Photosynthetica 2014, 52(2):233-246 | DOI: 10.1007/s11099-014-0027-8

Parameter inversion estimation in photosynthetic models: Impact of different simulation methods

H. B. Wang1,*, M. G. Ma1, Y. M. Xie1, X. F. Wang1, J. Wang2
1 Cold and Arid Regions Remote Sensing Observation System Experimental Station, Cold and Arid Regions Environment and Engineering Research Institute (CAREERI), Chinese Academy of Sciences, Lanzhou, China
2 Lanzhou Institute of Arid Meteorology, China Meteorological Administration, Lanzhou, China

When we apply ecological models in environmental management, we must assess the accuracy of parameter estimation and its impact on model predictions. Parameters estimated by conventional techniques tend to be nonrobust and require excessive computational resources. However, optimization algorithms are highly robust and generally exhibit convergence of parameter estimation by inversion with nonlinear models. They can simultaneously generate a large number of parameter estimates using an entire data set. In this study, we tested four inversion algorithms (simulated annealing, shuffled complex evolution, particle swarm optimization, and the genetic algorithm) to optimize parameters in photosynthetic models depending on different temperatures. We investigated if parameter boundary values and control variables influenced the accuracy and efficiency of the various algorithms and models. We obtained optimal solutions with all of the inversion algorithms tested if the parameter bounds and control variables were constrained properly. However, the efficiency of processing time use varied with the control variables obtained. In addition, we investigated if temperature dependence formalization impacted optimally the parameter estimation process. We found that the model with a peaked temperature response provided the best fit to the data.

Keywords: optimization algorithms; PN, Ci curve; parameter estimation

Received: March 25, 2013; Accepted: September 16, 2013; Published: June 1, 2014Show citation

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Wang, H.B., Ma, M.G., Xie, Y.M., Wang, X.F., & Wang, J. (2014). Parameter inversion estimation in photosynthetic models: Impact of different simulation methods. Photosynthetica52(2), 233-246. doi: 10.1007/s11099-014-0027-8.
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References

  1. Bernacchi, C.J., Pimentel, C., Long, S.P.: In vivo temperature response functions of parameters required to model RuBPlimited photosynthesis. - Plant Cell Environ. 26: 1419-1430, 2003. Go to original source...
  2. Bernacchi, C.J., Portis, A.R., Nakano, H., et al.: Temperature response of mesophyll conductance: Implications for the determination of Rubisco enzyme kinetics and for limitations to photosynthesis in vivo. - Plant Physiol. 130: 1992-1998, 2002.
  3. Bernacchi, C.J., Singsaas, E.L., Pimentel, C., et al.: Improved temperature response functions for models of Rubisco-limited photosynthesis. - Plant Cell Environ. 24: 253-259, 2001. Go to original source...
  4. Duan, Q., Sorooshian, S., Gupta, V.K.: Effective and efficient global optimization for conceptual rainfall-runoff models. - Water Resour. Res. 28: 1015-1031, 1992. Go to original source...
  5. Duan, Q.Y., Gupta, V.K., Sorooshian, S.: Shuffled complex evolution approach for effective and efficient global minimization. - J. Optimiz. Theory App. 76: 501-521, 1993. Go to original source...
  6. Dubois, J.B., Fiscus, E.L., Booker, F.L., et al.: Optimizing the statistical estimation of the parameters of the Farquhar-von Caemmerer-Berry model of photosynthesis. - New Phytol. 176: 402-414, 2007. Go to original source...
  7. Ethier, G.J., Livingston, N.J.: On the need to incorporate sensitivity to CO2 transfer conductance into the Farquhar-von Caemmerer-Berry leaf photosynthesis model. - Plant Cell Environ. 27: 137-153, 2004. Go to original source...
  8. Farquhar, G.D., von Caemmerer, S., Berry, J.A.: A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species. - Planta 149: 78-90, 1980. Go to original source...
  9. Farquhar, G.D., Wong, S.C.: An empirical model of stomatal conductance. - Aust. J. Plant Physiol. 11: 191-209, 1984. Go to original source...
  10. Goffe, W.L., Ferrier, G.D., Rogers, J.: Global optimization of statistical functions with simulated annealing. - J. Econometrics 60: 65-99, 1994. Go to original source...
  11. Gu, L., Pallardy, S.G., Tu, K., et al.: Reliable estimation of biochemical parameters from C3 leaf photosynthesis-intercellular carbon dioxide response curves. - Plant Cell Environ. 33: 1852-1874, 2010.
  12. Hanson, P.J., Amthor, J.S., Wullschleger, S.D., et al.: Oak forest carbon and water simulations: Model intercomparisons and evaluations against independent data. - Ecol. Monogr. 74: 443-489, 2004. Go to original source...
  13. Harley, P.C., Thomas, R.B., Reynolds, J.F., Strain, B.R.: Modeling photosynthesis of cotton grown in elevated CO2. - Plant Cell Environ. 15: 271-282, 1992. Go to original source...
  14. Kattge, J., Knorr, W.: Temperature acclimation in a biochemical model of photosynthesis: a reanalysis of data from 36 species. - Plant Cell Environ. 30: 1176-1190, 2007. Go to original source...
  15. Kennedy, J., Eberhart, R.C.: Particle swarm optimization. - Proceedings of IEEE international conference on neural networks. Pp: 1942-1948, 1995.
  16. Kosugi, Y., Matsuo, N.: Seasonal fluctuations and temperature dependence of leaf gas exchange parameters of co-occurring evergreen and deciduous trees in a temperate broad-leaved forest. - Tree Physiol. 26: 1173-1184, 2006. Go to original source...
  17. Kosugi, Y., Shibata, S., Kobashi, S.: Parameterization of the CO2 and H2O gas exchange of several temperate deciduous broadleaved trees at the leaf scale considering seasonal changes. - Plant Cell Environ. 26: 285-301, 2003. Go to original source...
  18. Kruger, J.: Simulated annealing: a tool for data assimilation in to an almost steady model state. - J. Phys. Oceanogr. 23: 679-688, 1993. Go to original source...
  19. Leuning, R.: Scaling to a common temperature improves the correlation between the photosynthesis parameters Jmax and Vcmax. - J. Exp. Bot. 48: 345-347, 1997. Go to original source...
  20. Leuning, R.: Temperature dependence of two parameters in a photosynthesis model. - Plant Cell Environ. 25: 1205-1210, 2002. Go to original source...
  21. Long, S.P., Bernacchi, C.J.: Gas exchange measurements, what can they tell us about the underlying limitations to photosynthesis? Procedures and sources of error. - J. Exp. Bot. 54: 2393-2401, 2003. Go to original source...
  22. Long, S.P., Postl, W.F., Bolhár-Nordenkampf, H.R.: Quantum yields for uptake of carbon dioxide in C3 vascular plants of contrasting habitats and taxonomic groupings. - Planta 189: 226-234, 1993. Go to original source...
  23. Manter, D.K., Kerrigan, J.: A/C-i curve analysis across a range of woody plant species: influence of regression analysis parameters and mesophyll conductance. - J. Exp. Bot. 55: 2581-2588, 2004. Go to original source...
  24. Matear, R.J.: Parameter optimization and analysis of ecosystem models using simulated annealing: A case study at Station P. - J. Mar. Res. 53: 571-607, 1995. Go to original source...
  25. Medlyn, B.E., Dreyer, E., Ellsworth, D., et al.: Temperature response of parameters of a biochemically based model of photosynthesisII. A review of experimental data. - Plant Cell Environ. 25: 1167-1179, 2002. Go to original source...
  26. Metropolis, N., Rosenbluth, A.W, Rosenbluth, M.N., et al.: Equation of state calculations by fast computing machines. - J. Chem. Phys. 21: 1087-1092, 1953. Go to original source...
  27. Miao, Z.W., Xu, M., Lathrop, J.R., Wang, Y.F.: Comparison of the A-C-c curve fitting methods in determining maximum ribulose 1.5-bisphosphate carboxylase/oxygenase carboxy-lation rate, potential light saturated electron transport rate and leaf dark respiration. - Plant Cell Environ. 32: 109-122, 2009. Go to original source...
  28. Nash, J.E., Sutcliffe, J.V.: River flow forecasting through conceptual models, part I: a discussion of principles. - J. Hydrol. 10: 282-290, 1970. Go to original source...
  29. Niinemets, U., Díaz-Espejo, A., Flexas, J., et al.: Importance of mesophyll diffusion conductance in estimation of plant photosynthesis in the field. - J. Exp. Bot. 60: 2271-2282, 2009. Go to original source...
  30. Ooka, R., Komamura, K.: Optimal design method for building energy systems using genetic algorithms. - Build. Environ. 44: 1538-1544, 2009. Go to original source...
  31. Parsopoulos, K.E., Vrahatis, M.N.: Recent approaches to global optimization problems through particle swarm optimization. - Nat. Comput. 1: 235-306, 2002. Go to original source...
  32. Patrick, L.D., Ogle, K., Tissue, D.T.: A hierarchical Bayesian approach for estimation of photosynthetic parameters of C3 plants. - Plant Cell Environ. 32: 1695-1709, 2009. Go to original source...
  33. Qian, T., Elings, A., Dieleman, J.A., et al.: Estimation of photosynthesis parameters for a modified Farquhar-von Caemmerer-Berry model using simultaneous estimation method and nonlinear mixed effects model. - Environ. Exp. Bot. 82: 66-73, 2012. Go to original source...
  34. Sedighizadeh, D., Masehian, E.: Particle swarm optimization methods, taxonomy and applications. - Int. J. Comp. Theor. Eng. 1: 1793-8201, 2009. Go to original source...
  35. Sharkey, T.D., Bernacchi, C.J., Farquhar, G.D., Singsaas, E.L.: Fitting photosynthetic carbon dioxide response curves for C3 leaves. - Plant Cell Environ. 30: 1035-1040, 2007. Go to original source...
  36. Sharkey, T.D., Berry, J.A., Raschke, K.: Starch and sucrose synthesis in Phaseolus vulgaris as affected by light, CO2, and abscisic acid. - Plant Physiol. 77: 617-620, 1985. Go to original source...
  37. Sitch, S., Smith, B., Prentice, I.C., et al.: Evaluation of ecosystem dynamics, plant geography and terrestrial carbon cycling in the LPJ dynamic global vegetation model. - Glob. Change Biol. 9: 161-185, 2003. Go to original source...
  38. Sorooshian, S., Duan, Q., Gupta, V.K.: Calibration of conceptual rainfall-runoffmodels using global optimization: application to the Sacramento soil moisture accounting model. - Water Resour. Res. 29: 1185-1194, 1993. Go to original source...
  39. Su, Y., Zhu, G., Miao, Z. et al.: Estimation of parameters of a biochemically based model of photosynthesis using a genetic algorithm. - Plant Cell Environ. 32: 1710-1723, 2009. Go to original source...
  40. Thornton, P.E., Law, B.E., Gholz, H.L., et al.: Modeling and measuring the effects of disturbance history and climate on carbon and water budgets in evergreen needleleaf forests. - Agr. Forest Meteorol. 113: 185-222, 2002. Go to original source...
  41. von Caemmerer, S., Evans, J,R., Hudson, G.S., Andrews, T.J.: The kinetics of ribulose-1,5-bisphosphate carboxylase/oxygenase in-vivo inferred from measurements of photosynthesis in leaves of transgenic tobacco. - Planta 195: 88-97, 1994. Go to original source...
  42. Vrugt, J.A., Gupta, H.V., Bouten, W., Sorooshian, S.: A Shuffled Complex Evolution Metropolis algorithm for optimization and uncertainty assessment of hydrologic model parameters. - Water Resour. Res. 39: 1201, 2003. Go to original source...
  43. Zhang, X.S., Srinivasan, R., Zhao, K.G., Van Liew. M.: Evaluation of global optimization algorithms for parameter calibration of a computationally intensive hydrologic model. - Hydrol. Process. 23: 430-441, 2009. Go to original source...