Average (± SE) prey crab crypsis index at five densities with (solid circles) and without (open circles) predator presence.

<p>The lines represent linear regressions for when predators were present (closed circles; crypsis = 0.732−(0.0134×density), R² = 0.172) and absent (open circles; crypsis = 0.551−(0.00971×density), R² = 0.106).</p

Ranking of functional response models in sand and shell habitats using AIC_c.

<p>Ranking of functional response models in sand and shell habitats using AIC_c.</p

The number of prey crabs eaten as a function of predator size (carapace length) in sand (closed circles) and shell (open circles) habitat.

<p>Lines represent linear regression. Equations are: 1) sand: prey eaten = −23.926 + (1.883×carapace length), R² = 0.895; and, 2) shell: prey eaten  = 1.373 + (0.00155×carapace length), R² = 0.0000568.</p

Supplement 1. MATLAB function files for modeling Macoma balthica populations, and trophic transfer under normoxic and hypoxic conditions.

<h2>File List</h2><div> <p><a href="MbPopModel.m">MbPopModel.m</a> (MD5: fbf47bb585a7f041100da16138dc8ab0)</p> <p><a href="Pop_and_Pred.m">Pop_and_Pred.m</a> (MD5: 435f0942c819b03520e41bea6ec7756e)</p> <p><a href="dA.m">dA.m</a> (MD5: 67e503d79e2373c3756d7eb322ae4a84)</p> <p><a href="typeIII.m">typeIII.m</a> (MD5: 3664dfa10b84d28960b8bd952e66e058)</p> <p><a href="typeIIIH.m">typeIIIH.m</a> (MD5: 7cc47c1e7de06bbf7fb824bcdb03b6e8)</p> <p><a href="typeIII_P.m">typeIII_P.m</a> (MD5: dc445d6b130c070b8f73ffbb9779b08f)</p> <p><a href="typeIIIH_P.m">typeIIIH_P.m</a> (MD5: f5cf34d4a88340c688394a1be50f9ad7)</p> </div><h2>Description</h2><div> <p><b>MbPopModel.m-</b> This MATLAB function will model the population of <i>Macoma balthica</i> over a user specified length of time. Required sub-functions that are called within this function are dA.m, which creates a population projection matrix using input parameters and tyepIII.m and typeIIIH.m which are a series of linked ordinary differential equations describing the population dynamics during the summer in normoxic and hypoxic areas of the river.</p> <p>The three inputs to the function are:<br> param- A vector with five parameters: <i>MN</i>, <i>MH</i>, <i>RH</i>, <i>RN</i>, <i>d</i><br> Where <i>M</i> is the proportion of the juvenile population that reproduces in their first year, and <i>R</i> is the number of recruits produced by each female, and d is the areal proportion of the river that remains normoxic.</p> <p>Inits(<i>JN</i>, <i>AN</i>, <i>JH</i>, <i>AH</i>)- A vector with the initial population density of the Juveniles (<i>J</i>), and Adults (<i>A</i>) in the normoxic (subscript <i>N</i>) and hypoxic (subscript <i>H</i>).</p> <p>J- the number of years the model is to be run for.</p> <p>Base parameter estimates used in the paper are:</p> <blockquote> -- TABLE: Please see in attached file. -- </blockquote> <p> </p> <p><b>Pop_and_Pred.m</b>- This MATLAB function will model the population (output <i>pop</i>) of <i>Macoma balthica</i> and provide an annual estimate of the biomass (output <i>B</i>) and number (output <i>N</i>) of clams consumed by blue crabs (<i>Callinectes sapidus</i>) and those that suffer non-predatory mortality. Required sub-functions that are called within this function are dA.m, which creates a population projection matrix using input parameters and tyepIIIP.m and typeIIIH_P.m which are a series of linked ordinary differential equations describing the population dynamics during the summer in normoxic and hypoxic areas of the river.</p> <p>The four inputs to the function are:<br> Mparam- A vector with five parameters: <i>MN</i>, <i>MH</i>, <i>RH</i>, <i>RN</i>, <i>d</i><br> Where <i>M</i> is the proportion of the juvenile population that reproduces in their first year, and <i>R</i> is the number of recruits produced by each female, and d is the areal proportion of the river that remains normoxic.</p> <p>Param- A vector with three parameters: <i>tH</i>, <i>mH</i>,<i> P</i><br> Where <i>tH</i> is the duration of hypoxia in days, <i>mH</i> is the non-predatory mortality rate in hypoxic areas and <i>P</i> is the proportional increase in predation under hypoxic conditions.</p> p>Inits(<i>JN</i>, <i>AN</i>, <i>JH</i>, <i>AH</i>)- A vector with the initial population density of the Juveniles (<i>J</i>), and Adults (<i>A</i>) in the normoxic (subscript <i>N</i>) and hypoxic (subscript <i>H</i>).<p></p> <p>J- the number of years the model is to be run for.</p> <p>Base parameter estimates used in the paper are:</p> <blockquote> -- TABLE: Please see in attached file. -- </blockquote> <p> </p> <p><b>dA.m</b>- Sub-function of MbPopModel and Pop_and_Pred that creates a population projection matrix using input parameters.</p> <p><b>typeIII</b>- Sub-function of MbPopModel that is a series of linked ordinary differential equations describing the population dynamics during the summer in normoxic areas of the river.</p> <p><b>typeIIIH</b>- Sub-function of MbPopModel that is a series of linked ordinary differential equations describing the population dynamics during the summer in hypoxic areas of the river.</p> <p><b>typeIII_P</b>- Sub-function of Pop_and_Pred that is a series of linked ordinary differential equations describing the population dynamics and predation during the summer in normoxic areas of the river.</p> <p><b>typeIIIH_P</b>- Sub-function of Pop_and_Pred that is a series of linked ordinary differential equations describing the population dynamics and predation during the summer in hypoxic areas of the river.</p> </div

Forward Scatter (FSC-H) versus Side Scatter (SSC-H) of hemolymph from <i>Chionoecetes bairdi</i>, Tanner Crab.

<p>Forward Scatter (FSC-H) versus Side Scatter (SSC-H) of hemolymph from <i>Chionoecetes bairdi</i>, Tanner Crab.</p

The calibration profile of Carboxy SNARF® for <i>Chionoecetes bairdi</i>, Tanner Crab.

<p>The slope of the line was used to calculate pH_i of semi-granular+ granular cells and hyalinocyte cells.</p

The percentage of phagocytic hemocytes in <i>Chionoecetes bairdi</i>, Tanner Crab, from each pH treatment.

<p>The error bars represent the standard error and a different letter indicates a significant difference between treatments.</p

Hemolymph pH (pH_e) and intracellular pH (pH_i) for semi-granular+granular cells (SGC+GC) and hyalinocyte cells (HC) from <i>Chionoecetes bairdi</i>, Tanner crab.

<p>The error bars represent the standard error and letters indicate significant differences between treatments.</p

Relationship between hemocyte function in and parameters measured in the adult <i>Chionoecetes bairdi</i>, Tanner Crab.

<p>The hemocyte function that showed an relationship include SGC+GC pH_i, phagocytosis, and % dead hemocytes relative to the adult parameters for number of eggs in second hatch, % viable/non-viable eggs, and calcium concentration.</p