The SalishSeaCast Project team have produced a number of refereed academic journal publications. If you use our model results, code, documentation, etc., please cite one or more of our publications as appropriate.
If our work is helpful or informative to you in a context where academic citation isn't possible we would appreciate you telling us with a quick email to Susan Allen <sallen@eos.ubc.ca>.
The Salish Sea NEMO model configuration and its ability to calculate tides and sea surface height was evaluated by hindcasting storm surge events that occurred between 2002 and 2011 in:
Soontiens, N., Allen, S., Latornell, D., Le Souef, K., Machuca, I., Paquin, J.-P., Lu, Y., Thompson, K., Korabel, V., 2016. Storm surges in the Strait of Georgia simulated with a regional model. Atmosphere-Ocean 54 1-21.
https://dx.doi.org/10.1080/07055900.2015.1108899
The seasonal variability of aragonite saturation and pH in the surface Strait of Georgia and their drivers were determined using a 1-D coupled biochemical-physical model in:
Moore-Maley, B. L., S. E. Allen, and D. Ianson, 2016. Locally-driven interannual variability of near-surface pH and ΩA in the Strait of Georgia. J. Geophys. Res. Oceans, 121(3), 1600–1625.
https://dx.doi.org/10.1002/2015JC011118
The sensitivity of the deep water renewal into the Strait of Georgia and of fresh water pulses into Juan de Fuca Strait to modelling choices affecting both turbulence and advection has been determined in:
Soontiens, N. and Allen, S. Modelling sensitivities to mixing and advection in a sill-basin estuarine system. Ocean Modelling, 112, 17-32.
https://dx.doi.org/10.1016/j.ocemod.2017.02.008
The 3 nutrient- 3 phytoplankton- 1.5 zooplankton compartment model described in Moore-Maley et al . (2016) was adapted to three dimensions and coupled to the Salish Sea NEMO model described by Soontiens et al. (2016). Description and evaluation of the model can be found in:
Olson, E. M., S. E. Allen, V. Do, M. Dunphy, and D. Ianson, 2020. Assessment of Nutrient Supply by a Tidal Jet in the Northern Strait of Georgia Based on a Biogeochemical Model. J. Geophys. Res. Oceans.
https://dx.doi.org/10.1029/2019JC015766
A cluster-based tool for model analysis and evaluation was developed and used to determine biophysical dynamics of the system in:
Jarníková, T., Olson, E. M., Allen, S. E., Ianson, D., and Suchy, K. D., 2021. A clustering approach to determine biophysical provinces and physical drivers of productivity dynamics in a complex coastal sea. Ocean Sci. Discuss., 1-36.
https://doi.org/10.5194/os-2021-66
The three-dimensional carbonate chemistry model was developed and used to determine the anthropogenic increase in Salish Sea coastal carbon content in:
Jarníková T., Ianson D., Allen S.E., Shao A.E., Olson E.M.. 2022. Anthropogenic carbon increase has caused critical shifts in aragonite saturation across a sensitive coastal system. Global Biogeochemical Cycles, 36(7).
@article{"Soontiens-etal-2016, author = "Soontiens, N. and Allen, S. and Latornell, D. and Le Souef, K. and Machuca, I. and Paquin, J.-P. and Lu, Y. and Thompson, K. and Korabel, V.", journal = "Atmosphere-Ocean", publisher = "Taylor and Francis", title = "Storm surges in the Strait of Georgia simulated with a regional model", year = "2016", volume = "54", number = "1", pages = "1-21", url = "https://dx.doi.org/10.1080/07055900.2015.1108899", abstract = "The Strait of Georgia is a large, semi-enclosed body of water between Vancouver Island and the mainland of British Columbia connected to the Pacific Ocean via Juan de Fuca Strait at the south and Johnstone Strait at the north. During the winter months, coastal communities along the Strait of Georgia are at risk of flooding caused by storm surges, a natural hazard that can occur when a strong storm coincides with high tide. This investigation produces storm surge hindcasts using a three-dimensional numerical ocean model for the Strait of Georgia and the surrounding bodies of water (Juan de Fuca Strait, Puget Sound, and Johnstone Strait) collectively known as the Salish Sea. The numerical model employs the Nucleus for European Modelling of the Ocean architecture in a regional configuration. The model is evaluated through comparisons of tidal elevation harmonics and storm surge with observations. Important forcing factors contributing to storm surges are assessed. It is shown that surges entering the domain from the Pacific Ocean make the most significant contribution to surge amplitude within the Strait of Georgia. Comparisons between simulations and high-resolution and low-resolution atmospheric forcing further emphasize that remote forcing is the dominant factor in surge amplitudes in this region. In addition, local wind patterns caused a slight increase in surge amplitude on the mainland side of the Strait of Georgia compared with Vancouver Island coastal areas during a major wind storm on 15 December 2006. Generally, surge amplitudes are found to be greater within the Strait of Georgia than in Juan de Fuca Strait.", doi = "10.1080/07055900.2015.1108899", }
@article {Moore-Maley-etal-2016, author = "Moore-Maley, Ben L. and Allen, Susan E. and Ianson, Debby", title = "Locally driven interannual variability of near-surface pH and ΩA in the Strait of Georgia", journal = "Journal of Geophysical Research: Oceans", year = "2016", volume = "121", number = "3", pages = "1600--1625", issn = "2169-9291", url = "https://dx.doi.org/10.1002/2015JC011118", keywords = "Biogeochemical cycles, processes, and modeling, Carbon cycling, Estuarine processes, Marginal and semi-enclosed seas, Ecosystems, structure, dynamics, and modeling, acidification, estuarine, ecosystem, modeling, shellfish, rivers", abstract = "Declines in mean ocean pH and aragonite saturation state (ΩA) driven by anthropogenic CO2 emissions have raised concerns regarding the trends of pH and ΩA in estuaries. Low pH and ΩA can be harmful to a variety of marine organisms, especially those with calcium carbonate shells, and so may threaten the productive ecosystems and commercial fisheries found in many estuarine environments. The Strait of Georgia is a large, temperate, productive estuarine system with numerous wild and aquaculture shellfish and finfish populations. We determine the seasonality and variability of near-surface pH and ΩA in the Strait using a one-dimensional, biophysical, mixing layer model. We further evaluate the sensitivity of these quantities to local wind, freshwater, and cloud forcing by running the model over a wide range of scenarios using 12 years of observations. Near-surface pH and ΩA demonstrate strong seasonal cycles characterized by low pH, aragonite-undersaturated waters in winter and high pH, aragonite-supersaturated waters in summer. The aragonite saturation horizon generally lies at ∼20 m depth except in winter and during strong Fraser River freshets when it shoals to the surface. Periods of strong interannual variability in pH and aragonite saturation horizon depth arise in spring and summer. We determine that at different times of year, each of wind speed, freshwater flux, and cloud fraction are the dominant drivers of this variability. These results establish the mechanisms behind the emerging observations of highly variable near-surface carbonate chemistry in the Strait.", doi = "10.1002/2015JC011118", }
@article{Soontiens-Allen-2017, author = "Soontiens, N. and Allen, S.", title = "Modelling sensitivities to mixing and advection in a sill-basin estuarine system", journal = "Ocean Modelling", year = "2017", volume = "112", number = "", pages = "17--32", issn = "1463-5003", url = "https://dx.doi.org/10.1002/2015JC011118", keywords = "Hollingsworth instability, Vertical mixing, Deep water renewal, Turbulence closures, Advection schemes, NEMO" abstract = "This study investigates the sensitivity of a high resolution regional ocean model to several choices in mixing and advection. The oceanographic process examined is a deep water renewal event in the Juan de Fuca Strait–Strait of Georgia sill-basin estuarine system located on the west coast of North America. Previous observational work has shown that the timing of the renewal events is linked to the spring/neap tidal cycle, and in turn, is sensitive to the amount of vertical mixing induced by tidal currents interacting with sills and complicated bathymetry. It is found that the model’s representation of deep water renewal is relatively insensitive to several mixing choices, including the vertical turbulence closure and direction of lateral mixing. No significant difference in deep or intermediate salinity was found between cases that used k−ϵk−ϵ versus k−ωk−ω closures and isoneutral versus horizontal lateral mixing. Modifications that had a stronger effect included those that involved advection such as modifying the salinity of the open boundary conditions which supply the source waters for the renewal event. The strongest impact came from the removal of the Hollingsworth instability, a kinetic energy sink in the energy-enstrophy discretization of the momentum equations. A marked improvement to the salinity of the deep water renewal suggests that the removal of the Hollingsworth instability will correct a fresh drift in the deep and intermediate waters in an operational version of this model.", doi = "10.1002/2015JC011118", }
@article{Olson-etal-2020, author = "Olson, E. M. and S. E. Allen and V. Do and M. Dunphy and D. Ianson", title = "Assessment of Nutrient Supply by a Tidal Jet in the Northern Strait of Georgia Based on a Biogeochemical Model", journal = "Journal of Geophysical Research: Oceans", year = "2020", url = "https://dx.doi.org/10.1029/2019JC015766", keywords = "nitrate, tidal jet, Discovery Passage, Strait of Georgia, biogeochemical model, new production", abstract = "We present a coupled three-dimensional biological-physical model for the Salish Sea and evaluate it by comparison to nitrate, silicate, and chlorophyll observations. It accurately reproduces nitrate concentrations with Willmott skill scores, root mean squared error, and bias ranging from 0.84–0.95, 4.02–6.5 μM, and −2.33–1.84 μM, respectively, compared to three independent discrete sample data sets. A prominent feature of the model output is a tidal jet emanating from Discovery Passage producing a downstream plume of elevated surface nitrate. The signal is present from April to September, when surface nitrate is otherwise drawn down. It has a weak but statistically significant correlation to Discovery Passage tidal velocity (R=0.37, p<0.01). Within the turbulent jet and associated plume, the average rate of vertical nitrate supply due to mixing and advection across a depth of roughly 6 m is 0.46 μmol m−2 s−1 between May 15, 2015, and August 20, 2015, compared to 0.10 μmol m−2 s−1 for the northern Strait of Georgia as a whole. Close to Discovery Passage, where velocities and shear are strongest, the majority of the vertical nitrate flux is due to mixing. As velocities weaken downstream, vertical advection becomes more important relative to mixing, but vertical velocities also decrease. The tidal pulses out of Discovery Passage drive waves that contribute net upward nitrate flux as far south as Cape Lazo, 40 km away. The nitrate supply drives new production, consistent with existing observations. Similar dynamics have been described in many other tidally influenced coastal systems.", doi = "10.1029/2019JC015766", }
@article{Jarnikova-etal-2021, author = "Jarníková, T., Olson, E. M., Allen, S. E., Ianson, D., and Suchy, K. D.", title = "A clustering approach to determine biophysical provinces and physical drivers of productivity dynamics in a complex coastal sea", journal = "Ocean Sci. Discuss.", year = "2021", url = "https://doi.org/10.5194/os-2021-66", abstract = "The balance between ocean mixing and stratification influences primary productivity through light limitation and nutrient supply in the euphotic ocean. Here, we apply a hierarchical clustering algorithm (Ward's method) to four factors relating to stratification and depth-integrated phytoplankton biomass extracted from a biophysical regional ocean model of the Salish Sea to assess spatial co-occurrence. Running the clustering algorithm on four years of model output, we identify distinct regions of the model domain that exhibit contrasting wind and freshwater input dynamics, as well as regions of varying watercolumn-averaged vertical eddy diffusivity and halocline depth regimes. The spatial regionalizations in physical variables are similar in all four analyzed years. We also find distinct interannually consistent biological zones. In the Northern Strait of Georgia and Juan de Fuca Strait, a deeper winter halocline and episodic summer mixing coincide with higher summer diatom abundance, while in the Fraser River stratified Central Strait of Georgia, shallower haloclines and stronger summer stratification coincide with summer flagellate abundance. Cluster based model results and evaluation suggest that the Juan de Fuca Strait supports more biomass than previously thought. Our approach elucidates probable physical mechanisms controlling phytoplankton abundance and composition. It also demonstrates a simple, powerful technique for finding structure in large datasets and determining boundaries of biophysical provinces.", doi = "10.5194/os-2021-66", }
@article{Jarnikova-etal-2022, author = "Jarníková T., Ianson D., Allen S.E., Shao A.E., Olson E.M.", title = "Anthropogenic Carbon Increase has Caused Critical Shifts in Aragonite Saturation Across a Sensitive Coastal System", journal = "Global Biogeochemical Cycles", year = "2022", volume = "36", number = "7", url = "https://doi.org/10.1029/2021GB007024", keywords = "coastal ocean acidification, carbon cycle, ocean acidification, sub-mesoscale ocean model, anthropogenic carbon, aragonite saturation", abstract = "Estuarine systems host a rich diversity of marine life that is vulnerable to changes in ocean chemistry due to addition of anthropogenic carbon. However, the detection and impact of secular carbon trends in these systems is complicated by heightened natural variability as compared to open-ocean regimes. We investigate biogeochemical changes between the pre-industrial (PI) and modern periods using a high-resolution, three-dimensional, biophysical model of the Salish Sea, a representative Northeast Pacific coastal system. While the seasonal amplitude of the air-sea difference in pCO2 has increased on average since pre-industrial times, the net CO2 source has changed little. Our simulations show that inorganic carbon has increased throughout the model domain by 29–39 mmol m−3 (28–38 µmol kg−1) from the pre-industrial to present. While this increase is modest in a global context, the region's naturally high inorganic carbon content and the low buffering capacity of the local carbonate system amplify the resultant effects. Notably, this increased carbon drives the estuary toward system-wide undersaturation of aragonite, negatively impacting shell-forming organisms. Undersaturation events were rare during the pre-industrial experiment, with 10%–25% of the domain undersaturated by volume throughout the year, while under present-day conditions, the majority (55%–75%) of the system experiences corrosive, undersaturated conditions year-round. These results are extended using recent global coastal observations to show that estuaries throughout the Pacific Rim have already undergone a similar saturation state regime shift.", doi = "10.1029/2021GB007024", }