Appendix A. Modeling the dynamics of the Oe and Oa soil carbon stocks.

Modeling the dynamics of the Oe and Oa soil carbon stocks

Location and size of adult Ficus aurea trees

This file contains the size and location of all reproductive adult Ficus aurea trees within 300 m of center plots. The column Sitecode matches the column of the same name in the "Center plots.csv" file. The DBH column is the diameter at breast height in cm of adult trees, Distance is distance from the trunk of the tree to the center of the center plot in m, and y and x are the coordinates in UTM (NAD83/ zone 17N) of each tree

Appendix B. Additional evidence for differential regulation, stand-age distributions, inventory patterns with elevation, and sensitivity analyses.

Additional evidence for differential regulation, stand-age distributions, inventory patterns with elevation, and sensitivity analyses

Counts of seedling figs and predictor variables in center plots

This data was collected in the field in fifty-two 30 m x 30 m plots in southwest Florida. SITECODE and IDENT columns are unique names for each plot, Y_PROJ and X_PROJ are the UTM coordinates (NAD83/ zone 17N) of the center of each plot, cabbage palms is the number of cabbage palms in each plot, aurea seedlings and microcarpa seedlings are counts of fig seedlings of Ficus aurea and Ficus microcarpa in each plot, canopy cover is estimated canopy cover over each plot (on a scale of 1-5), understory height represents the mean height of understory vegetation (in meters) in each plot and microcarpa and aurea DBH represent the summed DBH (in cm) of all reproductive adult figs in a 300 m radius around each plot

Supplement 1. Code for simulations and statistical models.

<h2>File List</h2><div> <p><a href="Menge_Latitudinal_Abundance_Model_Code.R">Menge_Latitudinal_Abundance_Model_Code.R</a> (MD5: 7917640d0c7cf0c449b97517fa29133d)</p> <p><a href="Menge_SuccessionDynamicsModel_Script.m">Menge_SuccessionDynamicsModel_Script.m</a> (MD5: e3bb898eef5b2e1d104cc90629d37120)</p> <p><a href="Menge_SuccessionDynamicsModel_Pars.m">Menge_SuccessionDynamicsModel_Pars.m</a> (MD5: 4f3456b66d123b4a957d5a21e74951d8)</p> <p><a href="Menge_SuccessionDynamicsModel_odes_ob_non.m">Menge_SuccessionDynamicsModel_odes_ob_non.m</a> (MD5: c32d1000d5a3c7047a5ed86d479e97ab)</p> <p><a href="Menge_SuccessionDynamicsModel_odes_fac_non.m">Menge_SuccessionDynamicsModel_odes_fac_non.m</a> (MD5: 401ad7cdb1a9d6d6785964231f133e82)</p> <p><a href="Menge_SuccessionDynamicsModel_Figures.m">Menge_SuccessionDynamicsModel_Figures.m</a> (MD5: e1e7346752dd3e7b8b6e9a101066a5a5)</p> <p><a href="Menge_SuccessionDynamicsModel_FigB8_Script.m">Menge_SuccessionDynamicsModel_FigB8_Script.m</a> (MD5: 9a482ad728fb63538bde2965c79a6041)</p> <p><a href="Menge_SuccessionDynamicsModel_Pars_3.m">Menge_SuccessionDynamicsModel_Pars_3.m</a> (MD5: 1ce6191d5cfc70061fd037ae6df80905)</p> <p><a href="Menge_SuccessionDynamicsModel_odes_fac_ob_non.m">Menge_SuccessionDynamicsModel_odes_fac_ob_non.m</a> (MD5: 7c1ba58eb3e7563bad78d2301d2a1da0)</p> <p><a href="Menge_SuccessionDynamicsModel_swa.m">Menge_SuccessionDynamicsModel_swa.m</a> (MD5: 2f0631669f3411753e287a264bd1ebd7)</p> <p><a href="Menge_SuccessionDynamicsModel_FigB8_Figure.m">Menge_SuccessionDynamicsModel_FigB8_Figure.m</a> (MD5: 9e4a1d2b02675b6c52f64e1e39f76bd5)</p> </div><h2>Description</h2><div> <p>This supplement contains files that consist of code for simulations and statistical analyses consisting of 1 .R (R) file for the "Latitudinal Abundance Model" and 10 .m (matlab) files for the "Succession Dynamics Model."</p> <p>The .R file, Menge_Latitudinal_Abundance_Model_Code.R, contains the statistical model code. It creates a dataframe with latitude and the 1-degree-latitude mean percent basal area occupied by N fixers (the data used in model fitting). It then creates variables for the abundance of each type in each habitat for given age distribution; these data were output from the Successional Dynamics Model and weighted by different age distributions. It then creates some functions needed for the model fitting exercise (as described in the text), and uses nls to fit the model to the data. Finally, it plots up the results. As currently set up, it creates Fig. 4 in the paper. To create Fig. B4–B7, some of the variables must be changed and the code rerun, as indicated in the code comments.</p> <p>The Successional Dynamics Model code is contained in the .m files. There are 5 .m files associated with running the simulation for Fig. 3. Menge_SuccessionDynamicsModel_Script.m is the main script. It calls Menge_SuccessionDynamicsModel_Pars.m to set the parameters, sets up the initial conditions for each simulation, runs the simulation(s), saves the data, and calls the script that makes the figure. Options in the file (used to create the different panels) are changing SevModNon and whichrun (as indicated in the code). The files Menge_SuccessionDynamicsModel_odes_ob_non.m and Menge_SuccessionDynamicsModel_odes_fac_non.m are the functions that describe the mathematical equations of the model, and are called in the main script with the function ode45. The file Menge_SuccessionDynamicsModel_Figures.m sets up the figure, loads the data for each panel (which must be made, first, from the main script), then fills out each panel.</p> <p>There are 5 .m files associated with running the simulation for Appendix B Fig. B8. The file Menge_SuccessionDynamicsModel_FigB8_Script.m is the main script. It initializes the parameter values for all three types (in the file Menge_SuccessionDynamicsModel_Pars_3.m), loops over habitat types and cost values (expressed as "psi," which is related to gamma in the paper by gamma = psi * c, with c = 120 per year), then numerically integrates the model Menge_SuccessionDynamicsModel_odes_fac_ob_non.m with the matlab function ode45, then weights the successional abundances by the FIA age distribution using the function Menge_SuccessionDynamicsModel_swa.m (also does so for the alternate age distributions, but these are not used in the figure), saves the data, then calls the figure script. The file Menge_SuccessionDynamicsModel_FigB8_Figure.m sets up the figure, loads the data, and fills out the panels. Editing of axis and panel labels directly on the pdf was done in Adobe Illustrator. Note that this run takes a long time.</p> </div

Appendix A. Theory-predicted N-fixing tree abundance in different habitats.

Theory-predicted N-fixing tree abundance in different habitats

Species-Independent Down-Regulation of Leaf Photosynthesis and Respiration in Response to Shading: Evidence from Six Temperate Tree Species

<div><p>The ability to down-regulate leaf maximum net photosynthetic capacity (Amax) and dark respiration rate (Rdark) in response to shading is thought to be an important adaptation of trees to the wide range of light environments that they are exposed to across space and time. A simple, general rule that accurately described this down-regulation would improve carbon cycle models and enhance our understanding of how forest successional diversity is maintained. In this paper, we investigated the light response of Amax and Rdark for saplings of six temperate forest tree species in New Jersey, USA, and formulated a simple model of down-regulation that could be incorporated into carbon cycle models. We found that full-sun values of Amax and Rdark differed significantly among species, but the rate of down-regulation (proportional decrease in Amax or Rdark relative to the full-sun value) in response to shade was not significantly species- or taxon-specific. Shade leaves of sun-grown plants appear to follow the same pattern of down-regulation in response to shade as leaves of shade-grown plants. Given the light level above a leaf and one species-specific number (either the full-sun Amax or full-sun Rdark), we provide a formula that can accurately predict the leaf's Amax and Rdark. We further show that most of the down regulation of per unit area Rdark and Amax is caused by reductions in leaf mass per unit area (LMA): as light decreases, leaves get thinner, while per unit mass Amax and Rdark remain approximately constant.</p></div

Relationship between normalized Amax or Rdark (measured value divided by species mean full-sun value) and light.

<p>Species code: GB = gray birch, WA = white ash, SM = sugar maple, WP = white pine, EH = eastern hemlock.</p

Maximum likelihood estimates (MLE) and 95% confidence limits for parameters in Model 3a.

<p>Units for per-area Amax and Rdark are µmol CO₂ m⁻² s⁻¹, and units for per-mass Amax and Rdark are 10⁻⁴ µmol CO₂ g⁻¹ s⁻¹.</p

Comparison of models of leaf maximum net photosynthetic capacity (Amax) and dark respiration rate (Rdark) in response to light level.

<p>The models here are the nine possible combinations of, (1) a single value of μ (i.e., full-sun Amax or Rdark) shared by all species, (2) separate μ for deciduous and conifer trees, (3) species-specific μ; and (a) a single value of D for all species, (b) separate D for deciduous and conifer species, (c) species-specific D. The data are normalized either by area or by mass (norm). The number of parameters (df) of each model includes the variance of the error term in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091798#pone.0091798.e001" target="_blank">Equation (1)</a>. R² is the coefficient of determination describing the overall fit of the model to data; and the Akaike Information Criterion (aic.ncor) is sample size-corrected following Bolker <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091798#pone.0091798-Bolker1" target="_blank">[35]</a>, , where k is the number of parameters, and n is the sample size. The AIC index without sample size-corrected showed the same results. The best model(s) (lowest aic.ncor) is highlighted in bold.</p