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  • 1
    Publication Date: 2013-05-28
    Description: Application of biogeochemical models to the study of marine ecosystems is pervasive, yet objective quantification of these models' performance is rare. Here, 12 lower trophic level models of varying complexity are objectively assessed in two distinct regions (equatorial Pacific and Arabian Sea). Each model was run within an identical one-dimensional physical framework. A consistent variational adjoint implementation assimilating chlorophyll-a, nitrate, export, and primary productivity was applied and the same metrics were used to assess model skill. Experiments were performed in which data were assimilated from each site individually and from both sites simultaneously. A cross-validation experiment was also conducted whereby data were assimilated from one site and the resulting optimal parameters were used to generate a simulation for the second site. When a single pelagic regime is considered, the simplest models fit the data as well as those with multiple phytoplankton functional groups. However, those with multiple phytoplankton functional groups produced lower misfits when the models are required to simulate both regimes using identical parameter values. The cross-validation experiments revealed that as long as only a few key biogeochemical parameters were optimized, the models with greater phytoplankton complexity were generally more portable. Furthermore, models with multiple zooplankton compartments did not necessarily outperform models with single zooplankton compartments, even when zooplankton biomass data are assimilated. Finally, even when different models produced similar least squares model-data misfits, they often did so via very different element flow pathways, highlighting the need for more comprehensive data sets that uniquely constrain these pathways.
    Type: Article , PeerReviewed
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  • 2
    Publication Date: 2019-05-06
    Description: Author Posting. © American Geophysical Union, 2018. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research-Oceans, 123(11), (2018): 7877-7895. doi: 10.1029/2018JC014290.
    Description: A three‐dimensional, primitive‐equation, ocean circulation model coupled with a Lagrangian particle‐tracking algorithm is used to investigate the dispersal and settlement of planktonic larvae released from discrete hydrothermal habitats on the East Pacific Rise segment at 9–10°N. Model outputs show that mean circulation is anticyclonic around the ridge segment, which consists of a northward flow along the western flank and a southward flow along the eastern flank. Those flank jets are dispersal expressways for the along‐ridge larval transport and strongly affect its overall direction and spatial‐temporal variations. It is evident from model results that the transform faults bounding the ridge segment and off axis topography (the Lamont Seamount Chain) act as topographic barriers to larval dispersal in the along‐ridge direction. Furthermore, the presence of an overlapping spreading center and an adjacent local topographic high impedes the southward along‐ridge larval transport. The model results suggest that larval recolonization within ridge‐crest habitats is enhanced by the anticyclonic circulation around the ridge segment, and the overall recolonization rate is higher for larvae having a short precompetency period and an altitude above the bottom sufficient to avoid influence by the near‐bottom currents Surprisingly, for larvae having a long precompetency period (〉10 days), the prolonged travel time allowed some of those larvae to return to their natal vent clusters, which results in an unexpected increase in connectivity among natal and neighboring sites. Overall, model‐based predictions of connectivity are highly sensitive to the larval precompetency period and vertical position in the water column.
    Description: The sediment‐trap data presented in this paper are included in Table S1. The bathymetric data used in the model can be downloaded from the Global Multi‐Resolution Topography (GMRT) Synthesis of Marine Geoscience Data System (MGDS) (https://www.gmrt.org/GMRTMapTool). The ocean current time series data used in this work were acquired in 2006‐2007 by Andreas Thurnherr at the Earth Institute of Columbia University. Those data can be accessed in the supporting information. D.J. McGillicuddy gratefully acknowledges support from the National Science Foundation and the Holger W. Jannasch and Columbus O'Donnell Iselin Shared Chairs for Excellence in Oceanography. L.S. Mullineaux acknowledges with gratitude support from the National Science Foundation and the Woods Hole Oceanographic Institution (WHOI) Ocean life fellowship. We appreciate the operation support from the Captain and crew of R/V Atlantis and the Alvin submersible group. We are thankful to V.K. Kosnyrev for developing the coupling interface between the ocean‐circulation and particle‐tracking models. We are grateful to J.W. Lavelle for his intellectual support for the modeling work presented in this paper. We thank Houshuo Jiang for sponsoring our use of the cluster computer at WHOI.
    Description: 2019-05-06
    Keywords: larva ; dispersal ; hydrothermal vent ; EPR ; connectivity ; supply
    Repository Name: Woods Hole Open Access Server
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  • 3
    Publication Date: 2017-01-05
    Description: Author Posting. © Elsevier B.V., 2006. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 53 (2006): 2632-2655, doi:10.1016/j.dsr2.2006.08.011.
    Description: An adjoint data assimilation approach was used to quantify the physical and biological controls on Calanus finmarchicus N3 to C stages on Georges Bank and its nearby environs. The mean seasonal cycle of vertically-averaged distributions, from 5 years of the GLOBEC Georges Bank Broad-Scale Surveys between January and June, was assimilated into a physical-biological model based on the climatological circulation. Large seasonal and spatial variability is present in the inferred supply sources, mortality rates, computed molting fluxes, and physical transports. Estimated mortalities fall within the range of observed rates, and exhibit stage structure that is consistent with earlier findings. Inferred off-bank initial conditions indicate that the deep basins in the Gulf of Maine are source regions of early-stage nauplii and late-stage copepodids in January. However, the population increase on Georges Bank from January to April is controlled mostly by local biological processes. Magnitudes of the physical transport terms are nearly as large as the mortality and molting fluxes, but their bank-wide averages are small in comparison to the biological terms. The hypothesis of local biological control is tested in a sensitivity experiment in which upstream sources are set to zero. In that solution, the lack of upstream sources is compensated by a decrease in mortality that is much smaller than the uncertainty in observational estimates.
    Description: This work was supported by the US GLOBEC Georges Bank program: Integration and Synthesis of Georges Bank Broad-Scale Survey Results, sponsored by NSF (OCE-0233800) and NOAA (NA17RJ1223).
    Keywords: Calanus finmarchicus ; Population dynamics ; Georges Bank ; Inverse modeling ; Adjoint method
    Repository Name: Woods Hole Open Access Server
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  • 4
    Publication Date: 2017-01-05
    Description: Author Posting. © American Geophysical Union, 2009. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 114 (2009): C09005, doi:10.1029/2008JC004948.
    Description: A persistent gyre at the mouth of the Bay of Fundy results from a combination of tidal rectification and buoyancy forcing. Here we assess recent interannual variability in the strength of the gyre using data assimilative model simulations. Realistic hindcast representations of the gyre are considered during cruises in 2005, 2006, and 2007. Assimilation of shipboard and moored acoustic Doppler current profiler velocities is used to improve the skill of the simulations, as quantified by comparison with nonassimilated drifter trajectories. Our hindcasts suggest a weakening of the gyre system during May 2005. Retention of simulated passive particles in the gyre during that period was highly reduced. A recovery of the dense water pool in the deep part of the basin by June 2006 resulted in a return to particle retention characteristics similar to climatology. Retention estimates reached a maximum during May 2007 (subsurface) and June–July 2007 (near surface). Interannual variability in the strength of the gyre was primarily modulated by the stratification of the dense water pool inside the Grand Manan Basin. These changes in stratification were associated with mixing conditions the preceding fall–winter and/or advectively driven modification of water mass properties.
    Description: The preparation of this paper was supported by NSF grant OCE-0430724, NIEHS grant 1P50-ES01274201 (Woods Hole Center for Oceans and Human Health), andNOAAgrant NA06NOS4780245 (GOMTOX). Additional support was provided by NSF grant DMS-0417769.
    Keywords: Bay of Fundy ; Model simulations ; Gyre hindcast
    Repository Name: Woods Hole Open Access Server
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  • 5
    Publication Date: 2017-01-04
    Description: Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 113 (2008): C10027, doi:10.1029/2007JC004480.
    Description: The characteristics of a persistent gyre in the mouth of the Bay of Fundy are studied using model simulations. A set of climatological runs are conducted to evaluate the relative importance of the different forcing mechanisms affecting the gyre. The main mechanisms are tidal rectification and density-driven circulation. Stronger circulation of the gyre occurs during the later part of the stratified season (July–August and September–October). The density-driven flow around the gyre is set up by weak tidal mixing in the deep basin in the central Bay of Fundy and strong tidal mixing on the shallow flanks around Grand Manan Island and western Nova Scotia. Spring river discharge has an important influence on near-surface circulation but only a small effect when averaged over the entire water column. Retention of particles in the gyre is controlled by the residual tidal circulation, increased frontal retention during stratified periods, wind stress, and interactions with the adjacent circulation of the Gulf of Maine. Residence times longer than 30 days are predicted for particles released in the proximity of the gyre.
    Description: The preparation of this paper was supported by NSF grant OCE-0430724 and NIEHS grant 1P50-ES01274201 (Woods Hole Center for Oceans and Human Health) and NOAA grant NA06NOS4780245 (GOMTOX). Additional support was provided by NSF grant DMS-0417769.
    Keywords: Bay of Fundy ; Model simulations ; Gyre climatology
    Repository Name: Woods Hole Open Access Server
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  • 6
    Publication Date: 2017-01-05
    Description: Author Posting. © American Geophysical Union, 2005. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 110 (2005): C10011, doi:10.1029/2004JC002807.
    Description: A data assimilative model hindcast of the Gulf of Maine (GOM) coastal circulation during an 11 day field survey in early summer 2003 is presented. In situ observations include surface winds, coastal sea levels, and shelf hydrography as well as moored and shipboard acoustic Doppler D current profiler (ADCP) currents. The hindcast system consists of both forward and inverse models. The forward model is a three-dimensional, nonlinear finite element ocean circulation model, and the inverse models are its linearized frequency domain and time domain counterparts. The model hindcast assimilates both coastal sea levels and ADCP current measurements via the inversion for the unknown sea level open boundary conditions. Model skill is evaluated by the divergence of the observed and modeled drifter trajectories. A mean drifter divergence rate (1.78 km d−1) is found, demonstrating the utility of the inverse data assimilation modeling system in the coastal ocean setting. Model hindcast also reveals complicated hydrodynamic structures and synoptic variability in the GOM coastal circulation and their influences on coastal water material property transport. The complex bottom bathymetric setting offshore of Penobscot and Casco bays is shown to be able to generate local upwelling and downwelling that may be important in local plankton dynamics.
    Description: This work was supported by CSCOR/COP/ NOAA as part of NOAA MERHAB program. DJM gratefully acknowledges support from JPL through the ocean vector wind science team. DRL and KWS acknowledge support of NOAA/COP ECOHAB program.
    Keywords: Data assimilation ; Coastal ocean modeling ; Gulf of Maine circulation
    Repository Name: Woods Hole Open Access Server
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  • 7
    Publication Date: 2017-01-05
    Description: Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 113 (2008): C07040, doi:10.1029/2007JC004602.
    Description: A coupled physical/biological modeling system was used to hindcast a massive Alexandrium fundyense bloom that occurred in the western Gulf of Maine in 2005 and to investigate the relative importance of factors governing the bloom's initiation and development. The coupled system consists of a state-of-the-art, free-surface primitive equation Regional Ocean Modeling System (ROMS) tailored for the Gulf of Maine (GOM) using a multinested configuration, and a population dynamics model for A. fundyense. The system was forced by realistic momentum and buoyancy fluxes, tides, river runoff, observed A. fundyense benthic cyst abundance, and climatological nutrient fields. Extensive comparisons were made between simulated (both physical and biological) fields and in situ observations, revealing that the hindcast model is capable of reproducing the temporal evolution and spatial distribution of the 2005 bloom. Sensitivity experiments were then performed to distinguish the roles of three major factors hypothesized to contribute to the bloom: (1) the high abundance of cysts in western GOM sediments; (2) strong ‘northeaster' storms with prevailing downwelling-favorable winds; and (3) a large amount of fresh water input due to abundant rainfall and heavy snowmelt. Model results suggest the following. (1) The high abundance of cysts in western GOM was the primary factor of the 2005 bloom. (2) Wind-forcing was an important regulator, as episodic bursts of northeast winds caused onshore advection of offshore populations. These downwelling favorable winds accelerated the alongshore flow, resulting in transport of high cell concentrations into Massachusetts Bay. A large regional bloom would still have happened, however, even with normal or typical winds for that period. (3) Anomalously high river runoff in 2005 resulted in stronger buoyant plumes/currents, which facilitated the transport of cell population to the western GOM. While affecting nearshore cell abundance in Massachusetts Bay, the buoyant plumes were confined near to the coast, and had limited impact on the gulf-wide bloom distribution.
    Description: Research support was provided through the Woods Hole Center for Oceans and Human Health, National Science Foundation (NSF) grant OCE-0430723 and National Institute of Environmental Health Science (NIEHS) grant 1-P50-ES012742-01, ECOHAB program through NSF grant OCE-9808173 and NOAA grant NA96OP0099, and GOMTOX program through NOAA grant NA06NOS4780245.
    Keywords: Gulf of Maine ; Harmful algal bloom ; Numerical modeling
    Repository Name: Woods Hole Open Access Server
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  • 8
    Publication Date: 2017-01-04
    Description: Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Deep Sea Research Part I: Oceanographic Research Papers 57 (2010): 880-892, doi:10.1016/j.dsr.2010.04.003.
    Description: We investigated planktonic larval transport processes along an axially symmetric mid-ocean ridge with characteristics similar to that of the East Pacific Rise (EPR) segment at 9-10°N. The hydrodynamic basis for this study is a primitive equation model implemented in two dimensions (depth and across-ridge), forced at the open boundaries to provide suitably realistic simulation of currents observed on the EPR ridge crest from May to November 1999. Three-dimensional trajectories of numerical larvae are computed assuming homogeneity in currents in the along-ridge direction. Larval dispersal fluctuates significantly in time. Transport distance decreases systematically with height above the bottom where numerical larvae are less subject to strong currents along the flanks of the ridge. The probability that the simulated larvae will be located near the ridge crest at settlement depends strongly on their behavioral characteristics (vertical position in the water column during the larval stage) and the length of their precompetency period.
    Description: We gratefully acknowledge the support of NSF grant OCE-0424953, which funded the Larval Dispersion along the Deep East Pacific Rise (LADDER) project. JWL was supported by the National Oceanic and Atmospheric Administration's (NOAA) Vents Program and by NOAA’s Pacific Marine Environmental Laboratory.
    Keywords: East Pacific Rise ; Larval transport ; Larval behavior ; Modeling ; Physical-biological interactions 2
    Repository Name: Woods Hole Open Access Server
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  • 9
    Publication Date: 2017-01-05
    Description: Author Posting. © American Meteorological Society 2005. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 22 (2005): 1267–1281, doi:10.1175/JTECH1760.1.
    Description: The focus of this paper is on the development of methodology for short-term (1–3 days) oceanic bioluminescence (BL) predictions and the optimization of spatial and temporal bioluminescence sampling strategies. The approach is based on predictions of bioluminescence with an advection–diffusion–reaction (tracer) model with velocities and diffusivities from a circulation model. In previous research, it was shown that short-term changes in some of the salient features in coastal bioluminescence can be explained and predicted by using this approach. At the same time, it was demonstrated that optimization of bioluminescence sampling prior to the forecast is critical for successful short-term BL predictions with the tracer model. In the present paper, the adjoint to the tracer model is used to study the sensitivity of the modeled bioluminescence distributions to the sampling strategies for BL. The locations and times of bioluminescence sampling prior to the forecast are determined by using the adjoint-based sensitivity maps. The approach is tested with bioluminescence observations collected during August 2000 and 2003 in the Monterey Bay, California, area. During August 2000, BL surveys were collected during a strong wind relaxation event, while in August 2003, BL surveys were conducted during an extended (longer than a week) upwelling-favorable event. The numerical bioluminescence predictability experiments demonstrated a close agreement between observed and model-predicted short-term spatial and temporal changes of the coastal bioluminescence.
    Description: This work has been supported by the Ocean Optics and Biology and Physical Oceanography Programs of the Office of Naval Research. Shulman’s support is through the NRL “Use of a Circulation Model to Enhance Predictability of Bioluminescence in the Coastal Ocean” project sponsored by the Office of Naval Research.
    Repository Name: Woods Hole Open Access Server
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  • 10
    Publication Date: 2017-01-04
    Description: Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of AAAS for personal use, not for redistribution. The definitive version was published in Science 332 (2011): 580-583, doi:10.1126/science.1201066.
    Description: Atmospheric forcing, which is known to have a strong influence on surface ocean dynamics and production, is typically not considered in studies of the deep sea. Our observations and models demonstrate an unexpected influence of surface-generated mesoscale eddies in the transport of hydrothermal vent efflux and of vent larvae away from the northern East Pacific Rise. Transport by these deep-reaching eddies provides a mechanism for spreading the hydrothermal chemical and heat-flux into the deep-ocean interior and for dispersing propagules hundreds of kilometers between isolated and ephemeral communities. Since the eddies interacting with the East Pacific Rise are formed seasonally and are sensitive to phenomena such as El Niño, they have the potential to introduce seasonal to interannual atmospheric variations into the deep sea.
    Description: Support was provided by NSF grants OCE-0424953, OCE-0425361 and OCE-0647948, WHOI grants from DOEI and the Ocean Venture Fund, a NDSEG graduate fellowship to D.K.A., and the WHOI Jannasch Chair for Excellence in Oceanography to L.S.M.
    Repository Name: Woods Hole Open Access Server
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