Time accumulated percentage of leaf area irradiated above photosynthetic saturation irradiance.

<p>The colour scale shows <i>H</i>^A_sat, the “percentage leaf area hours” above <i>E</i>_k, as a function of LAI and shading. (a) is for upright low wave action canopy structures, (b) is for the average over the high wave energy canopy positions. Contour lines are isoclines based on the mid value of <i>E</i>_k equal to 50 µmol quanta m⁻² s⁻¹ while the surrounding greyed region shows the limits for <i>E</i>_k of 45 to 55 µmol quanta m⁻² s⁻¹. The isoclines are located at <i>H</i>^A_sat of 50, 100, 200, and then steps of 100 up to 800% leaf area hours.</p

Time accumulated percentage of leaf area irradiated above photosynthetic saturation irradiance for low wave action and high wave action treatments, for <i>E</i>_k of 45 and 55 µmol quanta m⁻² s⁻¹.

<p>Error bars on high wave action treatment are the standard deviation over all 14 movement positions and hence indicate the range in the instantaneous canopy saturation state.</p

Trajectories of canopies from empirical shading experiment and hypothetical example.

<p>Underlying plot is as described in the caption of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111454#pone-0111454-g006" target="_blank">Figure 6a</a>.</p

Example canopy structures and positions used in the model treatments.

<p>(a)–(e) low wave action canopy position for the five LAI treatments A to E. (f)–(i) subset of time sequence positions under high wave action for canopy C, all 14 positions were used in the optical model. In all cases the canopy structure is notionally repeated in all horizontal directions such that the square substrate section tessellates.</p

Overview of modelling system.

<p>(a, b) empirical data informs construction of 3D canopy model (f), (c, d, e) A plane-parallel model estimates directional radiance incident on the top of the canopy, (f, g, h) a geometric optical model handles radiative transfer to and between leaf segments, (i, j) PAR distribution over leaf area is reduced to the percentage of the canopy irradiated above leaf-level photosynthetic saturation, <i>E</i>_k.</p

Percentage of downwelling top of canopy PAR irradiance reaching the substrate, as a function of LAI.

<p>Results for empirical in-situ measurements (data 1 and 2) and modelled estimates (model) are shown. Curve fit to model data points is <i>y</i> = 100 * exp(−0.29×LAI).×(data 2) - are 26 individual coincident measurements of LAI and irradiance above and below the canopy. ⊡ (data 1) is a single point based on a site mean of 13 LAI determinations from 2.84 to 4.09 and a set of associated but not spatially co-incident light measurements, error bars are one S.D. The four encircled points are the outliers referred to in the text. Transmittance data collection is described in McMahon and Lavery 2014 and corresponding LAI is unpublished data from Lavery et al. 2009. • are 25 model runs including both those described in detail and some additional runs. In the models runs solar zenith angle was approximately 28°.</p

Distribution of leaf saturation state in the canopy in terms of percentage of leaf area at midday.

<p>Treatments are upright low wave action canopy positions and the average over the high wave action movement positions (left columns), and the same for 50% shading (right columns), for the five LAI treatments. The estimated photosynthetic saturation irradiances, <i>E</i>_k, of 45 and 55 µmol quanta m⁻² s⁻¹ inferred from Masini and Manning (1997) are shown as vertical dotted lines.</p

Validation data

Validation data used to validate the DBN model for Amphibolis in Jurien Bay, Halophila at Hay Point, and Zostera at Gladstone (supporting information S4 through S6, respectively)

Recruitment Rate from Seeds

DBN CPT (visualised in supporting information S7

Rate of Recovery in Shoot Density

DBN CPT (visualised in supporting information S7