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2008

Caress, D.W., H. Thomas, W.J. Kirkwood, R. McEwen, R. Henthorn, D.A. Clague, C.K. Paull, J.B. Paduan, and K.L. Maier. 2008. High-resolution multibeam, sidescan, and subbottom surveys of seamounts, submarine canyons, deep-sea fan channels, and gas seeps using the MBARI AUV D. Allan B.. Marine Habitat Mapping Technology for Alaska: 47–70.

Carr, S.D., X.J. Capet, J.C. McWilliams, J.T. Pennington, and F.P. Chavez. 2008. The influence of diel vertical migration on zooplankton transport and recruitment in an upwelling region: Estimates from a coupled behavioral-physical model. Fisheries Oceanography, 17: 1–15. http://dx.doi.org/10.1111/j.1365-2419.2007.00447.x

Chavez, F.P., A. Bertrand, R. Guevara, P. Soler, and J. Csirke. 2008. The northern Humboldt Current System: Brief history, present status and a view towards the future. Progress in Oceanography, 79: 95–105. http://dx.doi.org/10.1016/j.pocean.2008.10.012

Cokelet, E.D., N. Tervalon, and J.G. Bellingham. 2008. Hydrography of the West Spitsbergen Current, Svalbard Branch: Autumn 2001. Journal of Geophysical Research, 113. http://dx.doi.org/10.1029/2007JC004150

Collins, A.G., B. Bentlage, A. Lindner, D. Lindsay, S.H.D. Haddock, G. Jarms, J.L. Norenburg, T. Jankowski, and P. Cartwright. 2008. Phylogenetics of Trachylina (Cnidaria: Hydrozoa) with new insights on the evolution of some problematical taxa. Journal of the Marine Biological Association of the United Kingdom, 88: 1673–1685. http://dx.doi.org/10.1017/S0025315408001732

Cuvelier, M.L., A. Ortiz, E. Kim, H. Moehlig, D.E. Richardson, J.F. Heidelberg, J.M. Archibald, and A.Z.  Worden. 2008. Widespread distribution of a unique marine protistan lineage. Environmental Microbiology, 10: 1621–1634. http://dx.doi.org/10.1111/j.1462-2920.2008.01580.x

Davis, A.S., D.A. Clague, B.L. Cousens, R. Keaten, and J.B. Paduan. 2008. Geochemistry of basalt from the North Gorda segment of the Gorda Ridge: Evolution toward ultra-slow spreading ridge lavas due to decreasing magma supply. Geochemistry, Geophysics, Geosystems, 9. http://dx.doi.org/10.1029/2007GC001775

Demir, E., K.J. Coyne, M.A. Doblin, S.M. Handy, and D.A. Hutchins. 2008. Assessment of microzooplankton grazing on Heterosigma akashiwo using a species-specific approach combining quantitative real time PCR (QPCR) and dilution methods. Microbial Ecology, 55: 583–584.

Deschamps, P., H. Moreau, A.Z. Worden, D. Dauvillée, and S.G. Ball. 2008. Early gene duplication within chloroplastida and its correspondence with relocation of starch metabolism to chloroplasts. Genetics, 178: 2373–2387. http://dx.doi.org/10.1534/genetics.108.087205

Dixon, J.E., D.A. Clague, B. Cousens, M.L. Monsalve and M.L. Uhl. 2008. Carbonatite and silicate melt metasomatism of the mantle surrounding the Hawaiian plume: Evidence from volatiles, trace elements, and radiogenic isotopes in rejuvenated-stage lavas from Niihau, Hawaii. Geochemistry, Geophysics, Geosystems, 9: 1–34. http://dx.doi.org/10.1029/2008GC002076

Drazen, J.C., B.N. Popp, C.A. Choy, T. Clemente, L. DeForest, and K.L. Smith Jr. 2008. Bypassing the abyssal benthic food web: Macrourid diet in the eastern North Pacific inferred from stomach content and stable isotope analyses. Limnology and Oceanography, 53: 2644–2654. http://dx.doi.org/10.4319/lo.2008.53.6.2644

Dunn, C.W., A. Hejnol, D.Q. Matus, K. Pang, W.E. Browne, S.A. Smith, E. Seaver, G.W. Rouse, M. Obst, G.D. Edgecombe, M.V. Sorensen, S.H.D. Haddock, A. Schmidt-Rhaesa, A. Okusu, R.M. Kristensen, W.C. Wheeler, M.Q. Martindale, and G. Giribet. 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature, 452: 745–749. http://dx.doi.org/10.1038/nature06614

Elrod, V.A., K.S. Johnson, S.E. Fitzwater, and J.N. Plant. 2008. A long-term, high-resolution record of surface water iron concentrations in the upwelling-driven central California region. Journal of Geophysical Research, 113: 1–13. http://dx.doi.org/10.1029/2007JC004610

Freon, P., C. Werner, and F.P. Chavez. 2008. Conjectures on the influence of climate change on ocean ecosystems dominated by small pelagic fish. Climate Change and Small Pelagic Fish: 312–343.

Friederich, G.E., J. Ledesma, O. Ulloa, and F.P.  Chavez. 2008. Air-sea carbon dioxide fluxes in the coastal southeastern tropical Pacific. Progress in Oceanography, 79: 156–166. http://dx.doi.org/10.1016/j.pocean.2008.10.001

Génio, L., S.B. Johnson, R.C. Vrijenhoek, M.R. Cunha, P.A. Tyler, S. Kiel, and C.T.S. Little. 2008. New record of “Bathymodiolusmauritanicus Cosel 2002 from the Gulf of Cadiz (NE Atlantic) mud volcanoes. Journal of Shellfish Research, 27: 53–61.

Goffredi, S.K., W.J. Jones, H. Erhlich, A. Springer, and R.C. Vrijenhoek. 2008. Epibiotic bacteria associated with the recently discovered Yeti crab, Kiwa hirsuta. Environmental Microbiology, 10: 2623–2634. http://dx.doi.org/10.1111/j.1462-2920.2008.01684.x

Greenfield, D., R. Marin III, G.J. Doucette, C. Mikulski, S. Jensen, B. Roman, N. Alvarado, and C.A. Scholin. 2008. Field applications of the second-generation Environmental Sample Processor (ESP) for remote detection of harmful algae: 2006–2007. Limnology and Oceanography: Methods, 6: 667–679.

Guillou, L., M. Viprey, A. Chambouvet, R.M. Welsh, A.R. Kirkham, R. Massanna, D.J. Scanlan, and A.Z. Worden. 2008. Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata). Environmental Microbiology, 10: 3349–3365. http://dx.doi.org/10.1111/j.1462-2920.2008.01731.x

Haddock, S. H. D. 2008. Reconsidering evidence for potential climate-related increases in jellyfish. Limnology and Oceanography, 53: 2759–2762.

Handy, S.H., E. Demir, K.J. Coyne, C.E. Hare, K.J. Portune, and D.A. Hutchins. 2008. Using quantitative PCR analyses to investigate competition between dinoflagellates and raphidophytes at various N:P ratios. Harmful Algae, 7: 599–613.

Harvey, J.B.J., M.S. Hoy, and R.J. Rodriguez. 2008. Molecular detection of native and invasive marine invertebrate larvae present in ballast and open water environmental samples collected in Puget Sound. Journal of Experimental Marine Biology and Ecology, 369: 93–99.

Hein, J.R., D.A. Clague, R.A. Koski, R.W. Embley, and R.E. Dunham. 2008. Metalliferous Sediment and a Silica-Hematite Deposit within the Blanco Fracture Zone, Northeast Pacific. Marine Georesources & Geotechnology, 26: 317–339. http://dx.doi.org/10.1080/10641190802430986

Hester, K.C., E.T. Peltzer, W. Kirkwood, and P.G. Brewer. 2008. Unanticipated consequences of ocean acidification: A noisier ocean at lower pH. Geophysical Research Letters, 35: 1–5. http://dx.doi.org/10.1029/2008GL034913

Holm, C.S., Z. Chase, H.W. Jannasch, and K.S. Johnson. 2008. Development and initial deployments of an autonomous in situ instrument for long-term monitoring of copper (II) in the marine environment. Limnology and Oceanography: Methods, 6: 336–346.

Jannasch, H.W., L.J. Coletti, K.S. Johnson, S.E. Fitzwater, J.A. Needoba, and J.N. Plant. 2008. The Land/Ocean Biogeochemical Observatory: A robust networked mooring system for continuously monitoring complex biogeochemical cycles in estuaries. Limnology and Oceanography: Methods, 6: 263–276.

Johnson, K.S., and J.A. Needoba. 2008. Mapping the spatial variability of plankton metabolism using nitrate and oxygen sensors on an autonomous underwater vehicle. Limnology and Oceanography, 53: 2237–2250. http://dx.doi.org/10.4319/lo.2008.53.5_part_2.2237

Jones, W.J., C.M. Preston, R. Marin III, C.A. Scholin, and R.C. Vrijenhoek. 2008. A robotic molecular method for in situ detection of marine invertebrate larvae. Molecular Ecology Resources, 8: 540–550. http://dx.doi.org/10.1111/j.1471-8286.2007.02021.x

Jones, W.J., S.B. Johnson, G.W. Rouse, and R.C. Vrijenhoek. 2008. Marine worms (genus Osedax) colonize cow bones. Proceedings of the Royal Society B, 275: 387–391. http://dx.doi.org/10.1098/rspb.2007.1437

Kessler, J.D., W.S. Reeburgh, D.L. Valentine, F.S. Kinnaman, E.T. Peltzer, P.G. Brewer, J. Southon, and S.C. Tyler. 2008. A survey of methane isotope abundance (14C, 13C, 2H) from five nearshore marine basins that reveals unusual radiocarbon levels in subsurface waters. Journal of Geophysical Research, 113: 1–13. http://dx.doi.org/10.1029/2008JC004822

Kildow, J. 2008. Phase II Florida's Ocean and Coastal Economies Report: 219.

Kildow, J. 2008. The Influence of Coastal Preservation and Restoration on Coastal Real Estate Value. In The Economic and Market Value of Coasts and Estuaries, Restore America’s Estuaries: 116–131.

Kudela, R.M., J.P. Ryan, M.D. Blakely, J.Q. Lane, and T.D. Peterson. 2008. Linking the physiology and ecology of Cochlodinium to better understand harmful algal bloom events: A comparative approach. Harmful Algae, 7: 278–292. http://dx.doi.org/10.1016/j.hal.2007.12.016

Lapham, L.L., J.P. Chanton, C.S. Martens, P.D. Higgley, H. Jannasch, and J.R. Woolsey. 2008. Measuring temporal variability in pore-fluid chemistry to assess gas hydrate stability: Development of a continuous pore-fluid array. Environmental Science and Technology, 42: 7368–7373.

McCann, M., and K. Gomes. 2008. Oceanographic data provenance tracking with the Shore Side Data System. Proceedings of the Second International Provenance and Annotation Workshop: 309–322.

McGann, C., F. Py, K. Rajan, H. Thomas, R. Henthorn, and R. McEwen. 2008. A deliberative architecture for AUV control. Proceedings of the International Conference on Robotics and Automation: 1049–1054.

McGann, C., F. Py, K. Rajan, H. Thomas, R. Henthorn, and R. McEwen. 2008. Automated decision making for a new class of AUV science. Proceedings of the American Society of Limnology and Oceanography / Ocean Sciences Meeting.

McGann, C., F. Py, K. Rajan, H. Thomas, R. Henthorn, and R. McEwen. 2008. Preliminary results for model-based adaptive control of an autonomous underwater vehicle. Proceedings of the International Symposium on Experimental Robotics.

McGann, C., F. Py, K. Rajan, J. Ryan, and R. Henthorn. 2008. Adaptive control for autonomous underwater vehicles. Proceedings of the Association for the Advancement for Artificial Intelligence National Conference, 1319–1324.

Meduna, D., S.M. Rock, and R. McEwen. 2008. Low-cost terrain-relative navigation for long-range AUVs. Proceedings of the Marine Technology Society / Institute of Electrical and Electronics Engineers Oceans Conference.

Mikulski, C.M., Y.T. Park, K.L. Jones, C.K. Lee, W.A. Lim, C.A. Scholin, and G.J. Doucette. 2008. Development and field application of rRNA-targeted probes for the detection of Cochlodinium ploykrikoides in Korean coastal waters using whole cell and sandwich hybridization formats. Harmful Algae, 7: 347–359.

Monterey Bay Aquarium Research Institute. 2008. Ocean Science Summit Report: Climate Change and Ocean Health: 82.

Moore, W.S., W. Ussler III, and C.K. Paull. 2008. Short-lived radium isotopes in the Hawaiian margin: Evidence for large fluid fluxes through the Puna Ridge. Marine Chemistry, 109: 421–430. http://dx.doi.org/10.1016/j.marchem.2007.09.010

Moore, W.S., W. Ussler III, and C.K. Paull. 2008. Short-lived radium isotopes in the Hawaiian margin: Evidence for large fluxes through the Puna Ridge. Marine Chemistry, 109: 421–430. http://dx.doi.org/10.1016/j.marchem.2007.09.010

National Oceans Economics Program. 2008. California Ocean and Coastal Investment Study: Final Report: 34.

Nielsen, M.E., C.E. Reimers, H.K. White, S. Sharma, and P.R. Girguis. 2008. Sustainable energy from deep ocean cold seeps. Energy and Environmental Science, 1: 584–593. http://dx.doi.org/10.1039/b811899j

Nyholm, S.V., J. Robidart, and P.R. Girguis. 2008. Coupling metabolite flux to transcriptomics: Insights into the molecular mechanisms underlying primary productivity by the hydrothermal vent tubeworm Ridgeia piscesae. Biological Bulletin, 214: 255–265.

Pane, E.F., M. Grosell, and J.P. Barry. 2008. Hypercapnic tolerance of deep- and shallow-living crabs. Aquatic Biology, 4: 23–32.

Paull, C.K., and W. Ussler III. 2008. Re-evaluation of the significance of seafloor accumulations of methane-derived carbonates: Seepage or erosion indicators? Proceedings of the Sixth International Conference on Gas Hydrates.

Paull, C.K., W. Ussler III, W.R. Normark, and R. Keaten. 2008. Tracking the dispersal of DDT residue-bearing sediments onto the floor of the Santa Monica Basin. Progress in Pesticide Research: 17.

Paull, C.K., W.R. Normark, W. Ussler III, D.W. Caress, and R. Keaten. 2008. Association among active seafloor deformation, mound formation, and gas hydrate growth and accumulation with the seafloor of the Santa Monica Basin, offshore California. Marine Geology, 250: 258–275.

Peltzer, E.T., and P.G. Brewer. 2008. Beyond pH and temperature: Thermodynamic constraints imposed by global warming and ocean acidification on midwater respiration by marine animals. Proceedings of the International Council for the Exploration of the Sea Annual Science Conference.

Potuzak, M., A.R.L. Nichols, D.B. Dingwell, and D.A. Clague. 2008. Hyperquenched volcanic glass from Loihi Seamount, Hawaii. Earth and Planetary Science Letters, 270: 54–62. http://dx.doi.org/10.1016/j.epsl.2008.03.018

Rago, T.A., R. Michisaki, B. Marinovic, M. Blum, and K. Whitaker. 2008. Physical, Nutrient, and Biological Measurements of Coastal Waters off Central California in June 2008: 46.

Rago, T.A., R. Michisaki, B. Marinovic, M. Blum, and K. Whitaker. 2008. Physical, Nutrient, and Biological Measurements of Coastal Waters off Central California in November 2007: 70.

Ramp, S.R., D.E. Barrick, T. Ito, and M.J. Cook. 2008. Variability of the Kuroshio Current south of Sagami Bay as observed by long-range coastal HF radar. Journal of Geophysical Research, 113. http://dx.doi.org/10.1029/2007JC004132

Rienecker, E.R., J.P. Ryan, R. Marin III, M. Blum, C. Dietz, and F.P. Chavez. 2008. Synoptic mapping of the phytoplankton size distribution, with applications to the ecology of red tides and harmful algal blooms. Limnology and Oceanography: Methods, 6: 153–161.

Robbens, S., P. Rouzé, J.M. Cock, J. Spring, A.Z. Worden, and Y.J. Van de Peer. 2008. The FTO gene, implicated in human obesity, is found only in vertebrates and marine algae. Molecular Evolution, 66: 80–84. http://dx.doi.org/10.1007/s00239-007-9059-z

Rouse, G.W., K. Worsaae, S.B. Johnson, W.J. Jones, and R.C. Vrijenhoek. 2008. Acquisition of dwarf male "harems" by recently settled females of Osedax roseus n. sp. (Siboglinidae; Annelida). Biological Bulletin, 214: 67–82. http://dx.doi.org/10.2307/25066661

Ruhl, H.A., J.A. Ellena, and K.L. Smith Jr. 2008. Connections between climate, food limitation, and carbon cycling in abyssal sediment communities. Proceedings of the National Academy of Sciences, 105: 17006–17011. http://dx.doi.org/10.1073/pnas.0803898105

Ryan, J.P., J.F.R. Gower, S.A. King, W.P. Bissett, A.M. Fischer, R.M. Kudela, Z. Kolber, F. Mazzillo, E.R. Rienecker, and F.P. Chavez. 2008. A coastal ocean extreme bloom incubator. Geophysical Research Letters, 35. http://dx.doi.org/10.1029/2008GL034081

Ryan, J.P., M.A. McManus, J.D. Paduan, and F.P. Chavez. 2008. Phytoplankton thin layers within coastal upwelling system fronts. Marine Ecology Progress Series, 354: 21–34.

Saba, V., J. Spotila, F.P. Chavez, and J. Musick. 2008. Bottom-up and climate forcing on the worldwide populations of leatherback turtles. Ecology, 89: 1414–1427.

Schnitzler, C.E., R.J. Keenan, R. McCord, A. Matysik, L.M. Christianson, and S.H.D. Haddock. 2008. Spectral diversity of fluorescent proteins from the anthozoan Corynactis californica. Marine Biotechnology, 10: 328–342. http://dx.doi.org/10.1007/s10126-007-9072-7

Scholin, C.A., G.J. Doucette, and A.D. Cembella. 2008. Prospects for developing automated systems for in situ detection of harmful algae and their toxins. Real-Time Coastal Observing Systems for Ecosystem Dynamics and Harmful Algal Blooms: 413–462.

Smith Jr., K.L., H.A. Ruhl, R.S. Kaufmann, and M. Kahru. 2008. Tracing abyssal food supply back to upper-ocean processes over a 17-year time series in the Northeast Pacific. Limnology and Oceanography, 53: 2655–2667.

Solomon, E.A., M. Kastner, H. Jannasch, G. Robertson, and Y. Weinstein. 2008. Dynamic fluid flow and chemical fluxes associated with a seafloor gas hydrate deposit on the northern Gulf of Mexico slope.. Earth and Planetary Science Letter, 270: 95–105. http://dx.doi.org/10.1016/j.epsl.2008.03.024

Staaf, D.J., S. Camarillo-Coop, S.H.D. Haddock, A.C. Nyack, J. Payne, R. Ramirez-Rojo, C.A. Salinas-Zavala, B.A. Seibel, L. Trueblood, C. Widmer, and W.F. Gilly. 2008. Natural egg mass deposition by the Humboldt squid (Dosidicus gigas) in the Gulf of California and characteristics of hatchlings and paralarvae . Journal of the Marine Biological Association of the United Kingdom, 88: 759–770. http://dx.doi.org/10.1017/S0025315408001422

Strutton, P.G., W. Evans, and F.P. Chavez. 2008. Equatorial Pacific chemical and biological variability, 1997–2003. Global Biogeochemical Cycles, 22. http://dx.doi.org/10.1029/2007GB003045

Turcotte, M.M., M.N. Pires, R.C. Vrijenhoek, and D.N. Reznick. 2008. Maternal provisioning in livebearing fish species and their hybrids (Poeciliidae: Poeciliopsis). Functional Ecology, 22: 1118–1124. http://dx.doi.org/10.1111/j.1365-2435.2008.01461.x

Ussler III, W., and C.K. Paull. 2008. Detection of methane sources along the California continental margin using water column anomalies. Proceedings of the Sixth International Conference on Gas Hydrates.

Ussler III, W., and C.K. Paull. 2008. Rates of anaerobic oxidation of methane and authigenic carbonate mineralization in methane-rich deep-sea sediments inferred from models and geochemical profiles. Earth and Planetary Science Letters, 266: 271–287.

Vrijenhoek, R.C. 2008. Valuing what most will never see. Trends in Ecology & Evolution, 23: 10–11.

Vrijenhoek, R.C., P.C. Collins, and C.L. Van Dover. 2008. Bone-eating marine worms: Habitat specialists or generalists?. Proceedings of the Royal Society B, 275: 1963–1964. http://dx.doi.org/10.1098/rspb.2008.0350

Walz, P.M., W.J. Kirkwood, E.T. Peltzer, K.C. Hester, and P.G. Brewer. 2008. Creating controlled CO2 perturbation experiments on the seafloor — Development of FOCE techniques. Proceedings of the Marine Technology Society / Institute of Electrical and Electronics Engineers Kobe Techno Meeting.

Wang, K., D. Klimov, and Z. Kolber. 2008. Long period grating-based ocean pH sensor in an SMS fiber. Proceedings of SPIE, 6932.

Wheat, C.G., P. Fryer, A.T. Fisher, S. Hulme, H. Jannasch, M.J. Mottl, and K. Becker. 2008. Borehole observations of fluid flow from South Chamorro Seamount, an active serpentinite mud volcano in the Mariana forearc.. Earth and Planetary Science Letters, 267: 401–409. http://dx.doi.org/10.1016/j.epsl.2007.11.057

Won, Y.J., W.J. Jones, and R.C. Vrijenhoek. 2008. Absence of co-speciation between deep-sea mytilids and their thiotrophic endosymbionts. Journal of Shellfish Research, 27: 129–138.

Worden, A.Z., and F. Not. 2008. Ecology and diversity of picoeukaryotes. Microbial Ecology of the Oceans, Second Edition, 159–206.

Zedlitz, J., J. Graybeal, and N. Luttenberger. 2008. Using XML-based formats for marine data. Proceedings of the Ocean Sensors Workshop.

Zeidberg, L. D., and B. Robison. 2008. Reply to Watters et al.: Range expansion by the Humboldt squid. Proceedings of the National Academy of Sciences Online, 105. http://dx.doi.org/10.1073/pnas.0710602105

Zhang, Y., and J.G. Bellingham. 2008. An efficient method of selecting ocean observing locations for capturing the leading modes and reconstructing the full field. Journal of Geophysical Research, 113. http://dx.doi.org/10.1029/2007JC004327

2007

Adams, L., and G.I. Matsumoto. 2007. Investigating coastal processes and nitrate levels in the Elkhorn Slough using real-time data. Oceanography, 20: 200–204.

Allison, N., A.A. Finch, J.M. Webster, and D.A. Clague. 2007. Paleoenvironmental records from fossil corals: The effects of submarine diagenesis on temperature and climate estimates. Geochimica et Cosmochimica Acta, 71: 4693–4703.

Barde, J., D.R. Edgington, and J.C. Desconnets. 2007. A generic approach to manage metadata standards. OSGeo Journal, 3: 24–30.

Barry, J.P., and J.C. Drazen. 2007. Response of deep-sea scavengers to mild hypercapnia and the odor from a dead grenadier. Marine Ecology Progress Series, 350: 193–207.

Barry, J.P., P.J. Whaling, and R.K. Kochevar. 2007. Growth, production, and mortality of the chemosynthetic vesicomyid bivalve, Calyptogena kilmeri, from cold seeps off central California. Marine Ecology, 28: 169–182. http://dx.doi.org/10.1111/j.1439-0485.2007.00119.x

Bird, L.E., A.D. Sherman, and J. Ryan. 2007. Development of an active, large volume, discrete seawater sampler for autonomous underwater vehicles. Proceedings of the Marine Technology Society / Institute of Electrical and Electronics Engineers Oceans Conference.

Bird, L.E., C.K. Paull, and B. Hobson. 2007. Instrumentation for investigating submarine canyons: The development of a self-triggering event detector to investigate sediment transport events. Sea Technology, 48: 17–21.

Braby, C.E., G.W. Rouse, S.B. Johnson, W.J. Jones, and R.C. Vrijenhoek. 2007. Bathymetric and temporal variation among Osedax boneworms and associated megafauna on whale-falls in Monterey Bay, California. Deep-Sea Research Part I, 54: 1773–1791. http://dx.doi.org/10.1016/j.dsr.2007.05.014