A general method for parameter estimation in light-response models

Selecting appropriate initial values is critical for parameter estimation in nonlinear photosynthetic light response models. Failed convergence often occurs due to wrongly selected initial values when using currently available methods, especially the kind of local optimization. There are no reliable methods that can resolve the conundrum of selecting appropriate initial values. After comparing the performance of the Levenberg–Marquardt algorithm and other three algorithms for global optimization, we develop a general method for parameter estimation in four photosynthetic light response models, based on the use of Differential Evolution (DE). The new method was shown to successfully provide good fits (R2 > 0.98) and robust parameter estimates for 42 datasets collected for 21 plant species under the same initial values. It suggests that the DE algorithm can efficiently resolve the issue of hyper initial-value sensitivity when using local optimization methods. Therefore, the DE method can be applied to fit the light-response curves of various species without considering the initial values.

[1]  Yang Xiang,et al.  Generalized Simulated Annealing for Global Optimization: The GenSA Package , 2013, R J..

[2]  J. Prieto,et al.  Modelling photosynthetic-light response on Syrah leaves with different exposure. , 2015 .

[3]  D. Xing,et al.  Rapid determination of the damage to photosynthesis caused by salt and osmotic stresses using delayed fluorescence of chloroplasts , 2008, Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology.

[4]  R. Gordon,et al.  Photosynthetic Response of Carrots to Varying Irradiances , 2003, Photosynthetica.

[5]  Ruigang Yang,et al.  How Far Can We Go with Local Optimization in Real-Time Stereo Matching , 2006, Third International Symposium on 3D Data Processing, Visualization, and Transmission (3DPVT'06).

[6]  D. Posada,et al.  Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests. , 2004, Systematic biology.

[7]  E. Ögren,et al.  Photosynthetic light-response curves , 1993, Planta.

[8]  J. H. Bassman,et al.  Gas exchange characteristics of Populus trichocarpa, Populus deltoides and Populus trichocarpa x P. deltoides clones. , 1991, Tree physiology.

[9]  L. Samuelson,et al.  Leaf Physiological and Morphological Responses to Shade in Grass-Stage Seedlings and Young Trees of Longleaf Pine , 2012 .

[10]  Trevor Platt,et al.  Mathematical formulation of the relationship between photosynthesis and light for phytoplankton , 1976 .

[11]  Duli Zhao,et al.  Sugarcane Leaf Photosynthesis and Growth Characters during Development of Water‐Deficit Stress , 2013 .

[12]  Fatih Emre Boran,et al.  Optimization of module, shaft diameter and rolling bearing for spur gear through genetic algorithm , 2010, Expert Syst. Appl..

[13]  B. Marshall,et al.  A Model for C3 Leaves Describing the Dependence of Net Photosynthesis on Irradiance , 1980 .

[14]  Adrian Hilton,et al.  Visual Analysis of Humans - Looking at People , 2013 .

[15]  Sönke Hartmann,et al.  A competitive genetic algorithm for resource-constrained project scheduling , 1998 .

[16]  T. Sharkey,et al.  Stomatal conductance and photosynthesis , 1982 .

[17]  Fernando E. Miguez,et al.  Nonlinear Regression Models and Applications in Agricultural Research , 2015 .

[18]  Z. Ye A new model for relationship between irradiance and the rate of photosynthesis in Oryza sativa , 2007, Photosynthetica.

[19]  Leon G. Higley,et al.  Effects of Insect Herbivory on Physiological and Biochemical (Oxidative Enzyme) Responses of the Halophyte Atriplex subspicata (Chenopodiaceae) , 2006 .

[20]  J. Reynolds,et al.  The nonrectangular hyperbola as a photosynthetic light response model: geometrical interpretation and estimation of the parameter , 1987 .

[21]  A coupled model of stomatal conductance and photosynthesis for winter wheat , 2008, Photosynthetica.

[22]  René Thomsen,et al.  A comparative study of differential evolution, particle swarm optimization, and evolutionary algorithms on numerical benchmark problems , 2004, Proceedings of the 2004 Congress on Evolutionary Computation (IEEE Cat. No.04TH8753).

[23]  Vijay P. Singh,et al.  Frequency analysis of droughts using the Plackett copula and parameter estimation by genetic algorithm , 2010 .

[24]  J. Thornley,et al.  DYNAMIC MODEL OF LEAF PHOTOSYNTHESIS WITH ACCLIMATION TO LIGHT AND NITROGEN , 1998 .

[25]  Xiao-Shan Gao,et al.  Geometric constraint satisfaction using optimization methods , 1999, Comput. Aided Des..

[26]  L. Kirkman,et al.  Growth and photosynthetic responses of the federally endangered shrub, Lindera melissifolia (Lauraceae), to varied light environments. , 2005, American journal of botany.

[27]  C. Tsallis,et al.  Generalized simulated annealing , 1995, cond-mat/9501047.

[28]  Robert L. Smith,et al.  Simulated annealing for constrained global optimization , 1994, J. Glob. Optim..

[29]  Rainer Storn,et al.  Differential Evolution – A Simple and Efficient Heuristic for global Optimization over Continuous Spaces , 1997, J. Glob. Optim..

[30]  J. Ehleringer,et al.  Carbon Isotope Discrimination and Photosynthesis , 1989 .

[31]  T. Rzigui,et al.  Light acclimation of leaf gas exchange in two Tunisian cork oak populations from contrasting environmental conditions , 2015 .

[32]  M. Alberdi,et al.  Pruning severity affects yield, fruit load and fruit and leaf traits of 'Brigitta' blueberry , 2014 .

[33]  F. Sarhan,et al.  Potential for increased photosynthetic performance and crop productivity in response to climate change: role of CBFs and gibberellic acid , 2014, Front. Chem..