Bibliography - Charles A Stock

1. Lee, Hyun-Chul, Thomas L Delworth, Anthony Rosati, Rong Zhang, Whit G Anderson, Fanrong Zeng, Charles A Stock, Anand Gnanadesikan, Keith W Dixon, and Stephen M Griffies, January 2013: Impact of climate warming on upper layer of the Bering Sea. Climate Dynamics, 40(1-2), DOI:10.1007/s00382-012-1301-8.
   [ Abstract ]

   The impact of climate warming on the upper layer of the Bering Sea is investigated by using a high-resolution coupled global climate model. The model is forced by increasing atmospheric CO2 at a rate of 1% per year until CO2 reaches double its initial value (after 70 years), after which it is held constant. In response to this forcing, the upper layer of the Bering Sea warms by about 2�C in the southeastern shelf and by a little more than 1�C in the western basin. The wintertime ventilation to the permanent thermocline weakens in the western Bering Sea. After CO2 doubling, the southeastern shelf of the Bering Sea becomes almost ice-free in March, and the stratification of the upper layer strengthens in May and June. Changes of physical condition due to the climate warming would impact the pre-condition of spring bio-productivity in the southeastern shelf.

2. Friedland, K D., and Charles A Stock, et al., January 2012: Pathways between Primary Production and Fisheries Yields of Large Marine Ecosystems. PLoS-ONE, 7(1), DOI:10.1371/journal.pone.0028945.
   [ Abstract ]

   The shift in marine resource management from a compartmentalized approach of dealing with resources on a species basis to an approach based on management of spatially defined ecosystems requires an accurate accounting of energy flow. The flow of energy from primary production through the food web will ultimately limit upper trophic-level fishery yields. In this work, we examine the relationship between yield and several metrics including net primary production, chlorophyll concentration, particle-export ratio, and the ratio of secondary to primary production. We also evaluate the relationship between yield and two additional rate measures that describe the export of energy from the pelagic food web, particle export flux and mesozooplankton productivity. We found primary production is a poor predictor of global fishery yields for a sample of 52 large marine ecosystems. However, chlorophyll concentration, particle-export ratio, and the ratio of secondary to primary production were positively associated with yields. The latter two measures provide greater mechanistic insight into factors controlling fishery production than chlorophyll concentration alone. Particle export flux and mesozooplankton productivity were also significantly related to yield on a global basis. Collectively, our analyses suggest that factors related to the export of energy from pelagic food webs are critical to defining patterns of fishery yields. Such trophic patterns are associated with temperature and latitude and hence greater yields are associated with colder, high latitude ecosystems.

3. Hare, J A., and Charles A Stock, et al., December 2012: Cusk (Brosme brosme) and climate change: assessing the threat to a candidate marine fish species under the US Endangered Species Act. ICES Journal of Marine Science, 69(10), DOI:10.1093/icesjms/fss160.
   [ Abstract ]

   In the Northwest Atlantic Ocean cusk (Brosme brosme) has declined dramatically, primarily as a result of fishing activities. These declines have led to concern about its status, which has prompted reviews under the US Endangered Species Act and the Canadian Species at Risk Act. Changes in distribution and abundance of a number of marine fish in the Northwest Atlantic have been linked to climate variability and change, suggesting that both fishing and climate may affect the status of cusk. Our goal was to evaluate potential effects of climate change on Northwest Atlantic cusk distribution. Coupling a species niche model with the output from an ensemble of climate models, we projected cusk distribution in the future. Our results indicate cusk habitat in the region will shrink and fragment, which is a result of a spatial mismatch between high complexity seafloor habitat and suitable temperature. The importance of habitat patch connectivity for cusk is poorly understood, so the population-level consequences of climate-related habitat fragmentation are uncertain. More broadly, climate change may reduce appropriate thermal habitat and increase habitat fragmentation for other cold-water species in the region; thereby, increasing the potential for regional overexploitation and extirpation.

4. Hollowed, A B., E Curchitser, Charles A Stock, and C I Zhang, in press: Trade-offs associated with different modeling approaches for assessment of fish and shellfish responses to climate change. Climatic Change. DOI:10.1007/s10584-012-0641-z. 12/12.
   [ Abstract ]

   Considerable progress has been made in integrating carbon, nutrient, phytoplankton and zooplankton dynamics into global-scale physical climate models. Scientists are exploring ways to extend the resolution of the biosphere within these Earth system models (ESMs) to include impacts on global distribution and abundance of commercially exploited fish and shellfish. This paper compares different methods for modeling fish and shellfish responses to climate change on global and regional scales. Several different modeling approaches are considered including: direct applications of ESM’s, use of ESM output for estimation of shifts in bioclimatic windows, using ESM outputs to force single- and multi-species stock projection models, and using ESM and physical climate model outputs to force regional bio-physical models of varying complexity and mechanistic resolution. We evaluate the utility of each of these modeling approaches in addressing nine key questions relevant to climate change impacts on living marine resources. No single modeling approach was capable of fully addressing each question. A blend of highly mechanistic and less computationally intensive methods is recommended to gain mechanistic insights and to identify model uncertainties.

5. Kearney, K, Charles A Stock, K Aydin, and Jorge L Sarmiento, July 2012: Coupling planktonic ecosystem and fisheries food web models for a pelagic ecosystem: Description and validation for the subarctic Pacific. Ecological Modelling, 237-238, DOI:10.1016/j.ecolmodel.2012.04.006.
   [ Abstract ]

   We provide a modeling framework that fully couples a one-dimensional physical mixed layer model, a biogeochemical model, and an upper trophic level fisheries model. For validation purposes, the model has been parameterized for the pelagic Eastern Pacific Subarctic Gyre ecosystem. This paper presents a thorough description of the model itself, as well as an ensemble-based parameterization process that allows the model to incorporate the high level of uncertainty associated with many upper trophic level predator-prey processes. Through a series of model architecture experiments, we demonstrate that the use of a consistent functional response for all predator-prey interactions, as well as the use of density-dependent mortality rates for planktonic functional groups, are important factors in reproducing annual and seasonal observations. We present the results of a 50-year climatological simulation, which demonstrates that under contemporary physical forcing, the model is capable of reproducing long-term seasonal dynamics in primary production and biogeochemical cycling, while maintaining steady-state coexistence of upper trophic level functional groups at levels consistent with observations.

6. Saba, Vincent S., and Charles A Stock, et al., November 2012: Projected response of an endangered marine turtle population to climate change. Nature Climate Change, 2, DOI:10.1038/nclimate1582.
   [ Abstract ]

   Assessing the potential impacts of climate change on individual species and populations is essential for the stewardship of ecosystems and biodiversity. Critically endangered leatherback turtles in the eastern Pacific Ocean are excellent candidates for such an assessment because their sensitivity to contemporary climate variability has been substantially studied1, 2, 3, 4. If incidental fisheries mortality is eliminated, this population still faces the challenge of recovery in a rapidly changing climate. Here we combined an Earth system model5, climate model projections assessed by the Intergovernmental Panel on Climate Change6 and a population dynamics model to estimate a 7% per decade decline in the Costa Rica nesting population over the twenty-first century. Whereas changes in ocean conditions had a small effect on the population, the ~2.5 °C warming of the nesting beach was the primary driver of the decline through reduced hatching success and hatchling emergence rate. Hatchling sex ratio did not substantially change. Adjusting nesting phenology or changing nesting sites may not entirely prevent the decline, but could offset the decline rate. However, if future observations show a long-term decline in hatching success and emergence rate, anthropogenic climate mitigation of nests (for example, shading, irrigation)7, 8 may be able to preserve the nesting population.

7. Tomillo, P S., Vincent S Saba, G S Blanco, Charles A Stock, F V Paladino, and J R Spotila, May 2012: Climate Driven Egg and Hatchling Mortality Threatens Survival of Eastern Pacific Leatherback Turtles. PLoS-ONE, 7(5), DOI:10.1371/journal.pone.0037602.
   [ Abstract ]

   Egg-burying reptiles need relatively stable temperature and humidity in the substrate surrounding their eggs for successful development and hatchling emergence. Here we show that egg and hatchling mortality of leatherback turtles (Dermochelys coriacea) in northwest Costa Rica were affected by climatic variability (precipitation and air temperature) driven by the El Nin˜o Southern Oscillation (ENSO). Drier and warmer conditions associated with El Nin˜o increased egg and hatchling mortality. The fourth assessment report of the Intergovernmental Panel on Climate Change (IPCC) projects a warming and drying in Central America and other regions of the World, under the SRES A2 development scenario. Using projections from an ensemble of global climate models contributed to the IPCC report, we project that egg and hatchling survival will rapidly decline in the region over the next 100 years by ,50–60%, due to warming and drying in northwestern Costa Rica, threatening the survival of leatherback turtles. Warming and drying trends may also threaten the survival of sea turtles in other areas affected by similar climate changes.

8. Song, H, R Ji, Charles A Stock, K Kearney, and Z Wang, March 2011: Interannual variability in phytoplankton blooms and plankton productivity over the Nova Scotian Shelf and in the Gulf of Maine. Marine Ecology Progress Series, 426, DOI:10.3354/meps09002.
   [ Abstract ]

   A 1D ecosystem model, driven by surface heat and wind forcing and relaxed toward observed salinity profiles, was applied to simulate the interannual and decadal scale variability of phytoplankton blooms and plankton production from 1984 to 2007 in the Nova Scotian Shelf (NSS) and Gulf of Maine (GoM) region. The model captured the mean observed timing and magnitude of the spring (SPB) and fall phytoplankton bloom (FPB) in both systems, as well as observed interannual variations in SPB peak timing. Model simulations for both the GoM and NSS exhibited marked interannual variability in SPB and FPB timing (±2 to 3 wk) and magnitude (up to ~1 mg chlorophyll m–3). Earlier SPBs and delayed FPBs are linked to enhanced water column stability generated by less saline surface water or sharper salinity gradients over the top 50 m of the water column. The modeled variation in annual primary productivity, mesozooplankton productivity, and particle export flux was modest (<10% of the mean). Years with high primary production were weakly associated with early SPBs (GoM: r = –0.205; NSS: r = –0.51), but there was no significant relationship with water column stability. This suggests that variation in annual productivity in the GoM and NSS reflects a combination of variation in light limitation (which is alleviated by increased water column stability) and nutrient limitation (which is exacerbated by increased water column stability) that offset and are of near equal importance when averaged over the year. Interannual variations in fisheries production due to changes in annual productivity are thus likely secondary to profound shifts in fisheries recruitment and production that have been linked to variations in SPB and FPB timing.

9. Stock, Charles A., Thomas L Delworth, John P Dunne, Stephen M Griffies, R Rykaczewski, Jorge L Sarmiento, Ronald J Stouffer, and Gabriel A Vecchi, et al., January 2011: On the use of IPCC-class models to assess the impact of climate on Living Marine Resources. Progress in Oceanography, 88(1-4), DOI:10.1016/j.pocean.2010.09.001.
   [ Abstract ]

   The study of climate impacts on Living Marine Resources (LMRs) has increased rapidly in recent years with the availability of climate model simulations contributed to the assessment reports of the Intergovernmental Panel on Climate Change (IPCC). Collaboration between climate and LMR scientists and shared understanding of critical challenges for such applications are essential for developing robust projections of climate impacts on LMRs. This paper assesses present approaches for generating projections of climate impacts on LMRs using IPCC-class climate models, recommends practices that should be followed for these applications, and identifies priority developments that could improve current projections. Understanding of the climate system and its representation within climate models has progressed to a point where many climate model outputs can now be used effectively to make LMR projections. However, uncertainty in climate model projections (particularly biases and inter-model spread at regional to local scales), coarse climate model resolution, and the uncertainty and potential complexity of the mechanisms underlying the response of LMRs to climate limit the robustness and precision of LMR projections. A variety of techniques including the analysis of multi-model ensembles, bias corrections, and statistical and dynamical downscaling can ameliorate some limitations, though the assumptions underlying these approaches and the sensitivity of results to their application must be assessed for each application. Developments in LMR science that could improve current projections of climate impacts on LMRs include improved understanding of the multi-scale mechanisms that link climate and LMRs and better representations of these mechanisms within more holistic LMR models. These developments require a strong baseline of field and laboratory observations including long time-series and measurements over the broad range of spatial and temporal scales over which LMRs and climate interact. Priority developments for IPCC-class climate models include improved model accuracy (particularly at regional and local scales), inter-annual to decadal-scale predictions, and the continued development of earth system models capable of simulating the evolution of both the physical climate system and biosphere. Efforts to address these issues should occur in parallel and be informed by the continued application of existing climate and LMR models.

10. Song, H, R Ji, Charles A Stock, and Z Wang, November 2010: Phenology of phytoplankton blooms in the Nova Scotian Shelf–Gulf of Maine region: remote sensing and modeling analysis. Journal of Plankton Research, 32(11), DOI:10.1093/plankt/fbq086.
    [ Abstract ]

    Remotely sensed ocean color data and numerical modeling have been used to study the phenology of both spring and fall phytoplankton blooms (FPBs) in the Nova Scotian Shelf (NSS)–Gulf of Maine (GoM) region. The ocean color data reveal a general pattern of westward progression of the spring phytoplankton bloom (SPB), and an eastward progression of the FPB in the NSS–GoM region. The spatial pattern of mean chlorophyll concentration in spring is similar to that in fall, with a lower concentration in the NSS and higher in the GoM. Interannually, there is a weak but significant tendency for years with earlier (delayed) SPBs to be followed by delayed (earlier) FPBs, but the mean chlorophyll concentrations during SPBs are not correlated with those during FPBs. The interannual variability of SPB timing is significantly correlated with sea surface salinity (SSS), but the FPB timing is correlated with both SSS and sea surface temperature. The process-oriented numerical modeling experiments suggest that (i) salinity is the main factor influencing the bloom timing and magnitude in the NSS–GoM region, especially for the timing of SPBs; (ii) compared to buoyancy forcing induced by vertical salinity gradients, the impact of surface heating and surface wind stress on the blooms variability is much weaker; and (iii) the nutrient level controls the bloom magnitude, but only has a minor effect on bloom timing. This study provides a quantitative estimation of relationship between changes in local/ remote environmental forcing and phytoplankton phenological shifts, thus improving our understanding on the possible impact of climate change on coastal/shelf ecosystems.

11. Stock, Charles A., and John P Dunne, January 2010: Controls on the ratio of mesozooplankton production to primary production in marine ecosystems. Deep-Sea Research, Part I, 57(1), DOI:10.1016/j.dsr.2009.10.006.
    [ Abstract ]

    An ecosystem model was used to (1) determine the extent to which global trends in the ratio of mesozooplankton production to primary production (referred to herein as the “z-ratio”) can be explained by nutrient enrichment, temperature, and euphotic zone depth, and (2) quantitatively diagnose the mechanisms driving these trends. Equilibrium model solutions were calibrated to observed and empirically derived patterns in phytoplankton biomass and growth rates, mesozooplankton biomass and growth rates, and the fraction of phytoplankton that are large (>5 μm ESD). This constrained several otherwise highly uncertain model parameters. Most notably, half-saturation constants for zooplankton feeding were constrained by the biomass and growth rates of their prey populations, and low zooplankton basal metabolic rates were required to match observations from oligotrophic ecosystems. Calibrated model solutions had no major biases and produced median z-ratios and ranges consistent with estimates. However, much of the variability around the median values in the calibration dataset (72 points) could not be explained. Model results were then compared with an extended global compilation of z-ratio estimates (>10 000 points). This revealed a modest yet significant (r=0.40) increasing trend in z-ratios from values 0.01–0.04 to 0.1–0.2 with increasing primary productivity, with the transition from low to high z-ratios occurring at lower primary productivity in cold-water ecosystems. Two mechanisms, both linked to increasing phytoplankton biomass, were responsible: (1) zooplankton gross growth efficiencies increased as their ingestion rates became much greater than basal metabolic rates and (2) the trophic distance between primary producers and mesozooplankton shortened as primary production shifted toward large phytoplankton. Mechanism (1) was most important during the transition from low to moderate productivity ecosystems and mechanism (2) was responsible for a relatively abrupt transition to values >0.1 in high productivity ecosystems. Substantial z-ratio variations overlying these mean trends remained unexplained by these mechanisms. Potential sources of this variability include zooplankton patchiness, unresolved effects of advection and unsteady dynamics, unresolved shifts in mesozooplankton sizes and species, and unresolved aspects of zooplankton bioenergetics. Comparison of the modeled z-ratio patterns and mechanisms diagnosed herein with those obtained using models with expanded biological dynamics embedded in global circulation models will help further elucidate the causes of this variation.

12. McGillicuddy, Jr, D J., and Charles A Stock, et al., 2008: Modeling blooms of Alexandrium fundyense in the Gulf of Maine In Real-time Observing Systems for Marine Ecosystems Dynamics and Harmful Algal Blooms, Paris, France, UNESCO Publishing, 599-626.
13. Stock, Charles A., T M Powell, and S A Levin, November 2008: Bottom-up and top-down forcing in a simple size-structured plankton dynamics model. Journal of Marine Systems, 74(1-2), DOI:10.1016/j.jmarsys.2007.12.004.
    [ Abstract ]

    A size-structured plankton dynamics model is developed and used to explore the effects of variations in bottom-up and top-down forcing upon the biomass spectrum, size-structured patterns in primary production, and the flux of energy from primary producers to fish. Parameters and mechanisms controlling the steady-state model response to bottom-up forcing via nutrient enrichment and top-down forcing via fluctuations in planktivorous fish are first diagnosed. Results are then compared with mean observed biomass spectra from three ecosystems spanning a broad range of productivity. Solutions using parameters within empirical ranges can recreate trends in the biomass spectrum across these systems. The zooplankton gross growth efficiency is critical for matching the steady-state slopes of the spectra. Variability in export sources and zooplankton half-saturation constants both provide ways of matching the mean biomass. Results support the model's potential to provide mechanistic insights and testable quantitative hypotheses for the dynamics underlying observed biomass spectra.

14. Stock, Charles A., et al., November 2007: Blooms of the toxic dinoflagellate Alexandrium fundyense in the western Gulf of Maine in 1993 and 1994: A comparative modeling study. Continental Shelf Research, 27(19), DOI:10.1016/j.csr.2007.06.008.
    [ Abstract ]

    Blooms of the toxic dinoflagellate Alexandrium fundyense commonly occur in the western Gulf of Maine but the amount of toxin observed in coastal shellfish is highly variable. In this study, a coupled physical–biological model is used to investigate the dynamics underlying the observed A. fundyense abundance and shellfish toxicity in 1993 (a high toxicity year) and 1994 (low toxicity year). The physical model simulates the spring circulation, while the biological model estimates the germination and population dynamics of A. fundyense based on laboratory and field data. The model captures the large-scale aspects of the initiation and development of A. fundyense blooms during both years, but small-scale patchiness and the dynamics of bloom termination remain problematic. In both cases, the germination of resting cysts accounts for the magnitude of A. fundyense populations early in the spring. Simulations with low net A. fundyense growth rates capture the mean observed concentration during the bloom peak, which is of similar magnitude during both years. There is little evidence that large-scale changes in biological dynamics between 1993 and 1994 were a primary driver of the differences in shellfish toxicity. Results instead suggest that the persistent southwesterly flow of the western Maine Coastal Current led to A. fundyense populations of similar alongshore extent by late May of both years. This period coincides with peak cell abundance in the region. Variations in wind forcing (downwelling favorable in 1993, upwelling favorable in 1994) and subsequent cell transport (inshore in 1993, offshore in 1994) in early June then provides a plausible explanation for the dramatic mid-June differences in shellfish toxicity throughout the western Gulf of Maine.

15. Anderson, D M., and Charles A Stock, et al., September 2005: Alexandrium fundyense cyst dynamics in the Gulf of Maine. Deep-Sea Research, Part II, 52(19-21), DOI:10.1016/j.dsr2.2005.06.014.
    [ Abstract ]

    The flux of cells from germinated cysts is critical in the population dynamics of many dinoflagellates. Here, data from a large-scale cyst survey are combined with surveys in other years to yield an Alexandrium fundyense cyst distribution map for the Gulf of Maine that is massive in geographic extent and cyst abundance. The benthic cyst population extends nearly 500 km alongshore. Embedded within it are several distinct accumulation zones or “seedbeds,” each 3000–5000 km² in area. Maximal cyst abundances range from 2–20×10⁶ cysts m⁻². Cysts are equally or more abundant in deeper sediment layers; nearshore, cysts are fewer by a factor of 10 or more. This cyst distribution reflects sedimentary dynamics and the location of blooms in overlying surface waters. The flux of germinated cells from sediments was estimated using a combination of laboratory measurements of cyst germination and autofluorescence and observations of cyst autofluorescence in the field. These measurements constrained a germination function that, when applied to the cyst distribution map, provided an estimate of the germination inoculum for a physical/biological numerical model. In the laboratory studies, virtually all cysts incubated at different temperatures and light regimes became autofluorescent, but the rate of development was slower at lower temperatures, with no difference between light and dark incubations. Germination rates were highest at elevated temperatures, and were 2-fold greater in the light than in the dark. Laboratory and field fluorescence measurements suggest that>70% of the cysts in the top cm of sediment would germinate over a 60–90 day period in offshore waters. The combination of laboratory germination experiments and numerical modeling predicts nearly 100% germination of cysts in the top cm of sediment and resulting early season cell concentrations that are comparable in magnitude to observed cell distributions. It cannot account for late-season peaks in cell abundance that are heavily influenced by vegetative growth. Cyst germination flux from deep-water (>50 m) cyst seedbeds is 14X the flux in shallow waters. A conceptual model is proposed that is consistent with observed and modeled A. fundyense cyst and motile cell distributions and dynamics in the Gulf of Maine. Cysts germinate within the Bay of Fundy seedbed, causing localized, recurrent blooms that are self-seeding and “propagatory” in nature, supplying cells that populate the eastern segment of the Maine Coastal Current (MCC) and eventually deposit cysts offshore of Penobscot and Casco Bays. These cysts serve as a seed population for western Maine blooms that are transported to the west by the western segment of the MCC, where cells are removed either by mortality or advection from the region. Without the localized, “incubator” characteristic of the Bay of Fundy bloom zone, A. fundyense populations in the Gulf of Maine should diminish through time. Their persistence over many decades highlights the effectiveness of the mechanisms described here.

16. He, R, and Charles A Stock, et al., October 2005: Data assimilative hindcast of the Gulf of Maine coastal circulation. Journal of Geophysical Research, 110, C10011, DOI:10.1029/2004JC002807.
    [ Abstract ]

    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.

17. Stock, Charles A., et al., September 2005: Evaluating hypotheses for the initiation and development of Alexandrium fundyense blooms in the western Gulf of Maine using a coupled physical–biological model. Deep-Sea Research, Part II, 52(19-21), DOI:10.1016/j.dsr2.2005.06.022.
    [ Abstract ]

    A coupled physical/biological model and observations are used to investigate the factors governing the initiation and development of an Alexandrium fundyense bloom in the western Gulf of Maine (WGOM) during the spring of 1993 (March 19–June 6). The physical circulation is simulated using a 3D primitive equation model forced by climatological sea-surface elevation and observed winds, irradiance, and river outflow. This is coupled with a biological model constructed from laboratory and field data that estimates the germination and growth rates of A. fundyense as a function of environmental conditions. Four biological model structures of increasing complexity are considered, with each structure representing a hypothesis for factors controlling bloom initiation and development. The model/data fit is optimized over the uncertainty in the parameters to which the model is most sensitive. The significance of changes in the model/data fit between model structures is quantified using a maximum likelihood ratio test. The baseline biological model, which parameterizes growth as only a function of temperature, salinity, and light, severely over-estimates observed A. fundyense abundance in the late spring. It is thus rejected with greater than 99% confidence in favor of biological models that include a mortality term or a dependence of growth on dissolved inorganic nitrogen (DIN). The overall best-fit simulation uses both nitrogen dependence and mortality. However, simulations using one or the other of these factors could not be differentiated from the best-fit case with greater than 90% confidence. The best-fit model captures the general timing and magnitude of the observed bloom and some of its secondary features. However, considerable misfits may exist in the point-to-point comparison, and some regional misfits remain. Diagnosis of the cell budget suggests that germination from a large cyst bed offshore of Casco Bay provides the majority of cells comprising spring A. fundyense populations within the WGOM. The size of the modeled bloom is largely set by the size of this cyst-driven source. Transport of cells from the eastern Gulf of Maine becomes increasingly important later in the spring. Net growth of the modeled A. fundyense populations is first limited by low water temperatures and then by the combined influence of nitrogen limitation and mortality. This results in low domain-averaged net growth rates (<0.05 day⁻¹) throughout much of the simulation. However, rates are sometimes elevated locally and therefore add notable spatial structure to the bloom. Primary uncertainties within the biological model include spatial and temporal variability in mortality, and the influence of sediment dynamics and inter-annual variability in the cyst abundance on the size and spatial character of the cyst driven source. As the dynamics governing these processes become better understood, the approach herein can be extended to accommodate additional dynamical model complexity. However, the ability of the model/data comparison to constrain and support the inclusion of additional biological processes is dependent on both the availability of A. fundyense observations and the physical model skill.

18. McGillicuddy, Jr, D J., and Charles A Stock, et al., September 2003: A mechanism for offshore initiation of harmful algal blooms in the coastal Gulf of Maine. Journal of Plankton Research, 25(9), DOI:10.1093/plankt/25.9.1131.
    [ Abstract ]

    A combination of observations and model results suggest a mechanism by which coastal blooms of the toxic dinoflagellate Alexandrium fundyense can be initiated from dormant cysts located in offshore sediments. The mechanism arises from the joint effects of organism behavior and the wind-driven response of a surface-trapped plume of fresh water originating from riverine sources. During upwelling-favorable winds, the plume thins vertically and extends offshore; downwelling winds thicken the plume and confine it to the nearshore region. In the western Gulf of Maine, the offshore extent of the river plume during upwelling conditions is sufficient to entrain upward-swimming A. fundyense cells germinated from offshore cyst beds. Subsequent downwelling conditions then transport those populations towards the coast.

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