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<article xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:oasis="http://docs.oasis-open.org/ns/oasis-exchange/table" dtd-version="3.0"><?xmltex \makeatother\@nolinetrue\makeatletter?>
  <front>
    <journal-meta>
<journal-id journal-id-type="publisher">BG</journal-id>
<journal-title-group>
<journal-title>Biogeosciences</journal-title>
<abbrev-journal-title abbrev-type="publisher">BG</abbrev-journal-title>
<abbrev-journal-title abbrev-type="nlm-ta">Biogeosciences</abbrev-journal-title>
</journal-title-group>
<issn pub-type="epub">1726-4189</issn>
<publisher><publisher-name>Copernicus Publications</publisher-name>
<publisher-loc>Göttingen, Germany</publisher-loc>
</publisher>
</journal-meta>

    <article-meta>
      <article-id pub-id-type="doi">10.5194/bg-13-2011-2016</article-id><title-group><article-title>Challenges associated with modeling low-oxygen waters in Chesapeake Bay: a
multiple model comparison</article-title>
      </title-group><?xmltex \runningtitle{Multiple modeling low-oxygen waters}?><?xmltex \runningauthor{I.~D. Irby et al.}?>
      <contrib-group>
        <contrib contrib-type="author" corresp="yes" rid="aff1">
          <name><surname>Irby</surname><given-names>Isaac D.</given-names></name>
          <email>iirby@vims.edu</email>
        </contrib>
        <contrib contrib-type="author" corresp="yes" rid="aff1">
          <name><surname>Friedrichs</surname><given-names>Marjorie A. M.</given-names></name>
          <email>marjy@vims.edu</email>
        <ext-link>https://orcid.org/0000-0003-2828-7595</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Friedrichs</surname><given-names>Carl T.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff2">
          <name><surname>Bever</surname><given-names>Aaron J.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff3">
          <name><surname>Hood</surname><given-names>Raleigh R.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff4 aff5">
          <name><surname>Lanerolle</surname><given-names>Lyon W. J.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff6">
          <name><surname>Li</surname><given-names>Ming</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff7">
          <name><surname>Linker</surname><given-names>Lewis</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff8">
          <name><surname>Scully</surname><given-names>Malcolm E.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff9">
          <name><surname>Sellner</surname><given-names>Kevin</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Shen</surname><given-names>Jian</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff6">
          <name><surname>Testa</surname><given-names>Jeremy</given-names></name>
          
        <ext-link>https://orcid.org/0000-0003-0027-9761</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff3">
          <name><surname>Wang</surname><given-names>Hao</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff10">
          <name><surname>Wang</surname><given-names>Ping</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff11">
          <name><surname>Xia</surname><given-names>Meng</given-names></name>
          
        </contrib>
        <aff id="aff1"><label>1</label><institution>Virginia Institute of Marine Science, College of William &amp; Mary, P.O. Box 1346, Gloucester Point, VA 23062, USA</institution>
        </aff>
        <aff id="aff2"><label>2</label><institution>Anchor QEA, LLC, 130 Battery Street, Suite 400, San Francisco, CA 94111, USA</institution>
        </aff>
        <aff id="aff3"><label>3</label><institution>Horn Point Laboratory, University of Maryland Center for Environmental Science, P.O. Box 775, Cambridge, MD 21613, USA</institution>
        </aff>
        <aff id="aff4"><label>4</label><institution>NOAA/NOS/OCS Coast Survey Development Laboratory, 1315 East–West Highway, Silver Spring, MD 20910, USA</institution>
        </aff>
        <aff id="aff5"><label>5</label><institution>ERT Inc., 14401 Sweitzer Lane Suite 300, Laurel, MD 20707, USA</institution>
        </aff>
        <aff id="aff6"><label>6</label><institution>Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, P.O. Box 38, Solomons, MD 20688, USA</institution>
        </aff>
        <aff id="aff7"><label>7</label><institution>US Environmental Protection Agency Chesapeake Bay Program Office, 410 Severn Avenue, Annapolis, MD 21403, USA</institution>
        </aff>
        <aff id="aff8"><label>8</label><institution>Woods Hole Oceanographic Institution, Applied Ocean Physics and Engineering Department, Woods Hole, MA 02543, USA</institution>
        </aff>
        <aff id="aff9"><label>9</label><institution>Chesapeake Research Consortium, 645 Contees Wharf Road, Edgewater, MD 21037, USA</institution>
        </aff>
        <aff id="aff10"><label>10</label><institution>VIMS/Chesapeake Bay Program Office, 410 Severn Avenue, Annapolis, MD 21403, USA</institution>
        </aff>
        <aff id="aff11"><label>11</label><institution>Department of Natural Sciences, University of Maryland Eastern Shore, MD, USA</institution>
        </aff>
      </contrib-group>
      <author-notes><corresp id="corr1">Isaac D. Irby (iirby@vims.edu) and Marjorie A. M. Friedrichs (marjy@vims.edu)</corresp></author-notes><pub-date><day>6</day><month>April</month><year>2016</year></pub-date>
      
      <volume>13</volume>
      <issue>7</issue>
      <fpage>2011</fpage><lpage>2028</lpage>
      <history>
        <date date-type="received"><day>2</day><month>December</month><year>2015</year></date>
           <date date-type="rev-request"><day>21</day><month>December</month><year>2015</year></date>
           <date date-type="rev-recd"><day>8</day><month>March</month><year>2016</year></date>
           <date date-type="accepted"><day>9</day><month>March</month><year>2016</year></date>
      </history>
      <permissions>
<license license-type="open-access">
<license-p>This work is licensed under a Creative Commons Attribution 3.0 Unported License. To view a copy of this license, visit <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/3.0/">http://creativecommons.org/licenses/by/3.0/</ext-link></license-p>
</license>
</permissions><self-uri xlink:href="https://bg.copernicus.org/articles/13/2011/2016/bg-13-2011-2016.html">This article is available from https://bg.copernicus.org/articles/13/2011/2016/bg-13-2011-2016.html</self-uri>
<self-uri xlink:href="https://bg.copernicus.org/articles/13/2011/2016/bg-13-2011-2016.pdf">The full text article is available as a PDF file from https://bg.copernicus.org/articles/13/2011/2016/bg-13-2011-2016.pdf</self-uri>


      <abstract>
    <p>As three-dimensional (3-D) aquatic ecosystem models are used
more frequently for operational water quality forecasts and ecological
management decisions, it is important to understand the relative strengths
and limitations of existing 3-D models of varying spatial resolution and
biogeochemical complexity. To this end, 2-year simulations of the
Chesapeake Bay from eight hydrodynamic-oxygen models have been statistically
compared to each other and to historical monitoring data. Results show that
although models have difficulty resolving the variables typically thought to
be the main drivers of dissolved oxygen variability (stratification,
nutrients, and chlorophyll), all eight models have significant skill in
reproducing the mean and seasonal variability of dissolved oxygen. In
addition, models with constant net respiration rates independent of nutrient
supply and temperature reproduced observed dissolved oxygen concentrations
about as well as much more complex, nutrient-dependent biogeochemical models.
This finding has significant ramifications for short-term hypoxia forecasts
in the Chesapeake Bay, which may be possible with very simple oxygen
parameterizations, in contrast to the more complex full biogeochemical models
required for scenario-based forecasting. However, models have difficulty
simulating correct density and oxygen mixed layer depths, which are important
ecologically in terms of habitat compression. Observations indicate a much
stronger correlation between the depths of the top of the pycnocline and
oxycline than between their maximum vertical gradients, highlighting the
importance of the mixing depth in defining the region of aerobic habitat in
the Chesapeake Bay when low-oxygen bottom waters are present. Improvement in
hypoxia simulations will thus depend more on the ability of models to
reproduce the correct mean and variability of the depth of the physically
driven surface mixed layer than the precise magnitude of the vertical density
gradient.</p>
  </abstract>
    </article-meta>
  </front>
<body>
      

      <?xmltex \hack{\newpage}?>
<sec id="Ch1.S1" sec-type="intro">
  <title>Introduction</title>
      <p>Since the middle of the last century, anthropogenic impacts
have dramatically decreased water quality throughout the Chesapeake Bay
(Boesch et al., 2001), one of the largest estuaries in North America.
Land-use change along with the industrialization and urbanization of the
Chesapeake Bay watershed have caused dramatic increases in nutrient inputs to
the bay (Kemp et al., 2005), spurring additional primary production and
phytoplankton abundance (Harding Jr. and Perry, 1997). Because increased
primary production leads to more organic matter throughout the water column
that is eventually decomposed by bacteria, these increased nutrient inputs to
the bay have led to a corresponding decrease in dissolved oxygen (DO)
concentrations (Hagy et al., 2004). Hypoxia, generally defined as the
condition in which DO concentrations are below 2 <inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">mg</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">L</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>, usually
initiates seasonally in the northern portion of the bay and expands southward
as summer develops (Kemp et al., 2009; Testa and Kemp, 2014). Although
hypoxia in the Chesapeake Bay has likely existed since European colonization
(Cooper and Brush, 1991, 1993), recent studies have highlighted an
accelerated rise in the number and spatial extent of hypoxic, as well as
anoxic (DO concentrations <inline-formula><mml:math display="inline"><mml:mo>&lt;</mml:mo></mml:math></inline-formula> 0.2 <inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">mg</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">L</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>), events in the bay
since the 1950s, primarily attributed to increased anthropogenic nutrient
input (Hagy et al., 2004; Kemp et al., 2005; Gilbert et al., 2010). These
impacts are likely to be exacerbated by future climate change (Najjar et
al., 2010; Meire et al., 2013; Harding Jr. et al., 2015).</p>
      <p>Interest in the ecological impacts of reduced DO concentrations has been
elevated due to the observed proliferation of hypoxic events in the world's
coastal oceans, creating vast dead zone areas that compress suitable habitats
for many marine species (Diaz, 2001; Diaz and Rosenberg, 2008; Pierson et
al., 2009). Low-DO waters can greatly impact the abundance and health of
important ecological species, potentially resulting in suffocation and major
kills of fish, crabs, and shellfish (Breitburg, 2002; Ekau et al., 2010;
Levin et al., 2009). While the presence of DO concentrations
<inline-formula><mml:math display="inline"><mml:mo>&lt;</mml:mo></mml:math></inline-formula> 2 <inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">mg</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">L</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> have been shown to decrease the abundance of fish
larvae (Keister et al., 2000), some species can incur negative health impacts
and modify their behavior at significantly higher DO concentrations
(Vaquer-Sunyer and Duarte, 2008). DO concentrations of
<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 4 <inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">mg</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">L</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> have been found to compress demersal fish
habitat as fish seek out more oxygenated waters (Buchheister et al., 2013).
Zooplankton, a crucial food source for valuable species, have also been found
to exhibit changes in distribution and predation when subject to large
volumes of low-DO water, potentially leading to further impacts along the
food chain (Breitburg et al., 1997; Pierson et al., 2009). Invertebrates have
similarly been found to alter their behavior under low-DO conditions (Riedel
et al., 2014). In the Chesapeake Bay, multiple regulated fish species, such
as striped bass and American shad, require oxygen restoration targets as high
as 5 <inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">mg</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">L</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> (USEPA, 2010). The greatest impact of low DO
concentrations spatially will depend on the specific living resource;
however, temporally, late spring to early fall is of most concern. As a
result of the significant ecological importance of oxygen on living resources
in the bay, DO concentrations are used as a primary indicator in assessing
water quality for Chesapeake Bay regulations (Keisman and Shenk, 2013).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F1"><caption><p>Map of the Chesapeake Bay and its watershed.</p></caption>
        <?xmltex \igopts{width=227.622047pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/2011/2016/bg-13-2011-2016-f01.png"/>

      </fig>

      <p>Improving the health of the Chesapeake Bay has become a priority for the
Environmental Protection Agency (EPA) along with the six states and
Washington, DC that make up the bay watershed (Fig. 1), and together they
have committed to utilizing a suite of regulatory models to inform their
management decisions (USEPA, 2010). The Chesapeake Bay Program (CBP), a
regional partnership that has led and directed the restoration of the
Chesapeake Bay since 1983, has undertaken an extensive modeling effort of the
bay (Cerco and Cole, 1993; Cerco et al., 2002; Cerco and Noel, 2004, 2013).
This modeling system is being used by the CBP to estimate the aggregate
effect of changes in management practices, including land use, atmospheric
deposition, animal populations, and fertilizer and manure application.
Recently, the modeling system has been used to conduct scenario simulations
to assess management actions needed to achieve desired bay water quality
standards (USEPA, 2010). Ultimately this model was used to establish a
regulatory set of total maximum daily loads of nutrients and sediment
delivered from the watershed, with the goal of significantly improving water
quality throughout the bay (USEPA, 2010).</p>
      <p>Many 3-D hydrodynamic-oxygen models of varying complexity stemming from the
academic research community have also been used to simulate DO concentrations
throughout the Chesapeake Bay (Scully, 2010, 2013; Hong and Shen, 2013; Feng
et al., 2015; Testa et al., 2014; Y. Li et al., 2015). Bever et al. (2013)
specifically demonstrated that multiple models of varying complexity are able
to generate skillful estimates of hypoxic volume in the bay. Some of these
models are being used in the bay to simulate short-term and/or seasonal
forecasts of DO conditions. Furthermore, some models are also being used to
generate scenario forecasts, or projections, that assess the impact of
changes in management practices on estuarine DO concentrations, in some cases
taking into account the impacts of future changes in climate.</p>
      <p>As ecosystem and water quality models are increasingly used for operational
forecasts as well as scenario-based management decisions by the regulatory
and academic research communities, it is important to understand the relative
strengths and limitations of existing models of varying complexity. The
ability to discern which variables must be most accurately simulated in order
to adequately reproduce the temporal and spatial variability of bay oxygen
concentrations is a necessary prerequisite for fully understanding how
volumes of low-DO water are initiated and sustained within water quality
models. The utilization of multiple models can also inform projections by
providing independent confidence bounds for management decisions. To those
ends, the overarching goals of this research are to compare the relative
skill of various 3-D Chesapeake Bay models characterized
by different levels of biogeochemical complexity and spatial resolution, to
better understand factors limiting their ability to reproduce observed DO
distributions, and to suggest approaches for the continued improvement of
these models.</p>
</sec>
<sec id="Ch1.S2">
  <title>Methods</title>
<sec id="Ch1.S2.SS1">
  <title>Participating Chesapeake Bay models</title>
      <p>Eight 3-D models were evaluated in this study (Table 1), each of which
includes hydrodynamic and DO components. Among the eight models, there are
four different hydrodynamic base models. Models B, C, D, F, and G utilize the
Regional Ocean Modeling System (ROMS; Shchepetkin and McWilliams, 2005;
Haidvogel et al., 2008) that employs a structured grid with sigma layers in
the vertical dimension. Specifically, Models B, C, and F use a ROMS
implementation developed for the Chesapeake Bay based on Xu et al. (2012;
ChesROMS). Model D employs a ROMS implementation for the Chesapeake Bay based
on M. Li et al. (2005), while Model G uses the ROMS-based Chesapeake Bay
Operational Forecast System (CBOFS; Lanerolle et al., 2011). Models A, E, and
H each use a different hydrodynamic base model: the Curvilinear Hydrodynamics
in Three Dimensions model (CH3D; Cerco et al., 2010), the Finite-Volume
Community Ocean Model (FVCOM; Jiang and Xia, 2016), and the Hydrodynamic
Eutrophication Model – Environmental Fluid Dynamics Code (EFDC; Park et
al., 1995; Hong and Shen, 2012; Du and Shen, 2015), respectively. The only
model that employs a non-sigma vertical grid is Model A and the only model
utilizing an unstructured horizontal grid is Model E. While Model E contains
10 sigma vertical layers, all of the other sigma grids use 20 layers. All of
the grids vary in terms of their horizontal resolution, with Models A and G
utilizing the highest resolution horizontal grids.</p>

<?xmltex \floatpos{p}?><table-wrap id="Ch1.T1" orientation="landscape"><caption><p>Model characteristics.</p></caption><oasis:table frame="topbot"><?xmltex \begin{scaleboxenv}{.80}[.80]?><oasis:tgroup cols="9">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:colspec colnum="3" colname="col3" align="left"/>
     <oasis:colspec colnum="4" colname="col4" align="left"/>
     <oasis:colspec colnum="5" colname="col5" align="left"/>
     <oasis:colspec colnum="6" colname="col6" align="left"/>
     <oasis:colspec colnum="7" colname="col7" align="left"/>
     <oasis:colspec colnum="8" colname="col8" align="left"/>
     <oasis:colspec colnum="9" colname="col9" align="left"/>
     <oasis:thead>
       <oasis:row rowsep="1">

         <oasis:entry colname="col1">Model</oasis:entry>

         <oasis:entry colname="col2">A</oasis:entry>

         <oasis:entry colname="col3">B</oasis:entry>

         <oasis:entry colname="col4">C</oasis:entry>

         <oasis:entry colname="col5">D</oasis:entry>

         <oasis:entry colname="col6">E</oasis:entry>

         <oasis:entry colname="col7">F</oasis:entry>

         <oasis:entry colname="col8">G</oasis:entry>

         <oasis:entry colname="col9">H</oasis:entry>

       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>

         <oasis:entry colname="col1">Hydrodynamic</oasis:entry>

         <oasis:entry rowsep="1" colname="col2" morerows="1">CH3D-ICM</oasis:entry>

         <oasis:entry rowsep="1" colname="col3" morerows="1">ChesROMS-ECB</oasis:entry>

         <oasis:entry rowsep="1" colname="col4" morerows="1">ChesROMS-BGC</oasis:entry>

         <oasis:entry rowsep="1" colname="col5" morerows="1">ROMS-RCA</oasis:entry>

         <oasis:entry rowsep="1" colname="col6" morerows="1">FVCOM-ICM</oasis:entry>

         <oasis:entry rowsep="1" colname="col7" morerows="1">ChesROMS-CRM</oasis:entry>

         <oasis:entry rowsep="1" colname="col8" morerows="1">CBOFS-CRM</oasis:entry>

         <oasis:entry rowsep="1" colname="col9" morerows="1">EFDC-CRM</oasis:entry>

       </oasis:row>
       <oasis:row rowsep="1">

         <oasis:entry colname="col1">model-DO model</oasis:entry>

       </oasis:row>
       <oasis:row rowsep="1">

         <oasis:entry colname="col1">Grid structure</oasis:entry>

         <oasis:entry colname="col2">Structured</oasis:entry>

         <oasis:entry colname="col3">Structured</oasis:entry>

         <oasis:entry colname="col4">Structured</oasis:entry>

         <oasis:entry colname="col5">Structured</oasis:entry>

         <oasis:entry colname="col6">Unstructured</oasis:entry>

         <oasis:entry colname="col7">Structured</oasis:entry>

         <oasis:entry colname="col8">Structured</oasis:entry>

         <oasis:entry colname="col9">Structured</oasis:entry>

       </oasis:row>
       <oasis:row>

         <oasis:entry colname="col1">Average wet-cell</oasis:entry>

         <oasis:entry rowsep="1" colname="col2" morerows="1">1 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula></oasis:entry>

         <oasis:entry rowsep="1" colname="col3" morerows="1">1.8 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula></oasis:entry>

         <oasis:entry rowsep="1" colname="col4" morerows="1">1.8 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula></oasis:entry>

         <oasis:entry rowsep="1" colname="col5" morerows="1">1.89 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula></oasis:entry>

         <oasis:entry rowsep="1" colname="col6" morerows="1">1.26 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula></oasis:entry>

         <oasis:entry rowsep="1" colname="col7" morerows="1">1.8 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula></oasis:entry>

         <oasis:entry rowsep="1" colname="col8" morerows="1">0.565 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula></oasis:entry>

         <oasis:entry rowsep="1" colname="col9" morerows="1">1.2 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula></oasis:entry>

       </oasis:row>
       <oasis:row rowsep="1">

         <oasis:entry colname="col1">resolution</oasis:entry>

       </oasis:row>
       <oasis:row rowsep="1">

         <oasis:entry colname="col1">Vertical grid</oasis:entry>

         <oasis:entry colname="col2">1.52 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula></oasis:entry>

         <oasis:entry colname="col3">20 sigma</oasis:entry>

         <oasis:entry colname="col4">20 sigma</oasis:entry>

         <oasis:entry colname="col5">20 sigma</oasis:entry>

         <oasis:entry colname="col6">10 sigma</oasis:entry>

         <oasis:entry colname="col7">20 sigma</oasis:entry>

         <oasis:entry colname="col8">20 sigma</oasis:entry>

         <oasis:entry colname="col9">20 sigma</oasis:entry>

       </oasis:row>
       <oasis:row rowsep="1">

         <oasis:entry colname="col1">River forcing</oasis:entry>

         <oasis:entry colname="col2">CBP watershed model</oasis:entry>

         <oasis:entry colname="col3">DLEM watershed model</oasis:entry>

         <oasis:entry colname="col4">USGS data</oasis:entry>

         <oasis:entry colname="col5">USGS data</oasis:entry>

         <oasis:entry colname="col6">USGS data</oasis:entry>

         <oasis:entry colname="col7">USGS data</oasis:entry>

         <oasis:entry colname="col8">USGS data</oasis:entry>

         <oasis:entry colname="col9">USGS data</oasis:entry>

       </oasis:row>
       <oasis:row>

         <oasis:entry colname="col1">Sub-tidal elevation</oasis:entry>

         <oasis:entry colname="col2">Multiple efforts</oasis:entry>

         <oasis:entry colname="col3">Lewes, DE</oasis:entry>

         <oasis:entry colname="col4">Lewes, DE</oasis:entry>

         <oasis:entry colname="col5">Wachapreague, VA</oasis:entry>

         <oasis:entry colname="col6">TPXO Tidal</oasis:entry>

         <oasis:entry colname="col7">Lewes, DE</oasis:entry>

         <oasis:entry colname="col8">Ocean City, MD</oasis:entry>

         <oasis:entry colname="col9">Lewes, DE</oasis:entry>

       </oasis:row>
       <oasis:row rowsep="1">

         <oasis:entry colname="col1">at open boundary</oasis:entry>

         <oasis:entry colname="col2"/>

         <oasis:entry colname="col3">to Duck, NC</oasis:entry>

         <oasis:entry colname="col4">to Duck, NC</oasis:entry>

         <oasis:entry colname="col5">to Duck, NC</oasis:entry>

         <oasis:entry colname="col6">Model</oasis:entry>

         <oasis:entry colname="col7">to Duck, NC</oasis:entry>

         <oasis:entry colname="col8">to Duck, NC</oasis:entry>

         <oasis:entry colname="col9">to Duck, NC</oasis:entry>

       </oasis:row>
       <oasis:row rowsep="1">

         <oasis:entry colname="col1">Wind forcing</oasis:entry>

         <oasis:entry colname="col2">Multiple efforts</oasis:entry>

         <oasis:entry colname="col3">Thomas Point Light</oasis:entry>

         <oasis:entry colname="col4">NARR</oasis:entry>

         <oasis:entry colname="col5">NARR</oasis:entry>

         <oasis:entry colname="col6">NARR</oasis:entry>

         <oasis:entry colname="col7">NARR</oasis:entry>

         <oasis:entry colname="col8">NARR and NDBC buoys</oasis:entry>

         <oasis:entry colname="col9">NARR</oasis:entry>

       </oasis:row>
       <oasis:row>

         <oasis:entry colname="col1">Other atmospheric</oasis:entry>

         <oasis:entry colname="col2">Multiple efforts</oasis:entry>

         <oasis:entry colname="col3">NARR</oasis:entry>

         <oasis:entry colname="col4">NARR</oasis:entry>

         <oasis:entry colname="col5">NARR</oasis:entry>

         <oasis:entry colname="col6">NARR</oasis:entry>

         <oasis:entry colname="col7">NARR</oasis:entry>

         <oasis:entry colname="col8">NARR</oasis:entry>

         <oasis:entry colname="col9">Norfolk and</oasis:entry>

       </oasis:row>
       <oasis:row rowsep="1">

         <oasis:entry colname="col1">forcing</oasis:entry>

         <oasis:entry colname="col2"/>

         <oasis:entry colname="col3"/>

         <oasis:entry colname="col4"/>

         <oasis:entry colname="col5"/>

         <oasis:entry colname="col6"/>

         <oasis:entry colname="col7"/>

         <oasis:entry colname="col8"/>

         <oasis:entry colname="col9">Baltimore airports</oasis:entry>

       </oasis:row>
       <oasis:row>

         <oasis:entry colname="col1">Biogeochemical</oasis:entry>

         <oasis:entry colname="col2">High; 5 phytoplk.</oasis:entry>

         <oasis:entry colname="col3">High; 1 phytoplk.</oasis:entry>

         <oasis:entry colname="col4">High; 1 phytoplk.</oasis:entry>

         <oasis:entry colname="col5">High; 2 phytoplk.</oasis:entry>

         <oasis:entry colname="col6">High; 3 phytoplk.</oasis:entry>

         <oasis:entry colname="col7">Low; constant</oasis:entry>

         <oasis:entry colname="col8">Low; constant</oasis:entry>

         <oasis:entry colname="col9">Low; constant</oasis:entry>

       </oasis:row>
       <oasis:row rowsep="1">

         <oasis:entry colname="col1">complexity</oasis:entry>

         <oasis:entry colname="col2">groups</oasis:entry>

         <oasis:entry colname="col3">group</oasis:entry>

         <oasis:entry colname="col4">group</oasis:entry>

         <oasis:entry colname="col5">groups</oasis:entry>

         <oasis:entry colname="col6">groups</oasis:entry>

         <oasis:entry colname="col7">respiration</oasis:entry>

         <oasis:entry colname="col8">respiration</oasis:entry>

         <oasis:entry colname="col9">respiration</oasis:entry>

       </oasis:row>
       <oasis:row>

         <oasis:entry colname="col1">Model citation</oasis:entry>

         <oasis:entry colname="col2">Cerco et al. (2010)</oasis:entry>

         <oasis:entry colname="col3">Feng et al. (2015)</oasis:entry>

         <oasis:entry colname="col4">Brown et al. (2013)</oasis:entry>

         <oasis:entry colname="col5">Testa et al. (2014)</oasis:entry>

         <oasis:entry colname="col6">Jiang and Xia (2016)</oasis:entry>

         <oasis:entry colname="col7">Scully (2013)</oasis:entry>

         <oasis:entry colname="col8">Lanerolle et al. (2011)</oasis:entry>

         <oasis:entry colname="col9">Du and Shen (2015)</oasis:entry>

       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup><?xmltex \end{scaleboxenv}?></oasis:table></table-wrap>

      <p>These four hydrodynamic models are coupled to five different models used to
simulate DO (Table 1). Models A, B, C, D, and E utilize full biogeochemical
models that include various combinations of oxygen,
phytoplankton, zooplankton, and multiple inorganic and organic nutrients as state
variables.
Specifically, Models A and E employ a version of the Integrated Compartment
Model (ICM; Cerco et al., 2010; Jiang et al., 2015), Model B uses the
Estuarine Carbon Biogeochemistry model (ECB; Feng et al., 2015), Model C uses
the Biogeochemistry model (BGC; Brown et al., 2013), and Model D uses the
Row–Column AESOP model (RCA; Testa et al., 2014). In terms of food web
complexity the models vary considerably: Models B and C employ a single
phytoplankton group whereas Model D uses two phytoplankton groups, Model E
uses three, and Model A, the most complex of the participating models, uses
five.</p>
      <p>In contrast to the full biogeochemical models discussed above (Models A
through E), Models F, G, and H represent oxygen dynamics as simply as
possible and therefore do not utilize a full biogeochemical component.
Rather, the models impose a biological oxygen consumption rate that is
model-specific, but constant in both space and time. This component is
referred to as a constant-respiration model (CRM). In this model, DO is
introduced to the estuary via the river and ocean boundaries and is set to
saturation at the estuarine surface. This constant-respiration oxygen
parameterization (Scully, 2010) is simplistic, yet has been shown to
adequately represent Chesapeake Bay oxygen dynamics (Scully, 2010, 2013;
Bever et al., 2013).</p>
      <p>The major difference in forcing between the eight model implementations is
that Models A and B use riverine input derived from watershed models, whereas
Models C–H used the measured flow from United States Geological Survey
gauging stations, extrapolated using various techniques. Model A utilized the
CBP's regulatory watershed model (Shenk and Linker, 2013), while Model B
utilized the Dynamic Land Ecosystem Model (Yang et al., 2015a,
b; Tian et al., 2015). At the open boundary with the Atlantic
Ocean, Models B, C, D, F, G, and H utilize a sub-tidal elevation extrapolated
from tidal stations on either side of the open boundary. Model E uses the
TPXO tidal model, while Model A uses a mix of observational and model forcing
(Cerco et al., 2010). While Model B utilizes wind forcing based on
observations from the Thomas Point Light, Models C through H use wind
estimates from the North American Regional Reanalysis (NARR).</p>
      <p>The eight models used in this analysis have been developed for a variety of
purposes. Model A is a governmental regulatory model developed by the CBP
that has been extensively calibrated specifically to examine water quality
issues in the Chesapeake Bay (Cerco and Cole, 1993; Cerco and Noel, 2004,
2013; Cerco et al., 2010) and has been used in the development of the 2010
Chesapeake Bay Total Maximum Daily Load (USEPA, 2010). The National Oceanic
and Atmospheric Administration employs the hydrodynamic component of Model F
for operational forecasts of a variety of physical estuarine parameters for
the Chesapeake Bay
(<uri>http://www.tidesandcurrents.noaa.gov/ofs/cbofs/cbofs.html</uri>). The other
six models are academic models used in diverse research efforts focused on
the Chesapeake Bay but not necessarily specifically on DO dynamics.</p>
      <p>Finally, a ninth model is calculated as the mean of the results from the
eight models described above, and is referred to here as Model Mean, or
Model M.</p>
</sec>
<sec id="Ch1.S2.SS2">
  <title>Available Chesapeake Bay observations</title>
      <p>Model simulations were compared to cruise data from the CBP for 2004 and 2005
from 13 stations along the main stem of the bay (Table 2, Fig. 2). The years
2004 and 2005 were selected to represent relatively wet and average years,
respectively, and the 13 stations were chosen as they have been found to
offer optimal estimates of bay-wide hypoxic volume (Bever et al., 2013).
Stations were sampled on up to 34 cruises over the 2 years (Table 2),
generally twice a month from April to August and once a month for the
remainder of the year. Observational data can be downloaded from the CBP
Water Quality Database (<uri>http://www.chesapeakebay.net/data/downloads/cbp
water quality database 1984 present</uri>). Variables downloaded from the CBP website and used in this study
were temperature, salinity, DO, nitrate <inline-formula><mml:math display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> nitrite (hereafter abbreviated as
“nitrate”), and chlorophyll <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> (hereafter abbreviated as “chlorophyll”).
For most cruises, observations of temperature, salinity, and DO were made at
roughly 1 m intervals throughout the water column, whereas observations of
chlorophyll and nitrate were generally made only at the surface, bottom, and
sometimes one or two mid-water column locations. For further information on
available water quality observations, please see USEPA (2012). While these
observations were publicly available for model assessment during calibration
of all of the models, they represent a very small subset of the 30 years of
EPA observations across over 100 bay stations. The models compared here were
calibrated based on access to the larger data set and for conditions in the
bay in general, not specifically for the 13 stations and 2 years considered
here.</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T2"><caption><p>Characteristics of observation stations (from USEPA,
2012).</p></caption><oasis:table frame="topbot"><?xmltex \begin{scaleboxenv}{.93}[.93]?><oasis:tgroup cols="5">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="center"/>
     <oasis:colspec colnum="3" colname="col3" align="center"/>
     <oasis:colspec colnum="4" colname="col4" align="center"/>
     <oasis:colspec colnum="5" colname="col5" align="center"/>
     <oasis:thead>
       <oasis:row>  
         <oasis:entry colname="col1">Station</oasis:entry>  
         <oasis:entry colname="col2">Latitude</oasis:entry>  
         <oasis:entry colname="col3">Longitude</oasis:entry>  
         <oasis:entry colname="col4">Station depth</oasis:entry>  
         <oasis:entry colname="col5">No. of cruises</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">(<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N)</oasis:entry>  
         <oasis:entry colname="col3">(<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> W)</oasis:entry>  
         <oasis:entry colname="col4">(<inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula>)</oasis:entry>  
         <oasis:entry colname="col5"/>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">CB3.2</oasis:entry>  
         <oasis:entry colname="col2">39.1634</oasis:entry>  
         <oasis:entry colname="col3">76.3063</oasis:entry>  
         <oasis:entry colname="col4">12.1</oasis:entry>  
         <oasis:entry colname="col5">34</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">CB3.3C</oasis:entry>  
         <oasis:entry colname="col2">38.9951</oasis:entry>  
         <oasis:entry colname="col3">76.3597</oasis:entry>  
         <oasis:entry colname="col4">24.3</oasis:entry>  
         <oasis:entry colname="col5">34</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">CB4.1C</oasis:entry>  
         <oasis:entry colname="col2">38.8251</oasis:entry>  
         <oasis:entry colname="col3">76.3997</oasis:entry>  
         <oasis:entry colname="col4">32.3</oasis:entry>  
         <oasis:entry colname="col5">34</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">CB4.2C</oasis:entry>  
         <oasis:entry colname="col2">38.6448</oasis:entry>  
         <oasis:entry colname="col3">76.4177</oasis:entry>  
         <oasis:entry colname="col4">27.2</oasis:entry>  
         <oasis:entry colname="col5">34</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">CB4.3C</oasis:entry>  
         <oasis:entry colname="col2">38.5565</oasis:entry>  
         <oasis:entry colname="col3">76.4347</oasis:entry>  
         <oasis:entry colname="col4">26.9</oasis:entry>  
         <oasis:entry colname="col5">34</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">CB4.4</oasis:entry>  
         <oasis:entry colname="col2">38.4132</oasis:entry>  
         <oasis:entry colname="col3">76.3430</oasis:entry>  
         <oasis:entry colname="col4">30.3</oasis:entry>  
         <oasis:entry colname="col5">34</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">CB5.1</oasis:entry>  
         <oasis:entry colname="col2">38.3185</oasis:entry>  
         <oasis:entry colname="col3">76.2930</oasis:entry>  
         <oasis:entry colname="col4">34.1</oasis:entry>  
         <oasis:entry colname="col5">34</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">CB5.2</oasis:entry>  
         <oasis:entry colname="col2">38.13678</oasis:entry>  
         <oasis:entry colname="col3">76.2280</oasis:entry>  
         <oasis:entry colname="col4">30.6</oasis:entry>  
         <oasis:entry colname="col5">34</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">CB5.4</oasis:entry>  
         <oasis:entry colname="col2">37.8001</oasis:entry>  
         <oasis:entry colname="col3">76.1747</oasis:entry>  
         <oasis:entry colname="col4">31.1</oasis:entry>  
         <oasis:entry colname="col5">26</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">CB6.2</oasis:entry>  
         <oasis:entry colname="col2">37.4868</oasis:entry>  
         <oasis:entry colname="col3">76.1563</oasis:entry>  
         <oasis:entry colname="col4">10.5</oasis:entry>  
         <oasis:entry colname="col5">30</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">CB6.4</oasis:entry>  
         <oasis:entry colname="col2">37.2365</oasis:entry>  
         <oasis:entry colname="col3">76.2080</oasis:entry>  
         <oasis:entry colname="col4">10.2</oasis:entry>  
         <oasis:entry colname="col5">29</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">CB7.1</oasis:entry>  
         <oasis:entry colname="col2">37.6835</oasis:entry>  
         <oasis:entry colname="col3">75.9897</oasis:entry>  
         <oasis:entry colname="col4">20.9</oasis:entry>  
         <oasis:entry colname="col5">27</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">LE2.3</oasis:entry>  
         <oasis:entry colname="col2">38.0215</oasis:entry>  
         <oasis:entry colname="col3">76.3477</oasis:entry>  
         <oasis:entry colname="col4">20.1</oasis:entry>  
         <oasis:entry colname="col5">34</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup><?xmltex \end{scaleboxenv}?></oasis:table></table-wrap>

      <?xmltex \floatpos{t}?><fig id="Ch1.F2"><caption><p>Location of the CBP water quality monitoring stations used in this
study.</p></caption>
          <?xmltex \igopts{width=213.395669pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/2011/2016/bg-13-2011-2016-f02.png"/>

        </fig>

</sec>
<sec id="Ch1.S2.SS3">
  <title>Calculation of stratification and mixed layer depth</title>
      <p>Stratification of the density and oxygen fields was examined to identify the
maximum gradient of the pycnocline and oxycline as well as the depth of the
top of the pycnocline and oxycline. In open ocean studies, the depth of the
top of stratification is commonly referred to as the mixed layer depth (MLD),
although this term is less frequently used in the estuarine literature. As
the research presented here distinguishes between the depths of the top of
the pycnocline and that of the oxycline, these will be referred to
respectively as the density (<inline-formula><mml:math display="inline"><mml:mi mathvariant="italic">ρ</mml:mi></mml:math></inline-formula>) mixed layer depth (MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="italic">ρ</mml:mi></mml:msub></mml:math></inline-formula>) and the
oxygen mixed layer depth (MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula>). Density was calculated via a
classical density formula that is also utilized by the CBP for use in the
Chesapeake Bay (Fofonoff and Millard, 1983; USEPA, 2004) and is a function of
temperature and salinity.</p>
      <p>The CBP defines the top and bottom of stratification in order to distinguish
individual designated use areas for water quality management purposes (USEPA,
2004). They suggest that the top of the pycnocline be defined as the
shallowest occurrence of a density gradient of 0.1 <inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">kg</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">m</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">4</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> or
greater as resolved by CBP profile observations, which are typically spaced
at 0.5–2 m depth intervals. If density gradients throughout the water
column are less than 0.1 <inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">kg</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">m</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">4</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>, they define the water to be
unstratified. The 0.1 <inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">kg</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">m</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">4</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> threshold definition is designed to
identify any initiation of stratification that may serve to cut off vertical
mixing from a nearly perfectly well-mixed layer.</p>
      <p>While the CBP definition described above delineates between designated use
boundaries according to density, our research focuses on the relationship
between the pycnocline and oxycline, requiring an alternate definition that
can be applied to both the density and oxygen distributions. In addition, the
CBP definition often generates estimates for the depth of the top of the
pycnocline that are too shallow compared to the maximum depth of surface
mixing (Fig. 3). As a result, a percentage threshold criterion was developed
that identifies the bottom of the reasonably well-mixed layer, rather than
perfectly mixed layer, and is used in this analysis. The percentage threshold
method defines a density or DO profile as being stratified if a change of
10 % of the difference between the profile's maximum and minimum values
occurs within a single meter (Fig. 3). For example, if the maximum DO
concentration throughout the water column on an individual sampling date is
10 <inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">mg</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">L</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> and the minimum concentration is 1 <inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">mg</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">L</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>,
stratification is defined to be present if a difference of
0.9 <inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">mg</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">L</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> is present within 1 m. As recommended by the
CBP, the uppermost meter of the water column is not considered (USEPA, 2004).
The mixed layer depth is therefore defined as the shallowest level (below
1 m depth) where stratification is identified. The minimum stratification
criterion utilized in this analysis requiring a profile to pass the 10 %
threshold also ensures that observations where very little stratification
exists do not bias the stratification results while also allowing for a
single criterion to be used across multiple stratification variables.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F3" specific-use="star"><caption><p>Density and dissolved oxygen profiles for a mid-bay station (CB4.1C)
on <bold>(a)</bold> 13 January 2004 and <bold>(b)</bold> 14 June 2005, comparing the
0.1 <inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">kg</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">m</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">4</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> stratification definition used by the CBP
(MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mtext>CBP</mml:mtext></mml:msub></mml:math></inline-formula>) with the 10 % threshold definitions used here for
density (MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="italic">ρ</mml:mi></mml:msub></mml:math></inline-formula>) and oxygen (MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula>).</p></caption>
          <?xmltex \igopts{width=284.527559pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/2011/2016/bg-13-2011-2016-f03.png"/>

        </fig>

</sec>
<sec id="Ch1.S2.SS4">
  <title>Model skill metrics</title>
      <p>Simulations of the Chesapeake Bay from the eight models described above were
statistically compared to historical monitoring data using a variety of skill
metrics including root-mean squared difference (RMSD), bias, standard
deviation, and correlation coefficient. These metrics are illustrated on
Taylor and target diagrams (Taylor, 2001; Hofmann et al., 2008; Jolliff et
al., 2009), which offer a compact way of assessing model skill by displaying
a number of different skill metrics. Target diagrams illustrate the bias and
total RMSD of model output, which Taylor diagrams do not. Taylor diagrams
include quantitative information on the standard deviations and correlations
between the model output and the observations, which target diagrams do not.
Both diagrams, however, represent unbiased RMSD, sometimes called
“centered-pattern RMSD”. On target diagrams, a model symbol above the
horizontal axis overestimates the mean of the observations and a model symbol
to the right of the vertical axis overestimates the variability of the
observations. (See Hofmann et al. (2008) and Jolliff et al. (2009) for a more
detailed description of these diagrams.) On Taylor diagrams, a model symbol
lying on the horizontal axis exactly correlates to the observations and a
model symbol further from the origin than the observation symbol
overestimates the standard deviation of the observations. (See Taylor (2001) for a more detailed
description of these diagrams.)</p>
      <p>Taylor and target diagrams presented here are normalized to the standard
deviation of the observations, allowing multiple variables be represented on
the same plot. This also conveniently allows the unit circle on a target
diagram to represent the skill of a model defined as the mean of the
observations. In effect, this means that if a model falls within the unit
circle, it exhibits a skill that is greater than the skill obtained if one
were to simply use the mean of the observations. The Taylor and target plots
are either temporal (displaying model skill at a single station over the
study period) or spatial (displaying model skill during a single month over
the entire set of study stations). In addition, summary diagrams are
presented which combine both temporal (examining the seasonal changes at each
individual station) and spatial (examining differences across the bay during
an individual month) variability.</p>
      <p>Model skill was assessed using the hourly model output (daily for CH3D-ICM
chlorophyll and nitrate) that was nearest in time to that of the observation
and from the grid cell that encompassed the observation location. For months
with two observations, each observation was individually matched to the model
output and the skill statistics from those comparisons were averaged for that
month. The native horizontal resolution and bathymetry of the individual
model grids was preserved in the comparison so as not to bias the analysis
through varying interpolation methodologies. For stratification variables,
the models and observations were interpolated to a 1 m vertical grid that
extended only as deep as the individual models' bathymetry or deepest
observation in order to preserve the differences in bathymetric grids while
allowing for a direct comparison of the observations to the models.
Model–data comparisons at the bottom of the water column were not necessarily
based on the same depths, since in many cases the modeled bathymetry was
shallower (or at times, deeper) than the deepest data point at a given
station. In order to avoid issues with extrapolation and/or grid stretching,
data at the bottom of the water column were always compared with model
estimates from the deepest grid cell provided by each particular model.
Model–data comparisons for stratification and mixed layer depths only
included stations and times for which stratification was defined to exist in
both the observed and simulated fields.</p>
</sec>
</sec>
<sec id="Ch1.S3">
  <title>Results</title>
      <p>An analysis of model skill of the combined temporal and spatial variability
of DO at the surface and bottom of the water column, as well as at the
observed MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula>, indicates that all models, regardless of
biogeochemical complexity or spatial resolution, exhibit a high degree of
skill in reproducing observed DO (Fig. 4). Specifically, all models produce
DO concentrations at the surface and bottom that have a normalized total RMSD
less than 1. The same is true for nearly all models for DO at the observed
MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula>. However, most models underestimate observed DO both at the
surface and at the MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula> (Fig. 4a). The correlation between the
observed and modeled DO is relatively constant with depth (Fig. 4b), though
on average slightly higher at the bottom (0.85) than at the surface (0.80).
Further, on average, the models simulate DO at the surface and bottom better
than they do at the MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula>. No statistical difference exists
between the skill of models that utilize a full biogeochemical component and
those that utilize the simple constant-respiration oxygen parameterization.
Based on an analysis of variance (ANOVA) comparing the full biogeochemical
models to the CRM models, the two model types do not perform differently in
terms of their ability to reproduce the combined temporal and spatial
variability of bottom DO as measured by total RMSD (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi>p</mml:mi><mml:mo>=</mml:mo><mml:mn>0.48</mml:mn></mml:mrow></mml:math></inline-formula>). Overall,
Model M (the mean of the eight models) consistently performs better than any
individual model across all depths examined (Fig. 4).</p>
      <p>The monthly temporal variability of bottom DO at each station over the 2
years studied is resolved similarly well by all of the models (Fig. 5a), but
the models have difficulty simulating spatial DO variability during each
month (Fig. 5b). Due to the stations chosen for this analysis (Fig. 2), the
spatial variability being examined here is essentially the north to south
variability. Most models exhibit a latitudinal gradient with respect to their
skill in reproducing the temporal variability of bottom DO, with models
overestimating DO at the more northern stations (Fig. 5a). Some models differ
in their ability to reproduce summer (May–September) DO concentrations and
winter (October–April) DO concentrations (Fig. 5b). Models B, F, and G all
distinctively overestimate mean DO in the summer compared to the winter. In
contrast, Models A and C perform similarly well in both seasons (Fig. 5b). In
addition, all three constant respiration models, as well as Models D and E,
substantially underestimate DO at several stations in the winter.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F4"><caption><p>Normalized summary <bold>(a)</bold> target and <bold>(b)</bold> Taylor
diagrams illustrating model skill of dissolved oxygen at the surface,
MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula>, and bottom for 13 Chesapeake Bay stations in 2004–2005.
The “x” represents the skill of a model that perfectly reproduces the
observations. The dotted, dashed-dot, and dashed lines on the Taylor diagram
represent lines of constant standard deviation, correlation coefficient, and
unbiased RMSD, respectively.</p></caption>
        <?xmltex \igopts{width=213.395669pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/2011/2016/bg-13-2011-2016-f04.png"/>

      </fig>

      <p>All eight models generally resolve the pycnocline and oxycline with similar
skill (Fig. 6). All models consistently underestimate the mean and standard
deviation of the maximum strength of stratification within the pycnocline and
oxycline, defined herein as the maximum vertical gradients of density and
oxygen (Fig. 6a). All models, except for Model A (see Sect. 4.2), also
underestimate the mixed layer depth, regardless of whether it is computed in
terms of density or oxygen. (Note that these model symbols in Fig. 6a are
located above the <inline-formula><mml:math display="inline"><mml:mi>y</mml:mi></mml:math></inline-formula> axis despite this negative bias in MLD because the
vertical coordinate system is oriented upwards.) Thus, the models are
producing stratification that is both weaker than observed and higher
(shallower) in the water column. The correlation coefficient for these
metrics is low, ranging 0.1–0.6, and indicates that all models are missing
the majority of variability associated with the magnitude and location of the
pycnocline and oxycline (Fig. 6b). However, there is slightly more
consistency and better correlation coefficients among the models for the
strength of stratification than the depth of the mixed layers.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F5" specific-use="star"><caption><p>Normalized target diagrams for Models A–H demonstrating the
<bold>(a)</bold> temporal and <bold>(b)</bold> spatial skill in resolving the
variability of bottom dissolved oxygen concentrations. In <bold>(a)</bold> the
individual dots represent the 13 stations along the main stem of the
Chesapeake Bay. In <bold>(b)</bold> the dots represent the 24 months of
2004–2005 and are delineated by color: red is summer (May–September) and
blue is winter (October–April).</p></caption>
        <?xmltex \igopts{width=412.564961pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/2011/2016/bg-13-2011-2016-f05.png"/>

      </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F6"><caption><p>Normalized summary <bold>(a)</bold> target and <bold>(b)</bold> Taylor
diagram illustrating model skill of MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="italic">ρ</mml:mi></mml:msub></mml:math></inline-formula> and MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula>, max
<inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">d</mml:mi><mml:mi mathvariant="italic">ρ</mml:mi><mml:mo>/</mml:mo><mml:mi mathvariant="normal">d</mml:mi><mml:mi>z</mml:mi></mml:mrow></mml:math></inline-formula>, and max <inline-formula><mml:math display="inline"><mml:mrow><mml:mtext>dO</mml:mtext><mml:mo>/</mml:mo><mml:mi mathvariant="normal">d</mml:mi><mml:mi>z</mml:mi></mml:mrow></mml:math></inline-formula> at 13
Chesapeake Bay stations for 2004–2005. The “x” represents the skill of a
model that perfectly reproduces the observations. Since RMSD of
stratification is only computed at stations where both the observations and
model exhibit stratification, the Model Mean is not calculable for these
variables.</p></caption>
        <?xmltex \igopts{width=213.395669pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/2011/2016/bg-13-2011-2016-f06.png"/>

      </fig>

      <p>All eight models are also characterized by similar skill in representing the
temporal and spatial variability of density stratification and MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="italic">ρ</mml:mi></mml:msub></mml:math></inline-formula>
(Fig. 7). There is a latitudinal difference in skill of the models in
reproducing the magnitude of the pycnocline and MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="italic">ρ</mml:mi></mml:msub></mml:math></inline-formula>, with model
skill generally lower at the northern stations (Fig. 7a). Contrary to the
pattern shown for bottom DO (Fig. 5b), none of the models exhibit a
significant seasonal pattern between summer and winter in reproducing spatial
variability of <inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">d</mml:mi><mml:mi mathvariant="italic">ρ</mml:mi><mml:mo>/</mml:mo><mml:mi mathvariant="normal">d</mml:mi><mml:mi>z</mml:mi></mml:mrow></mml:math></inline-formula> or MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="italic">ρ</mml:mi></mml:msub></mml:math></inline-formula> (Fig. 7b).
However, Model A differentiates itself from the rest of the models in its
pattern of skill at reproducing the spatial and temporal variability of the
MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="italic">ρ</mml:mi></mml:msub></mml:math></inline-formula> (see Sect. 4.2). Temporal and spatial patterns for oxycline
stratification (<inline-formula><mml:math display="inline"><mml:mrow><mml:mtext>dO</mml:mtext><mml:mo>/</mml:mo><mml:mi mathvariant="normal">d</mml:mi><mml:mi>z</mml:mi></mml:mrow></mml:math></inline-formula>) and MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula> closely match
those of <inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">d</mml:mi><mml:mi mathvariant="italic">ρ</mml:mi><mml:mo>/</mml:mo><mml:mi mathvariant="normal">d</mml:mi><mml:mi>z</mml:mi></mml:mrow></mml:math></inline-formula> and MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="italic">ρ</mml:mi></mml:msub></mml:math></inline-formula> (not shown).</p>
      <p>All eight models reproduce the variability of bottom DO better than the
variables that are generally thought of as being the primary drivers of
hypoxic conditions, including stratification (Fig. 6), salinity, chlorophyll,
and nitrate (Fig. 8, Table 3). However, all models reproduce patterns in
temperature across the bay and through time better than any of the other
variables in this model comparison (Fig. 8). All eight models, as well as the
Model Mean, are characterized by very low bias in modeled temperature, and
correlation coefficients of approximately 0.99; this high skill results from
the very strong and predictable seasonal temperature variability. Even though
the five models with full biogeochemical components (Models A, B, C, D, E)
are characterized by large differences in their mechanistic approaches to
modeling nitrate and chlorophyll, they produce similar total RMSDs for all of
the variables examined at both the surface and the bottom (Table 3).</p>
      <p>The mean of the eight models (Model M) has a higher model skill (lower RMSD)
than any individual model across nearly every variable examined (Table 3). In
addition, for nearly all observations at all stations, the 95 %
confidence interval of all model hindcasts encapsulates the observed bottom
DO concentration (Fig. 9), even though any individual model may overestimate
or underestimate observed DO. Models generally fall into greater agreement
during the summer, when DO is low, and into lesser agreement in the winter
when DO is replete. While this study does not allow for a true interannual
comparison, it is interesting that at station CB4.1C the model
ensemble closely matches the timing of the drawdown of DO in the spring of
2004 (Fig. 9), whereas it produces a summer rather than spring initiation of hypoxic
conditions in 2005. In addition, the model ensemble produces a premature
relaxing of hypoxic conditions for both years at this observation station.</p>
      <p>In order to better understand the impact of stratification on DO
concentrations throughout the water column, the relationship between the
observed pycnocline strength and MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="italic">ρ</mml:mi></mml:msub></mml:math></inline-formula> were compared to the observed
oxycline strength and MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula>. Observations from 1998 to 2006
demonstrate that while there is not a strong correlation between the
strengths of the pycnocline and oxycline, there is a very strong correlation
between MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="italic">ρ</mml:mi></mml:msub></mml:math></inline-formula> and MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula> (Fig. 10). Depending on the
criteria used for defining the existence of stratification (see Sect. 2.3),
the correlation of the pycnocline and oxycline strengths range <inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi>r</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup><mml:mo>=</mml:mo><mml:mn>0.18</mml:mn></mml:mrow></mml:math></inline-formula>–0.26 and the correlations of MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="italic">ρ</mml:mi></mml:msub></mml:math></inline-formula> and MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula> range
<inline-formula><mml:math display="inline"><mml:mrow><mml:msup><mml:mi>r</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup><mml:mo>=</mml:mo><mml:mn>0.51</mml:mn></mml:mrow></mml:math></inline-formula>–0.82 (Table 4). Furthermore, correlation of the relationship
between the MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="italic">ρ</mml:mi></mml:msub></mml:math></inline-formula> and MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula> is stronger for more severe
stratification (Table 4). The relationship between the two mixed layer depths
is biased towards the MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula> being located slightly deeper in the
water column than the MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="italic">ρ</mml:mi></mml:msub></mml:math></inline-formula>. As the cut-off criteria for the existence
of stratification becomes more stringent, the relationship becomes closer to
<inline-formula><mml:math display="inline"><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>:</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:math></inline-formula>.</p>

      <?xmltex \floatpos{p}?><fig id="Ch1.F7" specific-use="star"><caption><p>Normalized target diagrams for Models A–H demonstrating the
<bold>(a)</bold> temporal and <bold>(b)</bold> spatial skill in resolving the
variability of the strength of density stratification (circles) and the depth
of pycnocline initiation (diamonds). In <bold>(a)</bold> the individual dots
represent the 13 stations along the main stem of the Chesapeake Bay. In
<bold>(b)</bold> the dots represent the 24 months of 2004–2005 and are
delineated by color: red is summer (May–September) and blue is winter
(October–April).</p></caption>
        <?xmltex \igopts{width=412.564961pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/2011/2016/bg-13-2011-2016-f07.png"/>

      </fig>

<?xmltex \floatpos{p}?><table-wrap id="Ch1.T3" specific-use="star"><caption><p>Mean and standard deviation (SD) of observations and total
normalized RMSD for each model. RMSD for each model except when not applicable (N/A).</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="11">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="right"/>
     <oasis:colspec colnum="3" colname="col3" align="center"/>
     <oasis:colspec colnum="4" colname="col4" align="center"/>
     <oasis:colspec colnum="5" colname="col5" align="center"/>
     <oasis:colspec colnum="6" colname="col6" align="center"/>
     <oasis:colspec colnum="7" colname="col7" align="center"/>
     <oasis:colspec colnum="8" colname="col8" align="center"/>
     <oasis:colspec colnum="9" colname="col9" align="center"/>
     <oasis:colspec colnum="10" colname="col10" align="center"/>
     <oasis:colspec colnum="11" colname="col11" align="center"/>
     <oasis:thead>
       <oasis:row>  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">Mean <inline-formula><mml:math display="inline"><mml:mo>±</mml:mo></mml:math></inline-formula> SD of Obs.</oasis:entry>  
         <oasis:entry rowsep="1" namest="col3" nameend="col11">Normalized RMSD </oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2"/>  
         <oasis:entry colname="col3">A</oasis:entry>  
         <oasis:entry colname="col4">B</oasis:entry>  
         <oasis:entry colname="col5">C</oasis:entry>  
         <oasis:entry colname="col6">D</oasis:entry>  
         <oasis:entry colname="col7">E</oasis:entry>  
         <oasis:entry colname="col8">F</oasis:entry>  
         <oasis:entry colname="col9">G</oasis:entry>  
         <oasis:entry colname="col10">H</oasis:entry>  
         <oasis:entry colname="col11">M</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">Surface temp. (<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C)</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mrow><mml:mn>17.44</mml:mn><mml:mo>±</mml:mo><mml:mn>8.82</mml:mn></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">0.13</oasis:entry>  
         <oasis:entry colname="col4">0.13</oasis:entry>  
         <oasis:entry colname="col5">0.12</oasis:entry>  
         <oasis:entry colname="col6">0.09</oasis:entry>  
         <oasis:entry colname="col7">0.13</oasis:entry>  
         <oasis:entry colname="col8">0.13</oasis:entry>  
         <oasis:entry colname="col9">0.16</oasis:entry>  
         <oasis:entry colname="col10">0.19</oasis:entry>  
         <oasis:entry colname="col11">0.10</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Bottom temp. (<inline-formula><mml:math display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C)</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mrow><mml:mn>15.75</mml:mn><mml:mo>±</mml:mo><mml:mn>8.02</mml:mn></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">0.24</oasis:entry>  
         <oasis:entry colname="col4">0.35</oasis:entry>  
         <oasis:entry colname="col5">0.35</oasis:entry>  
         <oasis:entry colname="col6">0.23</oasis:entry>  
         <oasis:entry colname="col7">0.22</oasis:entry>  
         <oasis:entry colname="col8">0.35</oasis:entry>  
         <oasis:entry colname="col9">0.17</oasis:entry>  
         <oasis:entry colname="col10">0.19</oasis:entry>  
         <oasis:entry colname="col11">0.23</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Surface salinity (PSU)</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mrow><mml:mn>10.92</mml:mn><mml:mo>±</mml:mo><mml:mn>4.32</mml:mn></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">0.37</oasis:entry>  
         <oasis:entry colname="col4">0.62</oasis:entry>  
         <oasis:entry colname="col5">0.53</oasis:entry>  
         <oasis:entry colname="col6">0.36</oasis:entry>  
         <oasis:entry colname="col7">0.46</oasis:entry>  
         <oasis:entry colname="col8">0.61</oasis:entry>  
         <oasis:entry colname="col9">0.57</oasis:entry>  
         <oasis:entry colname="col10">0.41</oasis:entry>  
         <oasis:entry colname="col11">0.35</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Bottom salinity (PSU)</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mrow><mml:mn>18.17</mml:mn><mml:mo>±</mml:mo><mml:mn>3.14</mml:mn></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">0.72</oasis:entry>  
         <oasis:entry colname="col4">0.85</oasis:entry>  
         <oasis:entry colname="col5">0.73</oasis:entry>  
         <oasis:entry colname="col6">1.55</oasis:entry>  
         <oasis:entry colname="col7">1.28</oasis:entry>  
         <oasis:entry colname="col8">0.78</oasis:entry>  
         <oasis:entry colname="col9">1.03</oasis:entry>  
         <oasis:entry colname="col10">0.97</oasis:entry>  
         <oasis:entry colname="col11">0.75</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Max. <inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">d</mml:mi><mml:mi mathvariant="italic">ρ</mml:mi><mml:mo>/</mml:mo><mml:mi mathvariant="normal">d</mml:mi><mml:mi>z</mml:mi></mml:mrow></mml:math></inline-formula> (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">kg</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">m</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">4</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>)</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mrow><mml:mn>1.64</mml:mn><mml:mo>±</mml:mo><mml:mn>1.15</mml:mn></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">1.03</oasis:entry>  
         <oasis:entry colname="col4">1.09</oasis:entry>  
         <oasis:entry colname="col5">1.07</oasis:entry>  
         <oasis:entry colname="col6">1.09</oasis:entry>  
         <oasis:entry colname="col7">1.25</oasis:entry>  
         <oasis:entry colname="col8">1.01</oasis:entry>  
         <oasis:entry colname="col9">1.23</oasis:entry>  
         <oasis:entry colname="col10">1.02</oasis:entry>  
         <oasis:entry colname="col11">N/A</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">MLD<inline-formula><mml:math display="inline"><mml:mi mathvariant="italic">ρ</mml:mi></mml:math></inline-formula> (m)</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mrow><mml:mn>5.32</mml:mn><mml:mo>±</mml:mo><mml:mn>3.99</mml:mn></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">1.01</oasis:entry>  
         <oasis:entry colname="col4">1.13</oasis:entry>  
         <oasis:entry colname="col5">1.11</oasis:entry>  
         <oasis:entry colname="col6">1.41</oasis:entry>  
         <oasis:entry colname="col7">1.39</oasis:entry>  
         <oasis:entry colname="col8">1.12</oasis:entry>  
         <oasis:entry colname="col9">1.38</oasis:entry>  
         <oasis:entry colname="col10">1.13</oasis:entry>  
         <oasis:entry colname="col11">N/A</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Surface DO (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">mg</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">L</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>)</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mrow><mml:mn>9.74</mml:mn><mml:mo>±</mml:mo><mml:mn>2.15</mml:mn></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">0.67</oasis:entry>  
         <oasis:entry colname="col4">0.58</oasis:entry>  
         <oasis:entry colname="col5">0.89</oasis:entry>  
         <oasis:entry colname="col6">0.80</oasis:entry>  
         <oasis:entry colname="col7">1.00</oasis:entry>  
         <oasis:entry colname="col8">0.63</oasis:entry>  
         <oasis:entry colname="col9">0.64</oasis:entry>  
         <oasis:entry colname="col10">0.69</oasis:entry>  
         <oasis:entry colname="col11">0.57</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">DO at MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula> (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">mg</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">L</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>)</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mrow><mml:mn>8.44</mml:mn><mml:mo>±</mml:mo><mml:mn>2.53</mml:mn></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">0.54</oasis:entry>  
         <oasis:entry colname="col4">0.57</oasis:entry>  
         <oasis:entry colname="col5">0.74</oasis:entry>  
         <oasis:entry colname="col6">0.93</oasis:entry>  
         <oasis:entry colname="col7">0.83</oasis:entry>  
         <oasis:entry colname="col8">0.81</oasis:entry>  
         <oasis:entry colname="col9">0.95</oasis:entry>  
         <oasis:entry colname="col10">1.09</oasis:entry>  
         <oasis:entry colname="col11">0.62</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Bottom DO (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">mg</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">L</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>)</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mrow><mml:mn>4.42</mml:mn><mml:mo>±</mml:mo><mml:mn>3.61</mml:mn></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">0.51</oasis:entry>  
         <oasis:entry colname="col4">0.59</oasis:entry>  
         <oasis:entry colname="col5">0.81</oasis:entry>  
         <oasis:entry colname="col6">0.61</oasis:entry>  
         <oasis:entry colname="col7">0.54</oasis:entry>  
         <oasis:entry colname="col8">0.46</oasis:entry>  
         <oasis:entry colname="col9">0.61</oasis:entry>  
         <oasis:entry colname="col10">0.60</oasis:entry>  
         <oasis:entry colname="col11">0.46</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Max. <inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">d</mml:mi><mml:mrow class="chem"><mml:mi mathvariant="normal">DO</mml:mi></mml:mrow><mml:mo>/</mml:mo><mml:mi mathvariant="normal">d</mml:mi><mml:mi>z</mml:mi></mml:mrow></mml:math></inline-formula> (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">mg</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">L</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">m</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>)</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mrow><mml:mn>1.81</mml:mn><mml:mo>±</mml:mo><mml:mn>1.12</mml:mn></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">1.19</oasis:entry>  
         <oasis:entry colname="col4">1.21</oasis:entry>  
         <oasis:entry colname="col5">1.34</oasis:entry>  
         <oasis:entry colname="col6">1.09</oasis:entry>  
         <oasis:entry colname="col7">1.35</oasis:entry>  
         <oasis:entry colname="col8">1.12</oasis:entry>  
         <oasis:entry colname="col9">1.23</oasis:entry>  
         <oasis:entry colname="col10">1.19</oasis:entry>  
         <oasis:entry colname="col11">N/A</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">MLDo (m)</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> <inline-formula><mml:math display="inline"><mml:mrow><mml:mn>6.62</mml:mn><mml:mo>±</mml:mo><mml:mn>4.01</mml:mn></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">1.24</oasis:entry>  
         <oasis:entry colname="col4">1.01</oasis:entry>  
         <oasis:entry colname="col5">1.10</oasis:entry>  
         <oasis:entry colname="col6">1.33</oasis:entry>  
         <oasis:entry colname="col7">1.33</oasis:entry>  
         <oasis:entry colname="col8">1.05</oasis:entry>  
         <oasis:entry colname="col9">1.30</oasis:entry>  
         <oasis:entry colname="col10">1.29</oasis:entry>  
         <oasis:entry colname="col11">N/A</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Surface Chl <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">mg</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">m</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>)</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mrow><mml:mn>11.19</mml:mn><mml:mo>±</mml:mo><mml:mn>9.04</mml:mn></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">0.92</oasis:entry>  
         <oasis:entry colname="col4">1.22</oasis:entry>  
         <oasis:entry colname="col5">1.60</oasis:entry>  
         <oasis:entry colname="col6">1.23</oasis:entry>  
         <oasis:entry colname="col7">0.89</oasis:entry>  
         <oasis:entry colname="col8">N/A</oasis:entry>  
         <oasis:entry colname="col9">N/A</oasis:entry>  
         <oasis:entry colname="col10">N/A</oasis:entry>  
         <oasis:entry colname="col11">1.16</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Bottom Chl <inline-formula><mml:math display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">mg</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">m</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>)</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mrow><mml:mn>9.02</mml:mn><mml:mo>±</mml:mo><mml:mn>11.52</mml:mn></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">0.87</oasis:entry>  
         <oasis:entry colname="col4">1.10</oasis:entry>  
         <oasis:entry colname="col5">1.07</oasis:entry>  
         <oasis:entry colname="col6">1.05</oasis:entry>  
         <oasis:entry colname="col7">1.01</oasis:entry>  
         <oasis:entry colname="col8">N/A</oasis:entry>  
         <oasis:entry colname="col9">N/A</oasis:entry>  
         <oasis:entry colname="col10">N/A</oasis:entry>  
         <oasis:entry colname="col11">0.90</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Surface nitrate (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">mmolN</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">m</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>)</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mrow><mml:mn>0.32</mml:mn><mml:mo>±</mml:mo><mml:mn>0.33</mml:mn></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">0.61</oasis:entry>  
         <oasis:entry colname="col4">0.79</oasis:entry>  
         <oasis:entry colname="col5">1.03</oasis:entry>  
         <oasis:entry colname="col6">0.61</oasis:entry>  
         <oasis:entry colname="col7">0.52</oasis:entry>  
         <oasis:entry colname="col8">N/A</oasis:entry>  
         <oasis:entry colname="col9">N/A</oasis:entry>  
         <oasis:entry colname="col10">N/A</oasis:entry>  
         <oasis:entry colname="col11">0.79</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Bottom nitrate (<inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">mmolN</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">m</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>)</oasis:entry>  
         <oasis:entry colname="col2"><inline-formula><mml:math display="inline"><mml:mrow><mml:mn>0.12</mml:mn><mml:mo>±</mml:mo><mml:mn>0.13</mml:mn></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">1.08</oasis:entry>  
         <oasis:entry colname="col4">1.38</oasis:entry>  
         <oasis:entry colname="col5">1.38</oasis:entry>  
         <oasis:entry colname="col6">0.92</oasis:entry>  
         <oasis:entry colname="col7">1.46</oasis:entry>  
         <oasis:entry colname="col8">N/A</oasis:entry>  
         <oasis:entry colname="col9">N/A</oasis:entry>  
         <oasis:entry colname="col10">N/A</oasis:entry>  
         <oasis:entry colname="col11">0.85</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T4"><caption><p>Pycnocline and oxycline correlation statistics (all correlations
have <inline-formula><mml:math display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula> values <inline-formula><mml:math display="inline"><mml:mo>≪</mml:mo></mml:math></inline-formula> 0.01).</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="4">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:colspec colnum="3" colname="col3" align="left"/>
     <oasis:colspec colnum="4" colname="col4" align="right"/>
     <oasis:thead>
       <oasis:row>  
         <oasis:entry colname="col1">Stratification</oasis:entry>  
         <oasis:entry colname="col2">Max. <inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">d</mml:mi><mml:mi mathvariant="italic">ρ</mml:mi><mml:mo>/</mml:mo><mml:mi mathvariant="normal">d</mml:mi><mml:mi>z</mml:mi></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">MLD<inline-formula><mml:math display="inline"><mml:mi mathvariant="italic">ρ</mml:mi></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4">Profiles</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">threshold</oasis:entry>  
         <oasis:entry colname="col2">vs.</oasis:entry>  
         <oasis:entry colname="col3">vs.</oasis:entry>  
         <oasis:entry colname="col4">with</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1">percentage ( %)</oasis:entry>  
         <oasis:entry colname="col2">max. <inline-formula><mml:math display="inline"><mml:mrow><mml:mtext>dO</mml:mtext><mml:mo>/</mml:mo><mml:mi mathvariant="normal">d</mml:mi><mml:mi>z</mml:mi></mml:mrow></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4">stratification</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">10</oasis:entry>  
         <oasis:entry colname="col2">0.18</oasis:entry>  
         <oasis:entry colname="col3">0.51</oasis:entry>  
         <oasis:entry colname="col4">1613</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">15</oasis:entry>  
         <oasis:entry colname="col2">0.22</oasis:entry>  
         <oasis:entry colname="col3">0.59</oasis:entry>  
         <oasis:entry colname="col4">1303</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">20</oasis:entry>  
         <oasis:entry colname="col2">0.22</oasis:entry>  
         <oasis:entry colname="col3">0.70</oasis:entry>  
         <oasis:entry colname="col4">916</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">25</oasis:entry>  
         <oasis:entry colname="col2">0.26</oasis:entry>  
         <oasis:entry colname="col3">0.82</oasis:entry>  
         <oasis:entry colname="col4">575</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

</sec>
<sec id="Ch1.S4">
  <title>Discussion</title>
<sec id="Ch1.S4.SS1">
  <title>How does the skill of various hydrodynamically based DO models
compare?</title>
      <p><disp-quote>
  <p>In examining the eight 3-D models in this study, there is not a
statistical difference between the ability of simple and complex models to
simulate the mean and monthly variability of bottom DO; in addition, models
with higher spatial resolution do not necessarily produce better estimates of
DO.</p>
</disp-quote></p>
      <p>Models currently simulating hypoxia throughout Chesapeake Bay compute oxygen
concentrations in essentially two distinct ways: they either utilize a simple
constant respiration model or a full biogeochemical model. In this study, the
relative skill of both types of models is compared. Specifically, in
examining results of the comparison between five biogeochemical models (A, B,
C, D, E) and three simplistic constant respiration models (F, G, H), the two
groups of models performed statistically similar in their skill of
reproducing bottom DO concentrations (Fig. 3, Table 3). These results support
those of Bever et al. (2013) who compared three constant respiration models
with the CBP regulatory model (Model A) and similarly found that all four of
the models were equally skillful in terms of reproducing the seasonal
variability in bottom DO throughout the bay in 2004 and 2005. Consistent with
the results of Scully (2013), this result implies that the seasonal
variability of DO in the Chesapeake Bay is primarily dependent on underlying
hydrodynamic mechanisms which are nearly identical for all eight models,
rather than on aspects related to the biogeochemical cycling which vary
dramatically between models and in fact are constant in three of the eight
models. It should be noted, however, that the 2 years studied here were
relatively wet years and an analysis of dry years may offer different
results.</p>
      <p>Many previous studies have examined the costs and benefits of adding
complexity to biogeochemical models. For example, increasing biogeochemical
complexity has been found to improve skill in some biogeochemical data
assimilative parameter optimization studies (Friedrichs et al., 2006, 2007;
Lehmann et al., 2009; Bagniewski et al., 2011; Ward et al., 2013; Xiao and
Friedrichs, 2014). The additional parameters associated with increased
complexity generally provide more parameters that are available for
additional tuning and subsequent improved model–data agreement. This is in
contrast to the results of this analysis demonstrating that increased
biogeochemical complexity does not necessarily improve model–data agreement.
In this case, the increase in model complexity has likely outpaced the
ability of the researchers to fully tune the model to the available
observations. However, even past studies that have invoked formal parameter
optimization methodologies, such as genetic algorithms and variational
adjoint methods (Friedrichs et al., 2007; Ward et al., 2010; Xiao and
Friedrichs, 2014), have found that under certain conditions, adding too much
complexity does not necessarily improve model skill and in fact can decrease
model skill and portability, primarily due to artifacts resulting from
overtuning. This mirrors findings from the larger ecosystem modeling
community where the best-fit models are often those with intermediate
complexity (Fulton et al., 2003).</p>
      <p>In this study, horizontal grid resolution differed significantly between
model implementations, with the most highly resolved grid (Model G) including
more than 9 times more grid cells than the lower resolution grids
(Table 1). A certain degree of resolution is clearly required to successfully
simulate dynamic processes, and a model with 8–10 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula> resolution will
not be able to correctly simulate the hydrodynamic processes within the bay
(Feng et al., 2015). However, an increase in horizontal grid resolution from
<inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 1.8 to <inline-formula><mml:math display="inline"><mml:mo>∼</mml:mo></mml:math></inline-formula> 0.6 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula>, which results in a run-time change of
a factor of 9, or possibly of 27 if the time step is accordingly decreased
by a factor of 3, does not necessarily result in a significant
improvement in simulation skill of either stratification or bottom oxygen.
Although not shown here, additional sensitivity experiments with Model G
revealed that doubling the vertical resolution of this model had no
significant effect on the model's ability to resolve the depth of
stratification or the maximum magnitude of stratification. Thus, when
selecting the optimal model resolution for a simulation, it is critical to
weigh the advantages of increased resolution with the increased time required
for simulation. With a given level of computational resources, fewer
sensitivity experiments can be conducted with a model using a more highly
resolved grid.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F8"><caption><p>Normalized summary <bold>(a)</bold> target and <bold>(b)</bold> Taylor
diagram illustrating model skill of bottom temperature, salinity,
chlorophyll, nitrate, and dissolved oxygen at 13 Chesapeake Bay stations for
2004–2005. The “x” represents the skill of a model that perfectly
reproduces the observations.</p></caption>
          <?xmltex \igopts{width=213.395669pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/2011/2016/bg-13-2011-2016-f08.png"/>

        </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F9"><caption><p>Time series of bottom dissolved concentrations for station CB4.1C.
Red dots represent the 34 observations made during 2004–2005. Grey lines are
the individual model simulations. The dark blue line represents the Model
Mean while the cyan line represents the 95 % confidence interval of the
model simulations.</p></caption>
          <?xmltex \igopts{width=236.157874pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/2011/2016/bg-13-2011-2016-f09.png"/>

        </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F10"><caption><p>Scatter plots comparing observations of <bold>(a)</bold> the strengths
of stratification of the pycnocline and oxycline and <bold>(b)</bold> the oxygen-
and density-defined mixed layer depths. Size of the circles is proportional
to the number of observations. Observations are from 1998 to 2006 at the
13 Chesapeake Bay stations shown in Fig. 2.</p></caption>
          <?xmltex \igopts{width=236.157874pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/2011/2016/bg-13-2011-2016-f10.png"/>

        </fig>

      <p>Accurately simulating the observed spatial variability of DO (Fig. 4b) was a
greater challenge than simulating the temporal variability of DO (Fig. 4a)
for all eight models participating in this intercomparison. This is
especially true in the winter months when the vast majority of the bay is
oxygen replete and the models have difficulty representing the observed
variability from station to station. The majority of the models tend to
slightly overestimate mean bottom DO in the summer whereas multiple models
(e.g., Models D, E, F, and G) exhibit a strong negative bias during January
and/or February of 2005, primarily at stations in the middle to southern
portion of the bay's deep channel. Interestingly, increased biological
complexity and higher grid resolution do not completely resolve this issue,
as this is true for models utilizing full biogeochemical models (Models D, E)
as well as those using highly resolved model grids (Model G). This is likely
due to the ephemeral nature of the biological divers of DO.</p>
      <p>The strong performance of the constant respiration models implies that these
models may be excellent candidates for providing short-term bottom oxygen
forecasts. The high DO skill of the CRM models primarily results from the
fact that seasonal variations in physical processes (primarily wind mixing
and temperature) play a dominant role in controlling the seasonal cycle of
oxygen (Scully, 2013). Because the underlying hydrodynamic models all use
similar physical forcing, the constant respiration models are able to
simulate the seasonal cycle of DO with similar skill as the more complex
biogeochemical models. As a result, these simple models that are easier to
tune and require less in the way of computational resources than full
biogeochemical models, may be efficiently used to produce short-term (on the
order of days) DO forecasts. On the contrary, the more complex full
biogeochemical models will be necessary for scenario-based and long-term (on
the order of months to years) forecasting which requires that models respond
to prescribed changes in the biogeochemical environment, such as increased
rates of nutrient loading due to changes in land use, land cover, and/or
climate.</p>
</sec>
<sec id="Ch1.S4.SS2">
  <title>How does model skill of DO compare to that of the primary drivers
of DO variability?</title>
      <p><disp-quote>
  <p>Overall, model DO skill is greater than that of the variables generally
considered to drive DO variability, such as stratification, salinity, mixed
layer depth, chlorophyll, and nitrate; only modeled temperature has higher
skill than modeled DO.</p>
</disp-quote></p>
      <p>Since dissolved oxygen concentrations in the Chesapeake Bay are controlled by
physical processes (e.g., advection, wind mixing, heating/cooling, and
stratification), as well as biological processes (e.g., photosynthesis and
respiration), it is critical to understand the skill of the models in terms
of how well they reproduce the many factors influencing oxygen
concentrations. As expected, the five models containing a specific
biogeochemical model component had more difficulty simulating the observed
chlorophyll and nitrate concentrations than the physical variables
(temperature and salinity), both at the surface (Table 3) and the bottom
(Fig. 8). Replicating the correct location, magnitude, and timing of
phytoplankton blooms and nutrient cycling is a complex issue, and as a
result, these features are generally not well simulated in the models. While
the models generally simulate the total amount of chlorophyll adequately, it
is more uniformly spatially distributed in the models rather than in patchy
blooms as in nature, leading to the underestimation of chlorophyll
variability across all models. Although all models produced a relatively high
correlation between observed and modeled temperature and salinity (Fig. 8),
the correlation coefficients for chlorophyll and nitrate were much lower. The
correlations for observed vs. modeled DO was more similar to that of the
physical variables (temperature, salinity) than the biological variables
(chlorophyll and nitrate), highlighting that the seasonal variability in
bottom DO is regulated more by physical than biological factors. This also
explains the success of the constant respiration models, which by definition
contain no biological variability yet reproduce DO variability nearly as well
as the most complex biogeochemical models.</p>
      <p>In this study, model skill was also considerably higher for bottom oxygen
than it was for the vertical gradient of stratification and mixed layer
depths (Figs. 6, 8). The underestimation of the vertical gradient across all
models is largely due to the numerical diffusion that characterizes all of
these hydrodynamic models, but may also be partially due to an
underestimation of the winds or a lack of diffuse freshwater input around the
bay. Even though the models all underestimated the strength of stratification
(Figs. 4, 6), modeled stratification in summer was strong enough to prevent
mixing with the relatively well-oxygenated surface waters. This result
suggests, somewhat surprisingly, that simulating the correct vertical
gradient of stratification is not absolutely necessary for skillful bottom DO
simulations. Models need only simulate enough stratification to
effectively cut off vertical mixing in order to develop an isolated bottom
layer that can then experience a draw down in oxygen via respiration. In
addition, the models must also correctly simulate the horizontal advection of
oxygen (Scully, 2013; Y. Li et al., 2015). The fact that bottom DO is
simulated so well by the eight models analyzed here suggests that not only is
the advection of oxygen well represented in the models but also the strength
of stratification, i.e., the maximum vertical gradients of density and
oxygen, produced by these models is sufficient. Thus, although novel and
somewhat unexpected, these results are not contradictory to previous studies
demonstrating the importance stratification plays in initiating summer
hypoxia in the Chesapeake Bay (Murphy et al., 2011).</p>
      <p>Model skill in terms of reproducing observed mixed layer depths was likewise
much lower than model skill of reproducing observed oxygen concentrations.
All models, except Model A, produced mixed layer depths (MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula> and
MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="italic">ρ</mml:mi></mml:msub></mml:math></inline-formula>) that were generally too shallow in the water column (Fig. 6a).
Note that Model A is a regulatory model that has been used for many years by
the Chesapeake Bay Program, and has thus undergone more extensive calibration
aimed at matching the mean salinity and oxygen characteristics of the bay
(Cerco and Cole, 1993). Furthermore, Model A employs a <inline-formula><mml:math display="inline"><mml:mi>z</mml:mi></mml:math></inline-formula> grid that matches
the bathymetry in trench areas better than the sigma grids used by the other
models. Although Model A produced mixed layer depths that were generally in
the correct location within the water column (Fig. 6a), they were too
variable (Fig. 6b). This variability may partly be a result of the 1.5 m
<inline-formula><mml:math display="inline"><mml:mi>z</mml:mi></mml:math></inline-formula> grid employed by Model A causing large jumps between vertical grid cells
and hence resulting in overestimates of MLD variability. All other models use
sigma grids typically with more highly resolved vertical resolution at the
depth of maximum stratification.</p>
      <p>The two variables for which the models have greatest skill are DO and
temperature (Fig. 8). This is because oxygen variability is driven primarily
by seasonal variability in physical processes such as solubility and wind
mixing and to a lesser degree by variability in oxygen consumption (Scully,
2013). As a result, the models using a constant mean respiration rate produce
as realistic hypoxia simulations as the biogeochemically complex models.
Observations clearly show this strong seasonal variability in bottom DO
(Fig. 11a) and, to a slightly lesser extent, clear seasonal variability in DO
at the bottom of the bottom of the oxygen mixed layer (MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula>;
Fig. 11b). However, a seasonal cycle is not manifested in the MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula>
itself (Fig. 11c). The lack of such a strong seasonal cycle in the observed
mixed layer depths makes this a more difficult variable for the models to
simulate. As a result, the models can relatively skillfully simulate the
combined spatial and temporal variability of DO while simultaneously missing
the MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula>.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F11"><caption><p>Time series of observations at station CB4.1C from 2003 to 2006 for
<bold>(a)</bold> bottom dissolved oxygen, <bold>(b)</bold> dissolved oxygen at the
MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula>, and <bold>(c)</bold> MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula>.</p></caption>
          <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/2011/2016/bg-13-2011-2016-f11.png"/>

        </fig>

</sec>
<sec id="Ch1.S4.SS3">
  <?xmltex \opttitle{Why is it important for DO models to simulate the MLD${}_{\mathrm{O}}$
correctly?}?><title>Why is it important for DO models to simulate the MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula>
correctly?</title>
      <p><disp-quote>
  <p>Most of the aerobic habitat in the bay during the summer is located above the
MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula>, thus it is critical for living resource managers to use
models that accurately simulate this variable.</p>
</disp-quote></p>
      <p>On average, the models miss the observed depth of the MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula> by
3.4 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula>, which equates to roughly a 60 % error in the modeled mixed
layer depths. While the models have difficulty simulating the
MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula> throughout the entire year (Figs. 6, 7b), the summer months
are when the mismatch has the greatest potential to impact the available
habitat for oxygen-dependent species. Each year during this time period
low-oxygen waters occupy nearly the entire water column below the mixed
layer. At station CB4.1C, a representative mesohaline deep trough station,
the contours of low-oxygen (5 <inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">mg</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">L</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>) and hypoxic
(2 <inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">mg</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">L</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>) waters are located just below the MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula>
from late spring until late fall (Fig. 12). The severe depletion of oxygen
below the mixed layer compresses the habitable space at this station to
roughly 10 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula> (from a maximum of 32 <inline-formula><mml:math display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula>) during the annual
low-oxygen event.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F12"><caption><p>Time series of observations of dissolved oxygen and MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula>
contours at Station CB4.1C for 2004 and 2005.</p></caption>
          <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://bg.copernicus.org/articles/13/2011/2016/bg-13-2011-2016-f12.png"/>

        </fig>

      <p>The impact of habitat compression can be substantial, as many bay species
require DO concentrations well above the traditional hypoxic threshold
(USEPA, 2010). While not all of the main stem stations develop hypoxic water
each year, most mesohaline stations experience a dramatic drawdown of oxygen
to levels during the summer that effectively remove a large portion of the
bay from habitable space (Murphy et al., 2011; Schlenger et al., 2013).
Studies have shown that some species modify their behavior based on the
oxycline depth, which acts to constrict the habitable space in the water
column (Prince and Goodyear, 2006; Pierson et al., 2009; Elliott et
al., 2013). Since species can be negatively impacted by low-DO concentrations
as high as 5 <inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">mg</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">L</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> (Breitburg, 2002; Vaquer-Sunyer and Duarte,
2008; USEPA, 2010), the location of the oxycline is not only important for
habitat compression in the summer months but can also be important in the
winter months when an occasional lack of vertical mixing can substantially
decrease bottom DO concentrations. Furthermore, in order to accurately
estimate hypoxic volume, models must correctly simulate the depth of the
mixed layer, since the MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">O</mml:mi></mml:msub></mml:math></inline-formula> closely follows the depth of the
2 <inline-formula><mml:math display="inline"><mml:mrow><mml:mi mathvariant="normal">mg</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">L</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> contour.</p>
</sec>
<sec id="Ch1.S4.SS4">
  <title>How can DO simulations in the bay be improved for management of
water quality and living resources?</title>
      <p><disp-quote>
  <p>To better simulate DO conditions and summer habitat compression due to low-DO
water, simulations of the depth of the top of the pycnocline (MLD<inline-formula><mml:math display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="italic">ρ</mml:mi></mml:msub></mml:math></inline-formula>)
must be improved.</p>
</disp-quote></p>
      <p>Although the suite of models examined reproduce DO concentrations relatively
well overall (Fig. 4), the models typically overestimate summer habitat
compression by producing low DO concentrations too high in the water column
(Fig. 6). Observations from the Chesapeake Bay Program show a strong
correlation between the depths of the oxygen and density-defined mixed layers
(Fig. 10b). The models analyzed here also clearly exhibit a close
relationship between their skill in simulating the depths of the oxygen and
density-defined mixed layers (Fig. 6). These strong relationships between the
depths of the oxygen and density-defined mixed layers result from the fact
that the pycnocline represents the physical barrier that leads to the
development of the oxycline. Therefore, the inability of the models to
accurately simulate habitat compression is an artifact of their lack of skill
in simulating the depth of the density-defined mixed layer. In contrast, the
strength of density stratification is not well correlated to the strength of
oxygen stratification. This is because a relative wide range of intensities
of density stratification is still sufficient to cut off vertical mixing,
leading to the observed draw-down in bottom DO. Thus, even though all models
underestimate the strength of the pycnocline, they still produce enough
stratification to greatly reduce mixing. The results from this paper thus
indicate that to further improve DO simulations and better estimate
summertime habitat compression, it is even more critical for models to
accurately simulate the depth of the top of the pycnocline than to accurately
simulate the absolute strength of the pycnocline.</p>
</sec>
<sec id="Ch1.S4.SS5">
  <title>What is the utility of the multi-model ensemble and Model Mean?</title>
      <p><disp-quote>
  <p>The multi-model ensemble approach allows for the development of a model
mean, which taken as its own model, is the most skilled model when examining
the combined suite of variables analyzed in this study.</p>
</disp-quote></p>
      <p>The model skill assessment presented here demonstrates that the average of
all eight models, or five models in the case of chlorophyll and nitrate,
does better than any individual model if looking across the suite of
variables analyzed. This finding is similar to that of other studies that
examined the value of the Model Mean from a multi-model ensemble (e.g.,
Gneiting and Raftery, 2005; Hagedorn et al., 2005). While the concept of
using a multi-model ensemble has been most extensively employed by
atmospheric, climatic, and global circulation modelers, such as the
Intergovernmental Panel on Climate Change (e.g., Collins et al., 2013), the
tool's utility for aquatic ecosystem modeling is gaining traction (Meier et
al., 2012; Trolle et al., 2014; Janssen et al., 2015). As models are
increasingly used in regulatory decisions regarding aquatic ecosystems, a
cohort of similarly skilled models can be used to help inform a set of
confidence bounds around an environmental forecast. Due to the restrictions
placed on models used in regulatory actions, utilization of a multi-model
ensemble may not be realistic for all environmental and resource managers;
however, multiple models can be integrated into the decision-making process
even when the ultimate decision must be based on a single model. For
example, a confidence interval plot could help identify where regulatory
model output might be acting out of sync with other skilled water quality
models of the same system, thereby informing managers of the potential
shortfalls associated with the regulatory model. Furthermore, if the models
tend to be predicting similar DO concentrations, a cohort of models could
enhance the confidence in regulatory decisions based on a single regulatory
model (Friedrichs et al., 2012; Weller et al., 2013). Comparing multiple
models can also help inform how to better improve models in the future, as
this study has aimed to do.</p>
</sec>
</sec>
<sec id="Ch1.S5" sec-type="conclusions">
  <title>Conclusions</title>
      <p>All models analyzed here exhibited a high degree of skill in
simulating dissolved oxygen concentrations within the main stem of the
Chesapeake Bay in 2 years corresponding to relatively wet and average
years. Their high skill results from the fact that physical processes (e.g.,
solubility, wind-mixing, and advection) exert a first order influence on the
seasonal cycle of oxygen. As a result, the models' ability to reproduce
dissolved oxygen concentrations is independent of the complexity of the
biogeochemical parameterizations: the simplest constant respiration models
were found to reproduce observed oxygen concentrations as well as the most
biologically complex models. Essentially, all models are equally capable of
respiring most of the available oxygen in the lower water column during
summer.</p>
      <p>This study also suggests that for use as management tools for water quality
and living resources, it is more critical for these models to adequately
resolve the depth of the mixed layer than the absolute strength of
stratification (as long as modeled stratification is strong enough to limit
vertical mixing). This is critical because observations show that during
warmer months, oxygen-depleted water fills the water column to where
stratification limits further mixing, which effectively cuts off waters below
the mixed layer for use by the majority of the Chesapeake Bay's most
recognized and valued living resources. These results furthermore suggest
that modelers should focus their efforts on improving the hydrodynamics of
their models in an effort to improve simulations of mixed layer depth
dynamics and variability.</p>
      <p>These findings have significant ramifications for short-term bottom DO
forecasts, which may be successful with very simple oxygen parameterizations
embedded in hydrodynamic models. In contrast, scenario-based water quality
forecasts are likely to benefit from more complex models, which must
adequately reproduce the longer-term response of the oxygen field to changes
in nutrient and organic matter loads. This study also helps to demonstrate
how multiple community models from governmental agencies and academic
institutions may be used together to provide a model mean and a set of
confidence bounds for regulatory model results that could be used to inform
management decisions.</p>
</sec>
<sec id="Ch1.Sx1" specific-use="unnumbered">
  <title>Data Availability</title>
      <p>Observations used in this analysis can be downloaded from the Chesapeake Bay
Program's Water Quality Database website at
(<uri>http://www.chesapeakebay.net/data/downloads/cbpwaterqualitydatabase1984present</uri>).
Model output for the individual stations examined in this analysis can be
obtained by contacting Marjorie Friedrichs (marjy@vims.edu) or downloaded
from the Coastal &amp; Ocean Modeling Testbed – Estuarine Hypoxia THREDDS
server
(<uri>http://comt.sura.org/thredds/catalog/comt2/cb_hypoxia/catalog.html</uri>).</p>
</sec>

      
      </body>
    <back><ack><title>Acknowledgements</title><p>This work was supported by the NOAA IOOS program as part of the Coastal Ocean
Modeling Testbed. We thank Yun Li and Younjoo Lee for help with the ROMS-RCA
simulations used in this analysis and Ray Najjar for his insights and
comments. This is VIMS contribution 3520 and UMCES contribution 5130.
<?xmltex \hack{\newline}?><?xmltex \hack{\newline}?>
Edited by: K. Fennel</p></ack><ref-list>
    <title>References</title>

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    </app></app-group></back>
    <!--<article-title-html>Challenges associated with modeling low-oxygen waters in Chesapeake Bay: a
multiple model comparison</article-title-html>
<abstract-html><p class="p">As three-dimensional (3-D) aquatic ecosystem models are used
more frequently for operational water quality forecasts and ecological
management decisions, it is important to understand the relative strengths
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biogeochemical complexity. To this end, 2-year simulations of the
Chesapeake Bay from eight hydrodynamic-oxygen models have been statistically
compared to each other and to historical monitoring data. Results show that
although models have difficulty resolving the variables typically thought to
be the main drivers of dissolved oxygen variability (stratification,
nutrients, and chlorophyll), all eight models have significant skill in
reproducing the mean and seasonal variability of dissolved oxygen. In
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supply and temperature reproduced observed dissolved oxygen concentrations
about as well as much more complex, nutrient-dependent biogeochemical models.
This finding has significant ramifications for short-term hypoxia forecasts
in the Chesapeake Bay, which may be possible with very simple oxygen
parameterizations, in contrast to the more complex full biogeochemical models
required for scenario-based forecasting. However, models have difficulty
simulating correct density and oxygen mixed layer depths, which are important
ecologically in terms of habitat compression. Observations indicate a much
stronger correlation between the depths of the top of the pycnocline and
oxycline than between their maximum vertical gradients, highlighting the
importance of the mixing depth in defining the region of aerobic habitat in
the Chesapeake Bay when low-oxygen bottom waters are present. Improvement in
hypoxia simulations will thus depend more on the ability of models to
reproduce the correct mean and variability of the depth of the physically
driven surface mixed layer than the precise magnitude of the vertical density
gradient.</p></abstract-html>
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