A hierarchical Bayesian approach for estimation of photosynthetic parameters of C<sub>3</sub>plants

Patrick, Lisa; Ogle, Kiona; Tissue, David T.

doi:10.1111/j.1365-3040.2009.02029.x

Cited by 46 publications

(52 citation statements)

References 86 publications

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“…First, A-C i data are time-consuming to collect: each CO 2 response curve may take 1 h to set up and measure, particularly in stressed plants where stomatal closure may even prohibit such measurements. Second, a number of competing methods exist for fitting the data (Dubois et al, 2007;Sharkey et al, 2007;Patrick et al, 2009;Gu et al, 2010;Feng & Dietze, 2013) and, depending on the chosen method, parameter estimates may vary even for the same datasets (Miao et al, 2009;Niinemets et al, 2009). Many individual experimental studies tend to focus on only a small number of species and, more often than not, they concern plants grown and measured in controlled environments (laboratory or glasshouse).…”

Section: Introductionmentioning

confidence: 99%

A test of the ‘one‐point method’ for estimating maximum carboxylation capacity from field‐measured, light‐saturated photosynthesis

et al. 2015

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Key words: A-C i curve, leaf respiration during the day (R day ), maximum carboxylation rate (V cmax ), net photosynthetic rate at saturating irradiance and at ambient atmospheric CO 2 concentration (A sat ). SummarySimulations of photosynthesis by terrestrial biosphere models typically need a specification of the maximum carboxylation rate (V cmax ). Estimating this parameter using A-C i curves (net photosynthesis, A, vs intercellular CO 2 concentration, C i ) is laborious, which limits availability of V cmax data. However, many multispecies field datasets include net photosynthetic rate at saturating irradiance and at ambient atmospheric CO 2 concentration (A sat ) measurements, from which V cmax can be extracted using a 'one-point method'.We used a global dataset of A-C i curves (564 species from 46 field sites, covering a range of plant functional types) to test the validity of an alternative approach to estimate V cmax from A sat via this 'one-point method'.If leaf respiration during the day (R day ) is known exactly, V cmax can be estimated with an r 2 value of 0.98 and a root-mean-squared error (RMSE) of 8.19 lmol m À2 s À1 . However, R day typically must be estimated. Estimating R day as 1.5% of V cmax, we found that V cmax could be estimated with an r 2 of 0.95 and an RMSE of 17.1 lmol m À2 s À1 . The one-point method provides a robust means to expand current databases of fieldmeasured V cmax , giving new potential to improve vegetation models and quantify the environmental drivers of V cmax variation.

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Section: Introductionmentioning

confidence: 99%

A test of the ‘one‐point method’ for estimating maximum carboxylation capacity from field‐measured, light‐saturated photosynthesis

et al. 2015

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“…Bayesian hierarchical models have been developed in recent years for a number of environmental applications (Borsuk et al 2001;Lockwood et al 2001Lockwood et al , 2004Agarwal et al 2005;Goyal et al 2005;Cable et al 2009;Patrick et al 2009). The approach allows model inferences to be shared across sites (or other subunits, such as species) and yields both global and subunit-specific parameter estimates.…”

Section: Bayesian Statistical Formulation and Parameter Estimationmentioning

confidence: 97%

Bayesian hierarchical models for soil CO2 flux and leak detection at geologic sequestration sites

et al. 2011

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Proper characterizations of background soil CO 2 respiration rates are critical for interpreting CO 2 leakage monitoring results at geologic sequestration sites. In this paper, a method is developed for determining temperature-dependent critical values of soil CO 2 flux for preliminary leak detection inference. The method is illustrated using surface CO 2 flux measurements obtained from the AmeriFlux network fit with alternative models for the soil CO 2 flux versus soil temperature relationship. The models are fit first to determine pooled parameter estimates across the sites, then using a Bayesian hierarchical method to obtain both global and site-specific parameter estimates. Model comparisons are made using the deviance information criterion (DIC), which considers both goodness of fit and model complexity. The hierarchical models consistently outperform the corresponding pooled models, demonstrating the need for site-specific data and estimates when determining relationships for background soil respiration. A hierarchical model that relates the square root of the CO 2 flux to a quadratic function of soil temperature is found to provide the best fit for the AmeriFlux sites among the models tested. This model also yields effective prediction intervals, consistent with the upper envelope of the flux data across the modeled sites and temperature ranges. Calculation of upper prediction intervals using the proposed method can provide a basis for setting critical values in CO 2 leak detection monitoring at sequestration sites.

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“…At least three replicates were taken for each species, except for eucdiv, fluvir, gymsen, sclbir (n = 2) and pelafr and senpet (n = 1) (see Table 1 for species names). Four photosynthetic parameters (Table 2) were estimated by fitting a model developed by Patrick et al (2009) to the measured data.The model was fitted using MCMC sampling with the JAGS-software (Plummer 2003) and using the R coda package (Plummer et al 2006 Twenty-nine traits for the three growth forms shrub, shrub-sometimes-small-tree (SST) and tree were measured and compared. Mean values per growth form are shown with standard deviation.…”

Section: Photosynthesismentioning

confidence: 99%

How to tell a shrub from a tree: A life‐history perspective from a South African savanna

2014

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The ecological differences between 'shrubs' and 'trees' are surprisingly poorly understood and clear ecological definitions of these two constructs do not exist. It is not clear whether a shrub is simply a small tree or whether shrubs represent a distinct life-history strategy. This question is of special interest in African savannas, where shrubs and trees often co-dominate, but are often treated uniformly as 'woody plants' even though the tree to shrub ratio is an important determinant of ecosystem functioning. In this study we use data from a long-term fire experiment, together with a trait-based approach to test (i) if woody species usually classified as shrubs or trees in African savanna differ in key traits related to disturbance and resource use; and (ii) if these differences justify the interpretation of the two growth forms as distinct life-history strategies. We measured for 22 of the most common woody plant species of a South African savanna 27 plant traits related to plant architecture, life-history, leaf characteristics, photosynthesis and resprouting capacity. Furthermore we evaluated their performance during a long-term fire experiment. We found that woody plants authors call (i) shrubs; (ii) shrubs sometimes small trees; and (3) trees responded differently to long-term fire treatments. We additionally found significant differences in architecture, diameter-height-allometry, foliage density, resprouting vigour after fire, minimum fruiting height and foliar δ 13 C between these three woody plant types. We interpret these findings as evidence for at least two different life-history-strategies: an avoidance/adaptation strategy for shrubs (early reproduction + adaptation to minor disturbance) and an escape strategy for trees (promoted investment in height growth + delayed reproduction).

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A hierarchical Bayesian approach for estimation of photosynthetic parameters of C₃plants

Cited by 46 publications

References 86 publications

A test of the ‘one‐point method’ for estimating maximum carboxylation capacity from field‐measured, light‐saturated photosynthesis

A test of the ‘one‐point method’ for estimating maximum carboxylation capacity from field‐measured, light‐saturated photosynthesis

Bayesian hierarchical models for soil CO2 flux and leak detection at geologic sequestration sites

How to tell a shrub from a tree: A life‐history perspective from a South African savanna

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A hierarchical Bayesian approach for estimation of photosynthetic parameters of C3plants

Cited by 46 publications

References 86 publications

A test of the ‘one‐point method’ for estimating maximum carboxylation capacity from field‐measured, light‐saturated photosynthesis

A test of the ‘one‐point method’ for estimating maximum carboxylation capacity from field‐measured, light‐saturated photosynthesis

Bayesian hierarchical models for soil CO2 flux and leak detection at geologic sequestration sites

How to tell a shrub from a tree: A life‐history perspective from a South African savanna

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A hierarchical Bayesian approach for estimation of photosynthetic parameters of C₃plants