. Wegley-Kelly, C.A. Carlson, F. Rohwer, J.J. Leichter, A. Wyatt and J.E. Smith. 2011. Effects of coral reef benthic primary producers on dissolved organic carbon and microbial activity. PLoS One 6(11):e27973.
Hanson, K. 2011. Planktivorous fish link coral reef and oceanic food webs: causes and consequences of landscape-level patterns in fish behavior, diet and growth. PhD Dissertation, Scripps Institution of Oceanography. University of California San Diego, San Diego, CA.
Jaroensutasinee, M., K. Jaroensutasinee, T. Fountain, M. Nekrasov, S. Chumkiew, P. Noonsang, U. Kuhapong and S. Bainbridge. 2011. Coral sensor network at Racha Island, Thailand. In Jones, M. and C. Gries (ed.), Proceedings of the Environmental Information Management Conference 2011. Santa Barbara, CA September 28-29, 2011. Pp 82-86.
Johnson, M.K., S.J. Holbrook, R.J. Schmitt and A.J. Brooks. 2011. Fish communities on staghorn coral: effects of habitat characteristics and resident farmerfishes. Environmental Biology of Fishes 91:429-448.
Mayfield, A.B., L.-H. Wang, P.-C. Tang, T.-Y. Fan, Y.-Y. Hsiao, C.-L. Tsai and C.-S. Chen. 2011. Assessing the impacts of experimentally elevated temperature on the biological composition and molecular chaperone gene expression of a reef coral. PLoS One 6(10):e26529.
Melack, J.M., A.C. Finzi, D. Siegel, S. MacIntyre, C.E. Nelson, A.K. Aufdenkampe and M.L. Pace. 2011. Improving biogeochemical knowledge through technical innovation. Frontiers in Ecology and the Environment 9:37-43.
Mora, C., O. Aburto-Oropeza, A.A. Bocos, P.M. Ayotte, S. Banks, A.G. Bauman, M. Beger, S. Bessudo, D.J. Booth, E. Brokovich, A. Brooks, P. Chabanet, J. Cinner, J. Cortes, J.J. Cruz-Motta, A.C. Magana, E. DeMartini, G.J. Edgar, D.A. Feary, S.C.A. Ferse, A. Friedlander, K.J. Gaston, C. Gough, N.A.J. Graham, A. Green, H. Guzman, M. Kulbicki, Y. Letourneur, A.L. Perez, M. Loreau, Y. Loya, C. Martinez, I. Mascarenas-Osorio, T. Morove, M.-O. Nadon, Y. Nakamura, G. Paredes, N. Polunin, M.S. Pratchett, H.R. Bonilla, F. Rivera, E. Sala, S. Sandin, G. Soler, R. Stuart-Smith, E. Tessier, D.P. Tittensor, M. Tupper, P. Usseglio, L. Vigliola, L. Wantiez, I. Williams, S.K. Wilson and F.A. Zapata. 2011. Global human footprint on the linkage between biodiversity and ecosystem functioning in reef fishes. PloS Biology 9:e1000606.
Nelson, C.E., A.L. Alldredge, E.A. McCliment, L.A. Amaral-Zettler and C.A. Carlson. 2011. Depleted dissolved organic carbon and distinct bacterial communities in the water column of a rapid-flushing coral reef ecosystem. ISME Journal 5:1374-1387.
Padilla-Gamino, J.L., T.M. Weatherby, R.G. Waller and R.D. Gates. 2011. Formation and structural organization of the egg-sperm bundle of the scleractinian coral Montipora capita. Coral Reefs 30:371-380.
Salerno, J.L., D.R. Reineman, R.D. Gates and M.S. Rappe. 2011. The effect of a sub-lethal temperature elevation on the structure of bacterial communities associated with the coral Porites compressa. Journal of Marine Biology, 2011:Article ID 969173, 9 Pp.
Siegel, D.A., M.J. Behrenfeld, S. Maritorena, R.T. O’Malley and E. Fields. 2011. Global ocean phytoplankton. In Blunden, J., D.S. Arndt and M.O. Baringer (eds.) State of the Climate in 2010. Bulletin of the American Meteorological Society 92:S105-S108.
Stat, M, and R.D. Gates. 2011. Clade D Symbiodinium in scleractinian corals: a “nugget” of hope, a selfish opportunist, an ominous sign, or all of the above? Journal of Marine Biology, 2011:Article ID 730715, 9 Pp.
Stat, M., C.E. Bird, X. Pochon, L. Chasqui, L.J. Chauka, G.T. Concepcion, D. Logan, M. Takabayashi, R.J. Toonen and R.D. Gates. 2011. Variation in Symbiodinium ITS2 sequence assemblages among coral colonies. PLoS One 6:e15854.
Yau, A. J.-Y. 2011. Size-Based Approaches to Modeling and Managing Local Populations: A Case Study Using an Artisanal Fishery for Giant Clams, Tridacna maxima. PhD Dissertation, University of California Santa Barbara, Santa Barbara, CA.
Barshis, D.J., J.H. Stillman, R.D. Gates, R.J. Toonen, L.W. Smith and C. Birkeland. 2010. Protein expression and genetic structure of the coral Porites lobata in an environmentally extreme Samoan back reef: does host genotype limit phenotypic plasticity? Molecular Ecology 19:1705-1720.
Baskett, M.L., R.M. Nisbet, C.V. Kappel, P.J. Mumby and S.D. Gaines. 2010. Conservation management approaches to protecting the capacity for corals to respond to climate change: a theoretical comparison. Global Change Biology 16:1229-1246.
Brainard, R.E., S. Bainbridge, R. Brinkman, C.M. Eakin, J.-P. Gattuso, D. Gledhill, L. Gramer, J. Hendee, R.K. Hoeke, S.J. Holbrook, O. Hoegh-Guldberg, M. Lammers, D. Manzello, M. McManus, R. Moffitt, M. Monaco, J. Morgan, D. Obura, S. Planes, R.J. Schmitt, C. Steinberg, H. Sweatman, O.J. Vetter and K.B. Wong. 2010. An international network of coral reef ecosystem observing systems (I-CREOS). In Proceedings of OceanObs’09: Sustained Ocean Observations and Information for Society (Vol. 2), Venice, Italy, 21-25 September 2009, J. Hall, D.E. Harrison and D. Stammer, editors, ESA Publication WPP-306.
Colvard, N.B and P.J. Edmunds. 2010. The physiological response of tropical reef corals to light reflected from the benthos. In: Proceedings of the Society of Integrative and Comparative Biology. Seattle, WA. Integrative and Comparative Biology 50 (Supplement 1):E33-E33.
Green, D.H., P.J. Edmunds, X. Pochon and R.D. Gates. 2010. The effects of substratum type on the growth, mortality, and photophysiology of juvenile corals in St. John, US Virgin Islands. Journal of Experimental Marine Biology and Ecology 384:18-29.
Hofmann G.E., Barry J.P., Edmunds P.J., Gates R.D., Hutchins D.A., Klinger T. and M.A. Sewell. 2010. The effect of ocean acidification on calcifying organisms in marine ecosystems: an organism to ecosystem perspective. Annual Review of Ecology, Evolution and Systematics 41:127-147.
Jacobson, L.M. and P.J. Edmunds. 2010. Long-term changes in the concentration of zooplankton and particulate material over a fringing reef in St. John, US Virgin Islands. Bulletin of Marine Sciences 86:763-772.
Leray, M., R. Beldade, S.J. Holbrook, R.J. Schmitt, S. Planes and G. Bernardi. 2010. Allopatric divergence and speciation in coral reef fish: the three-spot Dascyllus, Dascyllus trimaculatus, species complex. Evolution 64:1218-1230.
Lesser, M. P., M. Slattery, M. Stat, M. Ojimi, R.D. Gates and A. Grottoli. 2010. Photoacclimatization by the coral Montastraea cavernosa in the mesophotic zone: light, food, and genetics. Ecology 91:990-1003.
Maritorena S., O.H.F. d’Andon, A. Mangin and D.A. Siegel. 2010. Merged satellite ocean color data products using a bio-optical model: characteristics, benefits and issues. Remote Sensing of Environment 114(8):1791-1804.
Mayfield, A.B., Y-Y Hsiao, T-Y Fan, C-S Chen and R.D. Gates. 2010. Evaluating the temporal stability of stress-activated protein kinase and cytoskeleton gene expression in the Pacific reef corals Pocillopora damicornis and Seriatopora hystrix . Journal of Experimental Marine Biology and Ecology 395:215-222.
Pochon, X., M. Stat, M. Takabayashi, L. Chasqui, L.J. Chauka, D.D.K. Logan and R.D. Gates. 2010. Comparison of endosymbiotic and free-living Symbiodinium (Dinophyceae) diversity in a Hawaiian reef environment. Journal of Phycology 46:53-65.
Wilson, S.K., M. Adjeroud, D.R. Bellwood, M.L. Berumen, D. Booth, Y.-M. Bozec, P. Chabanet, A. Cheal, J. Cinner, M. Depczynski, D.A. Feary, M. Gagliano, N.A.J. Graham, A.R. Halford, B.S. Halpern, A.R. Harborne, A.S. Hoey, S.J. Holbrook, G.P. Jones, M. Kulbiki, Y. Letourneur, T.L. De Loma, T. McClanahan, M.I. McCormick, M.G. Meekan, P.J. Mumby, P.L. Munday, M.C. Ohman, M.S. Pratchett, B. Riegl, M. Sano, R.J. Schmitt and C. Syms. 2010. Crucial knowledge gaps in current understanding of climate change impacts on coral reef fishes. Journal of Experimental Biology 213:894-900
Yancey, P.H., M. Heppenstall, S. Ly, R.M. Andrell, R.D. Gates, V.L. Carter and M. Hagedorn. 2010. Betaines and dimethylsulfoniopropionate as major osmolytes in Cnidaria with endosymbiotic dinoflagellates. Physiological and Biochemical Zoology 83:167-173.
Adjeroud, M., F. Michonneau, P.J. Edmunds, Y. Chancerelle, T. Lison de Loma, L. Penin, L. Thibaut, J. Vidal-Dupiol, B. Salvat and R. Galzin. 2009. Recurrent disturbances, recovery trajectories, and resilience of coral assemblages on a South Central Pacific reef. Coral Reefs 28:775-780.
Beldade, R., S.J. Holbrook, R.J. Schmitt, S. Planes and G. Bernardi. 2009. Isolation and characterization of eight polymorphic microsatellite markers from the orange-fin anemonefish, Amphiprion chrysopterus. Conservation Genetics Resources 1: 333-335.
Buenau, K.E. 2009. The shifting landscapes of competition: Modeling the roles of space, size, and facilitation in marine benthic communities. PhD Dissertation, University of California Santa Barbara, Santa Barbara, CA.
Fitt, W.K., R.D. Gates, O. Hoegh-Guldberg, J.C. Bythell, A. Jatkar, A.G. Grottoli, M. Gomez, P. Fisher, T.C. LaJeunesse, O. Pantos, R. Iglesias-Prieto, D.J. Franklin, L.J. Rodrigues, J.M. Torregiani, R. van Woesik and M.P. Lesser. 2009. Response of two species of Indo-Pacific corals, Porites cylindrica and Stylophora pistillata, to short term thermal stress: the host does matter in determining the tolerance of corals to bleaching. Journal of Experimental Marine Biology and Ecology 373:102-110.
Fountain, T., S. Tilak, P. Shin, S. Holbrook, R.J. Schmitt, A. Brooks, L. Washburn and D. Salazar. 2009. Digital Moorea cyberinfrastructure for coral reef monitoring. Proceedings of 5th International Conference on Intelligent Sensors, Sensor Networks and Information Processing (ISSNIP) 2009. Melbourne, Australia. IEEE Conferences Pp. 243-248.
Goldenheim, W.M. 2009. The effects of flow and temperature over multiple time scales on scleractinian growth and photo-physiology in Moorea, French Polynesia. MS Thesis, California State University Northridge, Northridge, CA.
Kane, C.N., A.J. Brooks, S.J. Holbrook and R.J. Schmitt. 2009. The role of microhabitat preference and social organization in determining the spatial distribution of a coral reef fish. Environmental Biology of Fishes 84:1-10.
Leray, M., R. Beldade, S.J. Holbrook, R.J. Schmitt, S. Planes and G. Bernardi. 2009. Isolation and characterization of 13 polymorphic nuclear microsatellite primers for the widespread Indo-Pacific three-spot damselfish, Dascyllus trimaculatus, and closely related D. auripinnis. Molecular Ecology Resources 9:213-215.
Muehllehner N. and P.J. Edmunds. 2009. Effects of ocean acidification and increased temperature on skeletal growth of two scleractinian corals, Pocillopora meandrina and Porites rus. Proceedings of the 11th International Coral Reef Symposium ICRS11 Proceedings Pp. 57-61.
Muller, E.B., F.J. Doyle, R.M. Nisbet, P. Edmunds and S. Kooijman. 2009. Dynamic energy budgets of syntropic symbiotic relationships between heterotrophic hosts and photoautotrophic symbionts. Comparative Biochemistry and Physiology A – Molecular and Integrative Physiology (Supplement) 153A:S145-S145.
Muller, E.B., S.A.L.M. Kooijman, P.J. Edmunds, F.J. Doyle and R.M. Nisbet. 2009. Dynamic energy budgets in syntrophic symbiotic relationships between heterotrophic hosts and photoautotrophic symbionts. Journal of Theoretical Biology 259:44-57.
Olson, N.D., T.D. Ainsworth, R.D. Gates and M. Takabayashi. 2009. Diazotrophic bacteria associated with Hawaiian Montipora corals: diversity and abundance in correlation with symbiotic dinoflagellates. Journal of Experimental Marine Biology and Ecology 371:140-146.
Putnam, H.M. and P.J.Edmunds. 2009. Responses of coral hosts and their algal symbionts to thermal heterogeneity. Proceedings of the 11th International Coral Reef Symposium ICRS11 Proceedings Pp. 393-397.
Spitler, M.I. 2009. Factors influencing the distribution and abundance of the dominant macroalgal species on coral reefs in Moorea, French Polynesia. MS Thesis, California State University Northridge, Northridge, CA.
Green, D.H., P.J. Edmunds and R.C. Carpenter. 2008. Increasing relative abundance of Porites astereoides on Caribbean reefs mediated by an overall decline in coral cover. Marine Ecology Progress Series 359:1-10.
Lison de Loma, T., C.W. Osenberg, J.S. Shima, Y. Chancerelle, N. Davies, A.J. Brooks and R. Galzin. 2008. A framework for assessing impacts of marine protected areas in Moorea (French Polynesia). Pacific Science 62:431-441.
Morrow, K.M. and R. Carpenter. 2008. Shallow kelp canopies mediate macroalgal composition: effects on the distribution and abundance of Corynactis californica (Corallimorpharia). Marine Ecology Progress Series 361:119-127.
Muehllehner, N. 2008. Growth and morphology in Acropora under increasing carbon dioxide and the effect of increased temperature and carbon dioxide on the photosynthesis and growth of Porites rus and Pocillopora meandrina. MS Thesis, California State University Northridge, Northridge, CA.
Price, N.N. 2008. Structuring processes for benthic communities: Habitat selection, facilitation, and competition on a coral reef. PhD Dissertation, University of California Santa Barbara, Santa Barbara, CA.
Rosman, J.H., J.L. Hench, J.R. Koseff and S.G. Monismith. 2008. Extracting Reynolds stresses from acoustic doppler current profiler measurements in wave-dominated environments. Journal of Atmospheric and Oceanic Technology 25:286-306.
Elahi, R. and P.J. Edmunds. 2007. Determinate growth and the scaling of photosynthetic energy intake in the solitary coral Fungia concinna (Verrill). Journal of Experimental Marine Biology and Ecology 349:183-193.
Hoegh-Guldberg, O., G. Muller-Parker, C.B. Cook, R.D. Gates, E. Gladfelter, R.K. Trench and V. Weiss. 2007. Len Muscatine (1932-2007) and his contributions to the understanding of algal-invertebrate endosymbiosis. Coral Reefs 26:731-739.
Holbrook, S.J., R.J. Schmitt, A.J. Brooks, T. Margalith, J. Burnsed, K. Seydel and H. Masui. 2007. The use of LED light lures to enhance larval settlement of coral reef fish. Pages 326-338 in T. Murata, editor. State of the Art: High Power LED Application Practices, Technical Information Institute Co. Ltd., Japan.
Leggat, W., T.A. Ainsworth, J.C. Bythell, S. Dove, R.D. Gates, O. Hoegh-Guldberg, R. Iglesias-Prieto and D. Yellowlees. 2007. The hologenome theory disregards the coral holobiont. Nature Reviews Microbiology 5(10) DOI: 10.1038/nrmicro1635-c1.
Lesser, M.P., J.C. Bythell, R.D. Gates, R.W. Johnstone and O. Hoegh-Guldberg. 2007. Are infectious diseases really killing corals? Alternative interpretations of the experimental and ecological data. Journal of Experimental Marine Biology and Ecology 346:36-44.
Ohlmann, C., P. White, L. Washburn, E. Terrill, B.M. Emery and M. Otero. 2007. Interpretation of coastal HF radar derived surface currents with high resolution drifter data. Journal of Atmospheric and Oceanic Technology 24:666-680.
Padilla-Gamino, J.L. and R.C. Carpenter. 2007. Thermal ecophysiology of Laurencia pacifica and Laurencia nidifica (Ceramiales, Rhodophyta) from tropical and warm-temperate regions. Journal of Phycology 43:686-692.
Penin, L., M. Adjeroud, M. Schrimm and H.S. Lenihan. 2007. High spatial variability in coral bleaching around Moorea (French Polynesia): patterns across locations and water depths. Comptes Rendus Biologies 330:171-181.
Schmitt, R.J. and S.J. Holbrook. 2007. Predicting the magnitude of temporal variation in young-of-year class strength of surfperch (Teleostei: Embiotocidae). The Raffles Bulletin of Zoology (Supplement) 14:155-160.
Talmage, S.C. 2007. Variation in abundance and carbon allocation for Sargassum mangarevense across gradients in herbivory and hydrodynamic exposure in Moorea, French Polynesia. MS Thesis, California State University Northridge, Northridge, CA.
Brooks, A.J. 2006. Digital Moorea: The implementation of a wireless sensor network for the monitoring of coral reefs. Proceedings of the Workshop on the Adoption of Sensor Networks by Coastal Managers. Pp. 11-16.
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.
Holbrook, S.J., A.J. Brooks and R.J. Schmitt. 2006. Relationships between live coral cover and reef fishes: implications for predicting effects of environmental disturbances. Proceedings of the 10th International Coral Reef Symposium ICRS10 Proceedings Pp. 241-249.
Schmitt, R.J. and S.J. Holbrook. 2006. Developmental delays, recruitment storage and adult attrition rates in local populations of a tropical damselfish. Proceedings of the 10th International Coral Reef Symposium ICRS10 Proceedings Pp. 232-240.
Stewart, H.L. 2006. Ontogenetic changes in buoyancy, breaking strength, extensibility, and reproductive investment in a drifting macroalga Turbinaria ornata (Phaeophyta). Journal of Phycology 42:43-50.
Lape, J.C.P. 2005. Factors influencing the quality of a refuge for coral reef fish: effects of microhabitat setting, size and inhabitants. MS Thesis, University of California Santa Barbara, Santa Barbara, CA.
Maritorena, S. and D.A. Siegel. 2005. Consistent merging of satellite ocean color data sets using a bio-optical model. Remote Sensing of Environment 94:429-440.
Siegel, D.A., S. Maritorena, N.B. Nelson, M.J. Behrenfeld and C.R. McClain. 2005. Colored dissolved organic matter and its influence on the satellite-based characterization of the ocean biosphere. Geophysical Research Letters 32:L20605.
Siegel, D.A., S. Maritorena and N.B. Nelson. 2005. Independence and interdependencies among global ocean color properties: reassessing the bio-optical assumption. Journal of Geophysical Research 110:C07011.
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