.. _Citations:

*********
Citations
*********

Model Configuration, Evaluation, and Storm Surge Hindcasting
============================================================

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`_

.. _https://dx.doi.org/10.1080/07055900.2015.1108899: https://www.tandfonline.com/doi/full/10.1080/07055900.2015.1108899

.. code-block:: tex

    @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 = "<p>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.</p>",
          doi = "10.1080/07055900.2015.1108899",
    }


Carbon Chemistry and Aragonite Saturation State
===============================================

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/10.1002/2015JC01111`_

.. _https://dx.doi.org/10.1002/2015JC01111: https://onlinelibrary.wiley.com/doi/abs/10.1002/2015JC011118

.. code-block:: tex

    @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 = "<p>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.</p>",
        doi = "10.1002/2015JC011118",
    }


Turbulence and Advective Mixing
===============================

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, **2017**.
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

.. code-block:: tex

    @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 = "<p>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.</p>",
        doi = "10.1002/2015JC011118",
    }


Salish Model Ecosystem-Lower Trophic (SMELT), the biological component of SalishSeaCast
=======================================================================================

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*, 25(8).
`https://dx.doi.org/10.1029/2019JC015766`_

.. _https://dx.doi.org/10.1029/2019JC015766: https://onlinelibrary.wiley.com/doi/10.1029/2019JC015766

.. code-block:: tex

    @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",
        volume = "25",
        number = "8",
        issn = "2169-9291",
        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",
    }


Cluster Analysis of Biophysical Dynamics
========================================

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`_

.. _https://doi.org/10.5194/os-2021-66: https://os.copernicus.org/preprints/os-2021-66/os-2021-66.pdf

.. code-block:: tex

    @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",
    }


SKOG, The Carbonate Chemistry Component of SalishSeaCast
========================================================

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).
`https://doi.org/10.1029/2021GB007024`_

.. _https://doi.org/10.1029/2021GB007024: https://onlinelibrary.wiley.com/doi/10.1029/2021GB007024

.. code-block:: tex

    @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",
    }


Zooplankton Spatial Distribution and Model Evaluation
=====================================================

SalishSeaCast was used to examine zooplankton dynamics in the Salish Sea and zooplankton
model classes were evaluated against a transboundary observation dataset in:

Suchy, K. D., Olson, E. M., Allen, S. E., Galbraith, M., Herrmann, B., Keister, J.E.,
Perry, R.I., Sastri, A. R., Young, K., **2023**.
Seasonal and regional variability of model-based zooplankton biomass in the Salish Sea and
evaluation against observations.
*Progress in Oceanography*, 219, 103171.
`https://doi.org/10.1016/j.pocean.2023.103171`_

.. _https://doi.org/10.1016/j.pocean.2023.103171: https://doi.org/10.1016/j.pocean.2023.103171

.. code-block:: tex

    @article{Suchy-etal-2023,
        author = "Suchy, K. D., Olson, E. M., Allen, S. E., Galbraith, M., Herrmann, B.,
    Keister, J.E., Perry, R.I., Sastri, A. R., Young, K.",
        title = "Seasonal and regional variability of model-based zooplankton biomass
    in the Salish Sea and evaluation against observations",
        journal = "Progress in Oceanography",
        year = "2023",
        volume = "219",
        pages = "103171",
        issn = "0079-6611",
        url = "https://doi.org/10.1016/j.pocean.2023.103171",
        keywords = "Zooplankton, Salish Sea, Biogeochemical model, Model evaluation,
    Transboundary studies, Strait of Georgia, Puget Sound",
        abstract = "We used a three-dimensional coupled biophysical model to examine
    zooplankton dynamics in the Salish Sea, NE Pacific. First, we evaluated the two
    zooplankton classes of the SalishSeaCast model using a transboundary zooplankton
    dataset comprised of observation data from the Canadian and United States waters
    of the Salish Sea from 2015 to 2019. Model zooplankton classes correspond to
    micro- and meso-zooplankton whose biomass is tightly coupled to phytoplankton
    through modelled food web dynamics (Z1) and mesozooplankton with life cycle-based
    seasonal grazing impacts (Z2). Overall, the model effectively captured seasonal
    patterns in observed biomass, although with slightly higher biomass estimates for
    both Z1 and Z2 (Bias = 0.10 and 0.08 g C m−2, respectively). Model fit varied
    regionally, with a weaker model fit being observed in nearshore regions.
    In addition, an autumn peak in Z2 was observed in the model, but not in the
    observations, suggesting some seasonal variations in model fit. Following the model
    evaluation, we used the model to determine seasonal and regional patterns of
    zooplankton grazing. Seasonally, the main peak in modelled zooplankton biomass
    increased in April or May in most of the regions defined within the Salish Sea and
    was driven by grazing on diatoms. Regionally, depth-integrated zooplankton biomass
    was consistently highest in areas adjacent to regions of strong tidal mixing.
    In addition, model-based zooplankton grazing was highest in the tidally mixed
    regions where phytoplankton biomass was high due to advection into the region
    despite low primary productivity. Our model-based results provide an opportunity
    to examine bottom-up food web processes at spatio-temporal scales not achievable
    with in situ sampling and help to elucidate key drivers of lower trophic level
    dynamics within the Salish Sea."
        doi = "10.1016/j.pocean.2023.103171",
    }