@article{allen:1996a, title = {Assessing Integrity of Weather Data for Reference Evapotranspiration Estimation}, author = {Allen, Richard G.}, year = {1996}, month = mar, journal = {Journal of irrigation and drainage engineering}, volume = {122}, number = {2}, pages = {97--106}, doi = {10.1061/(ASCE)0733-9437(1996)122:2(97)}, abstract = {Procedures and guidelines are recommended for assessing integrity, quality, and reasonableness of measured weather data and equipment calibration for automated and electronic agricultural weather stations. The procedures include calculation of hourly and 24-h clear sky envelopes for solar radiation, validation of net radiation measurements using calculation equations, and evaluation of expected trends and relationships between air vapor content and air temperature. The procedures for creating clear sky solar radiation envelopes include equations to account for the effects of atmospheric water vapor content and sun angle. Procedures for adjusting air temperature and air vapor content data are introduced to compensate for the aridity of the weather station environment. All of the guidelines are simple and straightforward, and can serve as preliminary ``filters'' by which to scrutinize weather measurements and as near real-time data flagging procedures for agricultural weather networks.} } @techreport{allen:1998a, title = {Crop Evapotranspiration - {{Guidelines}} for Computing Crop Water Requirements}, author = {Allen, Richard G. and Pereira, Luis S and Raes, Dirk and Smith, Martin}, year = {1998}, number = {56}, address = {Rome}, institution = {FAO} } @article{argles:2020a, title = {Robust {{Ecosystem Demography}} ({{RED}} Version 1.0): A Parsimonious Approach to Modelling Vegetation Dynamics in {{Earth}} System Models}, author = {Argles, Arthur P K and Moore, Jonathan R and Huntingford, Chris and Wiltshire, Andrew J and Harper, Anna B and Jones, Chris D and Cox, Peter M}, year = {2020}, journal = {Geoscientific Model Development}, volume = {13}, number = {9}, pages = {4067--4089}, doi = {10.5194/gmd-13-4067-2020}, langid = {english} } @article{Atkin:2015hk, title = {Global Variability in Leaf Respiration in Relation to Climate, Plant Functional Types and Leaf Traits.}, author = {Atkin, Owen K and Bloomfield, Keith J and Reich, Peter B and Tjoelker, Mark G and Asner, Gregory P. and Bonal, Damien and B{\"o}nisch, Gerhard and Bradford, Matt G and Cernusak, Lucas A and Cosio, Eric G and Creek, Danielle and Crous, Kristine Y and Domingues, Tomas F and Dukes, Jeffrey S and Egerton, John J G and Evans, John R and Farquhar, Graham D and Fyllas, Nikolaos M and Gauthier, Paul P G and Gloor, Emanuel and Gimeno, Teresa E and Griffin, Kevin L and Guerrieri, Rossella and Heskel, Mary A and Huntingford, Chris and Ishida, Fran{\c c}oise Yoko and Kattge, Jens and Lambers, Hans and Liddell, Michael J and Lloyd, Jon and Lusk, Christopher H and Martin, Roberta E and Maksimov, Ayal P and Maximov, Trofim C and Malhi, Yadvinder and Medlyn, Belinda E and Meir, Patrick and Mercado, Lina M and Mirotchnick, Nicholas and Ng, Desmond and Niinemets, {\"U}lo and O'Sullivan, Odhran S and Phillips, Oliver L and Poorter, Lourens and Poot, Pieter and Prentice, I. Colin and Salinas, Norma and Rowland, Lucy M and Ryan, Michael G and Sitch, Stephen and Slot, Martijn and Smith, Nicholas G and Turnbull, Matthew H and VanderWel, Mark C and Valladares, Fernando and Veneklaas, Erik J and Weerasinghe, Lasantha K and Wirth, Christian and Wright, Ian J. and Wythers, Kirk R and Xiang, Jen and Xiang, Shuang and {Zaragoza-Castells}, Joana}, year = {2015}, month = apr, journal = {New Phytologist}, volume = {206}, number = {2}, eprint = {25581061}, eprinttype = {pmid}, pages = {614--636}, doi = {10.1111/nph.13253}, abstract = {Leaf dark respiration (Rdark ) is an important yet poorly quantified component of the global carbon cycle. Given this, we analyzed a new global database of Rdark and associated leaf traits. Data for 899 species were compiled from 100 sites (from the Arctic to the tropics). Several woody and nonwoody plant functional types (PFTs) were represented. Mixed-effects models were used to disentangle sources of variation in Rdark . Area-based Rdark at the prevailing average daily growth temperature (T) of each site increased only twofold from the Arctic to the tropics, despite a 20{$^\circ$}C increase in growing T (8-28{$^\circ$}C). By contrast, Rdark at a standard T (25{$^\circ$}C, Rdark (25) ) was threefold higher in the Arctic than in the tropics, and twofold higher at arid than at mesic sites. Species and PFTs at cold sites exhibited higher Rdark (25) at a given photosynthetic capacity (Vcmax (25) ) or leaf nitrogen concentration ([N]) than species at warmer sites. Rdark (25) values at any given Vcmax (25) or [N] were higher in herbs than in woody plants. The results highlight variation in Rdark among species and across global gradients in T and aridity. In addition to their ecological significance, the results provide a framework for improving representation of Rdark in terrestrial biosphere models (TBMs) and associated land-surface components of Earth system models (ESMs).}, langid = {english} } @article{badeck:2005a, title = {Post-Photosynthetic Fractionation of Stable Carbon Isotopes between Plant Organs---a Widespread Phenomenon}, author = {Badeck, Franz-W. and Tcherkez, Guillaume and Nogu{\'e}s, Salvador and Piel, Cl{\'e}ment and Ghashghaie, Jaleh}, year = {2005}, journal = {Rapid Communications in Mass Spectrometry}, volume = {19}, number = {11}, pages = {1381--1391}, doi = {10.1002/rcm.1912}, abstract = {Abstract Discrimination against 13C during photosynthesis is a well-characterised phenomenon. It leaves behind distinct signatures in organic matter of plants and in the atmosphere. The former is depleted in 13C, the latter is enriched during periods of preponderant photosynthetic activity of terrestrial ecosystems. The intra-annual cycle and latitudinal gradient in atmospheric 13C resulting from photosynthetic and respiratory activities of terrestrial plants have been exploited for the reconstruction of sources and sinks through deconvolution by inverse modelling. Here, we compile evidence for widespread post-photosynthetic fractionation that further modifies the isotopic signatures of individual plant organs and consequently leads to consistent differences in {$\delta$}13C between plant organs. Leaves were on average 0.96‰ and 1.91‰ more depleted than roots and woody stems, respectively. This phenomenon is relevant if the isotopic signature of CO2-exchange fluxes at the ecosystem level is used for the reconstruction of individual sources and sinks. It may also modify the parameterisation of inverse modelling approaches if it leads to different isotopic signatures of organic matter with different residence times within the ecosystems and to a respiratory contribution to the average difference between the isotopic composition of plant organic matter and the atmosphere. We discuss the main hypotheses that can explain the observed inter-organ differences in {$\delta$}13C. Copyright {\copyright} 2005 John Wiley \& Sons, Ltd.} } @article{BerberanSantos:2009bk, title = {On the Barometric Formula inside the {{Earth}}}, author = {{Berberan-Santos}, Mario N and Bodunov, Evgeny N and Pogliani, Lionello}, year = {2009}, month = oct, journal = {Journal of Mathematical Chemistry}, volume = {47}, number = {3}, pages = {990--1004}, doi = {10.1007/s10910-009-9620-7}, langid = {english} } @article{berger:1978a, title = {Long-{{Term Variations}} of {{Daily Insolation}} and {{Quaternary Climatic Changes}}}, author = {Berger, Andr{\'e}L}, year = {1978}, month = dec, journal = {Journal of the Atmospheric Sciences}, volume = {35}, number = {12}, pages = {2362--2367}, issn = {0022-4928, 1520-0469}, doi = {10.1175/1520-0469(1978)035<2362:LTVODI>2.0.CO;2}, urldate = {2023-07-13}, abstract = {Abstract The first part of this note provides all trigonometrical formulas which allow the direct spectral analysis and the computation of those long-term variations of the earth's orbital elements which are of primary interest for the computation of the insolation. The elements are the eccentricity, the longitude of the perihelion, the processional parameter and the obliquity. This new formulary is much more simple to use than the ones previously designed and still provides excellent accuracy, mainly because it takes into account the influence of the most important higher order terms in the series expansions. The second part is devoted to the computation of the daily insolation both for calendar and solar dates.}, langid = {english} } @article{berger:1993a, title = {Insolation and {{Earth}}'s Orbital Periods}, author = {Berger, Andr{\'e} and Loutre, Marie-France and Tricot, Christian}, year = {1993}, journal = {Journal of Geophysical Research: Atmospheres}, volume = {98}, number = {D6}, pages = {10341--10362}, issn = {2156-2202}, doi = {10.1029/93JD00222}, urldate = {2024-08-02}, abstract = {Solar irradiance received on a horizontal surface depends on the solar output, the semimajor axis of the elliptical orbit of the Earth around the sun (a), the distance from the Earth to the sun (r), and the zenith distance (z). The spectrum of the distance, r, for a given value of the true longitude, {$\lambda$}, displays mainly the precessional periods and, with much less power, half precession periods, eccentricity periods, and some combination tones. The zenith distance or its equivalent, the elevation angle (E), is only a function of obliquity ({$\epsilon$}) for a given latitude, {$\phi$}, true longitude, and hour angle, H. Therefore the insolation at a given constant value of z is only a function of precession and eccentricity. On the other hand, the value of the hour angle, H, corresponding to this fixed value of z varies with {$\varepsilon$}, except for the equinoxes, where H corresponding to a constant z also remains constant through time. Three kinds of insolation have been computed both analytically and numerically: the instantaneous insolation (irradiance) at noon, the daily irradiation, and the irradiations received during particular time intervals of the day defined by two constant values of the zenith distance (diurnal irradiations). Mean irradiances (irradiations divided by the length of the time interval over which they are calculated) are also computed for different time intervals, like the interval between sunrise and sunset, in particular. Examples of these insolations are given in this paper for the equinoxes and the solstices. At the equinoxes, for each latitude, all insolations are only a function of precession (this invalidates the results obtained by Cerveny [1991]). At the solstices, both precession and obliquity are present, although precession dominates for most of the latitudes. Because the lengths of the astronomical seasons are secularly variable (in terms of precession only), a particular calendar day does not always correspond to the same position relative to the sun through geological time. Similarly, a given longitude of the Sun on its orbit does not correspond to the same calendar day. For example, 103 kyr ago, assuming arbitrarily that the spring equinox is always on March 21, autumn began on September 13, and 114 kyr ago, it began on September 27, the length of the summer season being 85 and 98 calendar days, respectively, at these remote times in the past.}, langid = {english} } @article{Bernacchi:2001kg, title = {Improved Temperature Response Functions for Models of {{Rubisco-limited}} Photosynthesis}, author = {Bernacchi, C J and Singsaas, E L and Pimentel, C and Portis Jr, A R and Long, S P}, year = {2001}, journal = {Plant, Cell \& Environment}, volume = {24}, number = {2}, pages = {253--259}, doi = {10.1111/j.1365-3040.2001.00668.x}, langid = {english} } @article{Bernacchi:2003dc, title = {In Vivo Temperature Response Functions of Parameters Required to Model {{RuBP-limited}} Photosynthesis}, author = {Bernacchi, C J and Pimentel, C and Long, S P}, year = {2003}, month = sep, journal = {Plant, Cell \& Environment}, volume = {26}, number = {9}, pages = {1419--1430}, doi = {10.1046/j.0016-8025.2003.01050.x}, abstract = {The leaf model of C3 photosynthesis of Farquhar, von Caemmerer \& Berry (Planta 149, 78--90, 1980) provides the basis for scaling carbon exchange from leaf to canopy and Earth-System models, and is wid...}, langid = {english} } @article{boyd:2015a, title = {Temperature Response of {{C4}} Photosynthesis: {{Biochemical}} Analysis of {{Rubisco}}, {{Phosphoenolpyruvate Carboxylase}} and {{Carbonic Anhydrase}} in {{Setaria}} Viridis.}, shorttitle = {Temperature Response of {{C4}} Photosynthesis}, author = {Boyd, Ryan Allen and Gandin, Anthony and Cousins, Asaph B}, year = {2015}, month = sep, journal = {Plant Physiology}, pages = {pp.00586.2015}, issn = {0032-0889, 1532-2548}, doi = {10.1104/pp.15.00586}, urldate = {2022-05-20}, langid = {english} } @article{brokaw:2000a, title = {The {{H}} for {{DBH}}}, author = {Brokaw, Nicholas and Thompson, Jill}, year = {2000}, month = apr, journal = {Forest Ecology and Management}, volume = {129}, number = {1}, pages = {89--91}, issn = {0378-1127}, doi = {10.1016/S0378-1127(99)00141-3}, urldate = {2025-06-27} } @article{cai:2020a, title = {Recent Trends in Gross Primary Production and Their Drivers: Analysis and Modelling at Flux-Site and Global Scales}, shorttitle = {Recent Trends in Gross Primary Production and Their Drivers}, author = {Cai, Wenjia and Prentice, Iain Colin}, year = {2020}, month = dec, journal = {Environmental Research Letters}, volume = {15}, number = {12}, pages = {124050}, issn = {1748-9326}, doi = {10.1088/1748-9326/abc64e}, urldate = {2022-05-16}, abstract = {Abstract Gross primary production (GPP) by terrestrial ecosystems is the largest flux in the global carbon cycle, and its continuing increase in response to environmental changes is key to land ecosystems' capacity to offset anthropogenic CO 2 emissions. However, the CO 2 - and climate-sensitivities of GPP vary among models. We applied the `P model'---a parameter-sparse and extensively tested light use efficiency (LUE) model, driven by CO 2 , climate and remotely sensed greenness data---at 29 sites with multi-year eddy-covariance flux measurements. Observed (both positive and negative) GPP trends at these sites were predicted, albeit with some bias. Increasing LUE (due to rising atmospheric CO 2 concentration) and green vegetation cover were the primary controls of modelled GPP trends across sites. Global GPP simulated by the same model increased by 0.46 {\textpm} 0.09 Pg C yr --2 during 1982--2016. This increase falls in the mid-range rate of simulated increase by the TRENDY v8 ensemble of state-of-the-art ecosystem models. The modelled LUE increase during 1900--2013 was 15\%, similar to a published estimate based on deuterium isotopomers. Rising CO 2 was the largest contributor to the modelled GPP increase. Greening, which may in part be caused by rising CO 2 , ranked second but dominated the modelled GPP change over large areas, including semi-arid vegetation on all continents. Warming caused a small net reduction in modelled global GPP, but dominated the modelled GPP increase in high northern latitudes. These findings strengthen the evidence that rising LUE due to rising CO 2 level and increased green vegetation cover (fAPAR) are the main causes of increasing GPP, and thereby, the terrestrial carbon sink.}, langid = {english} } @article{cai:2025a, title = {A Unifying Principle for Global Greenness Patterns and Trends}, author = {Cai, Wenjia and Zhu, Ziqi and Harrison, Sandy P. and Ryu, Youngryel and Wang, Han and Zhou, Boya and Prentice, Iain Colin}, year = {2025}, month = jan, journal = {Communications Earth \& Environment}, volume = {6}, number = {1}, pages = {19}, publisher = {Nature Publishing Group}, issn = {2662-4435}, doi = {10.1038/s43247-025-01992-0}, urldate = {2025-07-09}, abstract = {Vegetation cover regulates the exchanges of energy, water and carbon between land and atmosphere. Remotely-sensed fractional absorbed photosynthetically active radiation (fAPAR), a land-surface greenness measure, depends on carbon allocation to foliage while also controlling photon flux for photosynthesis. Here we use an equation with just two globally fitted parameters to describe annual maximum fAPAR as the smaller of a water-limited value transpiring a constant fraction of annual precipitation, and an energy-limited value maximizing annual plant growth. This minimalist description reproduces global greenness patterns and temporal trends in remote-sensing data, comparable to the best-performing dynamic global vegetation models. Widely observed greening is attributed principally to the influence of rising carbon dioxide on the light- and water-use efficiencies of photosynthesis; limited browning regions are attributed to drying. This research provides one key component of ecosystem function as a step towards more robust foundations for new-generation land ecosystem models.}, copyright = {2025 The Author(s)}, langid = {english} } @article{chen:2008a, title = {The Equation of State of Pure Water Determined from Sound Speeds}, author = {Chen, Chen-Tung and Fine, Rana A. and Millero, Frank J.}, year = {2008}, month = aug, journal = {The Journal of Chemical Physics}, volume = {66}, number = {5}, pages = {2142--2144}, issn = {0021-9606}, doi = {10.1063/1.434179}, urldate = {2023-07-04}, abstract = {The equation of state of water valid over the range 0--100\,{$^\circ$}C and 0--1000 bar has been determined from the high pressure sound velocities of Wilson, which were reanalyzed by Chen and Millero. The equation of state has a maximum error of {\textpm}0.01 bar-1 in isothermal compressibility and is in the form of a secant bulk modulus: K=V0P/(V0-V) =K0+AP+BP2, where K, K0, and V, V0 are the secant bulk moduli and specific volumes at applied pressures P and 0 (1 atm), respectively; A and B are temperature dependent parameters. The good agreement (to within 20{\texttimes}10-6 cm3\,g-1) of specific volumes calculated using the above equation with those obtained from other modifications of the Wilson sound velocity data demonstrates the reliability of the sound velocity method for determining equations of state.} } @article{colinprentice:1993a, title = {A Simulation Model for the Transient Effects of Climate Change on Forest Landscapes}, author = {Prentice, Iain Colin and Sykes, Martin T. and Cramer, Wolfgang}, year = {1993}, month = jan, journal = {Ecological Modelling}, volume = {65}, number = {1}, pages = {51--70}, issn = {0304-3800}, doi = {10.1016/0304-3800(93)90126-D}, urldate = {2024-10-15}, abstract = {Forests are likely to show complex transient responses to rapid changes in climate. The model described here simulates the dynamics of forest landscapes in a changing environment with simple phenomenological equations for tree growth processes and local environmental feedbacks. Tree establishment and growth rates are modified by species-specific functions describing the effects of winter and summer temperature limitations, accumulated annual foliage net assimilation and sapwood respiration as functions of temperature, CO2 fertilization, and growing-season drought. These functions provide external conditions for the simulation of patch-scale forest dynamics by a forest succession model, FORSKA, in which all of the trees on each 0.1 ha patch interact by competition for light and nutrients. The landscape is simulated as an array of such patches. The probability of disturbance on a patch is a power function of time since disturbance. Forest structure, composition and biomass simulated for the landscape average in boreal and temperate deciduous forests approach reasonable equilibrium values in 200--400 years. A climatic warning scenario is applied to central Sweden, where temperature and precipitation increases are shown to interact with each other and with soil water capacity in determining the transient and equilibrium responses of the forest landscape to climate change.} } @article{davis:2017a, title = {Simple Process-Led Algorithms for Simulating Habitats ({{SPLASH}} v.1.0): Robust Indices of Radiation, Evapotranspiration and Plant-Available Moisture}, shorttitle = {Simple Process-Led Algorithms for Simulating Habitats ({{SPLASH}} v.1.0)}, author = {Davis, Tyler W. and Prentice, I. Colin and Stocker, Benjamin D. and Thomas, Rebecca T. and Whitley, Rhys J. and Wang, Han and Evans, Bradley J. and {Gallego-Sala}, Angela V. and Sykes, Martin T. and Cramer, Wolfgang}, year = {2017}, month = feb, journal = {Geoscientific Model Development}, volume = {10}, number = {2}, pages = {689--708}, publisher = {Copernicus GmbH}, issn = {1991-959X}, doi = {10.5194/gmd-10-689-2017}, urldate = {2023-07-05}, abstract = {Bioclimatic indices for use in studies of ecosystem function, species distribution, and vegetation dynamics under changing climate scenarios depend on estimates of surface fluxes and other quantities, such as radiation, evapotranspiration and soil moisture, for which direct observations are sparse. These quantities can be derived indirectly from meteorological variables, such as near-surface air temperature, precipitation and cloudiness. Here we present a consolidated set of simple process-led algorithms for simulating habitats (SPLASH) allowing robust approximations of key quantities at ecologically relevant timescales. We specify equations, derivations, simplifications, and assumptions for the estimation of daily and monthly quantities of top-of-the-atmosphere solar radiation, net surface radiation, photosynthetic photon flux density, evapotranspiration (potential, equilibrium, and actual), condensation, soil moisture, and runoff, based on analysis of their relationship to fundamental climatic drivers. The climatic drivers include a minimum of three meteorological inputs: precipitation, air temperature, and fraction of bright sunshine hours. Indices, such as the moisture index, the climatic water deficit, and the Priestley--Taylor coefficient, are also defined. The SPLASH code is transcribed in C++, FORTRAN, Python, and R. A total of 1 year of results are presented at the local and global scales to exemplify the spatiotemporal patterns of daily and monthly model outputs along with comparisons to other model results.}, langid = {english} } @article{DeKauwe:2015im, title = {A Test of an Optimal Stomatal Conductance Scheme within the {{CABLE}} Land Surface Model}, author = {De Kauwe, M G and Kala, J and Lin, Y S and Pitman, A J and Medlyn, B E and Duursma, R A and Abramowitz, G and Wang, Y P and Miralles, D G}, year = {2015}, month = feb, journal = {Geoscientific Model Development}, volume = {8}, number = {2}, pages = {431--452}, publisher = {Copernicus GmbH}, doi = {10.5194/gmd-8-431-2015}, abstract = {{\textexclamdown}p{\textquestiondown}{\textexclamdown}strong class="journal-contentHeaderColor"{\textquestiondown}Abstract.{\textexclamdown}/strong{\textquestiondown} Stomatal conductance ({\textexclamdown}i{\textquestiondown}g{\textexclamdown}/i{\textquestiondown}{\textexclamdown}sub{\textquestiondown}s{\textexclamdown}/sub{\textquestiondown}) affects the fluxes of carbon, energy and water between the vegetated land surface and the atmosphere. We test an implementation of an optimal stomatal conductance model within the Community Atmosphere Biosphere Land Exchange (CABLE) land surface model (LSM). In common with many LSMs, CABLE does not differentiate between {\textexclamdown}i{\textquestiondown}g{\textexclamdown}/i{\textquestiondown}{\textexclamdown}sub{\textquestiondown}s{\textexclamdown}/sub{\textquestiondown} model parameters in relation to plant functional type (PFT), but instead only in relation to photosynthetic pathway. We constrained the key model parameter "{\textexclamdown}i{\textquestiondown}g{\textexclamdown}/i{\textquestiondown}{\textexclamdown}sub{\textquestiondown}1{\textexclamdown}/sub{\textquestiondown}", which represents plant water use strategy, by PFT, based on a global synthesis of stomatal behaviour. As proof of concept, we also demonstrate that the {\textexclamdown}i{\textquestiondown}g{\textexclamdown}/i{\textquestiondown}{\textexclamdown}sub{\textquestiondown}1{\textexclamdown}/sub{\textquestiondown} parameter can be estimated using two long-term average (1960--1990) bioclimatic variables: (i) temperature and (ii) an indirect estimate of annual plant water availability. The new stomatal model, in conjunction with PFT parameterisations, resulted in a large reduction in annual fluxes of transpiration ({\textasciitilde} 30\% compared to the standard CABLE simulations) across evergreen needleleaf, tundra and C4 grass regions. Differences in other regions of the globe were typically small. Model performance against upscaled data products was not degraded, but did not noticeably reduce existing model--data biases. We identified assumptions relating to the coupling of the vegetation to the atmosphere and the parameterisation of the minimum stomatal conductance as areas requiring further investigation in both CABLE and potentially other LSMs. We conclude that optimisation theory can yield a simple and tractable approach to predicting stomatal conductance in LSMs.{\textexclamdown}/p{\textquestiondown}}, date-added = {2021-11-11T14:04:21GMT}, date-modified = {2021-11-11T14:13:27GMT}, langid = {english}, local-url = {file://localhost/Users/dorme/References/Library.papers3/Articles/2015/De\%20Kauwe/Geoscientific\%20Model\%20Development\%202015\%20De\%20Kauwe.pdf}, rating = {0}, read = {Yes}, uri = {papers3://publication/doi/10.5194/gmd-8-431-2015} } @article{depury:1997a, title = {Simple Scaling of Photosynthesis from Leaves to Canopies without the Errors of Big-Leaf Models}, author = {De Pury, D. G. G. and Farquhar, G. D.}, year = {1997}, journal = {Plant, Cell \& Environment}, volume = {20}, number = {5}, pages = {537--557}, issn = {1365-3040}, doi = {10.1111/j.1365-3040.1997.00094.x}, urldate = {2025-07-07}, abstract = {In big-leaf models of canopy photosynthesis, the Rubisco activity per unit ground area is taken as the sum of activities per unit leaf area within the canopy, and electron transport capacity is similarly summed. Such models overestimate rates of photosynthesis and require empirical curvature factors in the response to irradiance. We show that, with any distribution of leaf nitrogen within the canopy (including optimal), the required curvature factors are not constant but vary with canopy leaf area index and leaf nitrogen content. We further show that the underlying reason is the difference between the time-averaged and instantaneous distributions of absorbed irradiance, caused by penetration of sunflecks and the range of leaf angles in canopies. These errors are avoided in models that treat the canopy in terms of a number of layers -- the multi-layer models. We present an alternative to the multi-layer model: by separately integrating the sunlit and shaded leaf fractions of the canopy, a single layered sun/shade model is obtained, which is as accurate and simpler. The model is a scaled version of a leaf model as distinct from an integrative approach.}, langid = {english} } @article{díaz:2016a, title = {The Global Spectrum of Plant Form and Function}, author = {D{\'i}az, Sandra and Kattge, Jens and Cornelissen, Johannes H C and Wright, Ian J. and Lavorel, Sandra and Dray, St{\'e}phane and Reu, Bj{\"o}rn and Kleyer, Michael and Wirth, Christian and Prentice, I. Colin and Garnier, Eric and B{\"o}nisch, Gerhard and Westoby, Mark and Poorter, Hendrik and Reich, Peter B and Moles, Angela T and Dickie, John and Gillison, Andrew N and Zanne, Amy E and Chave, J{\'e}r{\^o}me and Wright, S Joseph and Sheremet'ev, Serge N and Jactel, Herv{\'e} and Baraloto, Christopher and Cerabolini, Bruno and Pierce, Simon and Shipley, Bill and Kirkup, Donald and Casanoves, Fernando and Joswig, Julia S and G{\"u}nther, Angela and Falczuk, Valeria and R{\"u}ger, Nadja and Mahecha, Miguel D and Gorn{\'e}, Lucas D}, year = {2016}, month = jan, journal = {Nature}, volume = {529}, number = {7585}, pages = {167--171}, publisher = {Nature Publishing Group}, doi = {10.1038/nature16489}, abstract = {Nature 529, 167 (2016). doi:10.1038/nature16489}, date-added = {2021-06-14T12:23:21GMT}, date-modified = {2021-11-11T14:13:27GMT}, local-url = {file://localhost/Users/dorme/References/Library.papers3/Articles/2016/D\%C3\%ADaz/Nature\%202016\%20D\%C3\%ADaz.pdf}, rating = {0}, uri = {papers3://publication/doi/10.1038/nature16489} } @book{Duffie:2013a, title = {Solar {{Engineering}} of {{Thermal Processes}}}, author = {Duffie, John A. and Beckman, William A.}, year = {2013}, month = apr, publisher = {John Wiley \& Sons}, abstract = {The updated fourth edition of the "bible" of solar energy theory and applications Over several editions, Solar Engineering of Thermal Processes has become a classic solar engineering text and reference. This revised Fourth Edition offers current coverage of solar energy theory, systems design, and applications in different market sectors along with an emphasis on solar system design and analysis using simulations to help readers translate theory into practice. An important resource for students of solar engineering, solar energy, and alternative energy as well as professionals working in the power and energy industry or related fields, Solar Engineering of Thermal Processes, Fourth Edition features: Increased coverage of leading-edge topics such as photovoltaics and the design of solar cells and heaters A brand-new chapter on applying CombiSys (a readymade TRNSYS simulation program available for free download) to simulate a solar heated house with solar- heated domestic hot water Additional simulation problems available through a companion website An extensive array of homework problems and exercises}, googlebooks = {5uDdUfMgXYQC}, isbn = {978-1-118-41541-2}, langid = {english}, keywords = {Technology & Engineering / Electronics / General,Technology & Engineering / Mechanical,Technology & Engineering / Power Resources / General} } @article{Farquhar:1980ft, title = {A Biochemical Model of Photosynthetic {{CO2}} Assimilation in Leaves of {{C3}} Species.}, author = {Farquhar, G D and {von Caemmerer}, S and Berry, J A}, year = {1980}, month = jun, journal = {Planta}, volume = {149}, number = {1}, pages = {78--90}, doi = {10.1007/BF00386231}, abstract = {Various aspects of the biochemistry of photosynthetic carbon assimilation in C3 plants are integrated into a form compatible with studies of gas exchange in leaves. These aspects include the kinetic properties of ribulose bisphosphate carboxylase-oxygenase; the requirements of the photosynthetic carbon reduction and photorespiratory carbon oxidation cycles for reduced pyridine nucleotides; the dependence of electron transport on photon flux and the presence of a temperature dependent upper limit to electron transport. The measurements of gas exchange with which the model outputs may be compared include those of the temperature and partial pressure of CO2(p(CO2)) dependencies of quantum yield, the variation of compensation point with temperature and partial pressure of O2(p(O2)), the dependence of net CO2 assimilation rate on p(CO2) and irradiance, and the influence of p(CO2) and irradiance on the temperature dependence of assimilation rate.}, affiliation = {Department of Environmental Biology, Research School of Biological Sciences, Australian National University, P.O. Box 475, 2601, Canberra City, ACT, Australia.}, date-added = {2020-12-17T09:47:58GMT}, date-modified = {2020-12-17T09:49:44GMT}, langid = {english}, local-url = {file://localhost/Users/dorme/References/Library.papers3/Articles/1980/Farquhar/Planta\%201980\%20Farquhar.pdf}, pmid = {24306196}, rating = {0}, uri = {papers3://publication/doi/10.1007/BF00386231} } @article{farquhar:1982a, title = {On the Relationship between Carbon Isotope Discrimination and the Intercellular Carbon Dioxide Concentration in Leaves}, author = {Farquhar, Graham D and O'Leary, Marion H and Berry, Joseph A}, year = {1982}, journal = {Australian Journal of Plant Physiology}, volume = {9}, number = {2}, pages = {121}, issn = {1445-4408}, doi = {10.1071/PP9820121}, urldate = {2022-05-20}, abstract = {Theory is developed to explain the carbon isotopic composition of plants. It is shown how diffusion of gaseous COz can significantly affect carbon isotopic discrimination. The effects on discrimination by diffusion and carboxylation are integrated, yielding a simple relationship between discrimination and the ratio of the intercellular and atmospheric partial pressures of COZ. The effects of dark respiration and photorespiration are also considered, and it is suggested that they have relatively little effect on discrimination other than cia their effects on intercellular p(COz). It is also suggested that various environmental factors such as light, temperature, salinity and drought will also have effects via changes in intercellular p(C0,). A simple method is suggested for assessing water use efficiencies in the field.}, langid = {english} } @book{Fisher:1975tm, title = {Equation of State of Pure Water and Sea Water}, author = {Fisher, F H and Dial Jr, O E}, year = {1975}, publisher = {Scripps Institution of Oceanography}, date-added = {2020-11-30T12:27:10GMT}, date-modified = {2021-01-21T15:04:43GMT}, local-url = {file://localhost/Users/dorme/References/Library.papers3/Books/1975/Fisher/1975\%20Fisher.pdf}, rating = {0}, read = {Yes}, uri = {papers3://publication/uuid/5D2C2C96-7975-4AB9-8314-A988EFA489FF} } @article{frank:2015a, title = {Water-Use Efficiency and Transpiration across {{European}} Forests during the {{Anthropocene}}}, author = {Frank, D. C. and Poulter, B. and Saurer, M. and Esper, J. and Huntingford, C. and Helle, G. and Treydte, K. and Zimmermann, N. E. and Schleser, G.~H. and Ahlstr{\"o}m, A. and Ciais, P. and Friedlingstein, P. and Levis, S. and Lomas, M. and Sitch, S. and Viovy, N. and {Andreu-Hayles}, L. and Bednarz, Z. and Berninger, F. and Boettger, T. and D`Alessandro, C. M. and Daux, V. and Filot, M. and Grabner, M. and Gutierrez, E. and Haupt, M. and Hilasvuori, E. and Jungner, H. and {Kalela-Brundin}, M. and Krapiec, M. and Leuenberger, M. and Loader, N. J. and Marah, H. and {Masson-Delmotte}, V. and Pazdur, A. and Pawelczyk, S. and Pierre, M. and Planells, O. and Pukiene, R. and {Reynolds-Henne}, C. E. and Rinne, K. T. and Saracino, A. and Sonninen, E. and Stievenard, M. and Switsur, V. R. and Szczepanek, M. and {Szychowska-Krapiec}, E. and Todaro, L. and Waterhouse, J.~S. and Weigl, M.}, year = {2015}, month = jun, journal = {Nature Climate Change}, volume = {5}, number = {6}, pages = {579--583}, issn = {1758-6798}, doi = {10.1038/nclimate2614}, abstract = {Considering the combined effects of CO2 fertilization and climate change drivers on plant physiology leads to a modest increase in simulated European forest transpiration in spite of the effects of CO2-induced stomatal closure.} } @article{graven:2020a, title = {Changes to {{Carbon Isotopes}} in {{Atmospheric CO}} {\textsubscript{2}} {{Over}} the {{Industrial Era}} and {{Into}} the {{Future}}}, author = {Graven, Heather and Keeling, Ralph F. and Rogelj, Joeri}, year = {2020}, month = nov, journal = {Global Biogeochemical Cycles}, volume = {34}, number = {11}, issn = {0886-6236, 1944-9224}, doi = {10.1029/2019GB006170}, urldate = {2022-05-23}, abstract = {In this ``Grand Challenges'' paper, we review how the carbon isotopic composition of atmospheric CO2 has changed since the Industrial Revolution due to human activities and their influence on the natural carbon cycle, and we provide new estimates of possible future changes for a range of scenarios. Emissions of CO2 from fossil fuel combustion and land use change reduce the ratio of 13C/12C in atmospheric CO2 ({$\delta$}13CO2). This is because 12C is preferentially assimilated during photosynthesis and {$\delta$}13C in plant-derived carbon in terrestrial ecosystems and fossil fuels is lower than atmospheric {$\delta$}13CO2. Emissions of CO2 from fossil fuel combustion also reduce the ratio of 14C/C in atmospheric CO2 ({$\Delta$}14CO2) because 14C is absent in million-year-old fossil fuels, which have been stored for much longer than the radioactive decay time of 14C. Atmospheric {$\Delta$}14CO2 rapidly increased in the 1950s to 1960s because of 14C produced during nuclear bomb testing. The resulting trends in {$\delta$}13C and {$\Delta$}14C in atmospheric CO2 are influenced not only by these human emissions but also by natural carbon exchanges that mix carbon between the atmosphere and ocean and terrestrial ecosystems. This mixing caused {$\Delta$}14CO2 to return toward preindustrial levels in the first few decades after the spike from nuclear testing. More recently, as the bomb 14C excess is now mostly well mixed with the decadally overturning carbon reservoirs, fossil fuel emissions have become the main factor driving further decreases in atmospheric {$\Delta$}14CO2. For {$\delta$}13CO2, in addition to exchanges between reservoirs, the extent to which 12C is preferentially assimilated during photosynthesis appears to have increased, slowing down the recent {$\delta$}13CO2 trend slightly. A new compilation of ice core and flask {$\delta$}13CO2 observations indicates that the decline in {$\delta$}13CO2 since the preindustrial period is less than some prior estimates, which may have incorporated artifacts owing to offsets from different laboratories' measurements. Atmospheric observations of {$\delta$}13CO2 have been used to investigate carbon fluxes and the functioning of plants, and they are used for comparison with {$\delta$}13C in other materials such as tree rings. Atmospheric observations of {$\Delta$}14CO2 have been used to quantify the rate of air-sea gas exchange and ocean circulation, and the rate of net primary production and the turnover time of carbon in plant material and soils. Atmospheric observations of {$\Delta$}14CO2 are also used for comparison with {$\Delta$}14C in other materials in many fields such as archaeology, forensics, and physiology. Another major application is the assessment of regional emissions of CO2 from fossil fuel combustion using {$\Delta$}14CO2 observations and models. In the future, {$\delta$}13CO2 and {$\Delta$}14CO2 will continue to change. The sign and magnitude of the changes are mainly determined by global fossil fuel emissions. We present here simulations of future {$\delta$}13CO2 and {$\Delta$}14CO2 for six scenarios based on the shared socioeconomic pathways (SSPs) from the 6th Coupled Model Intercomparison Project (CMIP6). Applications using atmospheric {$\delta$}13CO2 and {$\Delta$}14CO2 observations in carbon cycle science and many other fields will be affected by these future changes. We recommend an increased effort toward making coordinated measurements of {$\delta$}13C and {$\Delta$}14C across the Earth System and for further development of isotopic modeling and model-data analysis tools.}, langid = {english} } @article{groner:2025a, title = {Harmonizing Nature's Timescales in Ecosystem Models}, author = {Groner, Vivienne P. and Cook, Jacob and Orme, C. David L. and Amarasekare, Priyanga and {Comyn-Platt}, Edward and Rallings, Taran and Joshi, Jaideep and Ewers, Robert M.}, year = {2025}, month = apr, journal = {Trends in Ecology \& Evolution}, pages = {S0169534725000746}, issn = {01695347}, doi = {10.1016/j.tree.2025.03.011}, urldate = {2025-05-06}, langid = {english} } @article{haxeltine:1996a, title = {A {{General Model}} for the {{Light-Use Efficiency}} of {{Primary Production}}}, author = {Haxeltine, A. and Prentice, I. C.}, year = {1996}, journal = {Functional Ecology}, volume = {10}, number = {5}, eprint = {2390165}, eprinttype = {jstor}, pages = {551--561}, publisher = {[British Ecological Society, Wiley]}, issn = {0269-8463}, doi = {10.2307/2390165}, urldate = {2025-03-13}, abstract = {1. Net primary production (NPP) by terrestrial ecosystems appears to be proportional to absorbed photosynthetically active radiation (APAR) on a seasonal and annual basis. This observation has been used in `diagnostic' models that estimate NPP from remotely sensed vegetation indices. In `prognostic' process-based models carbon fluxes are more commonly integrated with respect to leaf area index assuming invariant leaf photosynthetic parameters. This approach does not lead to a proportional relationship between NPP and APAR. However, leaf nitrogen content and Rubisco activity are known to vary seasonally and with canopy position, and there is evidence that this variation takes place in such a way as to nearly optimize total canopy net photosynthesis. 2. Using standard formulations for the instantaneous response of leaf net photosynthesis to APAR, we show that the optimized canopy net photosynthesis is proportional to APAR. This theory leads to reasonable values for the maximum (unstressed) light-use efficiency of gross and net primary production of C\textsubscript{3} plants at current ambient CO\textsubscript{2}, comparable with empirical estimates for agricultural crops and forest plantations. 3. By relating the standard formulations to the Collatz-Farquhar model of photosynthesis, we show that a range of observed physiological responses to temperature and CO\textsubscript{2} can be understood as consequences of the optimization. These responses include the CO\textsubscript{2} fertilization response and stomatal closure in C\textsubscript{3} plants, the increase of leaf N concentration with decreasing growing season temperature, and the downward acclimation of leaf respiration and N content with increasing ambient CO\textsubscript{2}. The theory provides a way to integrate diverse experimental observations into a general framework for modelling terrestrial primary production.} } @article{ellenberg:1967a, title = {A {{Key}} to {{Raunkiaer}} Plant Life Forms with Revised Subdivisions}, author = {Ellenberg, H. and {Mueller-Dombois}, Dieter}, year = {1967}, month = jan, journal = {Berichte des Geobotanischen Institutes der Eidg. Techn. Hochschule Stiftung R{\"u}bel}, volume = {37}, pages = {56--73} } @article{henderson-sellers:1984a, title = {A New Formula for Latent Heat of Vaporization of Water as a Function of Temperature}, author = {{Henderson-Sellers}, B.}, year = {1984}, journal = {Quarterly Journal of the Royal Meteorological Society}, volume = {110}, number = {466}, pages = {1186--1190}, issn = {1477-870X}, doi = {10.1002/qj.49711046626}, urldate = {2023-07-04}, abstract = {Existing formulae and approximations for the latent heat of vaporization of water, Lv, are reviewed. Using an analytical approximation to the saturated vapour pressure as a function of temperature, a new, temperature-dependent function for Lv is derived.}, copyright = {Copyright {\copyright} 1984 Royal Meteorological Society}, langid = {english} } @article{hengl:2017a, title = {{{SoilGrids250m}}: {{Global}} Gridded Soil Information Based on Machine Learning}, shorttitle = {{{SoilGrids250m}}}, author = {Hengl, Tomislav and de Jesus, Jorge Mendes and Heuvelink, Gerard B. M. and Gonzalez, Maria Ruiperez and Kilibarda, Milan and Blagoti{\'c}, Aleksandar and Shangguan, Wei and Wright, Marvin N. and Geng, Xiaoyuan and {Bauer-Marschallinger}, Bernhard and Guevara, Mario Antonio and Vargas, Rodrigo and MacMillan, Robert A. and Batjes, Niels H. and Leenaars, Johan G. B. and Ribeiro, Eloi and Wheeler, Ichsani and Mantel, Stephan and Kempen, Bas}, year = {2017}, month = feb, journal = {PLOS ONE}, volume = {12}, number = {2}, pages = {e0169748}, publisher = {Public Library of Science}, issn = {1932-6203}, doi = {10.1371/journal.pone.0169748}, urldate = {2023-07-05}, abstract = {This paper describes the technical development and accuracy assessment of the most recent and improved version of the SoilGrids system at 250m resolution (June 2016 update). SoilGrids provides global predictions for standard numeric soil properties (organic carbon, bulk density, Cation Exchange Capacity (CEC), pH, soil texture fractions and coarse fragments) at seven standard depths (0, 5, 15, 30, 60, 100 and 200 cm), in addition to predictions of depth to bedrock and distribution of soil classes based on the World Reference Base (WRB) and USDA classification systems (ca. 280 raster layers in total). Predictions were based on ca. 150,000 soil profiles used for training and a stack of 158 remote sensing-based soil covariates (primarily derived from MODIS land products, SRTM DEM derivatives, climatic images and global landform and lithology maps), which were used to fit an ensemble of machine learning methods---random forest and gradient boosting and/or multinomial logistic regression---as implemented in the R packages ranger, xgboost, nnet and caret. The results of 10--fold cross-validation show that the ensemble models explain between 56\% (coarse fragments) and 83\% (pH) of variation with an overall average of 61\%. Improvements in the relative accuracy considering the amount of variation explained, in comparison to the previous version of SoilGrids at 1 km spatial resolution, range from 60 to 230\%. Improvements can be attributed to: (1) the use of machine learning instead of linear regression, (2) to considerable investments in preparing finer resolution covariate layers and (3) to insertion of additional soil profiles. Further development of SoilGrids could include refinement of methods to incorporate input uncertainties and derivation of posterior probability distributions (per pixel), and further automation of spatial modeling so that soil maps can be generated for potentially hundreds of soil variables. Another area of future research is the development of methods for multiscale merging of SoilGrids predictions with local and/or national gridded soil products (e.g. up to 50 m spatial resolution) so that increasingly more accurate, complete and consistent global soil information can be produced. SoilGrids are available under the Open Data Base License.}, langid = {english}, keywords = {Agricultural soil science,Forecasting,Glaciers,Machine learning,Remote sensing,Shannon index,Soil pH,Trees} } @article{Heskel:2016fg, title = {Convergence in the Temperature Response of Leaf Respiration across Biomes and Plant Functional Types}, author = {Heskel, Mary A and O'Sullivan, Odhran S and Reich, Peter B and Tjoelker, Mark G and Weerasinghe, Lasantha K and Penillard, Aurore and Egerton, John J G and Creek, Danielle and Bloomfield, Keith J and Xiang, Jen and Sinca, Felipe and Stangl, Zsofia R and {Martinez-de la Torre}, Alberto and Griffin, Kevin L and Huntingford, Chris and Hurry, Vaughan and Meir, Patrick and Turnbull, Matthew H and Atkin, Owen K}, year = {2016}, month = apr, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {14}, pages = {3832--3837}, doi = {10.1073/pnas.1520282113}, date-added = {2020-11-30T13:55:54GMT}, date-modified = {2020-11-30T14:42:52GMT}, langid = {english}, local-url = {file://localhost/Users/dorme/References/Library.papers3/Articles/2016/Heskel/PNAS\%202016\%20Heskel.pdf}, rating = {0}, uri = {papers3://publication/doi/10.1073/pnas.1520282113} } @article{Huber:2009fy, title = {New International Formulation for the Viscosity of {{H2O}}}, author = {Huber, M L and Perkins, R A and Laesecke, A and Friend, D G and Sengers, J V and Assael, M J and Metaxa, I N and Vogel, E and Mare{\v s}, R and Miyagawa, K}, year = {2009}, month = jun, journal = {Journal of Physical and Chemical Reference Data}, volume = {38}, number = {2}, pages = {101--125}, doi = {10.1063/1.3088050}, date-added = {2020-12-02T09:52:51GMT}, date-modified = {2020-12-17T08:58:40GMT}, langid = {english}, local-url = {file://localhost/Users/dorme/References/Library.papers3/Articles/2009/Huber/Journal\%20of\%20Physical\%20and\%20Chemical\%20Reference\%20Data\%202009\%20Huber.pdf}, rating = {0}, uri = {papers3://publication/doi/10.1063/1.3088050} } @book{iqbal:1983a, title = {An Introduction to Solar Radiation}, author = {Iqbal, Mohammed}, year = {1983}, publisher = {Academic Press}, langid = {english} } @techreport{joshi:2022a, title = {Plant-{{FATE}}: {{Predicting}} the Adaptive Responses of Biodiverse Plant Communities Using Functional-Trait Evolution}, author = {Joshi, Jaideep and Prentice, Iain Colin and Br{\"a}nnstr{\"o}m, {\AA}ke and Singh, Shipra and Hofhansl, Florian and Dieckmann, Ulf}, year = {2022}, month = mar, number = {EGU22-9994}, institution = {Copernicus Meetings}, doi = {10.5194/egusphere-egu22-9994}, urldate = {2024-09-05}, langid = {english} } @article{Kattge:2007db, title = {Temperature Acclimation in a Biochemical Model of Photosynthesis: A Reanalysis of Data from 36 Species}, author = {Kattge, Jens and Knorr, Wolfgang}, year = {2007}, month = sep, journal = {Plant, Cell \& Environment}, volume = {30}, number = {9}, pages = {1176--1190}, doi = {10.1111/j.1365-3040.2007.01690.x}, abstract = {The Farquhar et al. model of C3 photosynthesis is frequently used to study the effect of global changes on the biosphere. Its two main parameters representing photosynthetic capacity, Vcmax and Jmax, have been observed to acclimate to plant growth temperature for single species, but a general formulation has never been derived. Here, we present a reanalysis of data from 36 plant species to quantify the temperature dependence of Vcmax and Jmax with a focus on plant growth temperature, ie the plants' average ambient {\dots}}, date-added = {2020-11-30T14:04:07GMT}, date-modified = {2020-12-02T16:14:05GMT}, langid = {english}, local-url = {file://localhost/Users/dorme/References/Library.papers3/Articles/2007/Kattge/Plant\%20Cell\%20\&\%20Environment\%202007\%20Kattge.pdf}, rating = {0}, read = {Yes}, uri = {papers3://publication/doi/10.1111/j.1365-3040.2007.01690.x} } @article{kennedy:2019a, title = {Implementing {{Plant Hydraulics}} in the {{Community Land Model}}, {{Version}} 5}, author = {Kennedy, Daniel and Swenson, Sean and Oleson, Keith W. and Lawrence, David M. and Fisher, Rosie and {Lola da Costa}, Antonio Carlos and Gentine, Pierre}, year = {2019}, month = feb, journal = {Journal of Advances in Modeling Earth Systems}, volume = {11}, number = {2}, pages = {485--513}, issn = {19422466}, doi = {10.1029/2018MS001500}, urldate = {2022-07-21}, abstract = {Version 5 of the Community Land Model (CLM5) introduces the plant hydraulic stress (PHS) configuration of vegetation water use, which is described and compared with the corresponding parameterization from CLM4.5. PHS updates vegetation water stress and root water uptake to better reflect plant hydraulic theory, advancing the physical basis of the model. The new configuration introduces prognostic vegetation water potential, modeled at the root, stem, and leaf levels. Leaf water potential replaces soil potential as the basis for stomatal conductance water stress, and root water potential is used to implement hydraulic root water uptake, replacing a transpiration partitioning function. Point simulations of a tropical forest site (Caxiuan{\~a}, Brazil) under ambient conditions and partial precipitation exclusion highlight the differences between PHS and the previous CLM implementation. Model description and simulation results are contextualized with a list of benefits and limitations of the new model formulation, including hypotheses that were not testable in previous versions of the model. Key results include reductions in transpiration and soil moisture biases relative to a control model under both ambient and exclusion conditions, correcting excessive dry season soil moisture stress in the control model. PHS implements hydraulic gradient root water uptake, which allows hydraulic redistribution and compensatory root water uptake and results in PHS utilizing a larger portion of the soil column to buffer shortfalls in precipitation. The new model structure, which bases water stress on leaf water potential, could have significant implications for vegetation-climate feedbacks, including increased sensitivity of photosynthesis to atmospheric vapor pressure deficit.}, langid = {english} } @phdthesis{lancelot:2020a, title = {A Novel Computational Model to Predict Forest Dynamics}, author = {Lancelot, Maxime}, year = {2020}, month = aug, affiliation = {Imperial College London}, date-added = {2020-11-30T12:25:21GMT}, date-modified = {2020-11-30T14:42:52GMT}, local-url = {file://localhost/Users/dorme/References/Library.papers3/Books/2020/Lancelot/2020\%20Lancelot.pdf}, rating = {0}, school = {Imperial College London}, uri = {papers3://publication/uuid/D73D9C6F-36C9-461D-A90C-784809C52BCB} } @article{lavergne:2020a, title = {Impacts of Soil Water Stress on the Acclimated Stomatal Limitation of Photosynthesis: {{Insights}} from Stable Carbon Isotope Data}, shorttitle = {Impacts of Soil Water Stress on the Acclimated Stomatal Limitation of Photosynthesis}, author = {Lavergne, Ali{\'e}nor and Sandoval, David and Hare, Vincent J. and Graven, Heather and Prentice, Iain Colin}, year = {2020}, month = dec, journal = {Global Change Biology}, volume = {26}, number = {12}, pages = {7158--7172}, issn = {1354-1013, 1365-2486}, doi = {10.1111/gcb.15364}, urldate = {2022-05-19}, abstract = {Atmospheric aridity and drought both influence physiological function in plant leaves, but their relative contributions to changes in the ratio of leaf internal to ambient partial pressure of CO2 ({$\chi$}) -- an index of adjustments in both stomatal conductance and photosynthetic rate to environmental conditions -- are difficult to disentangle. Many stomatal models predicting {$\chi$} include the influence of only one of these drivers. In particular, the least-cost optimality hypothesis considers the effect of atmospheric demand for water on {$\chi$} but does not predict how soils with reduced water further influence {$\chi$}, potentially leading to an overestimation of {$\chi$} under dry conditions. Here, we use a large network of stable carbon isotope measurements in C3 woody plants to examine the acclimated response of {$\chi$} to soil water stress. We estimate the ratio of cost factors for carboxylation and transpiration ({$\beta$}) expected from the theory to explain the variance in the data, and investigate the responses of {$\beta$} (and thus {$\chi$}) to soil water content and suction across seed plant groups, leaf phenological types and regions. Overall, {$\beta$} decreases linearly with soil drying, implying that the cost of water transport along the soil--plant--atmosphere continuum increases as water available in the soil decreases. However, despite contrasting hydraulic strategies, the stomatal responses of angiosperms and gymnosperms to soil water tend to converge, consistent with the optimality theory. The prediction of {$\beta$} as a simple, empirical function of soil water significantly improves {$\chi$} predictions by up to 6.3 {\textpm} 2.3\% (mean {\textpm} SD of adjusted-R2) over 1980--2018 and results in a reduction of around 2\% of mean {$\chi$} values across the globe. Our results highlight the importance of soil water status on stomatal functions and plant water-use efficiency, and suggest the implementation of trait-based hydraulic functions into the model to account for soil water stress.}, langid = {english} } @article{lavergne:2022a, title = {A Semi-Empirical Model for Primary Production, Isotopic Discrimination and Competition of {{C3}} and {{C4}} Plants}, author = {Lavergne, Ali{\'e}nor and Harrison, Sandy P. and Atsawawaranunt, Kamolphat and Dong, Ning and Prentice, Iain Colin}, year = {2022}, journal = {Global Ecology and Biogeography (submitted)} } @article{Li:2014bc, title = {Simulation of Tree-Ring Widths with a Model for Primary Production, Carbon Allocation, and Growth}, author = {Li, G and Harrison, S P and Prentice, I. C. and Falster, D}, year = {2014}, journal = {Biogeosciences (Online)}, volume = {11}, number = {23}, pages = {6711--6724}, doi = {10.5194/bg-11-6711-2014}, date-added = {2020-12-01T16:59:12GMT}, date-modified = {2021-11-11T13:59:21GMT}, langid = {english}, local-url = {file://localhost/Users/dorme/References/Library.papers3/Articles/2014/Li/Biogeosciences\%202014\%20Li.pdf}, rating = {0}, read = {Yes}, uri = {papers3://publication/doi/10.5194/bg-11-6711-2014} } @article{Lin:2015wh, title = {Optimal Stomatal Behaviour around the World}, author = {Lin, Yan-Shih and Medlyn, Belinda E and Duursma, Remko A and Prentice, I. Colin and Wang, Han and Baig, Sofia and Eamus, Derek and {de Dios}, Victor Resco and Mitchell, Patrick and Ellsworth, David S and {de Beeck}, Maarten Op and Wallin, Goran and Uddling, Johan and Tarvainen, Lasse and Linderson, Maj-Lena and Cernusak, Lucas A and Nippert, Jesse B and Ocheltree, Troy W and Tissue, David T and {Martin-StPaul}, Nicolas K and Rogers, Alistair and Warren, Jeff M and De Angelis, Paolo and Hikosaka, Kouki and Han, Qingmin and Onoda, Yusuke and Gimeno, Teresa E and Barton, Craig V M and Bennie, Jonathan and Bonal, Damien and Bosc, Alexandre and Low, Markus and {Macinins-Ng}, Cate and Rey, Ana and Rowland, Lucy and Setterfield, Samantha A and {Tausz-Posch}, Sabine and {Zaragoza-Castells}, Joana and Broadmeadow, Mark S J and Drake, John E and Freeman, Michael and Ghannoum, Oula and Hutley, Lindsay B and Kelly, Jeff W and Kikuzawa, Kihachiro and Kolari, Pasi and Koyama, Kohei and Limousin, Jean-Marc and Meir, Patrick and {Lola da Costa}, Antonio C and Mikkelsen, Teis N and Salinas, Norma and Sun, Wei and Wingate, Lisa}, year = {2015}, journal = {Nature Climate Change}, volume = {5}, number = {5}, pages = {459--464}, abstract = {Stomatal conductance is a land-surface attribute that links the water and carbon cycles. Analysis of a global database covering a wide range of plant functional types and biomes now provides a framework for predicting the behaviour of stomatal conductance that can be applied to model ecosystem productivity, energy balance and ecohydrological processes in a changing climate.}, date-added = {2021-11-11T14:12:05GMT}, date-modified = {2021-11-11T14:13:27GMT}, local-url = {file://localhost/Users/dorme/References/Library.papers3/Articles/2015/Lin/2015\%20Lin-2.pdf}, rating = {0}, uri = {papers3://publication/uuid/61D6E8CB-F257-4021-AC24-2DF4D72C298E} } @article{Linacre:1968a, title = {Estimating the Net-Radiation Flux}, author = {Linacre, E. T.}, year = {1968}, month = jan, journal = {Agricultural Meteorology}, volume = {5}, number = {1}, pages = {49--63}, issn = {0002-1571}, doi = {10.1016/0002-1571(68)90022-8}, urldate = {2024-08-02}, abstract = {A major influence controlling the water loss from irrigated crops is the net-radiation intensity Qn, but measurements of this are not normally available, and so attempts are often made to deduce it from other climatic data, such as the solar-radiation. Here it is shown that the relationship between net and solar-radiation intensities depends on the degree of cloudiness and the ambient temperature. By making appropriate assumptions, a series of expressions for Qn is derived, with decreasing accuracy but increasing simplicity of estimation. It appears that clouds lower the net-radiation intensity when it exceeds a critical value in the region of 0.02 cal./cm2 min, but increase it when the intensity is lower.} } @article{lloyd:2010a, title = {Optimisation of Photosynthetic Carbon Gain and Within-Canopy Gradients of Associated Foliar Traits for {{Amazon}} Forest Trees}, author = {Lloyd, J. and Pati{\~n}o, S. and Paiva, R. Q. and Nardoto, G. B. and Quesada, C. A. and Santos, A. J. B. and Baker, T. R. and Brand, W. A. and Hilke, I. and Gielmann, H. and Raessler, M. and Luiz{\~a}o, F. J. and Martinelli, L. A. and Mercado, L. M.}, year = {2010}, month = jun, journal = {Biogeosciences}, volume = {7}, number = {6}, pages = {1833--1859}, publisher = {Copernicus GmbH}, issn = {1726-4170}, doi = {10.5194/bg-7-1833-2010}, urldate = {2025-03-20}, abstract = {Vertical profiles in leaf mass per unit leaf area (MA), foliar 13C composition (\δ13C), nitrogen (N), phosphorus (P), carbon (C) and major cation concentrations were estimated for 204 rain forest trees growing in 57 sites across the Amazon Basin. Data was analysed using a multilevel modelling approach, allowing a separation of gradients within individual tree canopies (within-tree gradients) as opposed to stand level gradients occurring because of systematic differences occurring between different trees of different heights (between-tree gradients). Significant positive within-tree gradients (i.e. increasing values with increasing sampling height) were observed for MA and [C]DW (the subscript denoting on a dry weight basis) with negative within-tree gradients observed for \δ13C, [Mg]DW and [K]DW. No significant within-tree gradients were observed for [N]DW, [P]DW or [Ca]DW. The magnitudes of between-tree gradients were not significantly different to the within-tree gradients for MA, \δ13C, [C]DW, [K]DW, [N]DW, [P]DW and [Ca]DW. But for [Mg]DW, although there was no systematic difference observed between trees of different heights, strongly negative within-tree gradients were found to occur. When expressed on a leaf area basis (denoted by the subscript "A"), significant positive gradients were observed for [N]A, [P]A and [K]A both within and between trees, these being attributable to the positive intra- and between-tree gradients in MA mentioned above. No systematic within-tree gradient was observed for either [Ca]A or [Mg]A, but with a significant positive gradient observed for [Mg]A between trees (i.e. with taller trees tending to have a higher Mg per unit leaf area). Significant differences in within-tree gradients between individuals were observed only for MA, \δ13C and [P] A. This was best associated with the overall average [P]A for each tree, this also being considered to be a surrogate for a tree's average leaf area based photosynthetic capacity, Amax. A new model is presented which is in agreement with the above observations. The model predicts that trees characterised by a low upper canopy Amax should have shallow, or even non-existent, within-canopy gradients in Amax, with optimal intra-canopy gradients becoming sharper as a tree's upper canopy Amax increases. Nevertheless, in all cases it is predicted that the optimal within-canopy gradient in Amax should be substantially less than for photon irradiance. Although this is also shown to be consistent with numerous observations as illustrated by a literature survey of gradients in photosynthetic capacity for broadleaf trees, it is also in contrast to previously held notions of optimality. A new equation relating gradients in photosynthetic capacity within broadleaf tree canopies to the photosynthetic capacity of their upper canopy leaves is presented.}, langid = {english} } @article{long:1993a, title = {Quantum Yields for Uptake of Carbon Dioxide in {{C3}} Vascular Plants of Contrasting Habitats and Taxonomic Groupings}, author = {Long, S. P. and Postl, W. F. and {Bolh{\'a}r-Nordenkampf}, H. R.}, year = {1993}, month = feb, journal = {Planta}, volume = {189}, number = {2}, pages = {226--234}, issn = {1432-2048}, doi = {10.1007/BF00195081}, urldate = {2024-07-19}, abstract = {The maximum quantum yields ({$\phi$}a,c) for CO2 uptake in low-oxygen atmospheres were determined for 11 species of C3 vascular plants of diverse taxa, habitat and life form using an Ulbricht-sphere leaf chamber. Comparisons were also made between tissues of varied age within species. The species examined were Psilotum nudum (L.) P. Beauv., Davallia bullata Wall. ex Hook., Cycas revoluta Thunb., Araucaria heterophylla (Salisb.) Franco, Picea abies (L.) Karst., Nerium oleander L., Ruellia humilis Nutt., Pilea microphylla (L.) Karst., Beaucarnea stricta Lem., Oplismenus hirtellus (L.) P. Beauv. and Poa annua L. Quantum yields were calculated from the initial slopes of the response of CO2 uptake to the quantity of photons absorbed in conditions of diffuse lighting. Regression analysis of variance of the initial slopes of the response of CO2 uptake to photon absorption failed to show any statistically significant differences between age classes within species or between the mature photosynthetic organs of different species. The constancy of {$\phi$}a,c was apparent despite marked variation in the light-saturated rates of CO2 uptake within and between species. The mean {$\phi$}a,c was 0.093{\textpm}0.003 for 11 species. By contrast, surface absorptance varied markedly between species from 0.90 to 0.60, producing proportional variation in the quantum yield calculated on an incidentlight basis. The ratio of variable to maximum fluorescence emission at 695 nm for the same tissues also failed to show any statistically significant variation between species, with a mean of 0.838{\textpm}0.008. Mean values of {$\phi$}a,c reported here for C3 species, in the absence of photorespiration, are higher than reported in previous surveys of vascular plants, but consistent with recent estimates of the quantum yields of O2 evolution.}, langid = {english}, keywords = {C3 plant,CO2 uptake),Photosynthesis,Quantum yield (O2} } @article{maire:2012a, title = {The {{Coordination}} of {{Leaf Photosynthesis Links C}} and {{N Fluxes}} in {{C3 Plant Species}}}, author = {Maire, Vincent and Martre, Pierre and Kattge, Jens and Gastal, Fran{\c c}ois and Esser, Gerd and Fontaine, S{\'e}bastien and Soussana, Jean-Fran{\c c}ois}, year = {2012}, month = jun, journal = {PLOS ONE}, volume = {7}, number = {6}, pages = {e38345}, publisher = {Public Library of Science}, issn = {1932-6203}, doi = {10.1371/journal.pone.0038345}, urldate = {2025-03-13}, abstract = {Photosynthetic capacity is one of the most sensitive parameters in vegetation models and its relationship to leaf nitrogen content links the carbon and nitrogen cycles. Process understanding for reliably predicting photosynthetic capacity is still missing. To advance this understanding we have tested across C3 plant species the coordination hypothesis, which assumes nitrogen allocation to photosynthetic processes such that photosynthesis tends to be co-limited by ribulose-1,5-bisphosphate (RuBP) carboxylation and regeneration. The coordination hypothesis yields an analytical solution to predict photosynthetic capacity and calculate area-based leaf nitrogen content (Na). The resulting model linking leaf photosynthesis, stomata conductance and nitrogen investment provides testable hypotheses about the physiological regulation of these processes. Based on a dataset of 293 observations for 31 species grown under a range of environmental conditions, we confirm the coordination hypothesis: under mean environmental conditions experienced by leaves during the preceding month, RuBP carboxylation equals RuBP regeneration. We identify three key parameters for photosynthetic coordination: specific leaf area and two photosynthetic traits (k3, which modulates N investment and is the ratio of RuBP carboxylation/oxygenation capacity () to leaf photosynthetic N content (Npa); and Jfac, which modulates photosynthesis for a given k3 and is the ratio of RuBP regeneration capacity (Jmax) to). With species-specific parameter values of SLA, k3 and Jfac, our leaf photosynthesis coordination model accounts for 93\% of the total variance in Na across species and environmental conditions. A calibration by plant functional type of k3 and Jfac still leads to accurate model prediction of Na, while SLA calibration is essentially required at species level. Observed variations in k3 and Jfac are partly explained by environmental and phylogenetic constraints, while SLA variation is partly explained by phylogeny. These results open a new avenue for predicting photosynthetic capacity and leaf nitrogen content in vegetation models.}, langid = {english} } @article{mengoli:2022a, title = {Ecosystem {{Photosynthesis}} in {{Land}}-{{Surface Models}}: {{A First}}-{{Principles Approach Incorporating Acclimation}}}, shorttitle = {Ecosystem {{Photosynthesis}} in {{Land}}-{{Surface Models}}}, author = {Mengoli, Giulia and Agust{\'i}-Panareda, Anna and Boussetta, Souhail and Harrison, Sandy P. and Trotta, Carlo and Prentice, I. Colin}, year = {2022}, month = jan, journal = {Journal of Advances in Modeling Earth Systems}, volume = {14}, number = {1}, issn = {1942-2466, 1942-2466}, doi = {10.1029/2021MS002767}, urldate = {2022-05-26}, abstract = {Vegetation regulates land-atmosphere, water, and energy exchanges and is an essential component of land-surface models (LSMs). However, LSMs have been handicapped by assumptions that equate acclimated photosynthetic responses to the environment with the fast responses observable in the laboratory. The effects of acclimation can be taken into account by including PFT-specific values of photosynthetic parameters, but at the cost of increasing parameter requirements. Here, we develop an alternative approach for including acclimation in LSMs by adopting the P model, an existing light-use efficiency model for gross primary production (GPP) that implicitly predicts the acclimation of photosynthetic parameters on a weekly to monthly timescale via optimality principles. We demonstrate that it is possible to explicitly separate the fast and slow photosynthetic responses to environmental conditions, allowing the simulation of GPP at the sub-daily timesteps required for coupling in an LSM. The resulting model reproduces the diurnal cycles of GPP recorded by eddy-covariance flux towers in a temperate grassland and boreal, temperate and tropical forests. The best performance is achieved when biochemical capacities are adjusted to match recent midday conditions. Comparison between this model and the operational LSM in the European Centre for Medium-range Weather Forecasts climate model shows that the new model has better predictive power in most of the sites and years analyzed, particularly in summer and autumn. Our analyses suggest a simple and parameter-sparse method to include both instantaneous and acclimated responses within an LSM framework, with potential applications in weather, climate, and carbon-cycle modeling.}, langid = {english} } @article{mengoli:2023a, title = {A Global Function of Climatic Aridity Accounts for Soil Moisture Stress on Carbon Assimilation}, author = {Mengoli, Giulia and Harrison, Sandy P. and Prentice, I. Colin}, year = {2023}, month = jun, journal = {EGUsphere}, pages = {1--19}, publisher = {Copernicus GmbH}, doi = {10.5194/egusphere-2023-1261}, urldate = {2023-07-03}, abstract = {{$<$}p{$><$}strong class="journal-contentHeaderColor"{$>$}Abstract.{$<$}/strong{$>$} The coupling between carbon uptake and water loss through stomata implies that gross primary production (GPP) can be limited by soil water availability through reduced leaf area and/or reduced stomatal conductance. Vegetation and land-surface models typically assume that GPP is highest under well-watered conditions and apply a stress function to reduce GPP with declining soil moisture below a critical threshold, which may be universal or prescribed by vegetation type. It is unclear how well current schemes represent the water conservation strategies of plants in different climates. Here eddy-covariance flux data are used to investigate empirically how soil moisture influences the light-use efficiency (LUE) of GPP. Well-watered GPP is estimated using the P model, a first-principles LUE model driven by atmospheric data and remotely sensed green vegetation cover. Breakpoint regression is used to relate the daily value of the ratio \β(\θ) (flux-derived GPP/modelled well-watered GPP) to soil moisture, which is estimated using a generic water-balance model. Maximum LUE, even during wetter periods, is shown to decline with increasing climatic aridity index (AI). The critical soil-moisture threshold also declines with AI. Moreover, for any AI, there is a value of soil moisture at which \β(\θ) is maximized, and this value declines with increasing AI. Thus, ecosystems adapted to seasonally dry conditions use water more conservatively (relative to well-watered ecosystems) when soil moisture is high, but maintain higher GPP when soil moisture is low. An empirical non-linear function of AI expressing these relationships is derived by non-linear regression, and used to generate a \β(\θ) function that provides a multiplier for well-watered GPP as simulated by the P model. Substantially improved GPP simulation is shown during both unstressed and water-stressed conditions, compared to the reference model version that ignores soil-moisture stress, and to an earlier formulation in which maximum LUE was not reduced. This scheme may provide a step towards better-founded representations of carbon-water cycle coupling in vegetation and land-surface models.{$<$}/p{$>$}}, langid = {english} } @article{moore:2018a, title = {Equilibrium Forest Demography Explains the Distribution of Tree Sizes across {{North America}}}, author = {Moore, Jonathan R and Zhu, Kai and Huntingford, Chris and Cox, Peter M}, year = {2018}, month = aug, journal = {Environmental Research Letters}, volume = {13}, number = {8}, pages = {084019--10}, publisher = {IOP Publishing}, doi = {10.1088/1748-9326/aad6d1}, abstract = {Environmental Research Letters, 13(2018) 084019. doi:10.1088/1748-9326/aad6d1}, date-added = {2020-12-01T16:56:53GMT}, date-modified = {2020-12-17T08:58:39GMT}, local-url = {file://localhost/Users/dorme/References/Library.papers3/Articles/2018/Moore/Environ\%20Res\%20Lett\%202018\%20Moore.pdf}, rating = {0}, uri = {papers3://publication/doi/10.1088/1748-9326/aad6d1} } @article{murphy:2021a, title = {A Derivation Error That Affects Carbon Balance Models Exists in the Current Implementation of the Modified {{Arrhenius}} Function}, author = {Murphy, Bridget K. and Stinziano, Joseph R.}, year = {2021}, journal = {New Phytologist}, volume = {231}, number = {6}, pages = {2371--2381}, issn = {1469-8137}, doi = {10.1111/nph.16883}, urldate = {2024-07-25}, abstract = {Understanding biological temperature responses is crucial to predicting global carbon fluxes. The current approach to modelling temperature responses of photosynthetic capacity in large scale modelling efforts uses a modified Arrhenius equation. We rederived the modified Arrhenius equation from the source publication from 1942 and uncovered a missing term that was dropped by 2002. We compare fitted temperature response parameters between the correct and incorrect derivation of the modified Arrhenius equation. We find that most parameters are minimally affected, though activation energy is impacted quite substantially. We then scaled the impact of these small errors to whole plant carbon balance and found that the impact of the rederivation of the modified Arrhenius equation on modelled daily carbon gain causes a meaningful deviation of c. 18\% day-1. This suggests that the error in the derivation of the modified Arrhenius equation has impacted the accuracy of predictions of carbon fluxes at larger scales since {$>$} 40\% of Earth System Models contain the erroneous derivation. We recommend that the derivation error be corrected in modelling efforts moving forward.}, copyright = {{\copyright} 2020 The Authors New Phytologist {\copyright} 2020 New Phytologist Trust}, langid = {english}, keywords = {Arrhenius,carbon balance,gas exchange,modelling,photosynthesis,temperature} } @article{peng:2021a, title = {Global Climate and Nutrient Controls of Photosynthetic Capacity}, author = {Peng, Yunke and Bloomfield, Keith J and Cernusak, Lucas A and Domingues, Tomas F and Prentice, I. Colin}, year = {2021}, month = apr, journal = {Communications Biology}, pages = {1--9}, publisher = {Springer US}, doi = {10.1038/s42003-021-01985-7}, abstract = {Communications Biology, doi:10.1038/s42003-021-01985-7}, date-added = {2021-06-14T08:31:31GMT}, date-modified = {2021-11-11T14:13:27GMT}, local-url = {file://localhost/Users/dorme/References/Library.papers3/Articles/2021/Peng/Communications\%20Biology\%202021\%20Peng.pdf}, rating = {0}, uri = {papers3://publication/doi/10.1038/s42003-021-01985-7} } @article{Prentice:2014bc, title = {Balancing the Costs of Carbon Gain and Water Transport: Testing a New Theoretical Framework for Plant Functional Ecology}, author = {Prentice, I. Colin and Dong, Ning and Gleason, Sean M and Maire, Vincent and Wright, Ian J.}, year = {2014}, journal = {Ecology Letters}, volume = {17}, number = {1}, pages = {82--91}, doi = {10.1111/ele.12211}, date-added = {2020-12-01T13:22:48GMT}, date-modified = {2021-01-21T15:04:43GMT}, langid = {english}, local-url = {file://localhost/Users/dorme/References/Library.papers3/Articles/2014/Prentice/Ecol\%20Lett\%202014\%20Prentice.pdf}, rating = {0}, read = {Yes}, uri = {papers3://publication/doi/10.1111/ele.12211} } @article{purves:2008a, title = {Predicting and Understanding Forest Dynamics Using a Simple Tractable Model}, author = {Purves, Drew W. and Lichstein, Jeremy W. and Strigul, Nikolay and Pacala, Stephen W.}, year = {2008}, month = nov, journal = {Proceedings of the National Academy of Sciences}, volume = {105}, number = {44}, pages = {17018--17022}, issn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.0807754105}, urldate = {2022-06-20}, abstract = {The perfect-plasticity approximation (PPA) is an analytically tractable model of forest dynamics, defined in terms of parameters for individual trees, including allometry, growth, and mortality. We estimated these parameters for the eight most common species on each of four soil types in the US Lake states (Michigan, Wisconsin, and Minnesota) by using short-term ({$\leq$}15-year) inventory data from individual trees. We implemented 100-year PPA simulations given these parameters and compared these predictions to chronosequences of stand development. Predictions for the timing and magnitude of basal area dynamics and ecological succession on each soil were accurate, and predictions for the diameter distribution of 100-year-old stands were correct in form and slope. For a given species, the PPA provides analytical metrics for early-successional performance ( H 20 , height of a 20-year-old open-grown tree) and late-successional performance ( {\^Z} *, equilibrium canopy height in monoculture). These metrics predicted which species were early or late successional on each soil type. Decomposing {\^Z} * showed that ( i ) succession is driven both by superior understory performance and superior canopy performance of late-successional species, and ( ii ) performance differences primarily reflect differences in mortality rather than growth. The predicted late-successional dominants matched chronosequences on xeromesic ( Quercus rubra ) and mesic (codominance by Acer rubrum and Acer saccharum ) soil. On hydromesic and hydric soils, the literature reports that the current dominant species in old stands ( Thuja occidentalis ) is now failing to regenerate. Consistent with this, the PPA predicted that, on these soils, stands are now succeeding to dominance by other late-successional species (e.g., Fraxinus nigra , A. rubrum ).}, langid = {english} } @article{ryu:2011a, title = {Integration of {{MODIS}} Land and Atmosphere Products with a Coupled-Process Model to Estimate Gross Primary Productivity and Evapotranspiration from 1 Km to Global Scales}, author = {Ryu, Youngryel and Baldocchi, Dennis D. and Kobayashi, Hideki and {van Ingen}, Catherine and Li, Jie and Black, Andy and Beringer, Jason and {van Gorsel}, Eva and Knohl, Alexander and Law, Beverly E. and Roupsard, Olivier}, year = {2011}, month = dec, journal = {GLOBAL BIOGEOCHEMICAL CYCLES}, volume = {25}, number = {4} } @article{sandoval:in_prep, title = {Aridity and Growth Temperature Effects on Phio Manuscript}, author = {Sandoval, David}, year = {in\_prep}, journal = {Placeholder}, volume = {?}, pages = {??-??} } @article{Smith:2019dv, title = {Global Photosynthetic Capacity Is Optimized to the Environment}, author = {Smith, Nicholas G and Keenan, Trevor F and Colin Prentice, I and Wang, Han and Wright, Ian J. and Niinemets, {\"U}lo and Crous, Kristine Y and Domingues, Tomas F and Guerrieri, Rossella and Yoko Ishida, F and Kattge, Jens and Kruger, Eric L and Maire, Vincent and Rogers, Alistair and Serbin, Shawn P and Tarvainen, Lasse and Togashi, Henrique F and Townsend, Philip A and Wang, Meng and Weerasinghe, Lasantha K and Zhou, Shuang Xi}, year = {2019}, month = jan, journal = {Ecology Letters}, volume = {22}, number = {3}, pages = {506--517}, doi = {10.1111/ele.13210}, date-added = {2020-12-02T15:16:49GMT}, date-modified = {2021-01-25T10:03:32GMT}, langid = {english}, local-url = {file://localhost/Users/dorme/References/Library.papers3/Articles/2019/Smith/Ecol\%20Lett\%202019\%20Smith.pdf}, rating = {0}, read = {Yes}, uri = {papers3://publication/doi/10.1111/ele.13210} } @misc{stine_geyer:2001, title = {Power from the Sun}, author = {Stine, William and Geyer, Michael}, year = {2001}, journal = {Power from the sun.net}, howpublished = {http://www.powerfromthesun.net/book.html} } @article{stinziano:2021a, title = {Agreed -- There Is No Need to Switch the Modified {{Arrhenius}} Function Back to the Old Form}, author = {Stinziano, Joseph R. and Murphy, Bridget K.}, year = {2021}, journal = {New Phytologist}, volume = {231}, number = {6}, pages = {2117--2117}, issn = {1469-8137}, doi = {10.1111/nph.17565}, urldate = {2025-01-20}, copyright = {{\copyright} 2021 The Authors New Phytologist {\copyright} 2021 New Phytologist Foundation}, langid = {english} } @article{Stocker:2018be, title = {Quantifying Soil Moisture Impacts on Light Use Efficiency across Biomes}, author = {Stocker, Benjamin D and Zscheischler, Jakob and Keenan, Trevor F and Prentice, I. Colin and Penuelas, Josep and Seneviratne, Sonia I}, year = {2018}, month = mar, journal = {New Phytologist}, volume = {218}, number = {4}, pages = {1430--1449}, doi = {10.1111/nph.15123}, abstract = {Terrestrial primary productivity and carbon cycle impacts of droughts are commonly quantified using vapour pressure deficit (VPD) data and remotely sensed greenness, without accounting for soil moisture. However, soil moisture limitation is known to strongly affect plant physiology. Here, we investigate light use efficiency, the ratio of gross primary productivity (GPP) to absorbed light. We derive its fractional reduction due to soil moisture (fLUE), separated from VPD and greenness changes, using artificial neural networks trained {\dots}}, date-added = {2021-01-25T09:23:00GMT}, date-modified = {2021-01-28T15:58:46GMT}, langid = {english}, local-url = {file://localhost/Users/dorme/References/Library.papers3/Articles/2018/Stocker/New\%20Phytol.\%202018\%20Stocker.pdf}, rating = {0}, uri = {papers3://publication/doi/10.1111/nph.15123} } @article{Stocker:2020dh, title = {P-Model v1.0: An Optimality-Based Light Use Efficiency Model for Simulating Ecosystem Gross Primary Production}, author = {Stocker, Benjamin D and Wang, Han and Smith, Nicholas G and Harrison, Sandy P and Keenan, Trevor F and Sandoval, David and Davis, Tyler and Prentice, I. Colin}, year = {2020}, journal = {Geoscientific Model Development}, volume = {13}, number = {3}, pages = {1545--1581}, doi = {10.5194/gmd-13-1545-2020}, date-added = {2020-11-30T12:24:06GMT}, date-modified = {2021-01-28T11:55:51GMT}, langid = {english}, local-url = {file://localhost/Users/dorme/References/Library.papers3/Articles/2020/Stocker/Geoscientific\%20Model\%20Development\%202020\%20Stocker.pdf}, rating = {0}, read = {Yes}, uri = {papers3://publication/doi/10.5194/gmd-13-1545-2020} } @article{togashi:2018a, title = {Functional Trait Variation Related to Gap Dynamics in Tropical Moist forests{{{\textsubscript{A}}}} Vegetation Modelling Perspective}, author = {Togashi, Henrique F{\"u}rstenau and Atkin, Owen K and Bloomfield, Keith J and Bradford, Matt and Cao, Kunfang and Dong, Ning and Evans, Bradley J and Fan, Zexin and Harrison, Sandy P and Hua, Zhu and Liddell, Michael J and Lloyd, Jon and Ni, Jian and Wang, Han and Weerasinghe, Lasantha K and Prentice, Iain Colin}, year = {2018}, month = dec, journal = {Perspectives in Plant Ecology, Evolution and Systematics}, volume = {35}, pages = {52--64}, publisher = {Elsevier}, doi = {10.1016/j.ppees.2018.10.004}, abstract = {Perspectives in Plant Ecology, Evolution and Systematics, 35 (2018) 52-64. doi:10.1016/j.ppees.2018.10.004}, date-added = {2020-12-01T17:02:03GMT}, date-modified = {2020-12-17T08:58:40GMT}, local-url = {file://localhost/Users/dorme/References/Library.papers3/Articles/2018/Togashi/Perspectives\%20in\%20Plant\%20Ecology\%20Evolution\%20and\%20Systematics\%202018\%20Togashi.pdf}, rating = {0}, read = {Yes}, uri = {papers3://publication/doi/10.1016/j.ppees.2018.10.004} } @article{tsilingiris:2008a, title = {Thermophysical and Transport Properties of Humid Air at Temperature Range between 0 and 100{$^\circ$}{{C}}}, author = {Tsilingiris, P. T.}, year = {2008}, month = may, journal = {Energy Conversion and Management}, volume = {49}, number = {5}, pages = {1098--1110}, issn = {0196-8904}, doi = {10.1016/j.enconman.2007.09.015}, urldate = {2023-07-04}, abstract = {The aim of the present investigation is evaluation of the thermophysical and transport properties of moist air as a function of mixture temperature with relative humidity as a parameter, ranging between dry air and saturation conditions. Based on a literature review of the most widely available analytical procedures and methods, a number of developed correlations are presented, which are employed with recent gas mixture component properties as input parameters, to derive the temperature and humidity dependence of mixture density, viscosity, specific heat capacity, thermal conductivity, thermal diffusivity and Prandtl number under conditions corresponding to the total barometric pressure of 101.3kPa. The derived results at an accuracy level suitable for engineering calculations were plotted and compared with adequate accuracy with existing results from previous analytical calculations and measured data from earlier experimental investigations. The saturated mixture properties were also appropriately fitted, and the fitting expressions suitable for computer calculations are also presented.}, langid = {english}, keywords = {Density,Prandtl number,Specific heat capacity,Thermal conductivity,Thermal diffusivity,Thermophysical properties,Viscosity} } @article{voncaemmerer:2014a, title = {Carbon Isotope Discrimination as a Tool to Explore {{C4}} Photosynthesis}, author = {{von Caemmerer}, Susanne and Ghannoum, Oula and Pengelly, Jasper J. L. and Cousins, Asaph B.}, year = {2014}, month = jul, journal = {Journal of Experimental Botany}, volume = {65}, number = {13}, pages = {3459--3470}, issn = {1460-2431, 0022-0957}, doi = {10.1093/jxb/eru127}, urldate = {2022-05-20}, abstract = {Photosynthetic carbon isotope discrimination is a non-destructive tool for investigating C4 metabolism. Tuneable diode laser absorption spectroscopy provides new opportunities for making rapid, concurrent measurements of carbon isotope discrimination and CO2 assimilation over a range of environmental conditions, and this has facilitated the use of carbon isotope discrimination as a probe of C4 metabolism. In spite of the significant progress made in recent years, understanding how photosynthetic carbon isotope discrimination measured concurrently with gas exchange relates to carbon isotope composition of leaf and plant dry matter remains a challenge that requires resolution if this technique is to be successfully applied as a screening tool in crop breeding and phylogenetic research. In this review, we update our understanding of the factors and assumptions that underlie variations in photosynthetic carbon isotope discrimination in C4 leaves. Closing the main gaps in our understanding of carbon isotope discrimination during C4 photosynthesis may help advance research aimed at developing higher productivity and efficiency in key C4 food, feed, and biofuel crops.}, langid = {english} } @article{walker:2014a, title = {The Relationship of Leaf Photosynthetic Traits - {{Vcmaxand Jmax-}} to Leaf Nitrogen, Leaf Phosphorus, and Specific Leaf Area: A Meta-Analysis and Modeling Study}, author = {Walker, Anthony P and Beckerman, Andrew P and Gu, Lianhong and Kattge, Jens and Cernusak, Lucas A and Domingues, Tomas F and Scales, Joanna C and Wohlfahrt, Georg and Wullschleger, Stan D and Woodward, F Ian}, year = {2014}, month = jul, journal = {Ecology and Evolution}, volume = {4}, number = {16}, pages = {3218--3235}, doi = {10.1002/ece3.1173}, date-added = {2020-12-07T11:43:53GMT}, date-modified = {2020-12-17T08:58:39GMT}, langid = {english}, local-url = {file://localhost/Users/dorme/References/Library.papers3/Articles/2014/Walker/Ecology\%20and\%20Evolution\%202014\%20Walker.pdf}, rating = {0}, uri = {papers3://publication/doi/10.1002/ece3.1173} } @article{Wang:2017go, title = {Towards a Universal Model for Carbon Dioxide Uptake by Plants}, author = {Wang, Han and Prentice, I. Colin and Keenan, Trevor F and Davis, Tyler W and Wright, Ian J. and Cornwell, William K and Evans, Bradley J and Peng, Changhui}, year = {2017}, month = sep, journal = {Nature Plants}, pages = {1--8}, publisher = {Springer US}, doi = {10.1038/s41477-017-0006-8}, abstract = {Nature Plants, doi:10.1038/s41477-017-0006-8}, date-added = {2020-11-30T12:27:00GMT}, date-modified = {2021-01-28T09:14:19GMT}, local-url = {file://localhost/Users/dorme/References/Library.papers3/Articles/2017/Wang/Nature\%20Plants\%202017\%20Wang.pdf}, rating = {0}, read = {Yes}, uri = {papers3://publication/doi/10.1038/s41477-017-0006-8} } @article{wright:2003a, title = {Least-{{Cost Input Mixtures}} of {{Water}} and {{Nitrogen}} for {{Photosynthesis}}.}, author = {Wright, Ian~J. and Reich, Peter~B. and Westoby, Mark}, year = {2003}, month = jan, journal = {The American Naturalist}, volume = {161}, number = {1}, pages = {98--111}, publisher = {The University of Chicago Press}, issn = {0003-0147}, doi = {10.1086/344920}, urldate = {2025-07-08}, abstract = {In microeconomics, a standard framework is used for determining the optimal input mix for a two-input production process. Here we adapt this framework for understanding the way plants use water and nitrogen (N) in photosynthesis. The least-cost input mixture for generating a given output depends on the relative cost of procuring and using nitrogen versus water. This way of considering the issue integrates concepts such as water-use efficiency and photosynthetic nitrogen-use efficiency into the more inclusive objective of optimizing the input mix for a given situation. We explore the implications of deploying alternative combinations of leaf nitrogen concentration and stomatal conductance to water, focusing on comparing hypothetical species occurring in low- versus high-humidity habitats. We then present data from sites in both the United States and Australia and show that low-rainfall species operate with substantially higher leaf N concentration per unit leaf area. The extra protein reflected in higher leaf N concentration is associated with a greater drawdown of internal CO2, such that low-rainfall species achieve higher photosynthetic rates at a given stomatal conductance. This restraint of transpirational water use apparently counterbalances the multiple costs of deploying high-nitrogen leaves.} } @article{Wang:2020a, title = {Acclimation of Leaf Respiration Consistent with Optimal Photosynthetic Capacity}, author = {Wang, Han and Atkin, Owen K and Keenan, Trevor F and Smith, Nicholas G and Wright, Ian J. and Bloomfield, Keith J and Kattge, Jens and Reich, Peter B and Prentice, I. Colin}, year = {2020}, month = feb, journal = {Global Change Biology}, volume = {26}, number = {4}, pages = {2573--2583}, doi = {10.1111/gcb.14980}, date-added = {2020-11-30T12:23:58GMT}, date-modified = {2021-01-22T13:54:24GMT}, langid = {english}, local-url = {file://localhost/Users/dorme/References/Library.papers3/Articles/2020/Wang/Global\%20Change\%20Biol\%202020\%20Wang.pdf}, rating = {0}, read = {Yes}, uri = {papers3://publication/doi/10.1111/gcb.14980} } @book{Woolf:1968, title = {On the {{Computation}} of {{Solar Elevation Angles}} and the {{Determination}} of {{Sunrise}} and {{Sunset Times}}}, author = {Woolf, Harold M.}, year = {1968}, publisher = {{National Aeronautics and Space Administration}}, langid = {english} } @article{wullschleger:1993a, title = {Biochemical {{Limitations}} to {{Carbon Assimilation}} in {{C3 Plants}}---{{A Retrospective Analysis}} of the {{A}}/{{Ci Curves}} from 109 {{Species}}}, author = {Wullschleger, Stan D}, year = {1993}, month = may, journal = {Journal of Experimental Botany}, volume = {44}, number = {5}, pages = {907--920}, issn = {0022-0957}, doi = {10.1093/jxb/44.5.907}, urldate = {2025-03-20}, abstract = {Species-specific differences in the assimilation of atmospheric CO2 depends upon differences in the capacities for the biochemical reactions that regulate the gas-exchange process. Quantifying these differences for more than a few species, however, has proven difficult. Therefore, to understand better how species differ in their capacity for CO2 assimilation, a widely used model, capable of partitioning limitations to the activity of ribulose-1,5-bisphosphate carboxylase-oxygenase, to the rate of ribulose 1,5-bisphosphate regeneration via electron transport, and to the rate of triose phosphate utilization was used to analyse 164 previously published A/Ci, curves for 109 C3 plant species. Based on this analysis, the maximum rate of carboxylation, Vcmax, ranged from 6{$\mu$}mol m-2 s-1 for the coniferous species Picea abies to 194{$\mu$}mol m-2 s-1 for the agricultural species Beta vulgaris, and averaged 64{$\mu$}mol m-2 s-1 across all species. The maximum rate of electron transport, Jmax, ranged from 17{$\mu$}mol m-2 s-1 again for Picea abies to 372{$\mu$}mol m-2 s-1 for the desert annual Malvastrum rotundifolium, and averaged 134{$\mu$}mol m-2 s-1 across all species. A strong positive correlation between Vcmax and Jmax indicated that the assimilation of CO2 was regulated in a co-ordinated manner by these two component processes. Of the A/Ci curves analysed, 23 showed either an insensitivity or reversed-sensitivity to increasing CO2 concentration, indicating that CO2 assimilation was limited by the utilization of triose phosphates. The rate of triose phosphate utilization ranged from 4{$\cdot$}9 {$\mu$}mol m-2 s-1 for the tropical perennial Tabebuia rosea to 20{$\cdot$}1 {$\mu$}mol m-2 s-1 for the weedy annual Xanthium strumarium, and averaged 10{$\cdot$}1 {$\mu$}mol m-2 s-1 across all species.Despite what at first glance would appear to be a wide range of estimates for the biochemical capacities that regulate CO2 assimilation, separating these species-specific results into those of broad plant categories revealed that Vcmax and Jmax were in general higher for herbaceous annuals than they were for woody perennials. For annuals, Vcmax and Jmax averaged 75 and 154 {$\mu$}mol m-2 s-1, while for perennials these same two parameters averaged only 44 and 97 {$\mu$}mol m-2 s-1, respectively. Although these differences between groups may be coincidental, such an observation points to differences between annuals and perennials in either the availability or allocation of resources to the gas-exchange process.} } @article{yin:2021a, title = {No Need to Switch the Modified {{Arrhenius}} Function Back to the Old Form}, author = {Yin, Xinyou}, year = {2021}, journal = {New Phytologist}, volume = {231}, number = {6}, pages = {2113--2116}, issn = {1469-8137}, doi = {10.1111/nph.17341}, urldate = {2025-01-20}, copyright = {{\copyright} 2021 The Author New Phytologist {\copyright} 2021 New Phytologist Foundation}, langid = {english} } @Article{ harris:2020a, title = {Array programming with {NumPy}}, author = {Charles R. Harris and K. Jarrod Millman and St{\'{e}}fan J. van der Walt and Ralf Gommers and Pauli Virtanen and David Cournapeau and Eric Wieser and Julian Taylor and Sebastian Berg and Nathaniel J. Smith and Robert Kern and Matti Picus and Stephan Hoyer and Marten H. van Kerkwijk and Matthew Brett and Allan Haldane and Jaime Fern{\'{a}}ndez del R{\'{i}}o and Mark Wiebe and Pearu Peterson and Pierre G{\'{e}}rard-Marchant and Kevin Sheppard and Tyler Reddy and Warren Weckesser and Hameer Abbasi and Christoph Gohlke and Travis E. Oliphant}, year = {2020}, month = sep, journal = {Nature}, volume = {585}, number = {7825}, pages = {357--362}, doi = {10.1038/s41586-020-2649-2}, publisher = {Springer Science and Business Media {LLC}}, url = {https://doi.org/10.1038/s41586-020-2649-2} }